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Book ; Online ; Thesis: Grundbesitzklauseln in Doppelbesteuerungsabkommen.

Schreiber, Jacob [Verfasser]

2023

Author's details	Jacob Schreiber
Keywords	Recht ; Law
Subject code	sg340
Language	German
Publisher	Duncker & Humblot
Publishing place	Berlin
Document type	Book ; Online ; Thesis
ISBN	978-3-428-58786-5 ; 3-428-58786-3
Database	Digital theses on the web

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Article: Predicting chromatin conformation contact maps.

Min, Alan / Schreiber, Jacob / Kundaje, Anshul / Noble, William Stafford

bioRxiv : the preprint server for biology

2024

Abstract: Over the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin ... ...

Abstract	Over the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin architecture. Accordingly, making sense of the relationship between genome structure and function requires teasing apart two closely related questions: how does chromatin 3D structure change from one cell type to the next, and how do different measurements of that structure differ from one another, even when the two assays are carried out in the same cell type? In this work, we assemble a collection of chromatin 3D datasets-each represented as a 2D contact map- spanning multiple assay types and cell types. We then build a machine learning model that predicts missing contact maps in this collection. We use the model to systematically explore how genome 3D architecture changes, at the level of compartments, domains, and loops, between cell type and between assay types.
Language	English
Publishing date	2024-04-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.12.589240
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Machine learning for profile prediction in genomics.

Schreiber, Jacob / Singh, Ritambhara

Current opinion in chemical biology

2021 Volume 65, Page(s) 35–41

Abstract: A recent deluge of publicly available multi-omics data has fueled the development of machine learning methods aimed at investigating important questions in genomics. Although the motivations for these methods vary, a task that is commonly adopted is that ...

Abstract	A recent deluge of publicly available multi-omics data has fueled the development of machine learning methods aimed at investigating important questions in genomics. Although the motivations for these methods vary, a task that is commonly adopted is that of profile prediction, where predictions are made for one or more forms of biochemical activity along the genome, for example, histone modification, chromatin accessibility, or protein binding. In this review, we give an overview of the research works performing profile prediction, define two broad categories of profile prediction tasks, and discuss the types of scientific questions that can be answered in each.
MeSH term(s)	Chromatin/genetics ; Genome ; Genomics ; Machine Learning ; Protein Binding
Chemical Substances	Chromatin
Language	English
Publishing date	2021-06-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2021.04.008
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Article ; Online: Accelerating in silico saturation mutagenesis using compressed sensing.

Schreiber, Jacob / Nair, Surag / Balsubramani, Akshay / Kundaje, Anshul

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 14, Page(s) 3557–3564

Abstract: Motivation: In silico saturation mutagenesis (ISM) is a popular approach in computational genomics for calculating feature attributions on biological sequences that proceeds by systematically perturbing each position in a sequence and recording the ... ...

Abstract	Motivation: In silico saturation mutagenesis (ISM) is a popular approach in computational genomics for calculating feature attributions on biological sequences that proceeds by systematically perturbing each position in a sequence and recording the difference in model output. However, this method can be slow because systematically perturbing each position requires performing a number of forward passes proportional to the length of the sequence being examined. Results: In this work, we propose a modification of ISM that leverages the principles of compressed sensing to require only a constant number of forward passes, regardless of sequence length, when applied to models that contain operations with a limited receptive field, such as convolutions. Our method, named Yuzu, can reduce the time that ISM spends in convolution operations by several orders of magnitude and, consequently, Yuzu can speed up ISM on several commonly used architectures in genomics by over an order of magnitude. Notably, we found that Yuzu provides speedups that increase with the complexity of the convolution operation and the length of the sequence being analyzed, suggesting that Yuzu provides large benefits in realistic settings. Availability and implementation: We have made this tool available at https://github.com/kundajelab/yuzu.
MeSH term(s)	Mutagenesis ; Genomics/methods
Language	English
Publishing date	2022-05-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac385
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Article ; Online: fastISM: performant in silico saturation mutagenesis for convolutional neural networks.

Nair, Surag / Shrikumar, Avanti / Schreiber, Jacob / Kundaje, Anshul

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 9, Page(s) 2397–2403

Abstract: Motivation: Deep-learning models, such as convolutional neural networks, are able to accurately map biological sequences to associated functional readouts and properties by learning predictive de novo representations. In silico saturation mutagenesis ( ... ...

