tbuckley/cabot-search huggingface dataset:
CD36 family members are TCR-independent ligands for CD1 antigen–presenting molecules
Authors: Nicholas A. Gherardin, Samuel J. Redmond, Hamish E. G. McWilliam, Catarina F. Almeida, Katherine H. A. Gourley, Rebecca Seneviratna, Shihan Li, Robert De Rose, Fiona J. Ross, Catriona V. Nguyen-Robertson, Shian Su, Matthew E. Ritchie, Jose A. Villadangos, D. Branch Moody, Daniel G. Pellicci, Adam P. Uldrich, Dale I. Godfrey
Journal: Science Immunology (2021)

CD1 molecules bind CD36 family members, and blocking this interaction facilitates staining and study of CD1-restricted T cells.
MULTIDRUG RESISTANCE TRANSPORTERS AS MARKERS OF DECREASE OF TAMOXIFEN EFFICACY IN BREAST CANCER THERAPY
Authors: T.A. Bogush, E.A. Dudko, E.A. Bogush, A.B. Ravcheeva, R.J. Ramanauskaite, S.A. Tjulandin
Journal: Annals of Oncology (2011)
Respiratory disease, and treatment / thematic poster session large airway complications in severely ill patients with COVID 19
Authors: A. Anwar, N. Ramos-Bascon, A. Crerar-Gilbert, N. Barnes, B. Madden
Journal: American Journal of Respiratory and Critical Care Medicine (2021)

Introduction: Airway management of patients with Covid-19 is challenging. In addition to operator infection risk, the patient may have an acute severe lung injury with significant large airway inflammation. Under these circumstances, airway compromise may occur as a consequence of iatrogenic injury, bleeding or exuberant inflammatory response. Methods: We describe five severely unwell patients with COVID-19 who developed large airway complications. These comprised of tracheal tear, tracheal granulation tissue, bronchomalacia, tracheal diverticulum and oedematous glottitis. All were noted on thoracic computerized tomographic imaging and were also confirmed by bronchoscopy. Results: One had an iatrogenic 3cm tracheal tear associated with intubation using a stylet and presented with pneumomediastinum. He was managed conservatively and follow-up rigid bronchoscopy confirmed defect closure. A second patient developed granulation tissue formation superior to the site of entry of the tracheostomy tube insertion and this was successfully resected at rigid bronchoscopy prior to decannulation. Another patient developed left bronchomalacia and he was decannulated following successful insertion of a left main bronchial stent. The fourth patient has a persistent tracheal diverticulum that has been kept under prospective surveillance. One patient who had oedematous glottitis died from multiple organ failure. Conclusion: It is important to recognize that large airway complications can occur in critically ill patients with COVID 19. They can potentially lead to increased morbidity and mortality and may require specialist intervention. .
Bronchoscopic needle-based confocal laser endomicroscopy (nCLE) as a real-time detection tool for peripheral lung cancer
Authors: Tess Kramer, Lizzy Wijmans, Martijn de Bruin, Ton van Leeuwen, Teodora Radonic, Peter Bonta, Jouke T Annema
Journal: Thorax (2021)

Diagnosing peripheral lung cancer with the bronchoscope is challenging with near miss of the target lesion as major obstacle. Needle-based confocal laser endomicroscopy (nCLE) enables real-time microscopic tumour visualisation at the needle tip (smart needle).To investigate feasibility and safety of bronchoscopic nCLE imaging of suspected peripheral lung cancer and to assess whether nCLE imaging allows real-time discrimination between malignancy and airway/lung parenchyma.Patients with suspected peripheral lung cancer based on (positron emission tomography-)CT scan underwent radial endobronchial ultrasound (rEBUS) and fluoroscopy-guided flexible bronchoscopy. After rEBUS lesion detection, an 18G needle loaded with the CLE probe was inserted in the selected airway under fluoroscopic guidance. The nCLE videos were obtained at the needle tip, followed by aspirates and biopsies. The nCLE videos were reviewed and compared with the cytopathology of the corresponding puncture and final diagnosis. Five blinded raters validated nCLE videos of lung tumours and airway/lung parenchyma twice.The nCLE imaging was performed in 26 patients. No adverse events occurred. In 24 patients (92%) good to high quality videos were obtained (final diagnosis; lung cancer n=23 and organising pneumonia n=1). The nCLE imaging detected malignancy in 22 out of 23 patients with lung cancer. Blinded raters differentiated nCLE videos of malignancy from airway/lung parenchyma (280 ratings) with a 95% accuracy. The inter-observer agreement was substantial (κ=0.78, 95% CI 0.70 to 0.86) and intra-observer reliability excellent (mean±SD κ=0.81±0.05).Bronchoscopic nCLE imaging of peripheral lung lesions is feasible, safe and allows real-time lung cancer detection. Blinded raters accurately distinguished nCLE videos of lung cancer from airway/lung parenchyma, showing the potential of nCLE imaging as real-time guidance tool.
Transglutaminase 2 Inhibition for Prevention of Mucosal Damage in Celiac Disease
Authors: Bana Jabri
Journal: New England Journal of Medicine (2021)

