tbuckley/cabot-search huggingface dataset:
Mortality in adults with multidrug-resistant tuberculosis and HIV by antiretroviral therapy and tuberculosis drug use: an individual patient data meta-analysis
Authors: Gregory P Bisson, Mayara Bastos, Jonathon R Campbell, Didi Bang, James C Brust, Petros Isaakidis, Christoph Lange, Dick Menzies, Giovanni B Migliori, Jean W Pape, Domingo Palmero, Parvaneh Baghaei, Payam Tabarsi, Piret Viiklepp, Stalz Vilbrun, Jonathan Walsh, Suzanne M Marks
Journal: The Lancet (2020)
Treatment of Bilateral Synchronous Ocular Adnexa Marginal Zone Lymphoma: Consortium for Improving Survival of Lymphoma (CISL) Study
Authors: Sung Yong Oh, Jin Seok Kim, Ji Hyun Lee, Won Seog Kim, Seok Jin Kim, Dok Hyun Yoon, Jung Yong Hong, Won-Sik Lee, Hyo Jung Kim, Jong-Ho Won, Byeong Park, Soon Il Lee, Cheolwon Suh
Journal: Blood (2017)
Is It All About Revising, Correcting, and Transferring Genes?
Authors: Vasilija Rolfes, Uta Bittner, Heiner Fangerau, Karsten Weber
Journal: The American Journal of Bioethics (2020)

Bryan Cwik introduces a framework consisting of four categories (target, goal, outcome, and mechanics) to help differentiate between the many existing genetic germline interventions. This is becaus...
Facility-Wide Testing for SARS-CoV-2 in Nursing Homes — Seven U.S. Jurisdictions, March–June 2020
Authors: Kelly M. Hatfield, Sujan C. Reddy, Kaitlin Forsberg, Lauren Korhonen, Kelley Garner, Trent Gulley, Allison James, Naveen Patil, Carla Bezold, Najibah Rehman, Marla Sievers, Benjamin Schram, Tracy K. Miller, Molly Howell, Claire Youngblood, Hannah Ruegner, Rachel Radcliffe, Allyn Nakashima, Michael Torre, Kayla Donohue, Paul Meddaugh, Mallory Staskus, Brandon Attell, Caitlin Biedron, Peter Boersma, Lauren Epstein, Denise Hughes, Meghan Lyman, Leigh E. Preston, Guillermo V. Sanchez, Sukarma Tanwar, Nicola D. Thompson, Snigdha Vallabhaneni, Amber Vasquez, John A. Jernigan
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

Undetected infection with SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19) contributes to transmission in nursing homes, settings where large outbreaks with high resident mortality have occurred (1,2). Facility-wide testing of residents and health care personnel (HCP) can identify asymptomatic and presymptomatic infections and facilitate infection prevention and control interventions (3-5). Seven state or local health departments conducted initial facility-wide testing of residents and staff members in 288 nursing homes during March 24-June 14, 2020. Two of the seven health departments conducted testing in 195 nursing homes as part of facility-wide testing all nursing homes in their state, which were in low-incidence areas (i.e., the median preceding 14-day cumulative incidence in the surrounding county for each jurisdiction was 19 and 38 cases per 100,000 persons); 125 of the 195 nursing homes had not reported any COVID-19 cases before the testing. Ninety-five of 22,977 (0.4%) persons tested in 29 (23%) of these 125 facilities had positive SARS-CoV-2 test results. The other five health departments targeted facility-wide testing to 93 nursing homes, where 13,443 persons were tested, and 1,619 (12%) had positive SARS-CoV-2 test results. In regression analyses among 88 of these nursing homes with a documented case before facility-wide testing occurred, each additional day between identification of the first case and completion of facility-wide testing was associated with identification of 1.3 additional cases. Among 62 facilities that could differentiate results by resident and HCP status, an estimated 1.3 HCP cases were identified for every three resident cases. Performing facility-wide testing immediately after identification of a case commonly identifies additional unrecognized cases and, therefore, might maximize the benefits of infection prevention and control interventions. In contrast, facility-wide testing in low-incidence areas without a case has a lower proportion of test positivity; strategies are needed to further optimize testing in these settings.
Abstract 510: Type I Interferons Promote Atherosclerosis By Affecting Chemotaxis And Cell Death
Authors: Pieter Goossens, Marion J Gijbels, Alma Zernecke, Ingeborg van der Made, Linda Beckers, Wim A Buurman, Christian Weber, Ulrich Kalinke, Esther Lutgens, Menno P de Winther
Journal: Circulation (2008)

