tbuckley/cabot-search huggingface dataset:
Serrated neoplasia in the colorectum: gut microbiota and molecular pathways
Authors: Xing Kang, Ru Zhang, Thomas Ny Kwong, Rashid Ns Lui, William Kk Wu, Joseph Jy Sung, Jun Yu, Sunny H Wong
Journal: Gut Microbes (2020)

Colorectal cancer (CRC) is a heterogeneous disease with different gene expression patterns. There are two major colorectal carcinogenesis pathways: conventional adenoma-carcinoma pathway and alternative serrated neoplasia pathway. Apart from the conventional pathway that is typically initiated by characteristic APC mutation and chromosomal instability, the serrated neoplasia pathway is mainly characterized by mutations of BRAF or KRAS, microsatellite instability (MSI), and CpG island methylator phenotype (CIMP). Despite the malignant potential of serrated lesions, they can be easily overlooked during endoscopy screening and even in pathological assessment due to its anatomical location, morphology, and histological features. It has been shown that environmental factors especially the gut microbial composition play a key role in CRC pathogenesis. Thus, the preferential localization of serrated lesions in specific intestine areas suggest that niche-specific microbiota composition might intertwined with host genetic perturbations during the development of serrated lesions. Although serrated lesions and conventional adenomas are biologically different, most studies have focused on conventional adenomas, while the pathophysiology and role of microorganisms in the development of serrated lesions remain elusive. In this review, we discuss on the role of gut microbiota in the serrated neoplasia pathway of colorectal carcinogenesis and its specific clinical and molecular features, and summarize the potential mechanisms involved.
Interassociation consensus recommendations for pitch-side emergency care and personal protective equipment for elite sport during the COVID-19 pandemic
Authors: Lisa Hodgson, Gemma Phillips, Jonathan Gordon, Jonathan Hanson, John Maclean, Prabhat Mathema, Andrew Smith, Mark Woolcock, Charlotte M Cowie, Simon Kemp, Michael Patterson, Jo Larkin, Jerry Hill, Michael Rossiter, Niall Elliott, Pippa Bennett, Jonathan Power, Ari Pillay, Harjinder Singh, Craig Sheridan, Matthew Hurwood, Peter Riou, Anthony Bennison, Susan Chakraverty, Richard Tingay, Richard Higgins, Richard Weiler, Rod Jaques, Simon Spencer, Michael R Carmont, Jon Patricios
Journal: British Journal of Sports Medicine (2020)

The COVID-19 pandemic has necessitated many novel responses in healthcare including sport and exercise medicine. The cessation of elite sport almost globally has had significant economic implications and resulted in pressure to resume sport in very controlled conditions. This includes protecting pitch-side medical staff and players from infection. The ongoing prevalence of SARS-CoV-2 and the desire to resume professional sport required urgent best practice guidelines to be developed so that sport could be resumed as safely as possible. This set of best practice recommendations assembles early evidence for managing SARS-CoV-2 and integrates expert opinion to provide a uniform and pragmatic approach to enhance on-field and pitch-side safety for the clinician and player. The nature of SARS-CoV-2 transmission creates new hazards during resuscitation and emergency care and procedures. Recommendations for the use and type of personal protective equipment during on-field or pitch-side emergency medical care is provided based on the clinical scenario and projected risk of viral transmission.
Factors Associated with SARS-CoV-2 Infection (COVID) Severity and Mortality in Chronic Dialysis Patients
Authors: Eduardo K. Lacson, Gideon N. Aweh, Vladimir Ladik, Harold J. Manley, Carol Stewart, Doug Johnson
Journal: Journal of the American Society of Nephrology (2020)

