Computer Scientist
Oct 2019 –
Nov 2023
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-[{"authors":["admin"],"categories":null,"content":"Raphael Scheible is a computer scientist located at Freiburg im Breisgau in Germany. His research interests include medical computer science, natural language processing and medical imaging. He currently works at the Institute for AI and Informatics in Medicine (AIIM) at the The University Hospital Klinikum rechts der Isar of the Technical University of Munich, which is part of the DIFUTURE project.\nIn 2016 Raphael decided to accept Jesus Christ as his Lord and saviour and asked him to forgive all his sins. Consequently, he became a born again Christian. Now, he volunteers as a leader of a prayergroup at the local church Christengemeinde Freiburg. When he got born again and freed from the demons he was possessed of, his life changed dramatically for the better and he became a new person. Read more about it here.\nFurthermore, he loves hard music. Check out his spotify playlist.\n","date":1577566920,"expirydate":-62135596800,"kind":"taxonomy","lang":"en","lastmod":1577566920,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"https://raphiniert.com/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"Raphael Scheible is a computer scientist located at Freiburg im Breisgau in Germany. His research interests include medical computer science, natural language processing and medical imaging. He currently works at the Institute for AI and Informatics in Medicine (AIIM) at the The University Hospital Klinikum rechts der Isar of the Technical University of Munich, which is part of the DIFUTURE project.\nIn 2016 Raphael decided to accept Jesus Christ as his Lord and saviour and asked him to forgive all his sins.","tags":null,"title":"Raphael Scheible","type":"authors"},{"authors":["Raphael Scheible","Fabian Thomczyk","Patric Tippmann","Victor Jaravine","Martin Boeker"],"categories":[],"content":"","date":1606953600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"3e65c764500ec2b52f668f2473bcdc3d","permalink":"https://raphiniert.com/publication/scheible-gottbert-2020/","publishdate":"2020-12-08T15:33:47.904218Z","relpermalink":"/publication/scheible-gottbert-2020/","section":"publication","summary":"Lately, pre-trained language models advanced the field of natural language processing (NLP). The introduction of Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact and increased the relevance of pre-trained models. First, research in this field mainly started on English data followed by models trained with multilingual text corpora. However, current research shows that multilingual models are inferior to monolingual models. Currently, no German single language RoBERTa model is yet published, which we introduce in this work (GottBERT). The German portion of the OSCAR data set was used as text corpus. In an evaluation we compare its performance on the two Named Entity Recognition (NER) tasks Conll 2003 and GermEval 2014 as well as on the text classification tasks GermEval 2018 (fine and coarse) and GNAD with existing German single language BERT models and two multilingual ones. GottBERT was pre-trained related to the original RoBERTa model using fairseq. All downstream tasks were trained using hyperparameter presets taken from the benchmark of German BERT. The experiments were setup utilizing FARM. Performance was measured by the $F_1$ score. GottBERT was successfully pre-trained on a 256 core TPU pod using the RoBERTa BASE architecture. Even without extensive hyper-parameter optimization, in all NER and one text classification task, GottBERT already outperformed all other tested German and multilingual models. In order to support the German NLP field, we publish GottBERT under the AGPLv3 license.","tags":["\"Computer Science - Computation and Language\"","\"Computer Science - Machine Learning\""],"title":"GottBERT: a pure German Language Model","type":"publication"},{"authors":["Raphael Scheible","Dennis Kadioglu","Stephan Ehl","Marco Blum","Martin Boeker","Michael Folz","Bodo Grimbacher","Jens Göbel","Christoph Klein","Alexandra Nieters","Stephan Rusch","Gerhard Kindle","Holger Storf"],"categories":[],"content":"","date":1577836800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"ffa2b87a7411a5feea0a8fa479b0b0e4","permalink":"https://raphiniert.com/publication/scheible-enabling-2020/","publishdate":"2020-12-08T15:33:48.054508Z","relpermalink":"/publication/scheible-enabling-2020/","section":"publication","summary":"Background: The German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases ( Open-Source-Registersystem für Seltene Erkrankungen [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels. Objective: Data from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework. Methods: This paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest. Results: PID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation. Conclusions: The OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries. [JMIR Med Inform 2020;8(10):e17420]","tags":[],"title":"Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry","type":"publication"},{"authors":["Raphael Scheible"],"categories":null,"content":"As child I grew up catholic and I remember myself as praying regularly, well knowing and sensing when I did things that were not good for me and other people. On the other side, I ever had issues with my sexuality and eventually fell into bad habbits at a very early age as child. Early I had several girlfriends and way too early I had my first sexual encounters. Further, I fell into drug habbits, smoked weed and always was looking for freedom in my heart. When I was under alcoholic influence, I was a moron and sometimes treated people very unfair und unloving. I further started to play guitar in a band called Demon Seed, later they renamed to Frozen Infinity. The athmosphere in the band sessions were, let\u0026rsquo;s say, weired. I would say, we were a bunch of young guys dreaming of some success and playing at some events, which at least for me, never happened. I went to high-school, did my degree and just lived with my inner emptiness and powerlessness. In 2007 I did my Civil Service and in the last month of that life period I had a dramatic motorcycle accident.\n In the intensive care unit of the University Hospital in Freiburg after a heavy motor cycle accident in 2007. I nearly died and was very lucky to survive - a clear miracle. Nobody knew how I would end up. Anyhow, physical healing went incredibely fast. I instantly started to study Computer Science. My girlfriend at that time went on a US travel and I would say, I turned her trip to a real nightmare and hell on earth. Not intentionally, I just was so traumatized and something inside of me tormented me with a unnatural and completely unlogical fear of loosing her. In 2008 she quit the relationship, which was brutal to me. Consequently, I decided to start to train my body and to go into some healing process, i.e. psychologist sessions. On a tour to Padua in Italy, I remember myself sitting in a church, crying to God staring at the cross of Jesus. I wanted her back and it hurt so much and I wanted my emptyness to go away. Unfortunately, nothing happened into that direction. At the same time, I read the book The Art of Loving from Erich Fromm and afterwards I tried to start to love people out of myself. The effects were amazing, as relationsships grew. Unfortunately, I quickly went out of energy, out of love (the fuel of the human soul) and I turned to be a selfish, cold hearted human being in the proceeding years. I guess this was the turning point when I slowly decided that God does not exists. The society and humans started to piss me off and I hat much hatred inside my heart. I hoped to find freedom in another country. My new girlfriend and I decided to study abroad in Canada - but in different towns. She in Ottawa and I in Toronto. I lived outside of town. Here I was confronted with the hole in my heart and away from my usual life with my hole filling techniques were gone. Nothing seemed to help and consequently I got so depressed that I did not know what else to do. Blaming everybody and trying to grasp everything that could hold me, I wanted to travel back to Germany. But as I originally planned to travel around after the terms and my flat in Germany was sublet, I decided to stay in Canada and fight it through. After I changed the University to Kingston it became better, but still wasn\u0026rsquo;t amazing. I was empty inside as never before and still did not know how to solve this issue. Sports didn\u0026rsquo;t work, sex didn\u0026rsquo;t work, concentrated working wasn\u0026rsquo;t possible at all and drugs didn\u0026rsquo;t solve this issue. Again I turned the life of my girlfriend into a nightmare. Consequently, she betrayed me when someone made her very drunk. I utterly wanted to forgive her, but I couldn\u0026rsquo;t as cold hearted as I was. When we travelled around it was a pure nightmare for her, I would say.\nWhen I came back to Germany in Summer 2013 after visiting a friend in Columbia, she broke up - understandably. It was a supernatural moment. When she broke up, I thought that I should cry and I tried in vain. Then I had sudden freedom and decided to get some food a bit farer away. I cycled there and met an old flatmate who invited me to come by for a beer. On the very same evening, I met my wife. She was and still is a strong follower of Jesus and on that evening had a special visitor - an evangelical pastor - and living in the old flat where I was living years before. My wife and I became best friends and God started to show me his love through her. Although I was still trying to get my ex-girlfriend back, she started to attract me and we eventually became a couple. Futhermore, when I came back from Canada, I started to be active in politics as I thought, we must care more about this planet. This good intend went into an unhealthy extreme. I started to life vegan and judge other people for destroying the planet. My back then girlfriend and todays wife accompanied me on that path. Despite my good intentions, my heart became harder and harder. I did not care about myself very much and ran around in weird old clothings. For a period of time I even lived without a fridge. But all the effort I put into my lifestyle did not improve my inner status - no fulfillment, no peace, no freedom at all - quite the opposite.