tbuckley/cabot-search huggingface dataset:
OP0130 Unique ultrasonographic findings in patients with the hereditary inclusion body myopathy
Authors: GM Garofalo, R Adler, D Darvish, S Rafii, S Paget, L Kagen
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> Hereditary Inclusion Body Myopathy (HIBM) is an autosomal recessive disorder characterised histologically by the presence of beta amyloid fibrils in myofibers and clinically by muscle weakness and atrophy with quadriceps sparing. This disorder is seen in different ethnic groups including members of Iranian Jewish families where it has been mapped to chromosome 9p1-q1. The onset is usually in the 2nd to 3rd decade of life, with slow progression leading to severe involvement of multiple muscle groups, ultimately resulting in immobilisation. <h3>Objectives</h3> To demonstrate the facility of the use of grey scale and power Doppler sonography as a non-invasive diagnostic procedure in the evaluation of HIBM. <h3>Methods</h3> We studied 4 Iranian Jewish patients diagnosed with HIBM. Ultrasonographic examinations of the quadriceps femoris and hamstring muscle groups were carried out in these patients. Echogenicity, as determined by grey scale assessment, was used to detect disordered muscle structure and atrophy, and power Doppler sonography was used to assess vascularity. <h3>Results</h3> The initial symptom in all was “footdrop” due to anterior tibial muscle weakness. Two patients with disease duration of seven years developed pelvic girdle and shoulder girdle weakness. Two patients with twenty-eight years of disease were restricted to wheelchairs with severe myopathy of the upper and lower extremities. All had significant family histories consistent with HIBM. An unusual and unique pattern of central atrophy of muscle with peripheral sparing was observed in all four patients. Vascularity was markedly reduced in the affected areas with relatively increased blood flow in the peripherally-spared areas. We referred to this as a “fried-egg” or “bull’s eye” appearance. <h3>Conclusion</h3> Our study demonstrates the use of both grey scale and power Doppler sonography as a helpful non-invasive procedure in the evaluation of HIBM. Their ability to define a unique centrifugal, “fried-egg” myopatic abnormality may be diagnostic for this disorder.
Inferring Adaptive Introgression Using Hidden Markov Models
Authors: Jesper Svedberg, Vladimir Shchur, Solomon Reinman, Rasmus Nielsen, Russell Corbett-Detig
Journal: Molecular Biology and Evolution (2021)

Abstract Adaptive introgression—the flow of adaptive genetic variation between species or populations—has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
Clinical Neuroscience of Addiction: What Clinical Psychologists Need to Know and Why
Authors: Lara A. Ray, Erica N. Grodin
Journal: Annual Review of Clinical Psychology (2021)

The last three decades in psychological research have been marked by interdisciplinary science. Addiction represents a prime example of a disorder marked by a complex interaction among psychosocial and biological factors. This review highlights critical findings in the basic neuroscience of addiction and translates them into clinical language that can inform clinical psychologists in their research, teaching, and practice. From mechanisms of reward processing, learning and memory, allostasis, incentive-sensitization, withdrawal, tolerance, goal-directed decision making, habit learning, genetics, inflammation, and the microbiome, the common theme of this review is to illustrate the clinical utility of basic neuroscience research and to identify opportunities for clinical science. The thoughtful integration of basic and clinical science provides a powerful tool to fulfill the scientific mission of improving health care. Clinical psychologists have a crucial role to play in the translational science of addiction.
Management of congenital nephrotic syndrome: consensus recommendations of the ERKNet-ESPN Working Group
Authors: Olivia Boyer, Franz Schaefer, Dieter Haffner, Detlef Bockenhauer, Tuula Hölttä, Sandra Bérody, Hazel Webb, Marie Heselden, Beata S. Lipska-Zie˛tkiewicz, Fatih Ozaltin, Elena Levtchenko, Marina Vivarelli
Journal: Nature Reviews Nephrology (2021)

