tbuckley/cabot-search huggingface dataset:
The Potential Role of Lumateperone—Something Borrowed? Something New?
Authors: Joshua T. Kantrowitz
Journal: JAMA Psychiatry (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Psychiatry HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Psychiatry journal
Neonatal T Cells: A Reinterpretation
Authors: Brian D. Rudd
Journal: Annual Review of Immunology (2020)

Neonatal CD4 + and CD8 + T cells have historically been characterized as immature or defective. However, recent studies prompt a reinterpretation of the functions of neonatal T cells. Rather than a population of cells always falling short of expectations set by their adult counterparts, neonatal T cells are gaining recognition as a distinct population of lymphocytes well suited for the rapidly changing environment in early life. In this review, I will highlight new evidence indicating that neonatal T cells are not inert or less potent versions of adult T cells but instead are a broadly reactive layer of T cells poised to quickly develop into regulatory or effector cells, depending on the needs of the host. In this way, neonatal T cells are well adapted to provide fast-acting immune protection against foreign pathogens, while also sustaining tolerance to self-antigens.
An Event-driven Trial for Oral Treprostinil. Progress but Not the Holy Grail
Authors: Nicholas S. Hill, Harrison W. Farber, Ioana R. Preston
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

detailed information will also likely impact patient outcomes.Finally, this study suffers from underpowering, as it includes just 102 samples, less than half of which are the preinvasive AIS/MIA lesions of interest.Atypical alveolar hyperplasia, a presumed precursor of AIS, was not studied.Indeed, given the extensive genomic changes found in AIS/MIA, to truly understand early carcinogenesis, future studies must consider looking back to earlier preinvasive lesions, and even to the "normal" airways of smokers, as has been done in other tissues ( 14).Nevertheless, this study presents one of the largest cohorts published to date of preinvasive lung ADC, a rare disease state that is of great scientific interest given what it can teach us about cancer development.Several putative pathways for carcinogenesis are identified, providing candidates for experimental validation, and the implications for screening, diagnosis, and detection are significant.By stepping backward from invasive cancer into the earliest stages of carcinogenesis, this study represents an important step forward in our understanding of lung cancer evolution.
The Percentage of CD44-/CD24-/Lin- Cells in Primary Breast Tumors and Correlation Between Prognostic Factors
Authors: E. Yetimoglu, D. Cabuk, E. Karaoz, S. Kaya, S. Temiz, O. Acikgoz, K. Uygun, Z. Canturk, E. Yirmibesoglu, G. Aksu
Journal: Annals of Oncology (2012)
Association Between the Implementation of Hospital-Based Palliative Care and Use of Intensive Care During Terminal Hospitalizations
Authors: May Hua, Yewei Lu, Xiaoyue Ma, R. Sean Morrison, Guohua Li, Hannah Wunsch
Journal: JAMA Network Open (2020)

<h3>Importance</h3> The use of intensive care at the end of life continues to be common. Although the provision of palliative care has been advocated as a way to mitigate the use of high-intensity care, it is unknown whether implementation of hospital-based palliative care services is associated with reduced use of intensive care at the end of life. <h3>Objective</h3> To determine whether implementation of hospital-based palliative care services is associated with decreased intensive care unit (ICU) use during terminal hospitalizations. <h3>Design, Setting, and Participants</h3> This cohort study included 51 hospitals in New York State that either did or did not implement a palliative care program between 2008 and 2014. Hospitals that consistently had a palliative care program during the study period were excluded. Participants were adult patients who died during hospitalization. Data analysis was performed between January 2018 and July 2019. <h3>Exposure</h3> Implementation of a palliative care program. <h3>Main Outcomes and Measures</h3> The primary outcome was ICU use. A difference-in-differences analysis was performed using multilevel regression to assess the association between implementing a palliative care program and ICU use during terminal hospitalizations while adjusting for patient and hospital characteristics and time trends. <h3>Results</h3> During the study period, 73 370 patients (mean [SD] age, 76.5 [14.1] years; 38 467 [52.4%] women) died during hospitalization, of whom 37 628 (51.3%) received care in hospitals that implemented palliative care services and 35 742 (48.7%) received care in a hospital without palliative care implementation. Patients who received care in hospitals after implementation of palliative care services were less likely to receive intensive care than patients admitted to the same hospitals before implementation (49.3% vs 52.8%; difference 3.5%; 95% CI, 2.5%-4.5%;<i>P</i> &lt; .001). Compared with hospitals that never had a palliative care program, the implementation of palliative care was associated with a 10% reduction in ICU use during terminal hospitalizations (adjusted relative risk, 0.90; 95% CI, 0.85-0.95;<i>P</i> &lt; .001). <h3>Conclusions and Relevance</h3> The implementation of hospital-based palliative care services in New York State was associated with a modest reduction in ICU use during terminal hospitalizations.
A Very Persistent Cold
Authors: Fabrizia Faustinella
Journal: Annals of Internal Medicine (2020)