\n Me in my vegan lifestyle period in 2014. In 2016, a few weeks after my wife prayed to Jesus, that she cannot live like that anymore and seriously wanted to brake up, I accepted Jesus as my Lord and saviour (she didn\u0026rsquo;t tell me about that prayer): On one day she invited my flatmate, an agnostic, to join her for church service. At that point I was an anti-theist, convinced, that there is no God. I totally believed the idea that nothing created everything - which I can say as a scientist makes absolutely no sense. It is scientifically just impossible that nothing created everything. Further, I even did not accept the fact, that a human consists of soul, body and spirit. Furthermore, I was very narcistic and arrogant personality. I thought to have everything: nice girlfriend, good job and was convinced everything was going good in my life. Anyways, when my flatmate confirmed to join for church service, I decided to join as well. I joined them later at the church when service already started. Entering the church I thought these people are insane: Singing and rasing their arms, like they\u0026rsquo;re really feeling and something. Inside myself, everything was very dark and empty. When the preacher preached, I thought very arrogantly \u0026ldquo;when he knew, what I know he would think differently\u0026rdquo; because I was scientifecly very educated. At the end ot the service the pastor asked the crowd if someone wants to try Jesus. My friend raised his arm and so I did. We both went to the pastor and prayed a \u0026ldquo;sinners prayer\u0026rdquo;. When I spoke out, that I\u0026rsquo;m a sinner I honestly thought in my heart \u0026ldquo;indeed, I didn\u0026rsquo;t do everything right\u0026rdquo;. In the same night I had a very present dream, which was new to me. We started to follow Jesus, i.e. go to church services. Starting to read the Bible and things slowly changed inside of us. On one day, both of us had an extreme encounter with the holy spirit, when an apostle and a prophet of the church prayed for us. In my case, as I know today, back then I lost some demons. On that very day my friend and I knew, that Christ is Lord and the way to go. In my heart I suddenly arrived at some state I would call \u0026ldquo;home\u0026rdquo; and knew that I was looking for my entire life for that. The filling unconditional love that hit me the first time in that moment was so extrem and completely unearned. Funny fact: we were looking for truth, as we saw all the lies in the world. Final destination was the objective truth, which is a person, i.e. Jesus Christ: Jesus saith unto him, I am the way, the truth, and the life: no man cometh unto the Father, but by me1. We completely didn\u0026rsquo;t expect that. In August 2016 I became truly baptized, started to eat meet again and asked my wife to mary me. Continuing following Christ more and more I discovered his love, lost a lot of tears and got some of my emotions back. He furhter healed me from physical sicknesses and I didn\u0026rsquo;t require that much sleep anymore (12h+ vs. 7-8h). Finally, in 2017 my wife and I married.\n Wedding shooting in 2017. Before I encoutered God, I never wanted to marry or even wearing a suite like that. After my conversion to Jesus Christ, it wasn\u0026rsquo;t all that easy, yet. I still suffered from various bad emotional outbreaks and was somehow manipulative. In 2018 the holy spirit told me to fast a couple of days, i.e. only drink water and eat nothing, and so I did. At that time The Last Reformation carried out an event in town and a friend of mine co-ordinated it. So I helped them as well, inviting people on the street to a cinema presentation of their movie. In the evening of the that event, which was my second day fasting, a group of us went to a back yard and ate some pizza. Suddenly, the holy spirit started to work. People were freed from demons. After God worked through us (we touched somebody to pray, and he instantly fell on the ground), I had the feeling God wants to free me. When a couple of people prayed for me, i.e. commanding my demon out, the muscles on my entire back started to twist together as if someone inside or me was holding on it. With a loud shout the demon went out and I instantly felt freedom. I was astonished, as there was more freedom, than I already experienced. I felt like loosing tons of weight. After that experience again a lot changes in my life happened: I was able to grow in love, I heard God more clearly as the fear just went and I didn\u0026rsquo;t had to constantly fight against my old nature anymore. The doubtful voices which were in my head, especially when God spoke to me, disappeared - I became free at the 5. May 2018! That demon was all my life inside of me - one that required fast and prayer as Jesus told us thousands of years ago: Howbeit this kind goeth not out but by prayer and fasting2. After being spiritual free, God started a process to work on my soul. I\u0026rsquo;m still in this process and this seems to be lifelong adventure which sets me more and more free and makes me to the human God once planned me to be.\n Jesus is alive and you can encounter him. It is your decission to accept him as your God and saivor. You do not need to \u0026ldquo;believe\u0026rdquo; in the sense of hoping that it is true, what he did. He is the one who is going to start the faith as the Bible states it - but only by request. He gives you the holy spirit who re-establishes the relation to God the father. Faith in the Bible is \u0026ldquo;trusting\u0026rdquo; and therefore you need to know him - have a relationship, i.e. encounter him. Before my flatmate and I experienced God, we once said \u0026ldquo;it would be nice to have that believe but we simply cannot believe it\u0026rdquo;. That was very smart, as we humans even cannot believe out of our own as the Bible states. Therefore, it is a decission and makes it much easier and is based on maximal grace. It\u0026rsquo;s a complete gift which we can request from Jesus: Looking unto Jesus the author and finisher of our faith3.\n How does it work? Jesus died, because we all sin (are morally far away from what the Bible defines as love). We lie, we steel, we use God\u0026rsquo;s name in vain, are greedy, jealous, envy, proud, selfish and so forth. Therefore, we follow dead Gods based on success, harmony, safety, fun and reputation. These dead gods always want offering, that never suffices. They keep wanting more and more while destroying you. When we act against the moral law of God, it is called sin. Sin is the root of evil. Sin defiles our heart. Sin let\u0026rsquo;s enter fear into our character as we lose our identity and purpose. The consequence of sin is death in the spirit and as God is spirit we are separated from him. God and sin is not compatible, it would lead to death through astonishment. Therefore, when sin entered the world, he had to seperate himself from us. The emptiness in our soul is the consequence. Apart from God, trying to fill this inner vacuum, we destroy ourselves, our loved ones and our surroundings. This sounds very bad and it truly is. In this state, we are not capable to love unconditionally as Jesus Christ does. But the one and only living God is pure uncondontitional love and loves humanity so much, that he died for us and payed the fine. He became human in Jesus Christ. When he died completely sinless on the cross, he payed for everybody who accepts this perfect offering. In order to prove, that he is god, Jesus Christ raised from the dead. He is still alive and has the power to forgive and remove your sins. He can give you a new heart. Now there comes your chance: You can ask Jesus Christ right now for forgiveness and to fill you with the holy spirit by a simple prayer. Just speak out loud with your lips and your mouth the following words:\nJesus Christ, please forgive me all my sins and come into my life! Baptize me with the holy spirit and re-establish the relationship to my heavenly father. I accept you as my God and Saviour. Please make me to the human being you once planned me to be: an image of your perfect love. Please give me a new loving heart and remove all fear, hatred and darkness out of my life and free me now from every demonic power. In Jesus name - Amen.\nSteps to grow your relationship with God are prayer (talk to him) and especially reading the Bible. I recommend to start with the New Testament. Next step is water baptism and I recommend to do it quick - it has some serious spiritual effects, trust me! You can contact somebody of The Last Reformation. Also look for a local Bible based church that acknowledges Jesus Christ as God and saviour as it gives you guidance and spiritual protection. Jesus now gave you the power to see and overcome sin in your life, and most importantly to increase in love (as the Bible defines it) in order to become the human God once planned. God wants to restore you\u0026rsquo;re heart and make you pulling heaven down to make this dark world a brighter place.\nNow, it\u0026rsquo;s the time to rest and let him do his work in you:\nCome unto me, all ye that labour and are heavy laden, and I will give you rest. Take my yoke upon you, and learn of me; for I am meek and lowly in heart: and ye shall find rest unto your souls. For my yoke is easy, and my burden is light. 4\nGod bless you!\nWatch the following movie to see what God is still doing through his desciples today: The Bible, John 14:6 ^ The Bible, Matthew 14:21 ^ The Bible, Hebrews 12:2 ^ The Bible, Matthew 11:28-13 ^ ","date":1577566920,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1577566920,"objectID":"47734519599918f2fd76e1a729191523","permalink":"https://raphiniert.com/jesus/","publishdate":"2019-12-28T22:02:00+01:00","relpermalink":"/jesus/","section":"","summary":"How I met the one and only living God","tags":["Godly encounter","Jesus Christ","Unconditional Love"],"title":"Spiritual Life","type":"page"},{"authors":["Raphael Scheible"],"categories":["Bioinformatics"],"content":"","date":1577555479,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1577555479,"objectID":"47a2efa415310fe109a204c0410ea396","permalink":"https://raphiniert.com/project/miracum-pipe/","publishdate":"2019-12-28T18:51:19+01:00","relpermalink":"/project/miracum-pipe/","section":"project","summary":"Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.","tags":["Bioinformatics","Genetic Sequencing"],"title":"Miracum Pipe","type":"project"},{"authors":["Raphael Scheible","Stephan Rusch","David Guzman","Nizar Mahlaoui","Stephan Ehl","Gerhard Kindle"],"categories":[],"content":"","date":1576368000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440911,"objectID":"4974b303340f8c805b85d9e066b63b4a","permalink":"https://raphiniert.com/publication/scheible-new-2019/","publishdate":"2020-12-08T15:33:48.692746Z","relpermalink":"/publication/scheible-new-2019/","section":"publication","summary":"Primary Immunodeficiencies (PIDs) belong to the group of rare diseases. The European Society for Immunodeficiencies (ESID) operates an international research database application for continuous long-term documentation of patient data. The system is a web application which runs in a standard browser. Therefore, the system is easy to access from any location. Technically, the system is based on Gails backed by MariaDB with high standard security features to comply with the demands of a modern research platform.The ESID Online Database is accessible via the official website: https://esid.org/Working-Parties/Registry-Working-Party/ESID-Registry. A demo system is available via: https://cci-esid-reg-demo-app.uniklinik-freiburg.de/EERS with user demouser and password Demo-2019.","tags":[],"title":"The NEW ESID online database network","type":"publication"},{"authors":["Markus G. Seidel","Gerhard Kindle","Benjamin Gathmann","Isabella Quinti","Matthew