Abstract Congenital nephrotic syndrome (CNS) is a heterogeneous group of disorders characterized by nephrotic-range proteinuria, hypoalbuminaemia and oedema, which manifest in utero or during the first 3 months of life. The main cause of CNS is genetic defects in podocytes; however, it can also be caused, in rare cases, by congenital infections or maternal allo-immune disease. Management of CNS is very challenging because patients are prone to severe complications, such as haemodynamic compromise, infections, thromboses, impaired growth and kidney failure. In this consensus statement, experts from the European Reference Network for Kidney Diseases (ERKNet) and the European Society for Paediatric Nephrology (ESPN) summarize the current evidence and present recommendations for the management of CNS, including the use of renin–angiotensin system inhibitors, diuretics, anticoagulation and infection prophylaxis. Therapeutic management should be adapted to the clinical severity of the condition with the aim of maintaining intravascular euvolaemia and adequate nutrition, while preventing complications and preserving central and peripheral vessels. We do not recommend performing routine early nephrectomies but suggest that they are considered in patients with severe complications despite optimal conservative treatment, and before transplantation in patients with persisting nephrotic syndrome and/or a WT1 -dominant pathogenic variant.
A translational study to evaluate genomic markers and concordance with circulating-tumor DNA and circulating tumor cells to predict clinical outcomes in gastrointestinal and pancreatobiliary cancers: Valor trial.
Authors: Ayako Doi, Kumiko Umemoto, Tomoyo Oguri, Hiroyuki Takeda, Yoshiki Horie, Takashi Ogura, Takuro Mizukami, Naoki Izawa, Sungmok Jung, Byung Chul Kim, Yu Sunakawa
Journal: Journal of Clinical Oncology (2021)

TPS481 Background: Circulating tumor cells (CTCs) are cells that have shed into the vasculature or lymphatics from a primary tumor and are carried around the body in the blood circulation. The CTCs constitute seeds for the subsequent growth of additional tumors (metastases) in distant organs, a mechanism that is responsible for the vast majority of cancer-related deaths. Circulating-tumor DNA (ctDNA) includes DNA which derives from tumor necrosis or apoptosis; therefore, CTCs may potentially represent more precise tumor status compared to ctDNA. There have been few reports to assess the genomic concordance between ctDNA and CTCs in cancer patients. In addition, genomic analysis of ctDNA would find novel mechanism of resistance to anti-EGFR monoclonal antibody (mAb) in metastatic colorectal cancer (mCRC). RAS mutations in ctDNA are considered to be one of mechanism of resistance to anti-EGFR mAb in RAS wild-type mCRC. However, there is no data regarding CTCs when mCRC patients acquires resistance to anti-EGFR mAb. Methods: This translational study prospectively recruits patients with advanced/metastatic gastrointestinal and pancreatobiliary cancers (esophageal, gastric, pancreatic, biliary tract and colorectal cancers) who receive systemic chemotherapy in first- or second-line and mCRC with RAS wild-type tumors treated with anti-EGFR mAb in any lines, at St. Marianna University School of Medicine Hospital. We accumulate the clinical data regarding patients’ characteristics, treatment, and survival time. The primary objective is to evaluate genomic markers and concordance with ctDNA and CTCs in patients with advanced/metastatic gastrointestinal and pancreatobiliary cancers. Then, this study approaches to assess which biomarkers can predict clinical outcome more accurately. Secondary objectives include evaluating association between genomic status in ctDNA and clinical outcomes; association between genomic status in CTCs and clinical outcomes; comparing genomic change between ctDNA and CTCs in RAS wild-type mCRC patients treated with anti-EGFR mAb. Blood draw of total 10mL is performed for analyses of ctDNA and CTCs at 3 time points, pre-treatment of chemotherapy, 4 weeks after treatment start, and disease progression. Blood of 5mL is processed with CTCs enrichment using the CD-PRIME system (Clinomics Inc.) and remaining 5mL is used for the plasma preparation. Genomic alterations are measured using the customized cancer panel which allows the detection of mutations in 51 actionable genes. This study will enroll 70 patients with willing to undergo blood draws. Accrual is starting in May 2019. Clinical trial information: UMIN000036681.
Efficacy and safety of liposomal irinotecan plus fluorouracil/leucovorin after progression on conventional irinotecan-containing chemotherapy for metastatic pancreatic adenocarcinoma.
Authors: Kyunghye Bang, Jaekyung Cheon, Jae Ho Jeong, Hyeon-Su Im, Kyu-Pyo Kim, Baek-Yeol Ryoo, Changhoon Yoo
Journal: Journal of Clinical Oncology (2021)