Celiac disease is a T-cell–mediated enteropathy induced by dietary gluten that shares many features with organ-specific autoimmune disorders.1 Celiac disease requires the presence of autoantibodies directed against the endogenous enzyme tissue transglutaminase 2 and occurs selectively in persons in whom the HLA-DQ2 or HLA-DQ8 molecules, which harbor positively charged binding pockets, are expressed.1 These requirements were enigmatic given that gluten is an exogenous antigen that has very few negatively charged residues. The conundrum was solved with the discovery that autoantibodies are directed against transglutaminase 2,2 which forms a complex with gluten and increases its affinity for HLA-DQ2 and HLA-DQ8 by . . .
<i>QuickStats</i>: Age-Adjusted Percentage* of Adults Aged ≥18 Years Who Had an Influenza Vaccination in the Past 12 Months,<sup>†</sup> by Sex and Race/Ethnicity<sup>§</sup> — National Health Interview Survey, United States, 2019<sup>¶</sup>
Journal: MMWR Morbidity and Mortality Weekly Report (2021)
Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank
Authors: Joseph D. Szustakowski, Suganthi Balasubramanian, Erika Kvikstad, Shareef Khalid, Paola G. Bronson, Ariella Sasson, Emily Wong, Daren Liu, J. Wade Davis, Carolina Haefliger, A. Katrina Loomis, Rajesh Mikkilineni, Hyun Ji Noh, Samir Wadhawan, Xiaodong Bai, Alicia Hawes, Olga Krasheninina, Ricardo Ulloa, Alex E. Lopez, Erin N. Smith, Jeffrey F. Waring, Christopher D. Whelan, Ellen A. Tsai, John D. Overton, William J. Salerno, Howard Jacob, Sandor Szalma, Heiko Runz, Gregory Hinkle, Paul Nioi, Slavé Petrovski, Melissa R. Miller, Aris Baras, Lyndon J. Mitnaul, Jeffrey G. Reid, Oleg Moiseyenko, Carlos Rios, Saurabh Saha, Goncalo Abecasis, Nilanjana Banerjee, Christina Beechert, Boris Boutkov, Michael Cantor, Giovanni Coppola, Aris Economides, Gisu Eom, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Lukas Habegger, Marcus B. Jones, Rouel Lanche, Michael Lattari, Michelle LeBlanc, Dadong Li, Luca A. Lotta, Kia Manoochehri, Adam J. Mansfield, Evan K. Maxwell, Jason Mighty, Mrunali Nafde, Sean O’Keeffe, Max Orelus, Maria Sotiropoulos Padilla, Razvan Panea, Tommy Polanco, Manasi Pradhan, Ayesha Rasool, Thomas D. Schleicher, Deepika Sharma, Alan Shuldiner, Jeffrey C. Staples, Cristopher V. Van Hout, Louis Widom, Sarah E. Wolf, Sally John, Chia-Yen Chen, David Sexton, Varant Kupelian, Eric Marshall, Timothy Swan, Susan Eaton, Jimmy Z. Liu, Stephanie Loomis, Megan Jensen, Saranya Duraisamy, Jason Tetrault, David Merberg, Sunita Badola, Mark Reppell, Jason Grundstad, Xiuwen Zheng, Aimee M. Deaton, Margaret M. Parker, Lucas D. Ward, Alexander O. Flynn-Carroll, Caroline Austin, Ruth March, Menelas N. Pangalos, Adam Platt, Mike Snowden, Athena Matakidou, Sebastian Wasilewski, Quanli Wang, Sri Deevi, Keren Carss, Katherine Smith, Morten Sogaard, Xinli Hu, Xing Chen, Zhan Ye
Journal: Nature Genetics (2021)
Does Osteogenic Potential of Clonal Human Bone Marrow Mesenchymal Stem/Stromal Cells Correlate with Their Vascular Supportive Ability?
Authors: Suzanne M Watt, Alison Merryweather-Clarke, David Cook, Barbara Joo Lara, Emmanouela Repapi, Neil Ashley, Peng Hua
Journal: Blood (2017)
Building a sustainable infrastructure for covid-19 vaccinations long term
Authors: Simon Hodes, Azeem Majeed
Journal: BMJ (2021)