Buckland","Joris van Montfrans","Raphael Scheible","Stephan Rusch","Lukas M. Gasteiger","Bodo Grimbacher","Nizar Mahlaoui","Stephan Ehl","ESID Registry Working Party"," collaborators"],"categories":[],"content":"","date":1548979200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"819c0fb9e394bd5b6a6068b38181d4a3","permalink":"https://raphiniert.com/publication/seidel-european-2019/","publishdate":"2020-12-08T15:33:48.370904Z","relpermalink":"/publication/seidel-european-2019/","section":"publication","summary":"Patient registries are instrumental for clinical research in rare diseases. They help to achieve a sufficient sample size for epidemiological and clinical research and to assess the feasibility of clinical trials. The European Society for Immunodeficiencies (ESID) registry currently comprises information on more than 25,000 patients with inborn errors of immunity (IEI). The prerequisite of a patient to be included into the ESID registry is an IEI either defined by a defect in a gene included in the disease classification of the international union of immunological societies, or verified by applying clinical criteria. Because a relevant number of patients, including those with common variable immunodeficiency (CVID), representing the largest group of patients in the registry, remain without a genetic diagnosis, consensus on classification of these patients is mandatory. Here, we present clinical criteria for a large number of IEI that were designed in expert panels with an external review. They were implemented for novel entries and verification of existing data sets from 2014, yielding a substantial refinement. For instance, 8% of adults and 27% of children with CVID (176 of 1704 patients) were reclassified to 22 different immunodeficiencies, illustrating progress in genetics, but also the previous lack of standardized disease definitions. Importantly, apart from registry purposes, the clinical criteria are also helpful to support treatment decisions in the absence of a genetic diagnosis or in patients with variants of unknown significance.","tags":["\"Classification\"","\"Consensus\"","\"Diagnostic algorithm\"","\"Epidemiology\"","\"Guideline\"","\"Primary immune deficiency and immune dysregulation disorder (PIDD)\"","\"Primary immunodeficiency (PID)\"","\"Registry\""],"title":"The European Society for Immunodeficiencies (ESID) Registry Working Definitions for the Clinical Diagnosis of Inborn Errors of Immunity","type":"publication"},{"authors":["Sabine M. El-Helou","Anika-Kerstin Biegner","Sebastian Bode","Stephan R. Ehl","Maximilian Heeg","Maria E. Maccari","Henrike Ritterbusch","Carsten Speckmann","Stephan Rusch","Raphael Scheible","Klaus Warnatz","Faranaz Atschekzei","Renata Beider","Diana Ernst","Stev Gerschmann","Alexandra Jablonka","Gudrun Mielke","Reinhold E. Schmidt","Gesine Schürmann","Georgios Sogkas","Ulrich H. Baumann","Christian Klemann","Dorothee Viemann","Horst von Bernuth","Renate Krüger","Leif G. Hanitsch","Carmen M. Scheibenbogen","Kirsten Wittke","Michael H. Albert","Anna Eichinger","Fabian Hauck","Christoph Klein","Anita Rack-Hoch","Franz M. Sollinger","Anne Avila","Michael Borte","Stephan Borte","Maria Fasshauer","Anja Hauenherm","Nils Kellner","Anna H. Müller","Anett Ülzen","Peter Bader","Shahrzad Bakhtiar","Jae-Yun Lee","Ursula Heß","Ralf Schubert","Sandra Wölke","Stefan Zielen","Sujal Ghosh","Hans-Juergen Laws","Jennifer Neubert","Prasad T. Oommen","Manfred Hönig","Ansgar Schulz","Sandra Steinmann","Klaus Schwarz","Gregor Dückers","Beate Lamers","Vanessa Langemeyer","Tim Niehues","Sonu Shai","Dagmar Graf","Carmen Müglich","Marc T. Schmalzing","Eva C. Schwaneck","Hans-Peter Tony","Johannes Dirks","Gabriele Haase","Johannes G. Liese","Henner Morbach","Dirk Foell","Antje Hellige","Helmut Wittkowski","Katja Masjosthusmann","Michael Mohr","Linda Geberzahn","Christian M. Hedrich","Christiane Müller","Angela Rösen-Wolff","Joachim Roesler","Antje Zimmermann","Uta Behrends","Nikolaus Rieber","Uwe Schauer","Rupert Handgretinger","Ursula Holzer","Jörg Henes","Lothar Kanz","Christoph Boesecke","Jürgen K. Rockstroh","Carolynne Schwarze-Zander","Jan-Christian Wasmuth","Dagmar Dilloo","Brigitte Hülsmann","Stefan Schönberger","Stefan Schreiber","Rainald Zeuner","Tobias Ankermann","Philipp von Bismarck","Hans-Iko Huppertz","Petra Kaiser-Labusch","Johann Greil","Donate Jakoby","Andreas E. Kulozik","Markus Metzler","Nora Naumann-Bartsch","Bettina Sobik","Norbert Graf","Sabine Heine","Robin Kobbe","Kai Lehmberg","Ingo Müller","Friedrich Herrmann","Gerd Horneff","Ariane Klein","Joachim Peitz","Nadine Schmidt","Stefan Bielack","Ute Groß-Wieltsch","Carl F. Classen","Jessica Klasen","Peter Deutz","Dirk Kamitz","Lisa Lassay","Klaus Tenbrock","Norbert Wagner","Benedikt Bernbeck","Bastian Brummel","Eusebia Lara-Villacanas","Esther Münstermann","Dominik T. Schneider","Nadine Tietsch","Marco Westkemper","Michael Weiß","Christof Kramm","Ingrid Kühnle","Silke Kullmann","Hermann Girschick","Christof Specker","Elisabeth Vinnemeier-Laubenthal","Henriette Haenicke","Claudia Schulz","Lothar Schweigerer","Thomas G. Müller","Martina Stiefel","Bernd H. Belohradsky","Veronika Soetedjo","Gerhard Kindle","Bodo Grimbacher"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440911,"objectID":"14feedb6aea97c2cd1de00f8983f5eda","permalink":"https://raphiniert.com/publication/el-helou-german-2019/","publishdate":"2020-12-08T15:33:48.523772Z","relpermalink":"/publication/el-helou-german-2019/","section":"publication","summary":"Introduction: The German PID-NET registry was founded in 2009, serving as the first national registry of patients with primary immunodeficiencies (PID) in Germany. It is part of the European Society for Immunodeficiencies (ESID) registry. The primary purpose of the registry is to gather data on the epidemiology, diagnostic delay, diagnosis, and treatment of PIDs. Methods: Clinical and laboratory data was collected from 2,453 patients from 36 German PID centres in an online registry. Data was analysed with the software Stata® and Excel. Results: The minimum prevalence of PID in Germany is 2.72 per 100,000 inhabitants. Among patients aged 1 to 25, there was a clear predominance of males. The median age of living patients ranged between 7 and 40 years, depending on the respective PID. Predominantly antibody disorders were the most prevalent group with 57% of all 2,453 PID patients had (including 728 CVID patients). A gene defect was identified in 36% of patients. Familial cases were observed in 21% of patients. The age of onset for presenting symptoms ranged from birth to late adulthood (range 0 - 88 years). Presenting symptoms comprised infections (74%) and immune dysregulation (22%). Ninety-three patients were diagnosed without prior clinical symptoms. Regarding the general and clinical diagnostic delay, only severe combined immunodeficiency (SCID) had undergone a slight decrease within the last decade. However, both, SCID and hyper IgE- syndrome showed a substantial improvement in shortening the time between onset of symptoms and genetic diagnosis. Regarding treatment, 49 % of all patients received immunoglobulin G (IgG) substitution (70% - subcutaneous; 29% - intravenous; 1% - unknown). Three-hundred patients underwent at least one hematopoietic stem cell transplantation (HSCT). Five patients had gene therapy. Conclusion: The German PID-NET registry is a precious tool for physicians, researchers, the pharmaceutical industry, politicians, and ultimately the patients, for whom the outcomes will eventually lead to a more timely diagnosis and better treatment.","tags":["\"Primary immunodeficiency (PID)\"","\"clinical online database\"","\"CVID\"","\"ESID\"","\"European Society for Immunodeficiencies\"","\"gene therapy in PID\"","\"German PID-NET registry\"","\"HSCT = hematopoietic stem cell transplant\"","\"HSCT in PID\"","\"IgG substitution therapy\"","\"Immune System\"","\"PID prevalence\"","\"Prevalance\"","\"registry for primary immunodeficiency\""],"title":"The German National Registry of Primary Immunodeficiencies (2012–2017)","type":"publication"},{"authors":null,"categories":null,"content":" Datenschutz Die Betreiber dieser Seiten nehmen den Schutz Ihrer persönlichen Daten sehr ernst. 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Hierzu sowie zu weiteren Fragen zum Thema personenbezogene Daten können Sie sich jederzeit unter der im Impressum angegebenen Adresse an uns wenden.\nQuelle: eRecht24\n","date":1530140400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1530140400,"objectID":"18d05a63a1c8d7ed973cc51838494e41","permalink":"https://raphiniert.com/privacy/","publishdate":"2018-06-28T00:00:00+01:00","relpermalink":"/privacy/","section":"","summary":"Datenschutz Die Betreiber dieser Seiten nehmen den Schutz Ihrer persönlichen Daten sehr ernst. Wir behandeln Ihre personenbezogenen Daten vertraulich und entsprechend der gesetzlichen Datenschutzvorschriften sowie dieser Datenschutzerklärung.\nDie Nutzung unserer Website ist in der Regel ohne Angabe personenbezogener Daten möglich. Soweit auf unseren Seiten personenbezogene Daten (beispielsweise Name, Anschrift oder E-Mail-Adressen) erhoben werden, erfolgt dies, soweit möglich, stets auf freiwilliger Basis. Diese Daten werden ohne Ihre ausdrückliche Zustimmung nicht an Dritte weitergegeben.","tags":null,"title":"Datenschutzerklärung","type":"page"},{"authors":null,"categories":null,"content":" Angaben gemäß § 5 TMG Raphael Scheible\nSessenheimerstr. 6\n79110 Freiburg\nKontakt Telefon: 0761 290 800 60\nE- Mail: mail@raphiniert.com\nStreitschlichtung Wir sind nicht bereit oder verpflichtet, an Streitbeilegungsverfahren vor einer Verbraucherschlichtungsstelle teilzunehmen.\nHaftung für Inhalte Als Diensteanbieter sind wir gemäß § 7 Abs.1 TMG für eigene Inhalte auf diesen Seiten nach den allgemeinen Gesetzen verantwortlich. Nach §§ 8 bis 10 TMG sind wir als Diensteanbieter jedoch nicht verpflichtet, übermittelte oder gespeicherte fremde Informationen zu überwachen oder nach Umständen zu forschen, die auf eine rechtswidrige Tätigkeit hinweisen.\nVerpflichtungen zur Entfernung oder Sperrung der Nutzung von Informationen nach den allgemeinen Gesetzen bleiben hiervon unberührt. 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Bei Bekanntwerden von Rechtsverletzungen werden wir derartige Links umgehend entfernen.\nUrheberrecht Die durch die Seitenbetreiber erstellten Inhalte und Werke auf diesen Seiten unterliegen dem deutschen Urheberrecht. Die Vervielfältigung, Bearbeitung, Verbreitung und jede Art der Verwertung außerhalb der Grenzen des Urheberrechtes bedürfen der schriftlichen Zustimmung des jeweiligen Autors bzw. Erstellers. Downloads und Kopien dieser Seite sind nur für den privaten, nicht kommerziellen Gebrauch gestattet.\nSoweit die Inhalte auf dieser Seite nicht vom Betreiber erstellt wurden, werden die Urheberrechte Dritter beachtet. Insbesondere werden Inhalte Dritter als solche gekennzeichnet. Sollten Sie trotzdem auf eine Urheberrechtsverletzung aufmerksam werden, bitten wir um einen entsprechenden Hinweis. Bei Bekanntwerden von Rechtsverletzungen werden wir derartige Inhalte umgehend entfernen.