On Being a Doctor21 January 2020A Very Persistent ColdFabrizia Faustinella, MD, PhDFabrizia Faustinella, MD, PhDBaylor College of Medicine, Houston, Texas (F.F.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/M19-0326 Audio Reading - “A Very Persistent Cold” Audio. Virginia Hood, MD, reads “A Very Persistent Cold” by Fabrizia Faustinella, MD, PhD Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail The wind chimes were clinking forcefully that morning, buffeted by strong winds. Bitter-cold air was plunging into the south—an arctic blast, they said on the weather channel.My city stays warm during the winter months, but this was an extraordinary year. We were to expect freezing weather for several days. I worried that my beautiful hibiscus plants wouldn't survive. I wrapped them in sheets tightly taped all the way around to ward off the icy gusts. I caught a mild cold by fighting the chilling winds while trying to save the flowers.My wardrobe had no clothing suited for this ... Author, Article, and Disclosure InformationAffiliations: Baylor College of Medicine, Houston, Texas (F.F.)Corresponding Author: Fabrizia Faustinella, MD, PhD, 3718 South MacGregor Way, Houston, TX 77021; e-mail, [email protected]com. PreviousarticleNextarticle Advertisement Audio Reading - “A Very Persistent Cold” Audio. Virginia Hood, MD, reads “A Very Persistent Cold” by Fabrizia Faustinella, MD, PhD Your browser does not support the audio element. Audio player progress bar Step backward in current audio track Play current audio trackPause current audio track Step forward in current audio track Mute current audio trackUnmute current audio track 00:00/ FiguresReferencesRelatedDetails Metrics 21 January 2020Volume 172, Issue 2Page: 155-156KeywordsAntibioticsBoneComputersEmotionsShouldersSleepSneezingStarvationTemperatureUpper respiratory tract infections ePublished: 21 January 2020 Issue Published: 21 January 2020 Copyright & PermissionsCopyright © 2020 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
The <i>Toxoplasma gondii</i> virulence factor ROP16 acts in cis and trans, and suppresses T cell responses
Authors: Longfei Chen, David A. Christian, Joshua A. Kochanowsky, Anthony T. Phan, Joseph T. Clark, Shuai Wang, Corbett Berry, Jung Oh, Xiaoguang Chen, David S. Roos, Daniel P. Beiting, Anita A. Koshy, Christopher A. Hunter
Journal: The Journal of Experimental Medicine (2020)

The ability of Toxoplasma gondii to inject the rhoptry kinase ROP16 into host cells results in the activation of the transcription factors STAT3 and STAT6, but it is unclear how these events impact infection. Here, parasites that inject Cre-recombinase with rhoptry proteins were used to distinguish infected macrophages from those only injected with parasite proteins. Transcriptional profiling revealed that injection of rhoptry proteins alone was sufficient to induce an M2 phenotype that is dependent on STAT3 and STAT6, but only infected cells displayed reduced expression of genes associated with antimicrobial activity and protective immunity. In vivo, the absence of STAT3 or STAT6 improved parasite control, while the loss of ROP16 resulted in a marked reduction in parasite numbers and heightened parasite-specific T cell responses. Thus, ROP16 is a virulence factor that can act in cis and trans to promote M2 programs and which limits the magnitude of parasite-specific T cell responses.
Gender Differences in Authorship of Critical Care Literature
Authors: Kelly C. Vranas, David Ouyang, Amber L. Lin, Christopher G. Slatore, Donald R. Sullivan, Meeta Prasad Kerlin, Kathleen D. Liu, Rebecca M. Baron, Carolyn S. Calfee, Lorraine B. Ware, Scott D. Halpern, Michael A. Matthay, Margaret S. Herridge, Sangeeta Mehta, Angela J. Rogers
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

Gender gaps exist in academic leadership positions in critical care. Peer-reviewed publications are crucial to career advancement, and yet little is known regarding gender differences in authorship of critical care research.
DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Authors: Zilu Zhou, Bihui Xu, Andy Minn, Nancy R. Zhang
Journal: Genome biology (2020)

Abstract Although scRNA-seq is now ubiquitously adopted in studies of intratumor heterogeneity, detection of somatic mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that clusters single cells into genetically distinct subclones and reconstructs the phylogenetic tree relating the subclones. DENDRO utilizes transcribed point mutations and accounts for technical noise and expression stochasticity. We benchmark DENDRO and demonstrate its application on simulation data and real data from three cancer types. In particular, on a mouse melanoma model in response to immunotherapy, DENDRO delineates the role of neoantigens in treatment response.
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs
Authors: Katharina Jasmin Hoff
Journal: Genomics Proteomics & Bioinformatics (2019)