Background: From 2/17 to 5/29, 2020, Dialysis Clinic Inc  had 422 maintenance dialysis patients diagnosed with COVID from 90 clinics in 20 states  While prognostic factors in the general population have been reported, there is limited information regarding the US dialysis population  Methods: Over a 15 week period of observation, 96 patients died (22 7%) and 116 (27 5%) were not hospitalized (for up to 30 days post-COVID diagnosis), likely with milder illness  We compiled univariable associations with p;75 years, increasing to 74% of all deaths at age >;65 years  Wheelchair use also associated with higher death risk  Conclusions: Dialysis patients with low albumin and vintage ≧1 year associated with increased illness severity  It was surprising that a history of pneumonia vaccine associated with more severe illness - whether this reflects 'treatment by indication' bias vs  pulmonary immune activation by vaccination vs  chance finding is unclear  PVD also tended to increase illness severity but more importantly, was significantly associated with risk of death, independent of older age
Testing for Primary Aldosteronism and Mineralocorticoid Receptor Antagonist Use Among U.S. Veterans
Authors: Jordana B. Cohen, Debbie L. Cohen, Daniel S. Herman, John T. Leppert, James Brian Byrd, Vivek Bhalla
Journal: Annals of Internal Medicine (2020)

Primary aldosteronism is a common cause of treatment-resistant hypertension. However, evidence from local health systems suggests low rates of testing for primary aldosteronism.To evaluate testing rates for primary aldosteronism and evidence-based hypertension management in patients with treatment-resistant hypertension.Retrospective cohort study.U.S. Veterans Health Administration.Veterans with apparent treatment-resistant hypertension (n = 269 010) from 2000 to 2017, defined as either 2 blood pressures (BPs) of at least 140 mm Hg (systolic) or 90 mm Hg (diastolic) at least 1 month apart during use of 3 antihypertensive agents (including a diuretic), or hypertension requiring 4 antihypertensive classes.Rates of primary aldosteronism testing (plasma aldosterone-renin) and the association of testing with evidence-based treatment using a mineralocorticoid receptor antagonist (MRA) and with longitudinal systolic BP.4277 (1.6%) patients who were tested for primary aldosteronism were identified. An index visit with a nephrologist (hazard ratio [HR], 2.05 [95% CI, 1.66 to 2.52]) or an endocrinologist (HR, 2.48 [CI, 1.69 to 3.63]) was associated with a higher likelihood of testing compared with primary care. Testing was associated with a 4-fold higher likelihood of initiating MRA therapy (HR, 4.10 [CI, 3.68 to 4.55]) and with better BP control over time.Predominantly male cohort, retrospective design, susceptibility of office BPs to misclassification, and lack of confirmatory testing for primary aldosteronism.In a nationally distributed cohort of veterans with apparent treatment-resistant hypertension, testing for primary aldosteronism was rare and was associated with higher rates of evidence-based treatment with MRAs and better longitudinal BP control. The findings reinforce prior observations of low adherence to guideline-recommended practices in smaller health systems and underscore the urgent need for improved management of patients with treatment-resistant hypertension.National Institutes of Health.
National Trends in the US Public’s Likelihood of Getting a COVID-19 Vaccine—April 1 to December 8, 2020
Authors: Peter G. Szilagyi, Kyla Thomas, Megha D. Shah, Nathalie Vizueta, Yan Cui, Sitaram Vangala, Arie Kapteyn
Journal: JAMA (2020)

Sarah Kreps, PhD; Sandip Prasad, MD; John S. Brownstein, PhD; Yulin Hswen, PhD; Brian T. Garibaldi, MD, MEHP; Baobao Zhang, PhD; Douglas L. Kriner, PhD
Inforgraphic. Infographic and digital resources: the relationships between rugby union, and health and well-being
Authors: Steffan A Griffin, Nirmala Kanthi Panagodage Perera, Andrew Murray, Danny Glover, Jennifer Duncan, Samantha G Fawkner, Simon PT Kemp, Keith A Stokes, Paul Kelly
Journal: British Journal of Sports Medicine (2020)

Our scoping review was the first ‘big picture’ review to identify the relationships between rugby union, and health and well-being. Data suggest that all forms of rugby union (contact, non-contact and wheelchair) can provide moderate to vigorous physical activity, and can contribute to non-sedentary time, both of which have a raft of associated health and well-being benefits.1 National population surveys also consider rugby union as an activity that can provide muscle-strengthening/balance improvement when accrued for period of over 10 minutes,2 and ‘ball sports’ are generally considered to improve muscle function, bone health and balance.3