\nQuelle: https://www.e-recht24.de/impressum-generator.html\n","date":1530140400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1530140400,"objectID":"9b10c1f64082d3869fd4cb1f85809430","permalink":"https://raphiniert.com/terms/","publishdate":"2018-06-28T00:00:00+01:00","relpermalink":"/terms/","section":"","summary":"Angaben gemäß § 5 TMG Raphael Scheible\nSessenheimerstr. 6\n79110 Freiburg\nKontakt Telefon: 0761 290 800 60\nE- Mail: mail@raphiniert.com\nStreitschlichtung Wir sind nicht bereit oder verpflichtet, an Streitbeilegungsverfahren vor einer Verbraucherschlichtungsstelle teilzunehmen.\nHaftung für Inhalte Als Diensteanbieter sind wir gemäß § 7 Abs.1 TMG für eigene Inhalte auf diesen Seiten nach den allgemeinen Gesetzen verantwortlich. Nach §§ 8 bis 10 TMG sind wir als Diensteanbieter jedoch nicht verpflichtet, übermittelte oder gespeicherte fremde Informationen zu überwachen oder nach Umständen zu forschen, die auf eine rechtswidrige Tätigkeit hinweisen.","tags":null,"title":"Impressum","type":"page"},{"authors":["Maria Elena Maccari","Hassan Abolhassani","Asghar Aghamohammadi","Alessandro Aiuti","Olga Aleinikova","Catherine Bangs","Safa Baris","Federica Barzaghi","Helen Baxendale","Matthew Buckland","Siobhan O. Burns","Caterina Cancrini","Andrew Cant","Pascal Cathébras","Marina Cavazzana","Anita Chandra","Francesca Conti","Tanya Coulter","Lisa A. Devlin","J. David M. Edgar","Saul Faust","Alain Fischer","Marina Garcia-Prat","Lennart Hammarström","Maximilian Heeg","Stephen Jolles","Elif Karakoc-Aydiner","Gerhard Kindle","Ayca Kiykim","Dinakantha Kumararatne","Bodo Grimbacher","Hilary Longhurst","Nizar Mahlaoui","Tomas Milota","Fernando Moreira","Despina Moshous","Anna Mukhina","Olaf Neth","Benedicte Neven","Alexandra Nieters","Peter Olbrich","Ahmet Ozen","Jana Pachlopnik Schmid","Capucine Picard","Seraina Prader","William Rae","Janine Reichenbach","Stephan Rusch","Sinisa Savic","Alessia Scarselli","Raphael Scheible","Anna Sediva","Svetlana O. Sharapova","Anna Shcherbina","Mary Slatter","Pere Soler-Palacin","Aurelie Stanislas","Felipe Suarez","Francesca Tucci","Annette Uhlmann","Joris van Montfrans","Klaus Warnatz","Anthony Peter Williams","Phil Wood","Sven Kracker","Alison Mary Condliffe","Stephan Ehl"],"categories":[],"content":"","date":1514764800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"21d58a751c0b27763ecbd2aca5a8c64f","permalink":"https://raphiniert.com/publication/maccari-disease-2018/","publishdate":"2020-12-08T15:33:48.202087Z","relpermalink":"/publication/maccari-disease-2018/","section":"publication","summary":"Activated phosphoinositide 3-kinase (PI3K) δ Syndrome (APDS), caused by autosomal dominant mutations in PIK3CD (APDS1) or PIK3R1 (APDS2), is a heterogeneous primary immunodeficiency. While initial cohort-descriptions summarized the spectrum of clinical and immunological manifestations, questions about long-term disease evolution and response to therapy remain. The prospective European Society for Immunodeficiencies (ESID)-APDS registry aims to characterize the disease course, identify outcome predictors, and evaluate treatment responses. So far, 77 patients have been recruited (51 APDS1, 26 APDS2). Analysis of disease evolution in the first 68 patients pinpoints the early occurrence of recurrent respiratory infections followed by chronic lymphoproliferation, gastrointestinal manifestations, and cytopenias. Although most manifestations occur by age 15, adult-onset and asymptomatic courses were documented. Bronchiectasis was observed in 24/40 APDS1 patients who received a CT-scan compared with 4/15 APDS2 patients. By age 20, half of the patients had received at least one immunosuppressant, but 2-3 lines of immunosuppressive therapy were not unusual before age 10. Response to rapamycin was rated by physician visual analog scale as good in 10, moderate in 9, and poor in 7. Lymphoproliferation showed the best response (8 complete, 11 partial, 6 no remission), while bowel inflammation (3 complete, 3 partial, 9 no remission) and cytopenia (3 complete, 2 partial, 9 no remission) responded less well. Hence, non-lymphoproliferative manifestations should be a key target for novel therapies. This report from the ESID-APDS registry provides comprehensive baseline documentation for a growing cohort that will be followed prospectively to establish prognostic factors and identify patients for treatment studies.","tags":["\"activated phosphoinositide 3-kinase δ syndrome\"","\"natural history\"","\"PIK3CD\"","\"PIK3R1\"","\"rapamycin\"","\"registry\""],"title":"Disease Evolution and Response to Rapamycin in Activated Phosphoinositide 3-Kinase δ Syndrome: The European Society for Immunodeficiencies-Activated Phosphoinositide 3-Kinase δ Syndrome Registry","type":"publication"},{"authors":["Raphael Scheible"],"categories":["Software"],"content":" Features Volume Renderer for use with MATLAB® extends MATLAB® by a GPU-accelerated volume render command that handles 3D volumetric data. The core application is implemented in C/C++. To guarantee fast computations the render process computes on the GPU. This is realized by NVIDIA® CUDA®. Furthermore Volume Renderer for use with MATLAB® provides the following features:\n Special memory management: Due to restricted GPU memory and the requirement to render more than one volume in one scene, we developed a special memory management to enable the rendering of huge data sets in separate rendering passes. Afterward these separately rendered images are combined to one image using MATLAB®. Generic illumination model: We developed a generic illumination model that is easy to extend with other illumination functions. The provided function is the Heneyey-Greenstein phase function. Stereo rendering: In some use cases there is a nice feature to work with stereo images. Thus, the renderer offers the possibility to render off-axis stereo images. High usability: To enable a high usability a MATLAB® interface consisting of several MATLAB® classes has been developed. Due to this interface it is uncomplicated to generate movies. More detailed explanation of the renderer and its background can be found in the documentation in the download section. We provide this software only for 64 bit Linux systems.\nIt was developed by Raphael Scheible supervised by Benjamin Ummenhofer and Junior-Prof Dr. Olaf Ronneberger and is maintained by Raphael Scheible.\nRequirements CUDA® capable NVIDIA® graphics device\n(at least Fermi™ architecture) Linux computer (64 bit) with installed NVIDIA® driver and CUDA® 4.2 MATLAB® (*) * tested and developed under R2010a; might work from 2009a as the OOP feature was introduced the renderer uses.\nExample The following video demonstrates the power of the renderer.\nprovided by Benjamin Ummenhofer, data from [1]\n Download Documentation: documentation-1.0.pdf\nmd5sum: 5af53f26fe5965eb7ac9d69a2c0050be Software: vrm-1.0.tar.gz\nmd5sum: f324f09f3b7845876e5caf50a71b2f12 Installation Copy the files of src/matlab/ and bin/ into your current working folder. From this locationyou can now easily call the renderer.\nIf you want to compile src/HeneyeyGreenstein.cc by yourself, use themex command in your MATLAB® environment:\nmex inputfile -output resultname\nFor a more detailed explanation of the mex command visit this website .\nAlternatively, you can use the HG.mexa64. This provides the command to build alookup table for the illumination setup. This is a compiled version of HeneyeyGrennstein.cc.\nIf you want to write your own illumination function, you can adaptHeneyeyGrennstein.cc accordingly.\nLicence The provided matlab code and C-code for building the Heneyey-Greenstein LUT are released under New BSD License .\nThe matlab binary files (render command and binary of Heneyey-Greenstein.h) are relesed under the following license:\nCopyright © 2012, Raphael Scheible All rights reserved. Redistribution and use of the software, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 2. No names of contributors may be used to endorse or promote products derivedfrom this software without specific prior written permission. 3. The project has to be non-commercial in which this softare is used. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \u0026quot;AS IS\u0026quot; AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Contact Feel free to contact Raphael Scheible with questions and issues. If you find a bug, please report it.\nUsing Volume Renderer for use with MATLAB® ? Please let me know if you are using Volume Renderer for use with MATLAB® as I am interested in how it is used in other research works.\nAcknowledgments Volume Renderer for use with MATLAB® was developed as a student project by Raphael Scheible at University of Freiburg supervised by Benjamin Ummenhofer and Junior-Prof. Dr. Olaf Ronneberger .\nReferences Ronneberger, O and Liu, K and Rath, M and Ruess, D and Mueller, T and Skibbe, H and Drayer, B and Schmidt, T and Filippi, A and Nitschke, R and Brox, T and Burkhardt, H and Driever, W. ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains . 2012. Nature Methods, 9(7):735\u0026ndash;742. ","date":1342282198,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1342282198,"objectID":"c0c82d59f25305347587acd7892e7f77","permalink":"https://raphiniert.com/project/volume-renderer/","publishdate":"2012-07-14T17:09:58+01:00","relpermalink":"/project/volume-renderer/","section":"project","summary":"GPU accelerated volume renderer for use with MATLAB®","tags":["volume renderer","software","3D image analysis"],"title":"Volume Renderer for use with MATLAB®","type":"project"},{"authors":null,"categories":["Web Development"],"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"9f74446337734f373c8dcc669e2df911","permalink":"https://raphiniert.com/project/theresascheible.de/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/project/theresascheible.de/","section":"project","summary":"The web page of the photographer and artist Theresa Scheible.","tags":["Homepage","Web Development"],"title":"theresascheible.de","type":"project"}]
\ No newline at end of file
