tbuckley/cabot-search huggingface dataset:
T‐cell immune profile in blood of systemic mastocytosis: Association with disease features
Authors: Alba Pérez‐Pons, Cristina Teodosio, María Jara‐Acevedo, Ana Henriques, Paula Navarro‐Navarro, Andrés C. García‐Montero, Iván Álvarez‐Twose, Quentin Lecrevisse, Rafael Fluxa, Laura Sánchez‐Muñoz, Carolina Caldas, Julio Pozo, Silvia Martín, Teresa Contreras Sanfeliciano, Carlos E. Pedreira, Vitor Botafogo, Oscar González‐López, Andrea Mayado, Alberto Orfao
Journal: Allergy (2024)

Abstract Background Systemic mastocytosis (SM) is a heterogeneous disease characterized by an expansion of KIT ‐mutated mast cells (MC). KIT ‐mutated MC display activated features and release MC mediators that might act on the tumour microenvironment and other immune cells. Here, we investigated the distribution of lymphocyte subsets in blood of patients with distinct subtypes of SM and determined its association with other disease features. Methods We studied the distribution of TCD4 + and TCD4 − cytotoxic cells and their subsets, as well as total NK‐ and B cells, in blood of 115 SM patients—38 bone marrow mastocytosis (BMM), 67 indolent SM (ISM), 10 aggressive SM (ASM)‐ and 83 age‐matched healthy donors (HD), using spectral flow cytometry and the EuroFlow Immunomonitoring panel, and correlated it with multilineage KIT D816V , the alpha‐tryptasemia genotype (HαT) and the clinical manifestations of the disease. Results SM patients showed decreased counts (vs. HD) of TCD4 − cytotoxic cells, NK cells and several functional subsets of TCD4 + cells (total Th1, Th2‐effector memory, Th22‐terminal effector and Th1‐like Tregs), together with increased T‐follicular‐helper and Th1/Th17‐like Treg counts, associated with different immune profiles per diagnostic subtype of SM, in multilineal versus MC‐restricted KIT D816V and in cases with a HαT + versus HαT − genotype. Unique immune profiles were found among BMM and ISM patients with MC‐restricted KIT D816V who displayed HαT, anaphylaxis, hymenoptera venom allergy, bone disease, pruritus, flushing and GI symptoms. Conclusion Our results reveal altered T‐ and NK‐cell immune profiles in blood of SM, which vary per disease subtype, the pattern of involvement of haematopoiesis by KIT D816V , the HαT genotype and specific clinical manifestations of the disease.
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding
Authors: Lingyan Zheng, Shuiyang Shi, Mingkun Lu, Pan Fang, Ziqi Pan, Hongning Zhang, Zhimeng Zhou, Hanyu Zhang, Minjie Mou, Shijie Huang, Lin Tao, Weiqi Xia, Honglin Li, Zhenyu Zeng, Shun Zhang, Yuzong Chen, Zhaorong Li, Feng Zhu
Journal: Genome biology (2024)

Abstract Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO families containing few annotated proteins. Herein, an innovative strategy named AnnoPRO was therefore constructed by enabling sequence-based multi-scale protein representation, dual-path protein encoding using pre-training, and function annotation by long short-term memory-based decoding. A variety of case studies based on different benchmarks were conducted, which confirmed the superior performance of AnnoPRO among available methods. Source code and models have been made freely available at: https://github.com/idrblab/AnnoPRO and https://zenodo.org/records/10012272
Navigating the uncertainty of critical illness: the role of a time-limited trial
Authors: Thanh Neville, Donald R. Sullivan, Eileen Rubin, Jacqueline M. Kruser
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"Navigating the uncertainty of critical illness: the role of a time-limited trial." American Journal of Respiratory and Critical Care Medicine, 209(3), pp. P1–P2
<i>Notes from the Field:</i> Severe <i>Vibrio vulnificus</i> Infections During Heat Waves — Three Eastern U.S. States, July–August 2023
Authors: Michael J. Hughes, Eileen Flaherty, Nicole Lee, Amy Robbins, Daniel L. Weller
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Vibrio vulnificus, a waterborne and foodborne pathogen, lives in estuarine environments and thrives in warmer waters.V. vulnificus can infect open wounds through contact with salt water, brackish water, or raw seafood; infections can also occur after consuming raw or undercooked seafood.In the United States, 150-200 V. vulnificus infections are reported to CDC annually, approximately 20% of which are fatal.*During June-August 2023, widespread heat waves and above-average sea surface temperatures occurred in the United States (1).During July-August 2023, public health officials in three eastern U.S. states (Connecticut, New York, and North Carolina) were notified of V. vulnificus infections associated with exposure to coastal waters and seafood, most of which were severe and led to septic shock or death.This report describes V. vulnificus infections among residents of these three states during the 2023 heat waves.
Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site
Authors: Andrew J. Thompson, Nicholas C. Wu, Angeles Canales, Chika Kikuchi, Xueyong Zhu, Beatriz Fernández de Toro, Francisco J. Cañada, Charli Worth, Shengyang Wang, Ryan McBride, Wenjie Peng, Corwin M. Nycholat, Jesús Jiménez-Barbero, Ian A. Wilson, James C. Paulson
Journal: Cell Host & Microbe (2024)
Lung Disease and Social Justice: Chronic Obstructive Pulmonary Disease as a Manifestation of Structural Violence
Authors: Parris J. Williams, Sara C. Buttery, Anthony A. Laverty, Nicholas S. Hopkinson
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