Type I interferons (IFN-Is) belong to a family of cytokines well known to mediate antiviral responses but also both pro- and anti-inflammatory immune cell functions. Clinically, they are used as an...
Application of 2015 Seronegative Neuromyelitis Optica Spectrum Disorder Diagnostic Criteria for Patients With Myelin Oligodendrocyte Glycoprotein IgG–Associated Disorders
Authors: Amy Kunchok, John J. Chen, Ruba S. Saadeh, Dean M. Wingerchuk, Brian G. Weinshenker, Eoin P. Flanagan, Sean J. Pittock
Journal: JAMA Neurology (2020)

This study evaluates the proportion of patients with myelin oligodendrocyte glycoprotein IgG–associated disorders who fulfill the seronegative neuromyelitis optica spectrum disorder criteria.
Increased expression of interleukin‐23A in lesional skin of patients with atopic dermatitis with psoriasiform reaction during dupilumab treatment
Authors: M. Napolitano, G. Caiazzo, G. Fabbrocini, A. Balato, R. Di Caprio, E. Scala, M. Scalvenzi, C. Patruno
Journal: British Journal of Dermatology (2020)
Racial differences in treatment and outcomes in multiple myeloma: a multiple myeloma research foundation analysis
Authors: Benjamin A. Derman, Jagoda Jasielec, Spencer S. Langerman, Wei Zhang, Andrzej J. Jakubowiak, Brian C.-H. Chiu
Journal: Blood Cancer Journal (2020)

Abstract Findings on racial differences in survival in multiple myeloma (MM) have been inconclusive. We assessed differences in outcomes between White and Black individuals among 639 newly diagnosed MM patients in the MM Research Foundation CoMMpass registry with baseline cytogenetic data. Survival curves were constructed using the Kaplan–Meier method. Hazard ratios and 95% confidence intervals were derived from Cox proportional hazard regression models. Age, gender, and stage were similar between Whites ( n = 526) and Blacks ( n = 113). Blacks had inferior overall survival (OS) compared with Whites and were less likely to receive triplet therapies or frontline autologous stem cell transplant (ASCT). The following factors were significantly associated with inferior OS in multivariate analysis: higher international staging system (ISS) score, ≥1 or ≥2 high-risk cytogenetic abnormalities (HRCA), high-risk gene expression profile (GEP), and lack of ASCT. Multivariate analysis in the Black subset found that only lack of ASCT was significantly associated with inferior OS. The receipt of both triplet induction and ASCT only partly abrogated the effect of race on survival. HRCA did not track with survival in Blacks, emphasizing the need for race-specific risk prognostication schema to guide optimal MM therapy.
The mechanical property and corrosion resistance of Mg-Zn-Nd alloy fine wires in vitro and in vivo
Authors: Ming Gao, Di Na, Xiangqiao Ni, Lihui Song, Iniobong P. Etim, Ke Yang, Lili Tan, Zheng Ma
Journal: Bioactive Materials (2020)

Titanium and its alloy are commonly used as surgical staples in the reconstruction of intestinal tract and stomach, however they cannot be absorbed in human body, which may cause a series of complications to influence further diagnosis. Magnesium and its alloy have great potential as surgical staples, because they can be degraded in human body and have good mechanical properties and biocompatibility. In this study, Mg-2Zn-0.5Nd (ZN20) alloy fine wires showed great potential as surgical staples. The ultimate tensile strength and elongation of ZN20 alloy fine wires were 248 MPa and 13%, respectively, which could be benefit for the deformation of the surgical staples from U-shape to B-shape. The bursting pressure of the wire was about 40 kPa, implying that it can supply sufficient mechanical support after anastomosis. Biochemical test and histological analysis illustrated good biocompatibility and biological safety of ZN20 alloy fine wire. The residual tensile stress formed on the outside of ZN20 fine wire during drawing would accelerate the corrosion. The second phase had a negative influence on corrosion property due to galvanic corrosion. The corrosion rate in vitro was faster than that in vivo due to the capsule formed on the surface of ZN20 alloy fine wire.
Use of electronic tools for evidence-based preparedness and response to the COVID-19 pandemic in the WHO African region
Authors: Benido Impouma, Caitlin M Wolfe, Franck Mboussou, Bridget Farham, Arish Bukhari, Antoine Flahault, Theresa M Lee, Tamayi Mlanda, Patricia Ndumbi, Roland Ngom, Charles Okot, Fleury Moussana, George Sie Williams, Alden Moussongo, Ambrose Talisuna, Francis Kasolo, Kamran Ahmed, Olivia Keiser
Journal: The Lancet Digital Health (2020)
An evolutionary driver of interspersed segmental duplications in primates
Authors: Stuart Cantsilieris, Susan M. Sunkin, Matthew E. Johnson, Fabio Anaclerio, John Huddleston, Carl Baker, Max L. Dougherty, Jason G. Underwood, Arvis Sulovari, PingHsun Hsieh, Yafei Mao, Claudia Rita Catacchio, Maika Malig, AnneMarie E. Welch, Melanie Sorensen, Katherine M. Munson, Weihong Jiang, Santhosh Girirajan, Mario Ventura, Bruce T. Lamb, Ronald A. Conlon, Evan E. Eichler
Journal: Genome biology (2020)