+[{"authors":["admin"],"categories":null,"content":"Raphael Scheible is a computer scientist located at Freiburg im Breisgau in Germany. His research interests include medical computer science, natural language processing and medical imaging. He currently works at the Institute for AI and Informatics in Medicine (AIIM) at the The University Hospital Klinikum rechts der Isar of the Technical University of Munich, which is part of the DIFUTURE project.\nIn 2016 Raphael decided to accept Jesus Christ as his Lord and saviour and asked him to forgive all his sins. Consequently, he became a born again Christian and is a member at the local church Christengemeinde Freiburg. When he got born again and freed from the demons he was possessed of, his life changed dramatically for the better and he became a new person. Read more about it here.\nFurthermore, he loves hard music. Check out his spotify playlist.\n","date":1577566920,"expirydate":-62135596800,"kind":"taxonomy","lang":"en","lastmod":1577566920,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"https://raphiniert.com/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"Raphael Scheible is a computer scientist located at Freiburg im Breisgau in Germany. His research interests include medical computer science, natural language processing and medical imaging. He currently works at the Institute for AI and Informatics in Medicine (AIIM) at the The University Hospital Klinikum rechts der Isar of the Technical University of Munich, which is part of the DIFUTURE project.\nIn 2016 Raphael decided to accept Jesus Christ as his Lord and saviour and asked him to forgive all his sins.","tags":null,"title":"Raphael Scheible","type":"authors"},{"authors":["Raphael Scheible","Fabian Thomczyk","Patric Tippmann","Victor Jaravine","Martin Boeker"],"categories":[],"content":"","date":1606953600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"3e65c764500ec2b52f668f2473bcdc3d","permalink":"https://raphiniert.com/publication/scheible-gottbert-2020/","publishdate":"2020-12-08T15:33:47.904218Z","relpermalink":"/publication/scheible-gottbert-2020/","section":"publication","summary":"Lately, pre-trained language models advanced the field of natural language processing (NLP). The introduction of Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact and increased the relevance of pre-trained models. First, research in this field mainly started on English data followed by models trained with multilingual text corpora. However, current research shows that multilingual models are inferior to monolingual models. Currently, no German single language RoBERTa model is yet published, which we introduce in this work (GottBERT). The German portion of the OSCAR data set was used as text corpus. In an evaluation we compare its performance on the two Named Entity Recognition (NER) tasks Conll 2003 and GermEval 2014 as well as on the text classification tasks GermEval 2018 (fine and coarse) and GNAD with existing German single language BERT models and two multilingual ones. GottBERT was pre-trained related to the original RoBERTa model using fairseq. All downstream tasks were trained using hyperparameter presets taken from the benchmark of German BERT. The experiments were setup utilizing FARM. Performance was measured by the $F_1$ score. GottBERT was successfully pre-trained on a 256 core TPU pod using the RoBERTa BASE architecture. Even without extensive hyper-parameter optimization, in all NER and one text classification task, GottBERT already outperformed all other tested German and multilingual models. In order to support the German NLP field, we publish GottBERT under the AGPLv3 license.","tags":["\"Computer Science - Computation and Language\"","\"Computer Science - Machine Learning\""],"title":"GottBERT: a pure German Language Model","type":"publication"},{"authors":["Raphael Scheible","Dennis Kadioglu","Stephan Ehl","Marco Blum","Martin Boeker","Michael Folz","Bodo Grimbacher","Jens Göbel","Christoph Klein","Alexandra Nieters","Stephan Rusch","Gerhard Kindle","Holger Storf"],"categories":[],"content":"","date":1577836800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"ffa2b87a7411a5feea0a8fa479b0b0e4","permalink":"https://raphiniert.com/publication/scheible-enabling-2020/","publishdate":"2020-12-08T15:33:48.054508Z","relpermalink":"/publication/scheible-enabling-2020/","section":"publication","summary":"Background: The German Network on Primary Immunodeficiency Diseases (PID-NET) utilizes the European Society for Immunodeficiencies (ESID) registry as a platform for collecting data. In the context of PID-NET data, we show how registries based on custom software can be made interoperable for better collaborative access to precollected data. The Open Source Registry System for Rare Diseases ( Open-Source-Registersystem für Seltene Erkrankungen [OSSE], in German) provides patient organizations, physicians, scientists, and other parties with open source software for the creation of patient registries. In addition, the necessary interoperability between different registries based on the OSSE, as well as existing registries, is supported, which allows those registries to be confederated at both the national and international levels. Objective: Data from the PID-NET registry should be made available in an interoperable manner without losing data sovereignty by extending the existing custom software of the registry using the OSSE registry framework. Methods: This paper describes the following: (1) the installation and configuration of the OSSE bridgehead, (2) an approach using a free toolchain to set up the required interfaces to connect a registry with the OSSE bridgehead, and (3) the decentralized search, which allows the formulation of inquiries that are sent to a selected set of registries of interest. Results: PID-NET uses the established and highly customized ESID registry software. By setting up a so-called OSSE bridgehead, PID-NET data are made interoperable according to a federated approach, and centrally formulated inquiries for data can be received. As the first registry to use the OSSE bridgehead, the authors introduce an approach using a free toolchain to efficiently implement and maintain the required interfaces. Finally, to test and demonstrate the system, two inquiries are realized using the graphical query builder. By establishing and interconnecting an OSSE bridgehead with the underlying ESID registry, confederated queries for data can be received and, if desired, the inquirer can be contacted to further discuss any requirements for cooperation. Conclusions: The OSSE offers an infrastructure that provides the possibility of more collaborative and transparent research. The decentralized search functionality includes registries into one search application while still maintaining data sovereignty. The OSSE bridgehead enables any registry software to be integrated into the OSSE network. The proposed toolchain to set up the required interfaces consists of freely available software components that are well documented. The use of the decentralized search is uncomplicated to use and offers a well-structured, yet still improvable, graphical user interface to formulate queries. [JMIR Med Inform 2020;8(10):e17420]","tags":[],"title":"Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry","type":"publication"},{"authors":["Raphael Scheible"],"categories":null,"content":"As child I grew up catholic and I remember myself as praying regularly, well knowing and sensing when I did things that were not good for me and other people. On the other side, I ever had issues with my sexuality and eventually fell into bad habbits at a very early age as child. Early I had several girlfriends and way too early I had my first sexual encounters. Further, I fell into drug habbits, smoked weed and always was looking for freedom in my heart. When I was under alcoholic influence, I was a moron and sometimes treated people very unfair und unloving. I further started to play guitar in a band called Demon Seed, later they renamed to Frozen Infinity. The athmosphere in the band sessions were, let\u0026rsquo;s say, weired. I would say, we were a bunch of young guys dreaming of some success and playing at some events, which at least for me, never happened. I went to high-school, did my degree and just lived with my inner emptiness and powerlessness. In 2007 I did my Civil Service and in the last month of that life period I had a dramatic motorcycle accident.\n In the intensive care unit of the University Hospital in Freiburg after a heavy motor cycle accident in 2007. I nearly died and was very lucky to survive - a clear miracle. Nobody knew how I would end up. Anyhow, physical healing went incredibely fast. I instantly started to study Computer Science. My girlfriend at that time went on a US travel and I would say, I turned her trip to a real nightmare and hell on earth. Not intentionally, I just was so traumatized and something inside of me tormented me with a unnatural and completely unlogical fear of loosing her. In 2008 she quit the relationship, which was brutal to me. Consequently, I decided to start to train my body and to go into some healing process, i.e. psychologist sessions. On a tour to Padua in Italy, I remember myself sitting in a church, crying to God staring at the cross of Jesus. I wanted her back and it hurt so much and I wanted my emptyness to go away. Unfortunately, nothing happened into that direction. At the same time, I read the book The Art of Loving from Erich Fromm and afterwards I tried to start to love people out of myself. The effects were amazing, as relationsships grew. Unfortunately, I quickly went out of energy, out of love (the fuel of the human soul) and I turned to be a selfish, cold hearted human being in the proceeding years. I guess this was the turning point when I slowly decided that God does not exists. The society and humans started to piss me off and I hat much hatred inside my heart. I hoped to find freedom in another country. My new girlfriend and I decided to study abroad in Canada - but in different towns. She in Ottawa and I in Toronto. I lived outside of town. Here I was confronted with the hole in my heart and away from my usual life with my hole filling techniques were gone. Nothing seemed to help and consequently I got so depressed that I did not know what else to do. Blaming everybody and trying to grasp everything that could hold me, I wanted to travel back to Germany. But as I originally planned to travel around after the terms and my flat in Germany was sublet, I decided to stay in Canada and fight it through. After I changed the University to Kingston it became better, but still wasn\u0026rsquo;t amazing. I was empty inside as never before and still did not know how to solve this issue. Sports didn\u0026rsquo;t work, sex didn\u0026rsquo;t work, concentrated working wasn\u0026rsquo;t possible at all and drugs didn\u0026rsquo;t solve this issue. Again I turned the life of my girlfriend into a nightmare. Consequently, she betrayed me when someone made her very drunk. I utterly wanted to forgive her, but I couldn\u0026rsquo;t as cold hearted as I was. When we travelled around it was a pure nightmare for her, I would say.\nWhen I came back to Germany in Summer 2013 after visiting a friend in Columbia, she broke up - understandably. It was a supernatural moment. When she broke up, I thought that I should cry and I tried in vain. Then I had sudden freedom and decided to get some food a bit farer away. I cycled there and met an old flatmate who invited me to come by for a beer. On the very same evening, I met my wife. She was and still is a strong follower of Jesus and on that evening had a special visitor - an evangelical pastor - and living in the old flat where I was living years before. My wife and I became best friends and God started to show me his love through her. Although I was still trying to get my ex-girlfriend back, she started to attract me and we eventually became a couple. Futhermore, when I came back from Canada, I started to be active in politics as I thought, we must care more about this planet. This good intend went into an unhealthy extreme. I started to life vegan and judge other people for destroying the planet. My back then girlfriend and todays wife accompanied me on that path. Despite my good intentions, my heart became harder and harder. I did not care about myself very much and ran around in weird old clothings. For a period of time I even lived without a fridge. But all the effort I put into my lifestyle did not improve my inner status - no fulfillment, no peace, no freedom at all - quite the opposite.