Ficolins are oligomeric lectins comprising a collagen-like and a fibrinogen-like domain, with a binding specificity for <i>N</i>-acetylglucosamine. It has been reported recently that L-ficolin/P35 associates with mannan-binding lectin (MBL)-associated serine proteases (MASP-1 and -2) and MBL-associated protein 19 (MAp19) in serum and forms complexes able to activate complement. Using surface plasmon resonance spectroscopy we have shown that recombinant MASP-1 and -2, their N-terminal CUB1 (module originally found in complement proteins C1r/C1s, Uegf, and bone morphogenetic protein-1)-epidermal growth factor (EGF)-CUB2 and CUB1-EGF segments, and MAp19 bind to immobilized L-ficolin/P35 in the presence of Ca<sup>2+</sup> ions. Comparable <i>K</i><sub><i>d</i></sub> values were obtained for the full-length proteases and their CUB1-EGF-CUB2 segments (9.2 and 10 nM for MASP-1 and 4.6 and 5.4 nM for MASP-2, respectively), whereas higher values were obtained for the CUB1-EGF segments (26.7, 15.6, and 14.3 nM for MASP-1, MASP-2, and MAp19). These values are in the same range as those determined for the interaction of these proteins with MBL. Binding was Ca<sup>2+</sup> dependent and was only partly sensitive to EDTA for MASP-1, MASP-2, and MASP-2 CUB1-EGF-CUB2. Half-maximal binding was obtained at comparable Ca<sup>2+</sup> concentrations for MASP-1 and MASP-2 (0.45 and 0.47 μM, respectively), their CUB1-EGF-CUB2 segments (0.37 and 0.72 μM), and their CUB1-EGF segments (0.31 and 0.79 μM). These values are lower than those determined in the case of MBL, indicating a difference between MBL and L-ficolin/P35 with respect to the Ca<sup>2+</sup> dependence of their interaction with the MASPs. Preincubation of the MASPs with soluble MBL inhibited subsequent binding to immobilized L-ficolin/P35 and, conversely, suggesting that these lectins compete with each other for binding to the MASPs in vivo.
Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in <i>Gynandropsis gynandra</i>
Authors: Chi-Fa Huang, Wen-Yu Liu, Mei-Yeh Jade Lu, Yi-Hua Chen, Maurice S B Ku, Wen-Hsiung Li
Journal: Molecular Biology and Evolution (2021)

Abstract In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C4 photosynthesis from C3 photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C4Gynandropsis gynandra and C3Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C4 photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO2 pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C3–C4 intermediate stage during the C4 evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C4 enzyme genes and their recruitment into the C4 pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C4 CO2 concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C4 photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C4 cycle. This study revealed how WDG may facilitate C4 photosynthesis evolution.
The role of the mitochondrial protein VDAC1 in inflammatory bowel disease: a potential therapeutic target
Authors: Ankit Verma, Srinivas Pittala, Belal Alhozeel, Anna Shteinfer-Kuzmine, Ehud Ohana, Rajeev Gupta, Jay H. Chung, Varda Shoshan-Barmatz
Journal: Molecular Therapy (2021)