Lung health, the development of lung disease, and how well a person with lung disease is able to live all depend on a wide range of societal factors. These systemic factors that adversely affect people and cause injustice can be thought of as "structural violence." To make the causal processes relating to chronic obstructive pulmonary disease (COPD) more apparent, and the responsibility to interrupt or alleviate them clearer, we have developed a taxonomy to describe this. It contains five domains:
<i>Notes from the Field:</i> Dengue Outbreak — Peru, 2023
Authors: César V. Munayco, Betsabet Yadira Valderrama Rosales, Susan Yanett Mateo Lizarbe, Carmen Rosa Yon Fabian, Ricardo Peña Sánchez, César Henry Vásquez Sánchez, Maria Paquita García, Carlos Padilla-Rojas, Victor Suárez, Liliana Sánchez-González, Forrest K. Jones, Luciana Kohatsu, Laura E. Adams, Juliette Morgan, Gabriela Paz-Bailey
Journal: MMWR Morbidity and Mortality Weekly Report (2024)
<i>QuickStats:</i> Percentage of Newborns Breastfed Between Birth and Discharge* from Hospital, by Maternal Age — National Vital Statistics System, 49 States† and the District of Columbia, 2021 and 2022
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

34 35-39 ≥40 Percentage Age group of mother, yrs 2021 2022* Breastfed between birth and discharge from hospital is defined as a newborn who received breast milk or colostrum during the period between birth and discharge from the hospital.† California does not report breastfeeding on birth certificates; approximately 11% of U.S. births in 2022 were to residents of California.Among 49 states and the District of Columbia, the percentage of newborns breastfed between birth and discharge from the hospital increased from 83.3% in 2021 to 85.2% in 2022.Increases were observed for each maternal age group; the largest increases occurred among younger maternal age groups (70.4% to 74.5% among mothers aged <20 years and 77.6% to 80.8% among mothers aged 20-24 years).Despite the recent increases in initiation of breastfeeding at birth among younger mothers, older mothers were still more likely to breastfeed their newborns (86.8% of those aged ≥40 years versus 74.5% of mothers aged <20 years).
Critical Care: A Special Issue of the Blue Journal
Authors: Carolyn S. Calfee, Michael O. Harhay, Edward J. Schenck, Niall D. Ferguson, Leo Heunks, Douglas B. White, Laurent J. Brochard
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"Critical Care: A Special Issue of the Blue Journal." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Early Estimates of Updated 2023–2024 (Monovalent XBB.1.5) COVID-19 Vaccine Effectiveness Against Symptomatic SARS-CoV-2 Infection Attributable to Co-Circulating Omicron Variants Among Immunocompetent Adults — Increasing Community Access to Testing Program, United States, September 2023–January 2024
Authors: Ruth Link-Gelles, Allison Avrich Ciesla, Josephine Mak, Joseph D. Miller, Benjamin J. Silk, Anastasia S. Lambrou, Clinton R. Paden, Philip Shirk, Amadea Britton, Zachary R. Smith, Katherine E. Fleming-Dutra
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

