tbuckley/cabot-search huggingface dataset:
Endoscopic ultrasound-guided rendezvous ERCP using a steerable access device
Authors: Mohamad K. Marrache, Abdulhameed Al-Sabban, Mohamad Itani, Jad Farha, Lea Fayad, Mouen A. Khashab, Vivek Kumbhari
Journal: Endoscopy (2020)

A 77-year-old woman with history of lung adenocarcinoma and bone metastasis presented with intractable nausea, nonbloody emesis, and abdominal pain. The patient was taking high doses of nonsteroidal anti-inflammatory drugs for pain from bone metastasis. Computed tomography demonstrated a duodenal stricture and dilated common bile duct. Liver function tests showed raised bilirubin and alkaline phosphatase.
Abstract 151: Software Annotation of Defibrillator Files: Ready for Prime Time?
Authors: Vishal Gupta, Robert Schmicker, Pamela Owens, Elizabete Aramendi, Ahamed Idris
Journal: Circulation (2019)

Introduction: Defibrillators record important information about the quality of chest compressions during CPR. Software made for reviewing defibrillator files automatically annotate and measure chest compression metrics. However, evidence is limited regarding the accuracy of such measurements. Objective: To compare chest compression fraction (CCF) and rate measurements made with software annotation vs. manual annotation of defibrillator files. Methods: This is a retrospective, observational study from the Dallas Fort-Worth site of the Resuscitation Outcomes Consortium. We reviewed chest compression waveforms from the bioimpedance channel of defibrillator recordings (Physio-Control Lifepak 12 and 15, Redmond, WA) of 100 prehospital patients enrolled in the DFW Cardiac Arrest Registry from 9/8/2018 to 3/9/2019. Included cases were ≥18 years, had presumed cardiac cause of arrest, and continuous chest compressions. We assessed chest compression waveforms from the time of initial CPR until the time the defibrillator was removed. A trained reviewer revised the software annotations by marking the start and end of CPR and adding or removing chest compressions. Software annotated and manual reviewer annotated measurements were compared for CCF and rate using intraclass correlation coefficient (ICC) statistical analysis. Results: Mean patient age was 63 years with 59% male. The mean (±SD) duration of CPR was 30.4 ± 10.6 min. The overall mean CCF for files annotated by software vs. manual annotation was 0.64 ± 0.19 vs. 0.86 ± 0.07, respectively, and the ICC was 0.14. For software vs. manual annotation, the overall mean rate was 109 ± 10 vs. 108 ± 10, respectively, and ICC was 0.99. The software misidentified epochs before the start of chest compressions, failed to capture epochs after resuscitation ended, and after return of spontaneous circulation, resulting in low ICC for CCF. The ICC was excellent for compression rate because the software only counted epochs where chest compressions were actually given. Conclusions: Software annotation performed poorly for chest compression fraction and very well for chest compression rate. Defibrillator files must be reviewed and annotated manually before quality of chest compression measurements are calculated.
Pharmacological prophylaxis versus pancreatic duct stenting plus pharmacological prophylaxis for prevention of post-ERCP pancreatitis: results are as yet inconclusive
Authors: Ashish Agarwal, Soumya Jagannath Mahapatra, Deepak Gunjan
Journal: Endoscopy (2020)