\n Me in my vegan lifestyle period in 2014. In 2016, a few weeks after my wife prayed to Jesus, that she cannot live like that anymore and seriously wanted to brake up, I accepted Jesus as my Lord and saviour (she didn\u0026rsquo;t tell me about that prayer): On one day she invited my flatmate, an agnostic, to join her for church service. At that point I was an anti-theist, convinced, that there is no God. I totally believed the idea that nothing created everything - which I can say as a scientist makes absolutely no sense. It is scientifically just impossible that nothing created everything. Further, I even did not accept the fact, that a human consists of soul, body and spirit. Furthermore, I was very narcistic and arrogant personality. I thought to have everything: nice girlfriend, good job and was convinced everything was going good in my life. Anyways, when my flatmate confirmed to join for church service, I decided to join as well. I joined them later at the church when service already started. Entering the church I thought these people are insane: Singing and rasing their arms, like they\u0026rsquo;re really feeling and something. Inside myself, everything was very dark and empty. When the preacher preached, I thought very arrogantly \u0026ldquo;when he knew, what I know he would think differently\u0026rdquo; because I was scientifecly very educated. At the end ot the service the pastor asked the crowd if someone wants to try Jesus. My friend raised his arm and so I did. We both went to the pastor and prayed a \u0026ldquo;sinners prayer\u0026rdquo;. When I spoke out, that I\u0026rsquo;m a sinner I honestly thought in my heart \u0026ldquo;indeed, I didn\u0026rsquo;t do everything right\u0026rdquo;. In the same night I had a very present dream, which was new to me. We started to follow Jesus, i.e. go to church services. Starting to read the Bible and things slowly changed inside of us. On one day, both of us had an extreme encounter with the holy spirit, when an apostle and a prophet of the church prayed for us. In my case, as I know today, back then I lost some demons. On that very day my friend and I knew, that Christ is Lord and the way to go. In my heart I suddenly arrived at some state I would call \u0026ldquo;home\u0026rdquo; and knew that I was looking for my entire life for that. The filling unconditional love that hit me the first time in that moment was so extrem and completely unearned. Funny fact: we were looking for truth, as we saw all the lies in the world. Final destination was the objective truth, which is a person, i.e. Jesus Christ: Jesus saith unto him, I am the way, the truth, and the life: no man cometh unto the Father, but by me1. We completely didn\u0026rsquo;t expect that. In August 2016 I became truly baptized, started to eat meet again and asked my wife to mary me. Continuing following Christ more and more I discovered his love, lost a lot of tears and got some of my emotions back. He furhter healed me from physical sicknesses and I didn\u0026rsquo;t require that much sleep anymore (12h+ vs. 7-8h). Finally, in 2017 my wife and I married.\n Wedding shooting in 2017. Before I encoutered God, I never wanted to marry or even wearing a suite like that. After my conversion to Jesus Christ, it wasn\u0026rsquo;t all that easy, yet. I still suffered from various bad emotional outbreaks and was somehow manipulative. In 2018 the holy spirit told me to fast a couple of days, i.e. only drink water and eat nothing, and so I did. At that time The Last Reformation carried out an event in town and a friend of mine co-ordinated it. So I helped them as well, inviting people on the street to a cinema presentation of their movie. In the evening of the that event, which was my second day fasting, a group of us went to a back yard and ate some pizza. Suddenly, the holy spirit started to work. People were freed from demons. After God worked through us (we touched somebody to pray, and he instantly fell on the ground), I had the feeling God wants to free me. When a couple of people prayed for me, i.e. commanding my demon out, the muscles on my entire back started to twist together as if someone inside or me was holding on it. With a loud shout the demon went out and I instantly felt freedom. I was astonished, as there was more freedom, than I already experienced. I felt like loosing tons of weight. After that experience again a lot changes in my life happened: I was able to grow in love, I heard God more clearly as the fear just went and I didn\u0026rsquo;t had to constantly fight against my old nature anymore. The doubtful voices which were in my head, especially when God spoke to me, disappeared - I became free at the 5. May 2018! That demon was all my life inside of me - one that required fast and prayer as Jesus told us thousands of years ago: Howbeit this kind goeth not out but by prayer and fasting2. After being spiritual free, God started a process to work on my soul. I\u0026rsquo;m still in this process and this seems to be lifelong adventure which sets me more and more free and makes me to the human God once planned me to be.\n Jesus is alive and you can encounter him. It is your decission to accept him as your God and saivor. You do not need to \u0026ldquo;believe\u0026rdquo; in the sense of hoping that it is true, what he did. He is the one who is going to start the faith as the Bible states it - but only by request. He gives you the holy spirit who re-establishes the relation to God the father. Faith in the Bible is \u0026ldquo;trusting\u0026rdquo; and therefore you need to know him - have a relationship, i.e. encounter him. Before my flatmate and I experienced God, we once said \u0026ldquo;it would be nice to have that believe but we simply cannot believe it\u0026rdquo;. That was very smart, as we humans even cannot believe out of our own as the Bible states. Therefore, it is a decission and makes it much easier and is based on maximal grace. It\u0026rsquo;s a complete gift which we can request from Jesus: Looking unto Jesus the author and finisher of our faith3.\n How does it work? Jesus died, because we all sin (are morally far away from what the Bible defines as love). We lie, we steel, we use God\u0026rsquo;s name in vain, are greedy, jealous, envy, proud, selfish and so forth. Therefore, we follow dead Gods based on success, harmony, safety, fun and reputation. These dead gods always want offering, that never suffices. They keep wanting more and more while destroying you. When we act against the moral law of God, it is called sin. Sin is the root of evil. Sin defiles our heart. Sin let\u0026rsquo;s enter fear into our character as we lose our identity and purpose. The consequence of sin is death in the spirit and as God is spirit we are separated from him. God and sin is not compatible, it would lead to death through astonishment. Therefore, when sin entered the world, he had to seperate himself from us. The emptiness in our soul is the consequence. Apart from God, trying to fill this inner vacuum, we destroy ourselves, our loved ones and our surroundings. This sounds very bad and it truly is. In this state, we are not capable to love unconditionally as Jesus Christ does. But the one and only living God is pure uncondontitional love and loves humanity so much, that he died for us and payed the fine. He became human in Jesus Christ. When he died completely sinless on the cross, he payed for everybody who accepts this perfect offering. In order to prove, that he is god, Jesus Christ raised from the dead. He is still alive and has the power to forgive and remove your sins. He can give you a new heart. Now there comes your chance: You can ask Jesus Christ right now for forgiveness and to fill you with the holy spirit by a simple prayer. Just speak out loud with your lips and your mouth the following words:\nJesus Christ, please forgive me all my sins and come into my life! Baptize me with the holy spirit and re-establish the relationship to my heavenly father. I accept you as my God and Saviour. Please make me to the human being you once planned me to be: an image of your perfect love. Please give me a new loving heart and remove all fear, hatred and darkness out of my life and free me now from every demonic power. In Jesus name - Amen.\nSteps to grow your relationship with God are prayer (talk to him) and especially reading the Bible. I recommend to start with the New Testament. Next step is water baptism and I recommend to do it quick - it has some serious spiritual effects, trust me! You can contact somebody of The Last Reformation. Also look for a local Bible based church that acknowledges Jesus Christ as God and saviour as it gives you guidance and spiritual protection. Jesus now gave you the power to see and overcome sin in your life, and most importantly to increase in love (as the Bible defines it) in order to become the human God once planned. God wants to restore you\u0026rsquo;re heart and make you pulling heaven down to make this dark world a brighter place.\nNow, it\u0026rsquo;s the time to rest and let him do his work in you:\nCome unto me, all ye that labour and are heavy laden, and I will give you rest. Take my yoke upon you, and learn of me; for I am meek and lowly in heart: and ye shall find rest unto your souls. For my yoke is easy, and my burden is light. 4\nGod bless you!