Abstract	Motivation: Deep-learning models, such as convolutional neural networks, are able to accurately map biological sequences to associated functional readouts and properties by learning predictive de novo representations. In silico saturation mutagenesis (ISM) is a popular feature attribution technique for inferring contributions of all characters in an input sequence to the model's predicted output. The main drawback of ISM is its runtime, as it involves multiple forward propagations of all possible mutations of each character in the input sequence through the trained model to predict the effects on the output. Results: We present fastISM, an algorithm that speeds up ISM by a factor of over 10× for commonly used convolutional neural network architectures. fastISM is based on the observations that the majority of computation in ISM is spent in convolutional layers, and a single mutation only disrupts a limited region of intermediate layers, rendering most computation redundant. fastISM reduces the gap between backpropagation-based feature attribution methods and ISM. It far surpasses the runtime of backpropagation-based methods on multi-output architectures, making it feasible to run ISM on a large number of sequences. Availability and implementation: An easy-to-use Keras/TensorFlow 2 implementation of fastISM is available at https://github.com/kundajelab/fastISM. fastISM can be installed using pip install fastism. A hands-on tutorial can be found at https://colab.research.google.com/github/kundajelab/fastISM/blob/master/notebooks/colab/DeepSEA.ipynb. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Neural Networks, Computer ; Mutagenesis ; Mutation
Language	English
Publishing date	2022-02-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac135
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Article: Mental Health Disparities among Pre-Clinical Medical Students at Saint Louis University during the COVID-19 Pandemic.

Chwa, Won Jong / Chong, Albert C / Lin, Sheryl / Su, Erin H / Sheridan, Chantal / Schreiber, Jacob / Zia, Stephanie K / Thompson, Keniesha

Behavioral sciences (Basel, Switzerland)

2024 Volume 14, Issue 2

Abstract: The COVID-19 pandemic disproportionately affected racial and ethnic minorities. Medical students were also particularly impacted as they coped with increased stressors due to delayed medical training and a high prevalence of mental health conditions. ... ...

Abstract	The COVID-19 pandemic disproportionately affected racial and ethnic minorities. Medical students were also particularly impacted as they coped with increased stressors due to delayed medical training and a high prevalence of mental health conditions. This study investigates mental health disparities of underrepresented in medicine (URM) students at the Saint Louis University School of Medicine (SLUSOM). An anonymous online survey was distributed to first- and second-year medical students at SLUSOM in February 2021. The survey queried demographic information, lifestyle factors, and pandemic-related and institutional concerns. Mental health was assessed via the Generalized Anxiety Disorder-7 (GAD-7) and the Patient Health Questionnaire-9 (PHQ-9). Statistical tests were run with SPSS, version 27. A convenience sample of 87 students responded to the survey. Students who were categorized as URM were significantly more likely to be at risk of major depressive disorder during the pandemic. Concern about a lack of financial support was significantly greater among students categorized as URM. Concerns regarding a lack of financial support, mental health support, and decreased quality of medical training significantly predicted PHQ-9 scores. Our findings revealed several key factors that may exacerbate mental health disparities among URM students during the pandemic. Providing adequate financial and academic resources for URMs may improve mental health outcomes for similar adverse events in the future.
Language	English
Publishing date	2024-01-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2651997-5
ISSN	2076-328X
ISSN	2076-328X
DOI	10.3390/bs14020089
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Article ; Online: Future Directions and Innovations in Venous Sinus Stenting.

Pandey, Abhinav / Schreiber, Craig / Garton, Andrew L A / Jung, Brandon / Goldberg, Jacob L / Kocharian, Gary / Carnevale, Joseph A / Boddu, Srikanth R

World neurosurgery

2024 Volume 184, Page(s) 387–394

Abstract: This review explores the future role of venous sinus stenting (VSS) in the management of idiopathic intracranial hypertension and pulsatile tinnitus. Despite its favorable safety profile and clinical outcomes compared with traditional treatments, VSS is ... ...

Abstract	This review explores the future role of venous sinus stenting (VSS) in the management of idiopathic intracranial hypertension and pulsatile tinnitus. Despite its favorable safety profile and clinical outcomes compared with traditional treatments, VSS is not yet the standard of care for these conditions, lacking high-level evidence data and guidelines for patient selection and indications. Current and recently completed clinical trials are expected to provide data to support the adoption of VSS as a primary treatment option. Additionally, VSS shows potential in treating other conditions, such as dural arteriovenous fistula and cerebral venous sinus thrombosis, and it is likely that the procedure will continue to see an expansion of its approved indications. The current lack of dedicated venous stenting technology is being addressed with promising advancements, which may improve procedural ease and patient outcomes. VSS also offers potential for expansion into modulation of brain electrophysiology via endovascular routes, offering exciting possibilities for neurodiagnostics and treatment of neurodegenerative disorders.
MeSH term(s)	Humans ; Treatment Outcome ; Pseudotumor Cerebri ; Stents ; Cranial Sinuses/surgery ; Endovascular Procedures/methods ; Intracranial Hypertension ; Retrospective Studies
Language	English
Publishing date	2024-04-08
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	2534351-8
ISSN	1878-8769 ; 1878-8750
ISSN (online)	1878-8769
ISSN	1878-8750
DOI	10.1016/j.wneu.2023.12.128
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Zs.A 1159: Show issues

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Article ; Online: Author Correction: Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome.

Schreiber, Jacob / Durham, Timothy / Bilmes, Jeffrey / Noble, William Stafford

Genome biology

2021 Volume 22, Issue 1, Page(s) 255

Language	English
Publishing date	2021-09-03
Publishing country	England
Document type	Published Erratum
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02470-4
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Article ; Online: Challenges in the use of Venous Sinus Stenting in the Treatment of Idiopathic Intracranial Hypertension and Pulsatile Tinnitus.