Recent studies have implicated mitochondrial dysfunction as a trigger of inflammatory bowel diseases, including Crohn's disease (CD) and ulcerative colitis (UC). We have investigated the role of the mitochondria gate-keeper protein, the voltage-dependent-anion channel 1 (VDAC1), in gastrointestinal inflammation and tested the effects of the newly developed VDAC1-interacting molecules, VBIT-4 and VBIT-12, on UC induced by dextran sulfate sodium (DSS) or trinitrobenzene sulphonic acid (TNBS) in mice. VDAC1, which controls metabolism, lipids transport, apoptosis, and inflammasome activation, is overexpressed in the colon of CD and UC patients and DSS-treated mice. VBIT-12 treatment of cultured colon cells inhibited the DSS-induced VDAC1 overexpression, oligomerization, and apoptosis. In the DSS-treated mice, VBIT-12 suppressed weight loss, diarrhea, rectal bleeding, pro-inflammatory cytokine production, crypt and epithelial cell damage, and focal inflammation. VBIT-12 also inhibited the infiltration of inflammatory cells, apoptosis, mtDNA release, and activation of caspase-1 and NRLP3 inflammasome to reduce the inflammatory response. The levels of the ATP-gated P
TP53 Germline Variations Influence the Predisposition and Prognosis of Acute Lymphoblastic Leukemia in Children
Authors: Maoxiang Qian, Xueyuan Cao, Meenakshi Devidas, Wenjian Yang, Cheng Cheng, Andrew Carroll, Nyla A. Heerema, Hui Zhang, Takaya Moriyama, Julie M. Gastier-Foster, Heng Xu, Elizabeth A. Raetz, Eric Larsen, Naomi Winick, W. Paul Bowman, Paul L. Martin, Elaine R. Mardis, Robert Fulton, Gerard Zambetti, Michael Borowitz, Brent Wood, Kim E. Nichols, William L. Carroll, Ching-Hon Pui, Charles G. Mullighan, William E. Evans, Stephen P. Hunger, Mary V. Relling, Mignon L. Loh, Jun J. Yang
Journal: Blood (2017)
Development of a radiation oncology-specific prospective data registry for clinical research and quality improvement: A clinical workflow-based solution.
Authors: Allen M. Chen, Pin-Chieh Wang, Darlene Verittupong, Weber Shao, Susan Ann McCloskey, Vincent Basehart, Michael L. Steinberg, Patrick Kupelian
Journal: Journal of Clinical Oncology (2016)

197 Background: The computerized ‘paperless’ medical recording system has transformed the modern health information system and serves as an idea platform for cancer registry development, particularly in a specialty like radiation oncology, where technological advances generate unprecedented amounts of data. Methods: From May 2011 to May 2015, physicians prospectively inputted data on patients seen during consultation in the Department of Radiation Oncology at UCLA. Using a customized interface established between an in-house registry and a commercially-available, hospital-based electronic medical record system (Epic Systems, Inc. Verona, WI), a parcel was created for data deposition, which was also linked to the Aria Treatment Planning Station (Varian Medical Systems, Inc., Palo Alto, CA). This registry was designed to assimilate into routine physician work-flow and was based on the completion of tabular entries, which were templated by disease sites. The total number of data fields per disease site ranged from 9 to 73 (median, 21). Results: A total of 7,646 patients were logged into the registry. Primary disease sites were prostate (N = 1,247), breast (N = 1157), head/neck (N = 726), central nervous system (N = 638), lung (N = 439), brain metastasis (N = 349), gastrointestinal (N = 238), gynecologic (N = 234), other (N = 2,618). The mean data capture completion rate by physicians was 55% (range, 32 to 65%); however, this rate did not differentiate between true incomplete (data available but not collected), versus data that was either unavailable, not required, or not applicable. A total of 46 independent, investigator-initiated research studies have been undertaken using queries supported by the registry from multiple access points, 8 of which were published in peer-reviewed journals. Conclusions: The development of a radiation oncology-specific registry not only enhanced research efficiency and facilitated quality assurance, but also fostered data reuse and promoted self-education by producing quality information to guide clinical practice. Our next steps include the integration of patient-reported outcomes through radiation oncology-specific surverys, the documentation of cost of delivery of care of specific treatment pathways, and the implementation of data collection processes in the community.
Wound Healing: From Passive to Smart Dressings
Authors: Mojtaba Farahani, Abbas Shafiee
Journal: Advanced Healthcare Materials (2021)

Abstract The universal increase in the number of patients with nonhealing skin wounds imposes a huge social and economic burden on the patients and healthcare systems. Although, the application of traditional wound dressings contributes to an effective wound healing outcome, yet, the complexity of the healing process remains a major health challenge. Recent advances in materials and fabrication technologies have led to the fabrication of dressings that provide proper conditions for effective wound healing. The 3D‐printed wound dressings, biomolecule‐loaded dressings, as well as smart and flexible bandages are among the recent alternatives that have been developed to accelerate wound healing. Additionally, the new generation of wound dressings contains a variety of microelectronic sensors for real‐time monitoring of the wound environment and is able to apply required actions to support the healing progress. Moreover, advances in manufacturing flexible microelectronic sensors enable the development of the next generation of wound dressing substrates, known as electronic skin, for real‐time monitoring of the whole physiochemical markers in the wound environment in a single platform. The current study reviews the importance of smart wound dressings as an emerging strategy for wound care management and highlights different types of smart dressings for promoting the wound healing process.
Has SARS-CoV-2 reached peak fitness?
Authors: Roberto Burioni, Eric J. Topol
Journal: Nature Medicine (2021)