382 Background: Liposomal irinotecan (nal-IRI) plus fluorouracil/leucovorin (5-FU/LV) has demonstrated its clinical benefit in patients with metastatic pancreatic adenocarcinoma (mPAC) who progressed on prior gemcitabine-based chemotherapy. However, its role in patients who previously treated with conventional irinotecan has not been investigated. We analyzed clinical outcomes of nal-IRI + 5-FU/LV in mPAC patients after progression on conventional irinotecan-containing chemotherapy. Methods: In this multicenter retrospective analysis, a total of 35 patients with mPAC who received nal-IRI + 5-FU/LV after progression on irinotecan-containing regimen, between January 2017 and March 2020, were included. The ratio of time-to-progression (TTP) with nal-IRI + 5-FU/LV to TTP with conventional irinotecan (TTPr) was correlated with duration and cumulative dose of prior conventional irinotecan. Results: The median age was 58 years (range, 35-73) and 16 patients (46%) were male. All patients received prior irinotecan as the component of FOLFIRINOX. The median duration of prior irinotecan was 4.6 months (range, 0.5-16.8) and median cumulative dose of prior irinotecan was 1230 mg (range, 150-4650). Objective response rate of nal-IRI + 5-FU/LV was 2.9% (1 partial response) and stable disease was achieved in 31.4% (n = 11). With median follow-up duration of 9.2 months [95% CI, 7.8-10.5], the median PFS and OS were 2.0 months [95% CI, 1.4-2.6] and 4.4 months [95% CI, 3.6-5.7], respectively. 6-month PFS rate was 16.3% and OS rate was 37.5%. The median TTPr was 0.41 (range 0.07-2.07) and this showed negative correlation between cumulative dose of prior irinotecan (R = -0.37, p = 0.041). There was a tendency for the negative correlation between TTPr and duration of prior irinotecan (R = -0.35, p = 0.062). Most common grade 3-4 toxicities were neutropenia (20%) and fatigue (8.6%). Conclusions: Nal-IRI + 5-FU/LV showed only modest efficacy for mPAC patients who progressed on conventional irinotecan-containing chemotherapy. Cumulative dose of prior conventional irinotecan may be correlated with the efficacy of nal-IRI + 5-FU/LV.
Engagement in Meaningful Activities Among Older Adults With Disability, Dementia, and Depression
Authors: Anna Oh, Siqi Gan, W. John Boscardin, Theresa A. Allison, Deborah E. Barnes, Kenneth E. Covinsky, Alexander K. Smith
Journal: JAMA Internal Medicine (2021)

trials.Among the 21 vaccines, 17 (81.0%)had at least 1 pivotal efficacy trial that used masking, 20 (95.2%) that used an active or placebo comparator group, and 8 (38.1%) approved based on a clinical primary end point; of these, the median vaccine efficacy was 91.9% (IQR, 79.6%-98.0%)(Table 2).Among the 5 vaccines for diseases for which no FDA-approved vaccine existed at time of approval, 4 (80%) used a clinical primary end point.Discussion | Since 2010, most novel vaccines approved by the FDA required about 8 years of clinical development and were based on evidence from a median of 7 clinical trials, including at least 2 pivotal efficacy trials that were randomized, masked, and used a comparator group.These pivotal efficacy trials enrolled a median of 5000 patients, who were followed up for serious adverse events for at least 6 months.Given the urgency of developing a COVID-19 vaccine, trials will need to be larger than those supporting prior vaccine approvals and include sufficient follow-up time for emergence of adverse effects.
Synthetic Pentasaccharide Fondaparinux (Arixtra®) Reduces Sepsis Induced Coagulopathy and Promotes Survival in the Baboon Model of E. coli Sepsis
Authors: Ravi Shankar Keshari, Robert Silasi, Narcis Ioan Popescu, Cristina Lupu, Charles Esmon, Florea Lupu
Journal: Blood (2017)
SAT0186 Knee joint arthroscopy and radiological stages in osteoarthritis (oa)
Authors: EY Panasyuk, ES Tsvetkova
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> <h3>Objectives</h3> To compare the findings of knee joint arthroscopy and radiological stages in osteoarthritis (OA). <h3>Methods</h3> Arthroscopy was carried out in twenty four knee OA (I-III degree by A. Larsen) patients by 'STORZ' apparatus with photoinsrumental set. Six basic zones of knee joint were analysed: patella, trochlears, a lateral and medial arthicular tibial and femoral surfaces. Cartilage damage was assessed by Bequin and Lockeir according 5 degrees: normal cartilage (0), cartilage fibrillation (I deg.), surface fissures and/or surface erosions baring subchondral bone (III deg), bared subchondral bone (IV deg.). Synovitis was analysed by 3 degrees: mild, moderate and severe. <h3>Results</h3> The character and depth of cartilage destruction in different zone of knee joint is not the same. Patella cartilage was damaged in all patients independently of radiological stages. Deep cartilage fissures were found in the 1st radiological OA stage in all areas of knee joint with the exception of lateral surface of the tibia. Synovitis intensity has no correlation with X-ray stages. <h3>Conclusion</h3> According to arthroscopy data there was no correlation between degree of articular destruction and 'early' radiological OA stages. Arthroscopy of OA knee joint is the method for real assessment of hyaline cartilage structural changes and synovial inflammation.
Platform trial of BI 754091, an anti-PD-1 antibody, in patients with previously treated advanced solid tumors: Combination with BI 836880, a VEGF/Ang2-blocking nanobody.
Authors: Maen A. Hussein, Johanna C. Bendell, Hendrik-Tobias Arkenau, Quincy S. Chu, Aaron Richard Hansen, Damijan Erzen, Zhichao Sun, Anthony Lucarelli, Ivor John Percent
Journal: Journal of Clinical Oncology (2021)