See also: Pharmacological prophylaxis versus pancreatic duct stenting plus pharmacological prophylaxis for prevention of post-ERCP pancreatitis in high risk patients: a randomized trialEndoscopy 2019; 51(10): 915-921DOI: 10.1055/a-0977-3119
Association of Opioids Prescribed to Family Members With Opioid Overdose Among Adolescents and Young Adults
Authors: Anh P. Nguyen, Jason M. Glanz, Komal J. Narwaney, Ingrid A. Binswanger
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Family members are cited as a common source of prescription opioids used for nonmedical reasons. However, the overdose risk associated with exposure to opioids prescribed to family members among adolescents and young adults is not well established. <h3>Objective</h3> To assess the association of opioids prescribed to family members with pharmaceutical opioid overdose among youth. <h3>Design, Setting, and Participants</h3> This cohort study included 45 145 family units with a total of 72 040 adolescents and young adults aged 11 to 26 years enrolled in a Kaiser Permanente Colorado health plan in 2006 and observed through June 2018. <h3>Exposures</h3> Opioid prescriptions and dosage dispensed to family members and youth in the past month. <h3>Main Outcomes and Measures</h3> Fatal pharmaceutical opioid overdoses identified in vital records and nonfatal pharmaceutical opioid overdoses identified in emergency department and inpatient settings. Time to first overdose was modeled using Cox regression. <h3>Results</h3> The study population consisted of 72 040 adolescents and young adults (mean [SD] age across follow-up, 19.3 [3.7] years; 36 646 [50.9%] girls and women) nested in 45 145 family units. Youth were more commonly exposed to prescription opioids dispensed to a family member than through their own prescriptions. During follow-up, 26 284 youth (36.5%) filled at least 1 opioid prescription, and 47 461 youth (65.9%) had at least 1 family member with a prescription. Exposure to family members with opioid prescriptions in the past month was associated with increased risk of pharmaceutical opioid overdose (adjusted hazard ratio [aHR], 2.17; 95% CI, 1.24-3.79) independent of opioids prescribed to youth (aHR, 6.62; 95% CI, 3.39-12.91). Concurrent exposure to opioid prescriptions from youth and family members was associated with substantially increased overdose risk (aHR, 12.99; 95% CI, 5.08-33.25). High dosage of total morphine milligram equivalents (MME) prescribed to family members in the past month was associated with youth overdose (0 MME vs &gt;0 to &lt;200 MME: aHR, 1.39; 95% CI, 0.51-3.81; 0 MME vs 200 to &lt;600 MME: aHR, 1.49; 95% CI, 0.59-3.77; 0 MME vs ≥600 MME: aHR, 2.93; 95% CI, 1.55-5.56). <h3>Conclusions and Relevance</h3> In this study of youth linked to family members, exposure to family members' prescribed opioids was associated with increased risk of pharmaceutical opioid overdose, independent of opioids prescribed to youth. Further interventions targeting youth and families are needed, including counseling patients about the risks of opioids to youth in their families.
Minimal phenotyping yields genome-wide association signals of low specificity for major depression
Authors: Na Cai, Joana A. Revez, Mark J. Adams, Till F. M. Andlauer, Gerome Breen, Enda M. Byrne, Toni-Kim Clarke, Andreas J. Forstner, Hans J. Grabe, Steven P. Hamilton, Douglas F. Levinson, Cathryn M. Lewis, Glyn Lewis, Nicholas G. Martin, Yuri Milaneschi, Ole Mors, Bertram Müller-Myhsok, Brenda W. J. H. Penninx, Roy H. Perlis, Giorgio Pistis, James B. Potash, Martin Preisig, Jianxin Shi, Jordan W. Smoller, Fabien Streit, Henning Tiemeier, Rudolf Uher, Sandra Van der Auwera, Alexander Viktorin, Myrna M. Weissman, Kenneth S. Kendler, Jonathan Flint
Journal: Nature Genetics (2020)
Abstract P6-03-18: The accumulation of IGFBP-1 results in EGFR/MAPK activation and drives the development of tamoxifen resistance in breast cancer cells
Authors: Yan Zheng
Journal: Cancer Research (2020)