to be an advantageous strategy.Of course, vaccination rates are restricted not only by antigen supply but also by the availability of vaccinators and clinical supplies, such as syringes.Nevertheless, antigen supply remains the greatest restriction for vaccines against COVID-19, and strategies that make the most of available antigen supply would maximize the number of lives saved by vaccination.More generally, in future pandemics, researchers and clinicians involved in vaccine development should consider identifying the appropriate vaccine dosage that can save the most lives for a limited amount of antigen, rather than just a dosage that balances efficacy and reactogenicity for the individual person.
Preventive Care in Type 2 Diabetes: Results of a Randomized, Controlled Trial in Community Pharmacies
Authors: Katja Prax, Karin Schmiedel, Tobias Hepp, Helmut Schlager, Kristina Friedland
Journal: Diabetes Care (2021)

The number of patients with diabetes is expected to increase by 51% worldwide within the next 25 years, with diabetes complications resulting in high health costs (1). Consequently, comprehensive diabetes care is essential to control disease progression. Pharmacists are able to contribute to diabetes care in different settings (2,3). However, large randomized controlled trials for community pharmacists are rare. Therefore, GLICEMIA 2.0 was developed to examine whether intensive pharmacist-delivered care in community pharmacies can effectively improve glycemic control and reduce risk for complications.

GLICEMIA 2.0 was a multicenter, cluster-randomized controlled trial in 26 German pharmacies randomly assigned to the control or intervention group. Pharmacists from each center were trained prior to the start of the trial for 1 day regarding how to conduct the study. Pharmacists of the intervention group received an additional day of training that included medication analysis and counseling of behavioral changes. The Freiburg Ethics Commission International, Freiburg, Germany, approved the trial (016/1826). Eligible participants had type 2 diabetes, BMI of at least 25 kg/m2, and HbA1c ≥7% (53 mmol/mol). Data were collected at baseline and after 6 and 12 months. The assessment included HbA1c (point of care; Abbott Afinion AS 100 Analyzer), fasting blood glucose, weight, and blood pressure.

Pharmacists supported the participants of the intervention group for 1 year in a protocol-defined lifestyle change …
Role for Platelets in Mediating Neutrophil Recruitment in TNF-α Induced Vaso-Occlusive Processes in Animals with Sickle Cell Anemia
Authors: Hanan Chweih, Juliete A.F. Silva, Wilson A. Ferreira, Pamela L. Brito, Erica M.F. Gotardo, Flavia C. Leonardo, Carla F Franco-Penteado, Fernando Ferreira Costa, Nicola Conran
Journal: Blood (2017)
Proton pump inhibitors and risk of colorectal cancer
Authors: Devin Abrahami, Emily Gibson McDonald, Mireille E Schnitzer, Alan N Barkun, Samy Suissa, Laurent Azoulay
Journal: Gut (2021)

Objective To determine whether proton pump inhibitors (PPIs) are associated with an increased risk of colorectal cancer, compared with histamine-2 receptor antagonists (H2RAs). Design The United Kingdom Clinical Practice Research Datalink was used to identify initiators of PPIs and H2RA from 1990 to 2018, with follow-up until 2019. Cox proportional hazards models were fit to estimate marginal HRs and 95% CIs of colorectal cancer. The models were weighted using standardised mortality ratio weights using calendar time-specific propensity scores. Prespecified secondary analyses assessed associations with cumulative duration, cumulative dose and time since treatment initiation. The number needed to harm was calculated at five and 10 years of follow-up. Results The cohort included 1 293 749 and 292 387 initiators of PPIs and H2RAs, respectively, followed for a median duration of 4.9 years. While the use of PPIs was not associated with an overall increased risk of colorectal cancer (HR: 1.02, 95% CI 0.92 to 1.14), HRs increased with cumulative duration of PPI use (&lt;2 years, HR: 0.93, 95% CI 0.83 to 1.04; 2–4 years, HR: 1.45, 95% CI 1.28 to 1.60; ≥4 years, HR: 1.60, 95% CI 1.42 to 1.80). Similar patterns were observed with cumulative dose and time since treatment initiation. The number needed to harm was 5343 and 792 for five and 10 years of follow-up, respectively. Conclusion While any use of PPIs was not associated with an increased risk of colorectal cancer compared with H2RAs, prolonged use may be associated with a modest increased risk of this malignancy.