TPS152 Background: Combining anti-programmed cell death protein 1 (PD-1) antibodies with other immuno-modulatory or targeted therapies may improve outcomes. NCT03697304 is an open-label, Phase II, platform trial assessing BI 754091, an anti-PD-1 antibody, combined with other agents. Here, we describe Module C in which BI 754091 will be combined with BI 836880, a humanized bispecific nanobody, that targets vascular endothelial growth factor (VEGF) and angiopoietin2 (Ang2). VEGF and Ang2 play key roles in tumor angiogenesis and have an immunosuppressive effect in the tumor microenvironment. Combining anti-VEGF/Ang2 with an anti-PD-1 therapy promotes an immunopermissive state supportive of T-cell-mediated tumor cell death. Methods: Patients are being enrolled in 5 cohorts: 1) locally advanced/metastatic gastric or gastroesophageal adenocarcinoma with ≥1 prior treatment (anti-PD-[L]1 naïve); 2) any advanced/metastatic solid tumor (excluding NSCLC and melanoma) with prior anti-PD-(L)1 treatment, which progressed after achieving at least stable disease (SD) for 4 months; 3) advanced/metastatic solid tumors with no benefit from prior anti-PD-(L)1 treatment (SD &lt;4 months); 4) locally advanced/metastatic microsatellite stable (MSS) colorectal cancer with ≥1 prior treatment (anti-PD-[L]1 naïve); 5) advanced MSS and mismatch-repair proficient endometrial carcinoma which progressed following 1 line of chemotherapy (anti-PD-[L]1 naïve). Patients will receive BI 836880 (720 mg every 3 weeks [Q3W] intravenously [IV]) and BI 754091 (240 mg Q3W IV). Treatment will continue until progressive disease, unacceptable toxicity, consent withdrawal, or for a maximum of 1 year (treatment may be extended in case of clinical benefit). The primary endpoint is objective response (OR; complete or partial response per RECIST v1.1 as assessed by the investigator). Secondary endpoints are duration of OR, disease control and progression-free survival. Safety will also be assessed. Approximately 30 patients will be enrolled per cohort at sites in North America and the United Kingdom. Clinical trial information: NCT03697304.
COVID-19 in liver transplant recipients: How big is the problem?
Authors: L. Pasulo, F. Leonardi, M. Tacelli, M. F. Zambelli, L. Del Prete, M. Triolo, M. De Giorgio, C. Farina, M. Colledan, S. Fagiuoli
Journal: Hepatology (2020)