Abstract Background The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brain evolution. We investigate the evolution of LCR16a, a putative driver of this phenomenon that encodes one of the most rapidly evolving human–ape gene families, nuclear pore interacting protein ( NPIP ). Results Comparative analysis shows that LCR16a has independently expanded in five primate lineages over the last 35 million years of primate evolution. The expansions are associated with independent lineage-specific segmental duplications flanking LCR16a leading to the emergence of large interspersed duplication blocks at non-orthologous chromosomal locations in each primate lineage. The intron-exon structure of the NPIP gene family has changed dramatically throughout primate evolution with different branches showing characteristic gene models yet maintaining an open reading frame. In the African ape lineage, we detect signatures of positive selection that occurred after a transition to more ubiquitous expression among great ape tissues when compared to Old World and New World monkeys. Mouse transgenic experiments from baboon and human genomic loci confirm these expression differences and suggest that the broader ape expression pattern arose due to mutational changes that emerged in cis. Conclusions LCR16a promotes serial interspersed duplications and creates hotspots of genomic instability that appear to be an ancient property of primate genomes. Dramatic changes to NPIP gene structure and altered tissue expression preceded major bouts of positive selection in the African ape lineage, suggestive of a gene undergoing strong adaptive evolution.
Days of Future Past: Reply to Open Peer Commentaries on “Revising, Correcting, and Transferring Genes”
Authors: Bryan Cwik
Journal: The American Journal of Bioethics (2020)

Imagine it is 1932, and you walk into your office one morning and open your (physical, print) copy of Nature to see an article by a British physicist, James Chadwick, entitled “Possible Existence o...
Functional heterogeneity of alveolar macrophage population based on expression of CXCL2
Authors: Shengjie Xu-Vanpala, M. Elizabeth Deerhake, Joshua D. Wheaton, Morgan E. Parker, Praveen R. Juvvadi, Nancie MacIver, Maria Ciofani, Mari L. Shinohara
Journal: Science Immunology (2020)

Pulmonary fungal infections generate heterogenous alveolar macrophage subpopulations.
Multifunctional Natural Polymer Nanoparticles as Antifibrotic Gene Carriers for CKD Therapy
Authors: Adam C. Midgley, Yongzhen Wei, Dashuai Zhu, Fangli Gao, Hongyu Yan, Anila Khalique, Wenya Luo, Huan Jiang, Xiangsheng Liu, Jiasen Guo, Chuangnian Zhang, Guowei Feng, Kai Wang, Xueyuan Bai, Wen Ning, Chao Yang, Qiang Zhao, Deling Kong
Journal: Journal of the American Society of Nephrology (2020)