\nWatch the following movie to see what God is still doing through his desciples today: The Bible, John 14:6 ^ The Bible, Matthew 14:21 ^ The Bible, Hebrews 12:2 ^ The Bible, Matthew 11:28-13 ^ ","date":1577566920,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1577566920,"objectID":"47734519599918f2fd76e1a729191523","permalink":"https://raphiniert.com/jesus/","publishdate":"2019-12-28T22:02:00+01:00","relpermalink":"/jesus/","section":"","summary":"How I met the one and only living God","tags":["Godly encounter","Jesus Christ","Unconditional Love"],"title":"Spiritual Life","type":"page"},{"authors":["Raphael Scheible"],"categories":["Bioinformatics"],"content":"","date":1577555479,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1577555479,"objectID":"47a2efa415310fe109a204c0410ea396","permalink":"https://raphiniert.com/project/miracum-pipe/","publishdate":"2019-12-28T18:51:19+01:00","relpermalink":"/project/miracum-pipe/","section":"project","summary":"Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.","tags":["Bioinformatics","Genetic Sequencing"],"title":"Miracum Pipe","type":"project"},{"authors":["Raphael Scheible","Stephan Rusch","David Guzman","Nizar Mahlaoui","Stephan Ehl","Gerhard Kindle"],"categories":[],"content":"","date":1576368000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440911,"objectID":"4974b303340f8c805b85d9e066b63b4a","permalink":"https://raphiniert.com/publication/scheible-new-2019/","publishdate":"2020-12-08T15:33:48.692746Z","relpermalink":"/publication/scheible-new-2019/","section":"publication","summary":"Primary Immunodeficiencies (PIDs) belong to the group of rare diseases. The European Society for Immunodeficiencies (ESID) operates an international research database application for continuous long-term documentation of patient data. The system is a web application which runs in a standard browser. Therefore, the system is easy to access from any location. Technically, the system is based on Gails backed by MariaDB with high standard security features to comply with the demands of a modern research platform.The ESID Online Database is accessible via the official website: https://esid.org/Working-Parties/Registry-Working-Party/ESID-Registry. A demo system is available via: https://cci-esid-reg-demo-app.uniklinik-freiburg.de/EERS with user demouser and password Demo-2019.","tags":[],"title":"The NEW ESID online database network","type":"publication"},{"authors":["Markus G. Seidel","Gerhard Kindle","Benjamin Gathmann","Isabella Quinti","Matthew Buckland","Joris van Montfrans","Raphael Scheible","Stephan Rusch","Lukas M. Gasteiger","Bodo Grimbacher","Nizar Mahlaoui","Stephan Ehl","ESID Registry Working Party"," collaborators"],"categories":[],"content":"","date":1548979200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"819c0fb9e394bd5b6a6068b38181d4a3","permalink":"https://raphiniert.com/publication/seidel-european-2019/","publishdate":"2020-12-08T15:33:48.370904Z","relpermalink":"/publication/seidel-european-2019/","section":"publication","summary":"Patient registries are instrumental for clinical research in rare diseases. They help to achieve a sufficient sample size for epidemiological and clinical research and to assess the feasibility of clinical trials. The European Society for Immunodeficiencies (ESID) registry currently comprises information on more than 25,000 patients with inborn errors of immunity (IEI). The prerequisite of a patient to be included into the ESID registry is an IEI either defined by a defect in a gene included in the disease classification of the international union of immunological societies, or verified by applying clinical criteria. Because a relevant number of patients, including those with common variable immunodeficiency (CVID), representing the largest group of patients in the registry, remain without a genetic diagnosis, consensus on classification of these patients is mandatory. Here, we present clinical criteria for a large number of IEI that were designed in expert panels with an external review. They were implemented for novel entries and verification of existing data sets from 2014, yielding a substantial refinement. For instance, 8% of adults and 27% of children with CVID (176 of 1704 patients) were reclassified to 22 different immunodeficiencies, illustrating progress in genetics, but also the previous lack of standardized disease definitions. Importantly, apart from registry purposes, the clinical criteria are also helpful to support treatment decisions in the absence of a genetic diagnosis or in patients with variants of unknown significance.","tags":["\"Classification\"","\"Consensus\"","\"Diagnostic algorithm\"","\"Epidemiology\"","\"Guideline\"","\"Primary immune deficiency and immune dysregulation disorder (PIDD)\"","\"Primary immunodeficiency (PID)\"","\"Registry\""],"title":"The European Society for Immunodeficiencies (ESID) Registry Working Definitions for the Clinical Diagnosis of Inborn Errors of Immunity","type":"publication"},{"authors":["Sabine M. El-Helou","Anika-Kerstin Biegner","Sebastian Bode","Stephan R. Ehl","Maximilian Heeg","Maria E. Maccari","Henrike Ritterbusch","Carsten Speckmann","Stephan Rusch","Raphael Scheible","Klaus Warnatz","Faranaz Atschekzei","Renata Beider","Diana Ernst","Stev Gerschmann","Alexandra Jablonka","Gudrun Mielke","Reinhold E. Schmidt","Gesine Schürmann","Georgios Sogkas","Ulrich H. Baumann","Christian Klemann","Dorothee Viemann","Horst von Bernuth","Renate Krüger","Leif G. Hanitsch","Carmen M. Scheibenbogen","Kirsten Wittke","Michael H. Albert","Anna Eichinger","Fabian Hauck","Christoph Klein","Anita Rack-Hoch","Franz M. Sollinger","Anne Avila","Michael Borte","Stephan Borte","Maria Fasshauer","Anja Hauenherm","Nils Kellner","Anna H. Müller","Anett Ülzen","Peter Bader","Shahrzad Bakhtiar","Jae-Yun Lee","Ursula Heß","Ralf Schubert","Sandra Wölke","Stefan Zielen","Sujal Ghosh","Hans-Juergen Laws","Jennifer Neubert","Prasad T. Oommen","Manfred Hönig","Ansgar Schulz","Sandra Steinmann","Klaus Schwarz","Gregor Dückers","Beate Lamers","Vanessa Langemeyer","Tim Niehues","Sonu Shai","Dagmar Graf","Carmen Müglich","Marc T. Schmalzing","Eva C. Schwaneck","Hans-Peter Tony","Johannes Dirks","Gabriele Haase","Johannes G. Liese","Henner Morbach","Dirk Foell","Antje Hellige","Helmut Wittkowski","Katja Masjosthusmann","Michael Mohr","Linda Geberzahn","Christian M. Hedrich","Christiane Müller","Angela Rösen-Wolff","Joachim Roesler","Antje Zimmermann","Uta Behrends","Nikolaus Rieber","Uwe Schauer","Rupert Handgretinger","Ursula Holzer","Jörg Henes","Lothar Kanz","Christoph Boesecke","Jürgen K. Rockstroh","Carolynne Schwarze-Zander","Jan-Christian Wasmuth","Dagmar Dilloo","Brigitte Hülsmann","Stefan Schönberger","Stefan Schreiber","Rainald Zeuner","Tobias Ankermann","Philipp von Bismarck","Hans-Iko Huppertz","Petra Kaiser-Labusch","Johann Greil","Donate Jakoby","Andreas E. Kulozik","Markus Metzler","Nora Naumann-Bartsch","Bettina Sobik","Norbert Graf","Sabine Heine","Robin Kobbe","Kai Lehmberg","Ingo Müller","Friedrich Herrmann","Gerd Horneff","Ariane Klein","Joachim Peitz","Nadine Schmidt","Stefan Bielack","Ute Groß-Wieltsch","Carl F. Classen","Jessica Klasen","Peter Deutz","Dirk Kamitz","Lisa Lassay","Klaus Tenbrock","Norbert Wagner","Benedikt Bernbeck","Bastian Brummel","Eusebia Lara-Villacanas","Esther Münstermann","Dominik T. Schneider","Nadine Tietsch","Marco Westkemper","Michael Weiß","Christof Kramm","Ingrid Kühnle","Silke Kullmann","Hermann Girschick","Christof Specker","Elisabeth Vinnemeier-Laubenthal","Henriette Haenicke","Claudia Schulz","Lothar Schweigerer","Thomas G. Müller","Martina Stiefel","Bernd H. Belohradsky","Veronika Soetedjo","Gerhard Kindle","Bodo Grimbacher"],"categories":[],"content":"","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440911,"objectID":"14feedb6aea97c2cd1de00f8983f5eda","permalink":"https://raphiniert.com/publication/el-helou-german-2019/","publishdate":"2020-12-08T15:33:48.523772Z","relpermalink":"/publication/el-helou-german-2019/","section":"publication","summary":"Introduction: The German PID-NET registry was founded in 2009, serving as the first national registry of patients with primary immunodeficiencies (PID) in Germany. It is part of the European Society for Immunodeficiencies (ESID) registry. The primary purpose of the registry is to gather data on the epidemiology, diagnostic delay, diagnosis, and treatment of PIDs. Methods: Clinical and laboratory data was collected from 2,453 patients from 36 German PID centres in an online registry. Data was analysed with the software Stata® and Excel. Results: The minimum prevalence of PID in Germany is 2.72 per 100,000 inhabitants. Among patients aged 1 to 25, there was a clear predominance of males. The median age of living patients ranged between 7 and 40 years, depending on the respective PID. Predominantly antibody disorders were the most prevalent group with 57% of all 2,453 PID patients had (including 728 CVID patients). A gene defect was identified in 36% of patients. Familial cases were observed in 21% of patients. The age of onset for presenting symptoms ranged from birth to late adulthood (range 0 - 88 years). Presenting symptoms comprised infections (74%) and immune dysregulation (22%). Ninety-three patients were diagnosed without prior clinical symptoms. Regarding the general and clinical diagnostic delay, only severe combined immunodeficiency (SCID) had undergone a slight decrease within the last decade. However, both, SCID and hyper IgE- syndrome showed a substantial improvement in shortening the time between onset of symptoms and genetic diagnosis. Regarding treatment, 49 % of all patients received immunoglobulin G (IgG) substitution (70% - subcutaneous; 29% - intravenous; 1% - unknown). Three-hundred patients underwent at least one hematopoietic stem cell transplantation (HSCT). Five patients had gene therapy. Conclusion: The German PID-NET registry is a precious tool for physicians, researchers, the pharmaceutical industry, politicians, and ultimately the patients, for whom the outcomes will eventually lead to a more timely diagnosis and better treatment.","tags":["\"Primary immunodeficiency (PID)\"","\"clinical online database\"","\"CVID\"","\"ESID\"","\"European Society for Immunodeficiencies\"","\"gene therapy in PID\"","\"German PID-NET registry\"","\"HSCT = hematopoietic stem cell transplant\"","\"HSCT in PID\"","\"IgG substitution therapy\"","\"Immune System\"","\"PID prevalence\"","\"Prevalance\"","\"registry for primary immunodeficiency\""],"title":"The German National Registry of Primary Immunodeficiencies (2012–2017)","type":"publication"},{"authors":null,"categories":null,"content":" Datenschutz Die Betreiber dieser Seiten nehmen den Schutz Ihrer persönlichen Daten sehr ernst. 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Hierzu sowie zu weiteren Fragen zum Thema personenbezogene Daten können Sie sich jederzeit unter der im Impressum angegebenen Adresse an uns wenden.\nQuelle: eRecht24\n","date":1530140400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1530140400,"objectID":"18d05a63a1c8d7ed973cc51838494e41","permalink":"https://raphiniert.com/privacy/","publishdate":"2018-06-28T00:00:00+01:00","relpermalink":"/privacy/","section":"","summary":"Datenschutz Die Betreiber dieser Seiten nehmen den Schutz Ihrer persönlichen Daten sehr ernst. Wir behandeln Ihre personenbezogenen Daten vertraulich und entsprechend der gesetzlichen Datenschutzvorschriften sowie dieser Datenschutzerklärung.\nDie Nutzung unserer Website ist in der Regel ohne Angabe personenbezogener Daten möglich. Soweit auf unseren Seiten personenbezogene Daten (beispielsweise Name, Anschrift oder E-Mail-Adressen) erhoben werden, erfolgt dies, soweit möglich, stets auf freiwilliger Basis. Diese Daten werden ohne Ihre ausdrückliche Zustimmung nicht an Dritte weitergegeben.","tags":null,"title":"Datenschutzerklärung","type":"page"},{"authors":null,"categories":null,"content":" Angaben gemäß § 5 TMG Raphael Scheible\nSessenheimerstr. 6\n79110 Freiburg\nKontakt Telefon: 0761 290 800 60\nE- Mail: mail@raphiniert.com\nStreitschlichtung Wir sind nicht bereit oder verpflichtet, an Streitbeilegungsverfahren vor einer Verbraucherschlichtungsstelle teilzunehmen.\nHaftung für Inhalte Als Diensteanbieter sind wir gemäß § 7 Abs.1 TMG für eigene Inhalte auf diesen Seiten nach den allgemeinen Gesetzen verantwortlich. Nach §§ 8 bis 10 TMG sind wir als Diensteanbieter jedoch nicht verpflichtet, übermittelte oder gespeicherte fremde Informationen zu überwachen oder nach Umständen zu forschen, die auf eine rechtswidrige Tätigkeit hinweisen.