Abstract Insulin-like growth factor (IGF) system plays a significantly role in cellular processes, including proliferation, survival, and mitogenesis. The IGF system consists of two soluble ligands, IGF-1 and IGF-2; two transmembrane receptors, IGF-1R and IGF-2R; and six high affinity IGF binding proteins, IGFBPs 1-6. Evidence shows that the IGF system is involved in breast cancer. For example, at least 50% of breast cancer tumors have elevated IGF-1R signaling; the level of circulating IGF-1 is found positively associated with the incident of estrogen receptor positive breast cancer. Tamoxifen, a selective estrogen receptor modulator and antagonist for estrogen receptor alpha (ERα) in breast tissue, is a commonly prescribed adjuvant treatment for patients presenting with ERα-positive breast cancer. However, tamoxifen resistance also occurs, and its exact mechanism is not well understood. Recently, we discovered that the accumulation of IGFBP-1 was stimulated by tamoxifen treatment, which subsequently prevented the activation of IGF-1R and inhibited the proliferation in MCF-7 cells. As a result, we hypothesized that the accumulation of IGFBP-1 due to the long-term tamoxifen exposure would result in tamoxifen resistance. In order to mimic the accumulation of IGFBP-1 after tamoxifen treatment, we employed MCF-7 and T-47D breast cancer cells to generate stable cell lines with IGFBP-1 overexpression. We found that the expression of IGF-1R was largely reduced in both MCF7-BP1 and T47D-BP1 cells, which was also observed in tamoxifen resistant MCF-7 and T-47D cells. Furthermore, we demonstrated that both MCF7-BP1 and T47D-BP1 were not responsive to tamoxifen, and epidermal growth factor receptor (EGFR) signaling pathway was significantly upregulated, as shown by higher levels of EGFR, phospho-EGFR (pEGFR), and phospho-Erk (pErk). Also, we found that the inhibition of Erk phosphorylation by MEK1 inhibitor PD98059 sensitized the stable cells to tamoxifen, showing that elevated pErk was protective against tamoxifen. Lastly, the transient knockdown of IGFBP-1 in MCF7-BP1 and T47D-BP1 resulted in significantly lower level of pErk and increased sensitivity to tamoxifen, further showing the role of IGFBP1 accumulation in the establishment of tamoxifen resistance and the activation of EGFR/MAPK pathway. Citation Format: Yan Zheng. The accumulation of IGFBP-1 results in EGFR/MAPK activation and drives the development of tamoxifen resistance in breast cancer cells [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-03-18.
Maintaining peak performance as an elite Paralympian
Authors: Bo Hedges
Journal: British Journal of Sports Medicine (2020)

I first started playing when I was 13 when my hometown got some wheelchairs and started a team. I know a lot of guys who are 10 years older than myself whose shoulders were pretty shot by the time they were 45, because all they did was push and push and did no counterbalance work. Being a daily wheelchair user, as well as playing wheelchair sport, that wear and tear is continuous and ongoing on the shoulders and the joints.

Trying to balance all of that while still playing becomes harder and harder over the years and the presence of a balanced workout becomes more important. When I first started playing wheelchair basketball, it was about learning how to train to be able to compete at the highest level with the best players in the world. As I have gotten older, it is all about training smarter, training with a purpose.

There is a lot more knowledge out there about wheelchair athletes now, and a lot of it comes down to just the willingness to try and sometimes, to fail. I have been fortunate to work with people that are willing to learn with you and willing to accept that they may not know everything that there is about working with a disabled athlete. Every disability is different and every athlete …
Response to: ‘Immune-mediated necrotizing myopathies and interstitial lung disease are predominant characteristics in anti-Ku positive patients with idiopathic inflammatory myopathies’ by Yang<i>et al</i>
Authors: Lionel Spielmann, Benoit Nespola, Alain Meyer
Journal: Annals of the Rheumatic Diseases (2020)

Correspondence responseTable 1 Myositis-specific and associated autoantibodies in our 15 patients with anti-Ku autoantibodies and elevated CK MSA and MAA Anti-Ku patients with elevated CK n=15 Anti-Jo1 0/15 Anti-PL7 0/13 Anti-PL12 0/13 Anti-OJ 0/9 Anti-EJ 0/9 Anti-Ha 0/9 Anti-Zo 0/9 Anti-KS 0/9 Anti-U1-RNP 0/15 Anti-PM/Scl 1/14 Anti-Mi2 0/12 Anti-MDA5 1/9 Anti-TIF1γ 2/9 Anti-NXP2 0/9 Anti-SAE 0/9 Anti-SRP 0/11 Anti-HMGCR 0/9 Total 2* *One patient was positive for both anti-MDA5 and anti-TIF1γ; another had anti-PM/scl and anti-TIF1γ.CK, creatine kinase; MAA, myositis-associated autoantibodies; MSA, myositis-specific autoantibodies.
Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties
Authors: Basak B. Ural, Stephen T. Yeung, Payal Damani-Yokota, Joseph C. Devlin, Maren de Vries, Paola Vera-Licona, Tasleem Samji, Catherine M. Sawai, Geunhyo Jang, Oriana A. Perez, Quynh Pham, Leigh Maher, P'ng Loke, Meike Dittmann, Boris Reizis, Kamal M. Khanna
Journal: Science Immunology (2020)