Progressive fibrosis is the underlying pathophysiological process of CKD, and targeted prevention or reversal of the profibrotic cell phenotype is an important goal in developing therapeutics for CKD. Nanoparticles offer new ways to deliver antifibrotic therapies to damaged tissues and resident cells to limit manifestation of the profibrotic phenotype.We focused on delivering plasmid DNA expressing bone morphogenetic protein 7 (BMP7) or hepatocyte growth factor (HGF)-NK1 (HGF/NK1) by encapsulation within chitosan nanoparticles coated with hyaluronan, to safely administer multifunctional nanoparticles containing the plasmid DNA to the kidneys for localized and sustained expression of antifibrotic factors. We characterized and evaluated nanoparticles in vitro for biocompatibility and antifibrotic function. To assess antifibrotic activity in vivo, we used noninvasive delivery to unilateral ureteral obstruction mouse models of CKD.Synthesis of hyaluronan-coated chitosan nanoparticles containing plasmid DNA expressing either BMP7 or NGF/NKI resulted in consistently sized nanoparticles, which-following endocytosis driven by CD44+ cells-promoted cellular growth and inhibited fibrotic gene expression in vitro. Intravenous tail injection of these nanoparticles resulted in approximately 40%-45% of gene uptake in kidneys in vivo. The nanoparticles attenuated the development of fibrosis and rescued renal function in unilateral ureteral obstruction mouse models of CKD. Gene delivery of BMP7 reversed the progression of fibrosis and regenerated tubules, whereas delivery of HGF/NK1 halted CKD progression by eliminating collagen fiber deposition.Nanoparticle delivery of HGF/NK1 conveyed potent antifibrotic and proregenerative effects. Overall, this research provided the proof of concept on which to base future investigations for enhanced targeting and transfection of therapeutic genes to kidney tissues, and an avenue toward treatment of CKD.
Gains of chromosome 17q common in high-risk neuroblastomas do not involve the topoisomerase IIα gene: FISH and quantitative-PCR (Q-PCR) studies of six neuroblastoma cell lines
Authors: Kyoung Jin P. Yoon, Marcus B. Valentine, Virginia A. Valentine, Susan T. Ragsdale, Mary K. Danks
Journal: Cancer Research (2004)

2724  Neuroblastoma (NB) is the most common extra cranial solid tumor of childhood. Only 20-40% of children diagnosed with stage 4 disease survive 5 years. Tumors from these patients frequently have non-reciprocal translocations that result gain of genetic material from chromosome 17q21-25. The topoisomerase IIα gene is located in this region of 17q (17q21-22). Since topo IIα inhibitors are commonly used for NB treatment, we asked whether the 17q translocations in NB cells resulted in increased copy number of the topo IIα gene and/or increased levels of topo IIα protein. We also examined whether topo IIα gene copy number correlated with sensitivity to the topo IIα inhibitors VP-16 and doxorubicin. We evaluated six NB cell lines (NB 1691, SK-N-AS, SK-N-SH, SJNB-1, IMR-32, and NB 1643) by fluorescence in situ hybridization (FISH) analysis using a 17q “paint” probe or a BAC probe (RP11-45506) to the terminus of 17q (17q25.3). We then compared FISH results with karyotype analyses to identify specific 17q translocations. Then Q-PCR was done to determine whether the topo IIα gene was amplified in NB cell lines containing gains of 17q. FISH analyses with both probes showed that all six NB cell lines harbored non-reciprocal translocations of 17q. The karyotype analyses showed translocations of 17q to chromosomes 1, 3, 11, 19 and 22. However, although all six NB cell lines contained gains of 17q material, only one NB cell line, SK-N-AS, showed an increased topo IIα gene dose of 2. Further, increased gene copy number did not correspond to an increase in protein expression or in increased sensitivity to VP-16 or doxorubicin. This study illustrates that the topo IIα gene does not participate in 17q translocations in 5/6 NB cell lines examined and that an increased topo IIα gene copy number does not predict sensitivity to topo IIα inhibitors. (Supported by CA79763, CA76202, CA21765 and by the American Lebanese Syrian Associated Charities.)
Effect of pegylated interferon-alpha-2a treatment on mental health during recent hepatitis C virus infection
Authors: Maryam Alavi, Jason Grebely, Gail V Matthews, Kathy Petoumenos, Barbara Yeung, Carolyn Day, Andrew R Lloyd, Ingrid Van Beek, John M Kaldor, Margaret Hellard, Gregory J Dore, Paul S Haber
Journal: Hepatology (2012)
Novel insights into the interplay between m6A modification and noncoding RNAs in cancer
Authors: You-Cai Yi, Xiao-Yu Chen, Jing Zhang, Jin-Shui Zhu
Journal: Molecular Cancer (2020)

N6-methyladenosine (m6A) is one of the most common RNA modifications in eukaryotes, mainly in messenger RNA (mRNA). Increasing evidence shows that m6A methylation modification acts an essential role in various physiological and pathological bioprocesses. Noncoding RNAs (ncRNAs), including miRNAs, lncRNAs and circRNAs, are known to participate in regulating cell differentiation, angiogenesis, immune response, inflammatory response and carcinogenesis. m6A regulators, such as METTL3, ALKBH5 and IGF2BP1 have been reported to execute a m6A-dependent modification of ncRNAs involved in carcinogenesis. Meanwhile, ncRNAs can target or modulate m6A regulators to influence cancer development. In this review, we provide an insight into the interplay between m6A modification and ncRNAs in cancer.
Revising, Correcting, and Transferring Genes
Authors: Bryan Cwik
Journal: The American Journal of Bioethics (2020)