‘Non-contact’ and …
Reprogramming microorganisms for the biosynthesis of astaxanthin via metabolic engineering
Authors: Xia Wan, Xue-Rong Zhou, Gabriel Moncalian, Lin Su, Wen-Chao Chen, Hang-Zhi Zhu, Dan Chen, Yang-Min Gong, Feng-Hong Huang, Qian-Chun Deng
Journal: Progress in Lipid Research (2020)
Early COVID-19 lockdown in Greece and idiopathic pulmonary fibrosis: a beneficial “impact” beyond any expectation
Authors: Spyros A. Papiris, Demosthenes Bouros, Katerina Markopoulou, Lykourgos Kolilekas, Andriana I. Papaioannou, Vasilios Tzilas, Argyrios Tzouvelekis, Eva Fouka, Despoina Papakosta, Zoe Daniil, Paschalis Steiropoulos, Athina Gogali, Ilias C. Papanikolaou, Areti Xyfteri, Aggeliki Haritou, Ioanna Korbila, Ioannis P. Tomos, Stylianos Loukides, Rita Bellelli, Georgia Kounti, Christina Rampiadou, Theodoros Karampitsakos, Ilias Dimeas, Paraskevi Kirgou, Andromachi Bompoki, Eirini Vasarmidi, Konstantinos Loverdos, Elvira-Markela Antonogiannaki, Myrto Blizou, Evangelos Bouros, Konstantinos Kagouridis, Maria Maniati, Anna Karakatsani, Katerina M. Antoniou, Effrosyni D. Manali
Journal: European Respiratory Journal (2020)

<b>During the lockdown, IPF patients experienced lower than expected COVID-19, suggesting that simple measures for the winter months, such as face masking, clean hands, physical distancing could be adopted as promising advances in non-pharmacological therapy</b>https://bit.ly/2ISi2EV
CD40 agonistic monoclonal antibody APX005M (sotigalimab) and chemotherapy, with or without nivolumab, for the treatment of metastatic pancreatic adenocarcinoma: an open-label, multicentre, phase 1b study
Authors: Mark H O'Hara, Eileen M O'Reilly, Gauri Varadhachary, Robert A Wolff, Zev A Wainberg, Andrew H Ko, George Fisher, Osama Rahma, Jaclyn P Lyman, Christopher R Cabanski, Rosemarie Mick, Pier Federico Gherardini, Lacey J Kitch, Jingying Xu, Theresa Samuel, Joyson Karakunnel, Justin Fairchild, Samantha Bucktrout, Theresa M LaVallee, Cheryl Selinsky, Jacob E Till, Erica L Carpenter, Cécile Alanio, Katelyn T Byrne, Richard O Chen, Ovid C Trifan, Ute Dugan, Christine Horak, Vanessa M Hubbard-Lucey, E John Wherry, Ramy Ibrahim, Robert H Vonderheide
Journal: The Lancet Oncology (2020)
Outpatient Initiation of Dialysis for AKI Requiring Dialysis Following Diagnosis of COVID-19
Authors: Kristine Kubisiak, Lorien S. Dalrymple, Norma J. Ofsthun, Yuping Sun, Franklin W. Maddux, Robert J. Kossmann, Jeffrey L. Hymes
Journal: Journal of the American Society of Nephrology (2020)

Kubisiak, Kristine; Dalrymple, Lorien S.; Ofsthun, Norma J.; Sun, Yuping; Maddux, Franklin W.; Kossmann, Robert J.; Hymes, Jeffrey L. Author Information
Detailed Long-Term Follow-Up of Patients Who Relapsed After the Nordic Mantle Cell Lymphoma Trials: MCL2 and MCL3
Authors: Christian Winther Eskelund, Kostas Dimopoulos, Arne Kolstad, Ingrid Glimelius, Riikka Räty, Lise Mette Rahbek Gjerdrum, Kristina Sonnevi, Pär Josefsson, Herman Nilsson-Ehle, Hans H. N. Bentzen, Unn Merete Fagerli, Outi Kuittinen, Jacob Haaber, Carsten Utoft Niemann, Lone Bredo Pedersen, Maria Torp Larsen, Christian Hartmann Geisler, Martin Hutchings, Mats Jerkeman, Kirsten Grønbæk
Journal: HemaSphere (2020)