The lungs contain a CD169 + interstitial macrophage subset localized to the bronchovascular tree that regulates lung inflammation.
Sixty seconds on . . . anosmia
Authors: Gareth Iacobucci
Journal: BMJ (2020)

While a high temperature and a new, continuous cough are the most established symptoms of covid-19, the World Health Organization is now examining how common it might be for infected people to experience a loss of smell (anosmia) or taste (ageusia).

A lot of respiratory viruses can cause problems with smell receptors. And there is evidence that previous coronaviruses have been associated with post-viral smell loss. …
Surviving Sepsis Campaign: guidelines on the management of critically ill adults with Coronavirus Disease 2019 (COVID-19)
Authors: Waleed Alhazzani, Morten Hylander Møller, Yaseen M. Arabi, Mark Loeb, Michelle Ng Gong, Eddy Fan, Simon Oczkowski, Mitchell M. Levy, Lennie Derde, Amy Dzierba, Bin Du, Michael Aboodi, Hannah Wunsch, Maurizio Cecconi, Younsuck Koh, Daniel S. Chertow, Kathryn Maitland, Fayez Alshamsi, Emilie Belley-Cote, Massimiliano Greco, Matthew Laundy, Jill S. Morgan, Jozef Kesecioglu, Allison McGeer, Leonard Mermel, Manoj J. Mammen, Paul E. Alexander, Amy Arrington, John E. Centofanti, Giuseppe Citerio, Bandar Baw, Ziad A. Memish, Naomi Hammond, Frederick G. Hayden, Laura Evans, Andrew Rhodes
Journal: Intensive Care Medicine (2020)

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, Coronavirus Disease 2019 (COVID-19), affecting thousands of people around the world. Urgent guidance for clinicians caring for the sickest of these patients is needed. We formed a panel of 36 experts from 12 countries. All panel members completed the World Health Organization conflict of interest disclosure form. The panel proposed 53 questions that are relevant to the management of COVID-19 in the ICU. We searched the literature for direct and indirect evidence on the management of COVID-19 in critically ill patients in the ICU. We identified relevant and recent systematic reviews on most questions relating to supportive care. We assessed the certainty in the evidence using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach, then generated recommendations based on the balance between benefit and harm, resource and cost implications, equity, and feasibility. Recommendations were either strong or weak, or in the form of best practice recommendations. The Surviving Sepsis Campaign COVID-19 panel issued 54 statements, of which 4 are best practice statements, 9 are strong recommendations, and 35 are weak recommendations. No recommendation was provided for 6 questions. The topics were: (1) infection control, (2) laboratory diagnosis and specimens, (3) hemodynamic support, (4) ventilatory support, and (5) COVID-19 therapy. The Surviving Sepsis Campaign COVID-19 panel issued several recommendations to help support healthcare workers caring for critically ill ICU patients with COVID-19. When available, we will provide new recommendations in further releases of these guidelines.
Diverse genetic mechanisms underlie worldwide convergent rice feralization
Authors: Jie Qiu, Lei Jia, Dongya Wu, Xifang Weng, Lijuan Chen, Jian Sun, Meihong Chen, Lingfeng Mao, Bowen Jiang, Chuyu Ye, Guilherme Menegol Turra, Longbiao Guo, Guoyou Ye, Qian-Hao Zhu, Toshiyuki Imaizumi, Beng-Kah Song, Laura Scarabel, Aldo Merotto, Kenneth M. Olsen, Longjiang Fan
Journal: Genome biology (2020)