Abstract Novel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. Such need has been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs, which can be hosted on any publicly available web server, allow browsing genomes via UCSC Genome Browser servers. The steps for creating custom Assembly Hubs are well documented and the required tools are publicly available. However, the number of steps for creating a novel Assembly Hub is large. In some cases, the format of input files needs to be adapted, which is a difficult task for scientists without programming background. Here, we describe MakeHub, a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated fashion. The pipeline also allows extending previously created Hubs by additional tracks. MakeHub is freely available for downloading at https://github.com/Gaius-Augustus/MakeHub.
Pre-emptive genomic surveillance of emerging ebolaviruses
Authors: Ignacio Postigo-Hidalgo, Carlo Fischer, Andres Moreira-Soto, Patricia Tscheak, Michael Nagel, Markus Eickmann, Jan Felix Drexler
Journal: Eurosurveillance (2020)

Genomic surveillance during ebolavirus outbreaks to elucidate transmission chains and develop diagnostic tests is delayed by the laborious development of variant-specific laboratory assays. We developed a new protocol combining 31 parallel PCR assays with Illumina/MinION-based sequencing, allowing generic ebolavirus genomic surveillance, validated using cell culture-derived Ebola, Reston, Sudan and Taï Forest virus at concentrations compatible with patient viral loads. Our approach enables pre-emptive genomic surveillance of ongoing and future ebolavirus outbreaks irrespective of variant divergence.
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways
Authors: Cigdem Sevim Bayrak, Peng Zhang, Martin Tristani-Firouzi, Bruce D. Gelb, Yuval Itan
Journal: Genome Medicine (2020)

Abstract Background Congenital heart disease (CHD) affects ~ 1% of live births and is the most common birth defect. Although the genetic contribution to the CHD has been long suspected, it has only been well established recently. De novo variants are estimated to contribute to approximately 8% of sporadic CHD. Methods CHD is genetically heterogeneous, making pathway enrichment analysis an effective approach to explore and statistically validate CHD-associated genes. In this study, we performed novel gene and pathway enrichment analyses of high-impact de novo variants in the recently published whole-exome sequencing (WES) data generated from a cohort of CHD 2645 parent-offspring trios to identify new CHD-causing candidate genes and mutations. We performed rigorous variant- and gene-level filtrations to identify potentially damaging variants, followed by enrichment analyses and gene prioritization. Results Our analyses revealed 23 novel genes that are likely to cause CHD, including HSP90AA1 , ROCK2 , IQGAP1 , and CHD4 , and sharing biological functions, pathways, molecular interactions, and properties with known CHD-causing genes. Conclusions Ultimately, these findings suggest novel genes that are likely to be contributing to CHD pathogenesis.
Climate emergency: new expert panel will set out how NHS can achieve net zero
Authors: Jacqui Wise
Journal: BMJ (2020)

NHS England is establishing an expert panel to set out how the NHS can get to “net zero” on greenhouse gases ahead of the national target of 2050, the world’s first major health service to do so.

The expert panel will examine changes that can be made to reduce the NHS’s carbon footprint by looking at its supply chain and energy use. It will submit an interim report to NHS England in the summer, and the final report is expected in the autumn, ahead of the COP26 climate change summit in Glasgow in November.

In the UK, healthcare is responsible for 5.4% of the country’s net emissions, says a recent a report from Health Care Without Harm.1 The causes of air pollution and climate change are often the same, and both contribute to increased pressure on health services. …
How to be involved in peer teaching
Authors: Rebecca Choong, Fiona Macauslan
Journal: BMJ (2020)

In peer teaching, learners are taught by those similar in age or at a similar educational stage. Many peer teaching programmes in medical school involve junior students being taught by senior students.1 Some evidence suggests that the closer learners are in training stage to their teacher, the better the learning outcomes.2 This might be because peers have better ideas of the relative importance of different topics.3 Students also say that peer teaching enables them to direct their own education.4

Peer teaching doesn’t just help learners—teachers can benefit too.45 It provides an opportunity for revision and furthering knowledge. Developing ways to explain challenging concepts to peers promotes effective communication skills, which are essential for working in teams and with patients.

This article provides some tips on how to set up a peer teaching initiative on the basis of the authors’ experiences.

### Small group bedside teaching

This type of teaching can be coordinated formally within a whole year group, or ad hoc by a group of students on placement. It is particularly useful preparation for OSCEs (objective structured clinical examinations) and is most effective in groups of three to five. Students take turns in playing the roles of examiner and candidate.