Background: In December 2019, a new contagious disease, named COVID-19 caused by a novel coronavirus (SARSCov- 2) emerged in Wuhan City, China Since February 2020 this disease has also spread to Italy Bergamo, where one of the most active liver transplant (LT) Italian center is located, has been one of the most affected cities by COVID-19 This study aimed to evaluate the impact of COVID-19 in liver transplant patients Methods: From April 1st, 2020, to May 15th, 2020, 660 adult liver transplant recipients were contacted by phone by the medical staff of the Transplant Center at the ASST-Papa Giovanni XXIII-Bergamo The presence of COVID-19 symptoms (fever, cough, dyspnea, asthenia, dysgeusia, anosmia, gastrointestinal complaints and/or myalgia) and contact at risk were investigated Results of RX chest, SARS-Cov-2 nose-swab and hospitalizations, when occurred, were recorded in symptomatic patients Results: Seventy-seven patients (11 7%) reported symptoms related to SARS-Cov-2 infection;patients were primarily males (72 7%), with a median age of 62 9 years (IQR 57 1-69 0) and a median time from LT of 73 6 months (IQR 36 5-135 8) A chest x-rays was performed in 25/77 symptomatic patients (32 5%) and in 17/25 (68 0%) an interstitial pneumonia was found;swabs were performed in 21/77 patients (27 3%) and 17 of them (81 0%) resulted positive Among symptomatic patients, all reported at least two symptoms and in 14 (18 2%) five symptoms were present  Three patients (3 9%) had been hospitalized for transplant-related reasons and 11 patients needed hospitalization because of COVID-19 (14 9%) All hospitalized patients were treated with antibiotics;high dose steroids were added to 8 patients and antiviral therapy (lopinavir/ritonavir) to 4 patients Nine patients (11 7%) needed oxygen therapy One patient died for non-COVID-19 related condition, 2 patients died for COVID-19 (2/76;2 6%) Mortality in hospitalized patients was 21 4% (3/14), COVIDrelated mortality-rate was 15 4% (2/13) and both patients died within one month after LT Conclusion: COVID-19 can affect liver transplant patients, however, in our experience, both the need for hospitalization and deaths do not exceed those observed among the general population
Lower or Higher Oxygenation Targets for Acute Hypoxemic Respiratory Failure
Authors: Olav L Schjørring, Thomas L Klitgaard, Anders Perner, Jørn Wetterslev, Theis Lange, Martin Siegemund, Minna Bäcklund, Frederik Keus, Jon H Laake, Matthew Morgan, Katrin M Thormar, Søren A Rosborg, Jannie Bisgaard, Annette E S Erntgaard, Anne-Sofie H Lynnerup, Rasmus L Pedersen, Elena Crescioli, Theis C Gielstrup, Meike T Behzadi, Lone M Poulsen, Stine Estrup, Jens P Laigaard, Cheme Andersen, Camilla B Mortensen, Björn A Brand, Jonathan White, Inge-Lise Jarnvig, Morten H Møller, Lars Quist, Morten H Bestle, Martin Schønemann-Lund, Maj K Kamper, Mathias Hindborg, Alexa Hollinger, Caroline E Gebhard, Núria Zellweger, Christian S Meyhoff, Mathias Hjort, Laura K Bech, Thorbjørn Grøfte, Helle Bundgaard, Lars H M Østergaard, Maria A Thyø, Thomas Hildebrandt, Bülent Uslu, Christoffer G Sølling, Nette Møller-Nielsen, Anne C Brøchner, Morten Borup, Marjatta Okkonen, Willem Dieperink, Ulf G Pedersen, Anne S Andreasen, Lone Buus, Tayyba N Aslam, Robert R Winding, Joerg C Schefold, Stine B Thorup, Susanne A Iversen, Janus Engstrøm, Maj-Brit N Kjær, Bodil S Rasmussen
Journal: New England Journal of Medicine (2021)

Patients with acute hypoxemic respiratory failure in the intensive care unit (ICU) are treated with supplemental oxygen, but the benefits and harms of different oxygenation targets are unclear. We hypothesized that using a lower target for partial pressure of arterial oxygen (Pao2) would result in lower mortality than using a higher target.
Factors associated with progression to death in patients with Lassa fever in Nigeria: an observational study
Authors: Jamie Strampe, Danny A Asogun, Emily Speranza, Meike Pahlmann, Ali Soucy, Sabrina Bockholt, Elisa Pallasch, Beate Becker-Ziaja, Sophie Duraffour, Nahid Bhadelia, Yemisi Ighodalo, Jennifer Oyakhilome, Emmanuel O Omomoh, Thomas Olokor, Donatus I Adomeh, Odia Ikponwonsa, Chris Aire, Ekaete Tobin, Nosa Akpede, Peter O Okokhere, Sylvanus A Okogbenin, George O Akpede, César Muñoz-Fontela, Ephraim Ogbaini-Emovon, Stephan Günther, John H Connor, Lisa Oestereich
Journal: The Lancet Infectious Diseases (2021)
Psychiatric Medication Use After Possible Neuroborreliosis—Reply
Authors: Malte M. Tetens, Anne-Mette Lebech, Lars H. Omland
Journal: JAMA Psychiatry (2021)

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