Abstract Background Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varieties. Despite increasing attention in recent years, a comprehensive understanding of the origins of weedy crop relatives and how a universal feralization process acts at the genomic and molecular level to allow the rapid adaptation to weediness are still yet to be explored. Results We use whole-genome sequencing to examine the origin and adaptation of 524 global weedy rice samples representing all major regions of rice cultivation. Weed populations have evolved multiple times from cultivated rice, and a strikingly high proportion of contemporary Asian weed strains can be traced to a few Green Revolution cultivars that were widely grown in the late twentieth century. Latin American weedy rice stands out in having originated through extensive hybridization. Selection scans indicate that most genomic regions underlying weedy adaptations do not overlap with domestication targets of selection, suggesting that feralization occurs largely through changes at loci unrelated to domestication. Conclusions This is the first investigation to provide detailed genomic characterizations of weedy rice on a global scale, and the results reveal diverse genetic mechanisms underlying worldwide convergent rice feralization.
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples
Authors: Jacob Schreiber, Jeffrey Bilmes, William Stafford Noble
Journal: Genome biology (2020)

Abstract Recent efforts to describe the human epigenome have yielded thousands of epigenomic and transcriptomic datasets. However, due primarily to cost, the total number of such assays that can be performed is limited. Accordingly, we applied an imputation approach, Avocado, to a dataset of 3814 tracks of data derived from the ENCODE compendium, including measurements of chromatin accessibility, histone modification, transcription, and protein binding. Avocado shows significant improvements in imputing protein binding compared to the top models in the ENCODE-DREAM challenge. Additionally, we show that the Avocado model allows for efficient addition of new assays and biosamples to a pre-trained model.
Abstract P6-08-14: Assessing the effectiveness of the NCCN genetic testing guidelines in identifying African American breast cancer patients with deleterious genetic mutations
Authors: Foluso O Ademuyiwa, Patricia Salyer, Yinjiao Ma, Sherri Fisher, Graham Colditz, Katherine Weilbaecher, Laura J Bierut
Journal: Cancer Research (2020)

Abstract Purpose: Approximately 10% of breast cancers are hereditary. Identifying women at high risk for hereditary breast and ovarian cancer allows for early detection, prevention, and individualized disease management for those diagnosed with breast cancer. There is limited data about breast cancer genetic risks among African Americans (AA) as the majority of the large studies have been conducted in European Americans. We examined the distribution of deleterious genetic mutations in AA breast cancer patients, and evaluated the effectiveness of the National Comprehensive Cancer Network (NCCN) guidelines for identifying AA women at high risk for deleterious genetic mutations. Methods: AA participants with breast cancer underwent an interview regarding health and family history, and a 30-gene saliva test. Medical records were accessed to determine whether participants had received prior genetic testing as part of usual care, results of previous testing, and cancer characteristics. Results: Two hundred and fifty participants were enrolled between February 2016 and May 2018. Twenty (8.0%) had a deleterious mutation in one of the 30 genes; BRCA2 had the highest frequency (40.0%). 187 (74.8%) met eligibility for testing based on NCCN guidelines. Only 110 (58.8%) of participants eligible for genetic testing, according to guidelines, had received prior testing as part of routine care. Using the 30-gene test, we identified deleterious mutations in 17 of 187 (9.1%) of those who met NCCN criteria for testing, and three of 63 (4.8%) of those who did not meet criteria for testing nonetheless had a deleterious mutation associated with breast cancer. Conclusions: Our results indicate that a large proportion of African American breast cancer patients who meet criteria for genetic testing do not receive it as part of routine care. Even in women who do not meet testing guidelines, nearly 5% have a known deleterious mutation associated with breast cancer. Citation Format: Foluso O Ademuyiwa, Patricia Salyer, Yinjiao Ma, Sherri Fisher, Graham Colditz, Katherine Weilbaecher, Laura J Bierut. Assessing the effectiveness of the NCCN genetic testing guidelines in identifying African American breast cancer patients with deleterious genetic mutations [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-14.
Abstract 10453: Carotid Intima Media Thickness, Pulse Wave Velocity and the Spatial QRS-T Angle
Authors: Theodora Elffers, Stella Trompet, Renée de Mutsert, Arie Maan, Peter Macfarlane, Hildo Lamb, Albert de Roos, Frits Rosendaal, Wouter Jukema
Journal: Circulation (2018)

Background: The spatial QRS-T angle (spQRSTa) has been studied as prognostic factor for cardiovascular (CV) events and mortality. To gain more insight in mechanisms involved in spQRSTa widening, we...