Mantle cell lymphoma (MCL) is an incurable disease with a highly variable clinical course. The prognosis after relapse is generally poor, and no standard of care exists. We investigated the postrelapse outcomes of 149 patients who were initially treated in the Nordic Lymphoma Group trials, MCL2 or MCL3, both representing intensive cytarabine-containing frontline regimens including autologous stem cell transplant. Patients with progression of disease before 24 months (POD24, n = 51, 34%) displayed a median overall survival of 6.6 months compared with 46 months for patients with later POD (n = 98, 66%; P &lt; 0.001). MCL international prognostic index, cell proliferation marker, blastoid morphology, and TP53 mutations showed independent prognostic value irrespective of POD24, and in a combined, exploratory risk score, patients with 0, 1, 2-3, or 4-5 high-risk markers, respectively, displayed a 5-year overall survival of 62%, 39%, 31%, and 0%. By a comparison of median progression-free survival of the different salvage therapies in the relapse setting, bendamustine-rituximab was superior to all other combination chemotherapy regimens; however, it was also associated with longer responses to last line of therapy. Collectively, we confirm the prognostic impact of POD24 and highlight the relevance of other biomarkers, and we emphasize the importance of novel therapies for patients with high-risk features at first POD.
Epidemiology of pleural empyema in English hospitals and the impact of influenza
Authors: David T. Arnold, Fergus W. Hamilton, Tim T. Morris, Tim Suri, Anna Morley, Vicky Frost, Ian B. Vipond, Andrew R. Medford, Rupert A. Payne, Peter Muir, Nick A. Maskell
Journal: European Respiratory Journal (2020)

Pleural empyema represents a significant healthcare burden due to extended hospital admissions and potential requirement for surgical intervention. This study aimed to assess changes in incidence and management of pleural empyema in England over the past 10 years and the potential impact of influenza on rates. Hospital Episode Statistics data were used to identify patients admitted to English hospitals with pleural empyema between 2008 and 2018. Linear regression was used to analyse the relationship between empyema rates and influenza incidence recorded by Public Health England. The relationship between influenza and empyema was further explored using serological data from a prospective cohort study of patients presenting with pleural empyema. Between April 2008 and March 2018 there were 55 530 patients admitted with pleural empyema. There was male predominance (67% versus 33%), which increased with age. Cases have increased significantly from 4447 in 2008 to 7268 in 2017. Peaks of incidence correlated moderately with rates of laboratory-confirmed influenza in children and young adults (r=0.30). For nine of the 10 years studied, the highest annual point incidence of influenza coincided with the highest admission rate for empyema (with a 2-week lag). In a cohort study of patients presenting to a single UK hospital with pleural empyema/infection, 24% (17 out of 72) had serological evidence of recent influenza infection, compared to 7% in seasonally matched controls with simple parapneumonic or cardiogenic effusions (p&lt;0.001). Rates of empyema admissions in England have increased steadily with a seasonal variation that is temporally related to influenza incidence. Patient-level serological data from a prospective study support the hypothesis that influenza may play a pathogenic role in empyema development.
Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes
Authors: José A. Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, Manuel Rubio, Chang Liu, Christian Kukat, David Ruiz, Bruno Huettel, Korbinian Schneeberger
Journal: Genome biology (2020)

Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes enabling separation of the whole-genome sequencing reads into haplotype-specific reads sets. After assembling the reads of each haplotype, the contigs are scaffolded to chromosome level using a genetic map derived from the gametes. We assemble the two genomes of a diploid apricot tree based on whole-genome sequencing of 445 individual pollen grains. The two haplotype assemblies (N50: 25.5 and 25.8 Mb) feature a haplotyping precision of greater than 99% and are accurately scaffolded to chromosome-level.
Collapsing/Sclerosing Glomerulopathy (CSG) and Acute Tubular Injury (ATI) in Patients with COVID-19
Authors: Sunil Sherchan, Mohamed Kahila, Jamrose K. Durrani, Isha Puri, Ibrahim A. Mohamed, Yohannes Melaku, Ernie Yap, Robert F. Leonardo, Subodh J. Saggi, Moro O. Salifu, Anthony D. Nicastri
Journal: Journal of the American Society of Nephrology (2020)