\nVerpflichtungen zur Entfernung oder Sperrung der Nutzung von Informationen nach den allgemeinen Gesetzen bleiben hiervon unberührt. 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Bei Bekanntwerden von Rechtsverletzungen werden wir derartige Links umgehend entfernen.\nUrheberrecht Die durch die Seitenbetreiber erstellten Inhalte und Werke auf diesen Seiten unterliegen dem deutschen Urheberrecht. Die Vervielfältigung, Bearbeitung, Verbreitung und jede Art der Verwertung außerhalb der Grenzen des Urheberrechtes bedürfen der schriftlichen Zustimmung des jeweiligen Autors bzw. Erstellers. Downloads und Kopien dieser Seite sind nur für den privaten, nicht kommerziellen Gebrauch gestattet.\nSoweit die Inhalte auf dieser Seite nicht vom Betreiber erstellt wurden, werden die Urheberrechte Dritter beachtet. Insbesondere werden Inhalte Dritter als solche gekennzeichnet. Sollten Sie trotzdem auf eine Urheberrechtsverletzung aufmerksam werden, bitten wir um einen entsprechenden Hinweis. Bei Bekanntwerden von Rechtsverletzungen werden wir derartige Inhalte umgehend entfernen.\nQuelle: https://www.e-recht24.de/impressum-generator.html\n","date":1530140400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1530140400,"objectID":"9b10c1f64082d3869fd4cb1f85809430","permalink":"https://raphiniert.com/terms/","publishdate":"2018-06-28T00:00:00+01:00","relpermalink":"/terms/","section":"","summary":"Angaben gemäß § 5 TMG Raphael Scheible\nSessenheimerstr. 6\n79110 Freiburg\nKontakt Telefon: 0761 290 800 60\nE- Mail: mail@raphiniert.com\nStreitschlichtung Wir sind nicht bereit oder verpflichtet, an Streitbeilegungsverfahren vor einer Verbraucherschlichtungsstelle teilzunehmen.\nHaftung für Inhalte Als Diensteanbieter sind wir gemäß § 7 Abs.1 TMG für eigene Inhalte auf diesen Seiten nach den allgemeinen Gesetzen verantwortlich. Nach §§ 8 bis 10 TMG sind wir als Diensteanbieter jedoch nicht verpflichtet, übermittelte oder gespeicherte fremde Informationen zu überwachen oder nach Umständen zu forschen, die auf eine rechtswidrige Tätigkeit hinweisen.","tags":null,"title":"Impressum","type":"page"},{"authors":["Maria Elena Maccari","Hassan Abolhassani","Asghar Aghamohammadi","Alessandro Aiuti","Olga Aleinikova","Catherine Bangs","Safa Baris","Federica Barzaghi","Helen Baxendale","Matthew Buckland","Siobhan O. Burns","Caterina Cancrini","Andrew Cant","Pascal Cathébras","Marina Cavazzana","Anita Chandra","Francesca Conti","Tanya Coulter","Lisa A. Devlin","J. David M. Edgar","Saul Faust","Alain Fischer","Marina Garcia-Prat","Lennart Hammarström","Maximilian Heeg","Stephen Jolles","Elif Karakoc-Aydiner","Gerhard Kindle","Ayca Kiykim","Dinakantha Kumararatne","Bodo Grimbacher","Hilary Longhurst","Nizar Mahlaoui","Tomas Milota","Fernando Moreira","Despina Moshous","Anna Mukhina","Olaf Neth","Benedicte Neven","Alexandra Nieters","Peter Olbrich","Ahmet Ozen","Jana Pachlopnik Schmid","Capucine Picard","Seraina Prader","William Rae","Janine Reichenbach","Stephan Rusch","Sinisa Savic","Alessia Scarselli","Raphael Scheible","Anna Sediva","Svetlana O. Sharapova","Anna Shcherbina","Mary Slatter","Pere Soler-Palacin","Aurelie Stanislas","Felipe Suarez","Francesca Tucci","Annette Uhlmann","Joris van Montfrans","Klaus Warnatz","Anthony Peter Williams","Phil Wood","Sven Kracker","Alison Mary Condliffe","Stephan Ehl"],"categories":[],"content":"","date":1514764800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1607440910,"objectID":"21d58a751c0b27763ecbd2aca5a8c64f","permalink":"https://raphiniert.com/publication/maccari-disease-2018/","publishdate":"2020-12-08T15:33:48.202087Z","relpermalink":"/publication/maccari-disease-2018/","section":"publication","summary":"Activated phosphoinositide 3-kinase (PI3K) δ Syndrome (APDS), caused by autosomal dominant mutations in PIK3CD (APDS1) or PIK3R1 (APDS2), is a heterogeneous primary immunodeficiency. While initial cohort-descriptions summarized the spectrum of clinical and immunological manifestations, questions about long-term disease evolution and response to therapy remain. The prospective European Society for Immunodeficiencies (ESID)-APDS registry aims to characterize the disease course, identify outcome predictors, and evaluate treatment responses. So far, 77 patients have been recruited (51 APDS1, 26 APDS2). Analysis of disease evolution in the first 68 patients pinpoints the early occurrence of recurrent respiratory infections followed by chronic lymphoproliferation, gastrointestinal manifestations, and cytopenias. Although most manifestations occur by age 15, adult-onset and asymptomatic courses were documented. Bronchiectasis was observed in 24/40 APDS1 patients who received a CT-scan compared with 4/15 APDS2 patients. By age 20, half of the patients had received at least one immunosuppressant, but 2-3 lines of immunosuppressive therapy were not unusual before age 10. Response to rapamycin was rated by physician visual analog scale as good in 10, moderate in 9, and poor in 7. Lymphoproliferation showed the best response (8 complete, 11 partial, 6 no remission), while bowel inflammation (3 complete, 3 partial, 9 no remission) and cytopenia (3 complete, 2 partial, 9 no remission) responded less well. Hence, non-lymphoproliferative manifestations should be a key target for novel therapies. This report from the ESID-APDS registry provides comprehensive baseline documentation for a growing cohort that will be followed prospectively to establish prognostic factors and identify patients for treatment studies.","tags":["\"activated phosphoinositide 3-kinase δ syndrome\"","\"natural history\"","\"PIK3CD\"","\"PIK3R1\"","\"rapamycin\"","\"registry\""],"title":"Disease Evolution and Response to Rapamycin in Activated Phosphoinositide 3-Kinase δ Syndrome: The European Society for Immunodeficiencies-Activated Phosphoinositide 3-Kinase δ Syndrome Registry","type":"publication"},{"authors":["Raphael Scheible"],"categories":["Software"],"content":" Features Volume Renderer for use with MATLAB® extends MATLAB® by a GPU-accelerated volume render command that handles 3D volumetric data. The core application is implemented in C/C++. To guarantee fast computations the render process computes on the GPU. This is realized by NVIDIA® CUDA®. Furthermore Volume Renderer for use with MATLAB® provides the following features:\n Special memory management: Due to restricted GPU memory and the requirement to render more than one volume in one scene, we developed a special memory management to enable the rendering of huge data sets in separate rendering passes. Afterward these separately rendered images are combined to one image using MATLAB®. Generic illumination model: We developed a generic illumination model that is easy to extend with other illumination functions. The provided function is the Heneyey-Greenstein phase function. Stereo rendering: In some use cases there is a nice feature to work with stereo images. Thus, the renderer offers the possibility to render off-axis stereo images. High usability: To enable a high usability a MATLAB® interface consisting of several MATLAB® classes has been developed. Due to this interface it is uncomplicated to generate movies. More detailed explanation of the renderer and its background can be found in the documentation in the download section. We provide this software only for 64 bit Linux systems.\nIt was developed by Raphael Scheible supervised by Benjamin Ummenhofer and Junior-Prof Dr. Olaf Ronneberger and is maintained by Raphael Scheible.\nRequirements CUDA® capable NVIDIA® graphics device\n(at least Fermi™ architecture) Linux computer (64 bit) with installed NVIDIA® driver and CUDA® 4.2 MATLAB® (*) * tested and developed under R2010a; might work from 2009a as the OOP feature was introduced the renderer uses.\nExample The following video demonstrates the power of the renderer.\nprovided by Benjamin Ummenhofer, data from [1]\n Download Documentation: documentation-1.0.pdf\nmd5sum: 5af53f26fe5965eb7ac9d69a2c0050be Software: vrm-1.0.tar.gz\nmd5sum: f324f09f3b7845876e5caf50a71b2f12 Installation Copy the files of src/matlab/ and bin/ into your current working folder. From this locationyou can now easily call the renderer.\nIf you want to compile src/HeneyeyGreenstein.cc by yourself, use themex command in your MATLAB® environment:\nmex inputfile -output resultname\nFor a more detailed explanation of the mex command visit this website .\nAlternatively, you can use the HG.mexa64. This provides the command to build alookup table for the illumination setup. This is a compiled version of HeneyeyGrennstein.cc.\nIf you want to write your own illumination function, you can adaptHeneyeyGrennstein.cc accordingly.\nLicence The provided matlab code and C-code for building the Heneyey-Greenstein LUT are released under New BSD License .\nThe matlab binary files (render command and binary of Heneyey-Greenstein.h) are relesed under the following license:\nCopyright © 2012, Raphael Scheible All rights reserved. Redistribution and use of the software, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 2. No names of contributors may be used to endorse or promote products derivedfrom this software without specific prior written permission. 3. The project has to be non-commercial in which this softare is used. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \u0026quot;AS IS\u0026quot; AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Contact Feel free to contact Raphael Scheible with questions and issues. If you find a bug, please report it.\nUsing Volume Renderer for use with MATLAB® ? Please let me know if you are using Volume Renderer for use with MATLAB® as I am interested in how it is used in other research works.\nAcknowledgments Volume Renderer for use with MATLAB® was developed as a student project by Raphael Scheible at University of Freiburg supervised by Benjamin Ummenhofer and Junior-Prof. Dr. Olaf Ronneberger .\nReferences Ronneberger, O and Liu, K and Rath, M and Ruess, D and Mueller, T and Skibbe, H and Drayer, B and Schmidt, T and Filippi, A and Nitschke, R and Brox, T and Burkhardt, H and Driever, W. ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains . 2012. Nature Methods, 9(7):735\u0026ndash;742. ","date":1342282198,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1342282198,"objectID":"c0c82d59f25305347587acd7892e7f77","permalink":"https://raphiniert.com/project/volume-renderer/","publishdate":"2012-07-14T17:09:58+01:00","relpermalink":"/project/volume-renderer/","section":"project","summary":"GPU accelerated volume renderer for use with MATLAB®","tags":["volume renderer","software","3D image analysis"],"title":"Volume Renderer for use with MATLAB®","type":"project"},{"authors":null,"categories":["Web Development"],"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"9f74446337734f373c8dcc669e2df911","permalink":"https://raphiniert.com/project/theresascheible.de/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/project/theresascheible.de/","section":"project","summary":"The web page of the photographer and artist Theresa Scheible.","tags":["Homepage","Web Development"],"title":"theresascheible.de","type":"project"}]
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