The distinction between germline and somatic gene editing is fundamental to the ethics of human gene editing. Multiple conferences of scientists, ethicists, and policymakers, and multiple professional bodies, have called for moratoria on germline gene editing, and editing of human germline cells is considered to be an ethical "red line" that either never should be crossed, or should only be crossed with great caution and care. However, as research on germline gene editing has progressed, it has become clear that not all germline interventions are alike, and that these differences make a significant moral difference, when it comes to ethical questions about research, regulation, clinical application, and medical justification. In this paper, I argue that, rather than lumping all germline interventions together, we should distinguish between revising, correcting, and transferring genes, and I assess the consequences of this move for the ethics of gene editing.
AB0407 HUMAN PAPILLOMA VIRUS (HPV) INFECTION AND CERVICAL CANCER PREVALENCE IN A PORTUGUESE UNIVERSITY HOSPITAL SINGLE-CENTER SYSTEMIC LUPUS ERYTHEMATOSUS COHORT
Authors: J. Sousa Morais, D. G. Oliveira, R. Faria, A. Almeida, M. Brandão, A. Marinho, I. Almeida, F. Farinha, C. Vasconcelos
Journal: Annals of the Rheumatic Diseases (2020)

Background: About 12% of women worldwide are infected with Human Papillomavirus (HPV), the most frequent cause of cervical cancer (CC) - very prevalent (~ 7,5%) and preventable. National screening efforts are in use in several countries, including Portugal. Patients with Systemic Lupus Erythematosus (SLE) are at increased risk of HPV infection and CC when compared to the healthy population. Objectives: To evaluate the prevalence of HPV infection and rate of incidence of cervical neoplastic lesions in a SLE patient cohort followed at a university hospital. Methods: Retrospective single-center (35 year long, 463 SLE patient cohort) review of all female SLE patients’ local and online national health care records on HPV vaccination and CC screening. Results: Of the 463 SLE patients, 420 were women (91%), of which 322 had records on of HPV infection or CC developed. Mean patients’ current age was 48 years and all had screening for cervical pathology in the last 3 years. Thirty-three patients (11%) had HPV infection diagnosed at a mean age of 44 years. Twenty-seven (8%) of SLE patients were vaccinated for HPV: 8 (22%) of the infected patients had the vaccine, half after the HPV infection. Despite HPV infection, 49 patients (15%) had developed some cervical lesion, of which 41 (84% of cervical lesion) were suggestive of malignancy, and ultimately CC was diagnosed in 20 women (41%; 6% of total women), with a mean age at diagnosis of 45 years. All CC patients had history of HPV infection, but only 3 women (15%; 0,9% of total women) had been vaccinated against HPV, 2 after the diagnoses of CC and 1 before. Conclusion: In our population the prevalence of HPV was higher than reported for the general population using the World Health Organization database, conforming the higher risk of HPV infection in SLE patients. The prevalence of cervical cancer, however, was similar to the healthy population. References: [1]https://www.who.int/immunization/diseases/hpv/en/ [2 ] Forman David (2012); “Global Burden of Human Papillomavirus and Related Diseases”, Vaccine, Elsevier Volume 30, Supplement 5, 20 November 2012 [3 ] Grein Ingrid (2016), Department of Pediatric Immunology and Rheumatology, Netherland (2016), HPV infection and vaccination in Systemic Lupus Erythematosus patients: what we really should know, Pediatric Rheumatology, 2016 Disclosure of Interests: : None declared
Inducible myocardial ischemia due to obstructive coronary artery disease is associated with subclinical LV dysfunction in patients with stable angina
Authors: C. Caselli, V. Lorenzoni, M. Lombardi, R. Sicari, A.J. Scholte, J. Knuuti, S.R. Underwood, A. Clerico, M. Emdin, D. Neglia
Journal: European Journal of Heart Failure (2016)
Prevalence of SARS-CoV-2 Infection Among Health Care Workers in a Tertiary Community Hospital
Authors: Allen Jeremias, James Nguyen, Joseph Levine, Simcha Pollack, William Engellenner, Avni Thakore, Charles Lucore
Journal: JAMA Internal Medicine (2020)

Filtration Efficiency of Hospital Face Mask Alternatives Available for Use During the COVID-19 Pandemic