Sherchan, Sunil; Kahila, Mohamed; Durrani, Jamrose K.; Puri, Isha; Mohamed, Ibrahim A.; Melaku, Yohannes; Yap, Ernie; Leonardo, Robert F.; Saggi, Subodh J.; Salifu, Moro O.; Nicastri, Anthony D. Author Information
Lysosomal lipoprotein processing in endothelial cells stimulates adipose tissue thermogenic adaptation
Authors: Alexander W. Fischer, Michelle Y. Jaeckstein, Kristina Gottschling, Markus Heine, Frederike Sass, Nils Mangels, Christian Schlein, Anna Worthmann, Oliver T. Bruns, Yucheng Yuan, Hua Zhu, Ou Chen, Harald Ittrich, Stefan K. Nilsson, Patrik Stefanicka, Jozef Ukropec, Miroslav Balaz, Hua Dong, Wenfei Sun, Rudolf Reimer, Ludger Scheja, Joerg Heeren
Journal: Cell Metabolism (2020)
Pandemic Spotlights In-home Colon Cancer Screening Tests
Authors: Mary Chris Jaklevic
Journal: JAMA (2020)

G. Caleb Alexander, MD, MS; Matthew Tajanlangit; James Heyward, MPH; Omar Mansour, MHS; Dima M. Qato, PharmD, MPH, PhD; Randall S. Stafford, MD, PhD
Association of the V122I Transthyretin Amyloidosis Genetic Variant With Cardiac Structure and Function in Middle-aged Black Adults
Authors: Arjun Sinha, Yinan Zheng, Drew Nannini, Yishu Qu, Lifang Hou, Sanjiv J. Shah, Clyde W. Yancy, Elizabeth M. McNally, Myriam Fornage, Joao Lima, Donald M. Lloyd-Jones, Laura J. Rasmussen-Torvik, Sadiya S. Khan
Journal: JAMA Cardiology (2020)

The variant V122I is commonly enriched in the transthyretin (TTR) gene in individuals of African ancestry and associated with greater risk of heart failure (HF) in older adulthood, after age 65 years. Prevention of HF may be most effective earlier in life, but whether screening with echocardiography can identify subclinical cardiac abnormalities during middle age to risk-stratify individuals appears to be unknown.
Efficacy of pembrolizumab in patients with pituitary carcinoma: report of four cases from a phase II study
Authors: Nazanin Majd, Steven G Waguespack, Filip Janku, Siqing Fu, Marta Penas-Prado, Mingxuan Xu, Anas Alshawa, Carlos Kamiya-Matsuoka, Shaan M Raza, Ian E McCutcheon, Aung Naing
Journal: Journal for ImmunoTherapy of Cancer (2020)