### Revision lectures

You …
Five-year impact of ICU-acquired neuromuscular complications: a prospective, observational study
Authors: Nathalie Van Aerde, Philippe Meersseman, Yves Debaveye, Alexander Wilmer, Jan Gunst, Michael P. Casaer, Frans Bruyninckx, Pieter J. Wouters, Rik Gosselink, Greet Van den Berghe, Greet Hermans
Journal: Intensive Care Medicine (2020)
Europe’s drug regulator wins court backing for data transparency policy
Authors: Clare Dyer
Journal: BMJ (2020)

The European Union’s highest court has decisively upheld the European Medicines Agency’s right to publish clinical trial data from drug companies’ applications to market their products in the EU.

In two keenly awaited judgments, the European Court of Justice has comprehensively rejected appeals by two companies against rulings in 2018 by the General Court of the European Union upholding the European Medicines Agency’s open data policy.12

In 2010 the agency adopted a policy of making available all documents underlying a successful drug licence application from January 2014, setting aside its previous presumption of confidentiality. But the move was resisted by pharmaceutical companies, which mounted legal challenges, arguing that their commercial confidentiality was at risk.

Now the European Court …
Treatment-free remission after first-line dasatinib discontinuation in patients with chronic myeloid leukaemia (first-line DADI trial): a single-arm, multicentre, phase 2 trial
Authors: Shinya Kimura, Jun Imagawa, Kazunori Murai, Masayuki Hino, Toshio Kitawaki, Masaya Okada, Hideo Tanaka, Motohiro Shindo, Takashi Kumagai, Takayuki Ikezoe, Nobuhiko Uoshima, Tsutomu Sato, Reiko Watanabe, Shugo Kowata, Masaya Hayakawa, Takaaki Hosoki, Kazuhiko Ikeda, Tsutomu Kobayashi, Yasutaka Kakinoki, Tetsuo Nishimoto, Naoki Takezako, Hirohiko Shibayama, Akifumi Takaori-Kondo, Hirohisa Nakamae, Atsushi Kawaguchi, Hiroshi Ureshino, Junichi Sakamoto, Yoji Ishida
Journal: The Lancet Haematology (2020)
Peptide Receptor Radionuclide Therapy Using 225Ac-DOTATOC Achieves Partial Remission in a Patient With Progressive Neuroendocrine Liver Metastases After Repeated β-Emitter Peptide Receptor Radionuclide Therapy
Authors: Jingjing Zhang, Harshad R. Kulkarni, Richard P. Baum
Journal: Clinical Nuclear Medicine (2019)

Abstract We present here a case with β-radiation–refractory metastatic neuroendocrine tumors, who demonstrated an excellent therapy response after 1 cycle of 225 Ac-DOTATOC, without any significant adverse effects even after 10 cycles of β-emitter peptide receptor radionuclide therapy followed by α-peptide receptor radionuclide therapy.
Abstract 475: Association Between Bystander Delay in Activating the Emergency Response System and Outcomes Following Out-Of-Hospital Cardiac Arrest: All-Japan National Utstein Registry
Authors: Tomoyoshi Tamura, Tomohisa SEKI, Masaru Suzuki, Junichi Sasaki
Journal: Circulation (2019)

Introduction: An emphasis on the chain of survival has contributed to improved outcomes of out-of-hospital cardiac arrest (OHCA). Although immediate recognition of cardiac arrest (CA) and activation of the emergency response system are the first links in the chain of survival, their impact on outcomes is unclear. Hypothesis: Delayed time from collapse to activation of the emergency response system (bystander delay) is associated with an unfavorable neurological outcome after adult OHCA. Methods: Data from the prospective, nationwide, population-based All-Japan Utstein Registry of the Fire and Disaster Management Agency between January 1, 2012 and December 31, 2016 were analyzed. Of the 625,916 eligible cases, 164,256 adult, non-traumatic, witnessed OHCA including bystander delay times (age, 79 [IQR, 67-86] years; 60% male) were studied. The primary outcome measure was favorable neurological outcome 1 month after an OHCA, defined as a score of 1 or 2 on the Cerebral Performance Category Scale. Results: The median bystander delay time of 2.0 [1.0-4.0] min was shorter among patients who achieved a favorable outcome as compared to 3.0 [1.0-6.0] min (P &lt; 0.001) for patients with an unfavorable outcome. In multivariable logistic regression analyses, bystander delay had an OR for favorable neurological outcome of 0.94 [95% CI, 0.93-0.97] after adjusting for age, sex, etiology of arrest, first documented rhythm, provision of bystander CPR, use of public access automated external defibrillator, epinephrine administration, time intervals of activation of the emergency response system and hospital arrival, and collapse to initiation of CPR, and regional location. Similarly, bystander delay was independently associated with reduced neurologically favorable survival among patients who received bystander CPR within one minute of collapse (adjusted OR, 0.97 [0.97-0.98]). Conclusions: Bystander delay was independently associated with decreased odds of neurologically favorable survival, even among patients for whom bystander CPR was immediately performed.