Pandey, Abhinav / Schreiber, Craig / Garton, Andrew L A / Jung, Brandon / Goldberg, Jacob L / Kocharian, Gary / Carnevale, Joseph A / Boddu, Srikanth R

World neurosurgery

2024 Volume 184, Page(s) 372–386

Abstract: Although numerous case series and meta-analyses have shown the efficacy of venous sinus stenting (VSS) in the treatment of idiopathic intracranial hypertension and idiopathic intracranial hypertension-associated pulsatile tinnitus, there remain numerous ... ...

Abstract	Although numerous case series and meta-analyses have shown the efficacy of venous sinus stenting (VSS) in the treatment of idiopathic intracranial hypertension and idiopathic intracranial hypertension-associated pulsatile tinnitus, there remain numerous challenges to be resolved. There is no widespread agreement on candidacy; pressure gradient and failed medical treatment are common indications, but not all clinicians require medical refractoriness as a criterion. Venous manometry, venography, and cerebral angiography are essential tools for patient assessment, but again disagreements exist regarding the best, or most appropriate, diagnostic imaging choice. Challenges with the VSS technique also exist, such as stent choice and deployment. There are considerations regarding postprocedural balloon angioplasty and pharmacologic treatment, but there is insufficient evidence to formalize postoperative decision making. Although complications of VSS are relatively rare, they include in-stent stenosis, hemorrhage, and subdural hematoma, and the learning curve for VSS presents specific challenges in navigating venous anatomy, emphasizing the need for wider availability of high-quality training. Recurrence of symptoms, particularly stent-adjacent stenosis, poses challenges, and although restenting and cerebrospinal fluid-diverting procedures are options, there is a need for clearer criteria for retreatment strategies. Despite these challenges, when comparing VSS with traditional cerebrospinal fluid-diverting procedures, VSS emerges as a favorable option, with strong clinical outcomes, lower complication rates, and cost-effectiveness. Further research is necessary to refine techniques and indications and address specific aspects of VSS to overcome these challenges.
MeSH term(s)	Humans ; Pseudotumor Cerebri/complications ; Pseudotumor Cerebri/diagnostic imaging ; Pseudotumor Cerebri/surgery ; Tinnitus/etiology ; Tinnitus/surgery ; Constriction, Pathologic/diagnostic imaging ; Constriction, Pathologic/surgery ; Constriction, Pathologic/complications ; Cranial Sinuses/diagnostic imaging ; Cranial Sinuses/surgery ; Stents/adverse effects ; Intracranial Hypertension/surgery ; Intracranial Hypertension/complications ; Treatment Outcome ; Retrospective Studies
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2534351-8
ISSN	1878-8769 ; 1878-8750
ISSN (online)	1878-8769
ISSN	1878-8750
DOI	10.1016/j.wneu.2023.12.164
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Article ; Online: "Everybody in this room can understand": A qualitative exploration of peer support during residency training.

Jain, Aarti / Tabatabai, Ramin / Schreiber, Jacob / Vo, Anne / Riddell, Jeffrey

AEM education and training

2022 Volume 6, Issue 2, Page(s) e10728

Abstract: Objectives: Though peer support groups are often utilized during residency training, the dynamics, content, and impact of social support offered through peer support are poorly understood. We explored trainee perceptions of the benefits, drawbacks, and ... ...

Abstract	Objectives: Though peer support groups are often utilized during residency training, the dynamics, content, and impact of social support offered through peer support are poorly understood. We explored trainee perceptions of the benefits, drawbacks, and optimal membership and facilitation of peer support groups. Methods: After engaging in a peer support program at an emergency medicine residency program, 15 residents and 4 group facilitators participated in four focus groups in 2018. Interview questions explored the dynamics of group interactions, types of support offered, and psychological impacts of participation. The authors conducted a reflexive thematic analysis of data, performing iterative coding and organization of interview transcripts. Results: Discussions with experienced senior residents and alumni normalized residents' workplace struggles and provided them with insights into the trajectory of their residency experiences. Vulnerable group dialogue was enhanced by the use of "insider" participants; however, residents acknowledged the potential contributions of mental health professionals. Though groups occasionally utilized maladaptive coping strategies and lacked actual solutions, they also enhanced residents' sense of belonging, willingness to share personal struggles, and ability to "reset" in the clinical environment. Conclusions: Participants offered insights into the benefits and drawbacks of peer support as well as optimal peer group composition and facilitation. Support groups may be more effective if they engage a complementary model of alumni and pre-briefed psychologist facilitators, avoid fatalism, and aim to foster intimate connections among residents. These findings can inform the development of future initiatives aiming to create a safe space for trainees to discuss workplace stressors.
Language	English
Publishing date	2022-04-01
Publishing country	United States
Document type	Journal Article
ISSN	2472-5390
ISSN (online)	2472-5390
DOI	10.1002/aet2.10728
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