Pituitary carcinoma is an aggressive tumor characterized by metastatic spread beyond the sellar region. Symptoms can be debilitating due to hormonal excess and survival is poor. Pituitary carcinomas recur despite conventional multimodality treatments. Given the recent advances in the use of immune checkpoint inhibitors (CPIs) to treat various solid cancers, there has been interest in exploring the role of immunotherapy for treating aggressive, refractory pituitary tumors. We treated 4 patients with pituitary carcinoma with pembrolizumab as part of a phase II clinical trial. Two patients (patients 1 and 2) with functioning corticotroph pituitary carcinomas (refractory to surgery, radiotherapy and chemotherapy) had partial radiographic (60% and 32% per Immune-Related Response Evaluation Criteria In Solid Tumors, respectively) and hormonal responses. Patient 1’s response continues 42 months after initiation of pembrolizumab and his tumor tissue obtained after treatment with temozolomide demonstrated a hypermutator phenotype with MSH2 and MSH6 gene mutations. Patient 2’s tumor after exposure to temozolomide was not sampled, but prior somatic mutational testing was negative. One patient with a non-functioning corticotroph tumor (patient 3) had a best response of stable disease for 4 months. One patient with a prolactin-secreting carcinoma (patient 4) had progressive disease. The latter 2 patients’ tumors did not demonstrate a hypermutator phenotype after treatment with temozolomide. Programmed death-ligand 1 staining was negative in all tumors. We report 2 cases of corticotroph pituitary carcinoma responsive to pembrolizumab after prior exposure to alkylating agents. The role of CPIs in treating patients with pituitary carcinoma, the relationship between tumor subtype and response to immunotherapy and mechanisms of hypermutation in this orphan disease require further study.Trial registration number: NCT02721732 .
Planning slow Mohs excision margins for lentigo maligna: a retrospective nonrandomized cohort study comparing reflectance confocal microscopy margin mapping vs. visual inspection with dermoscopy
Authors: J. M. Gao, J. J. Garioch, M. Fadhil, E. Tan, N. Shah, M. Moncrieff
Journal: British Journal of Dermatology (2020)
Longitudinal tracking of 97 esophageal adenocarcinomas using liquid biopsy sampling
Authors: E. Ococks, A.M. Frankell, N. Masque Soler, N. Grehan, A. Northrop, H. Coles, A.M. Redmond, G. Devonshire, J.M.J. Weaver, C. Hughes, K. Lehovsky, A. Blasko, B. Nutzinger, R.C. Fitzgerald, E. Smyth
Journal: Annals of Oncology (2021)

The incidence of esophageal adenocarcinoma (EAC) is rapidly rising and has a 5-year survival rate of <20%. Beyond TNM (tumor-node-metastasis) staging, no reliable risk stratification tools exist and no large-scale studies have profiled circulating tumor DNA (ctDNA) at relapse in EAC. Here we analyze the prognostic potential of ctDNA dynamics in EAC, taking into account clonal hematopoiesis with indeterminate potential (CHIP).
Impact of bedaquiline on treatment outcomes of multidrug-resistant tuberculosis in a high-burden country
Authors: Dumitru Chesov, Jan Heyckendorf, Sofia Alexandru, Ana Donica, Elena Chesov, Maja Reimann, Valeriu Crudu, Victor Botnaru, Christoph Lange
Journal: European Respiratory Journal (2020)

Background Evaluation of novel anti-tuberculosis (TB) drugs for the treatment of multidrug-resistant (MDR)-TB continues to be of high interest on the TB research agenda. We assessed treatment outcomes in patients with pulmonary MDR-TB who received bedaquiline-containing treatment regimens in the Republic of Moldova, a high-burden MDR-TB country. Method We systematically analysed the SIMETB national electronic TB database and performed a retrospective propensity score-matched comparison of treatment outcomes in a cohort of patients with MDR-TB who started treatment during 2016–2018 with a bedaquiline-containing regimen (bedaquiline cohort) and a cohort of patients treated without bedaquiline (non-bedaquiline cohort). Results Following propensity score matching, 114 patients were assigned to each cohort of MDR-TB patients. Patients in the bedaquiline cohort had a higher 6-month sputum culture conversion rate than those in the non-bedaquiline cohort (66.7% versus 40.3%; p&lt;0.001). Patients under bedaquiline-containing regimens had a higher cure rate assessed by both World Health Organization (WHO) and TBnet definitions (55.3% versus 24.6%; p=0.001 and 43.5% versus 19.6%; p=0.004, respectively), as well as a lower mortality rate (8.8% versus 20.2%; p&lt;0.001 and 10.9% versus 25.2%; p=0.01, respectively). In patients who previously failed on MDR-TB treatment, &gt;40% of patients achieved a cure with a bedaquiline-containing regimen. Conclusions Bedaquiline-based MDR-TB treatment regimens result in better disease resolution when compared with bedaquiline-sparing MDR-TB treatment regimens under programmatic conditions in a country with a high burden of MDR-TB.
Robot-assisted Radical Prostatectomy Using Single-port Perineal Approach: Technique and Single-surgeon Matched-paired Comparative Outcomes
Authors: Louis Lenfant, Juan Garisto, Guilherme Sawczyn, Clark A. Wilson, Alireza Aminsharifi, Soodong Kim, Zeyad Schwen, Riccardo Bertolo, Jihad Kaouk
Journal: European Urology (2020)