On September 12, 2023, CDC's Advisory Committee on Immunization Practices recommended updated 2023-2024 (updated) COVID-19 vaccination with a monovalent XBB.1.5-derived vaccine for all persons aged ≥6 months to prevent COVID-19, including severe disease. During fall 2023, XBB lineages co-circulated with JN.1, an Omicron BA.2.86 lineage that emerged in September 2023. These variants have amino acid substitutions that might increase escape from neutralizing antibodies. XBB lineages predominated through December 2023, when JN.1 became predominant in the United States. Reduction or failure of spike gene (S-gene) amplification (i.e., S-gene target failure [SGTF]) in real-time reverse transcription-polymerase chain reaction testing is a time-dependent, proxy indicator of JN.1 infection. Data from the Increasing Community Access to Testing SARS-CoV-2 pharmacy testing program were analyzed to estimate updated COVID-19 vaccine effectiveness (VE) (i.e., receipt versus no receipt of updated vaccination) against symptomatic SARS-CoV-2 infection, including by SGTF result. Among 9,222 total eligible tests, overall VE among adults aged ≥18 years was 54% (95% CI = 46%-60%) at a median of 52 days after vaccination. Among 2,199 tests performed at a laboratory with SGTF testing, VE 60-119 days after vaccination was 49% (95% CI = 19%-68%) among tests exhibiting SGTF and 60% (95% CI = 35%-75%) among tests without SGTF. Updated COVID-19 vaccines provide protection against symptomatic infection, including against currently circulating lineages. CDC will continue monitoring VE, including for expected waning and against severe disease. All persons aged ≥6 months should receive an updated COVID-19 vaccine dose.
Surveillance for Acute Flaccid Myelitis ― United States, 2018–2022
Authors: Erin R. Whitehouse, Adriana Lopez, Randall English, Halle Getachew, Terry Fei Fan Ng, Brian Emery, Shannon Rogers, Sarah Kidd
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Acute flaccid myelitis (AFM) is a serious neurologic condition primarily affecting children; AFM can cause acute respiratory failure and permanent paralysis.AFM is a rare but known complication of various viral infections, particularly those of enteroviruses (EVs).Increases in AFM cases during 2014, 2016, and 2018 were associated with EV-D68 infection.This report examines trends in confirmed AFM cases during 2018-2022 and patients' clinical and laboratory characteristics.The number of AFM cases was low during 2019-2022 (28-47 cases per year); the number of cases remained low in 2022 despite evidence of increased EV-D68 circulation in the United States.Compared with cases during the most recent peak year (2018), fewer cases during 2019-2021 had upper limb involvement, prodromal respiratory or febrile illness, or cerebrospinal fluid pleocytosis, and more were associated with lower limb involvement.It is unclear why EV-D68 circulation in 2022 was not associated with an increase in AFM cases or when the next increase in AFM cases will occur.Nonetheless, clinicians should continue to suspect AFM in any child with acute flaccid limb weakness, especially those with a recent respiratory or febrile illness.
The CoREST repressor complex mediates phenotype switching and therapy resistance in melanoma
Authors: Muzhou Wu, Ailish Hanly, Frederick Gibson, Robert Fisher, Samantha Rogers, Kihyun Park, Angelina Zuger, Kevin Kuang, Jay H. Kalin, Sarah Nocco, Matthew Cole, Amy Xiao, Filisia Agus, Adam Labadorf, Samuel Beck, Marianne Collard, Philip A. Cole, Rhoda M. Alani
Journal: Journal of Clinical Investigation (2024)

Virtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through nonmutational events. Although the epigenetic landscape is shown to be altered in therapy-resistant melanomas and other cancers, a specific targetable epigenetic mechanism has not been validated. Here, we evaluated the corepressor for element 1-silencing transcription factor (CoREST) epigenetic repressor complex and the recently developed bivalent inhibitor corin within the context of melanoma phenotype plasticity and therapeutic resistance. We found that CoREST was a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells led to phenotype reprogramming. Global assessment of transcript and chromatin changes conferred by corin revealed specific effects on histone marks connected to epithelial-mesenchymal transition-associated (EMT-associated) transcription factors and the dual-specificity phosphatases (DUSPs). Remarkably, treatment of BRAF inhibitor-resistant (BRAFi-R) melanomas with corin promoted resensitization to BRAFi therapy. DUSP1 was consistently downregulated in BRAFi-R melanomas, which was reversed by corin treatment and associated with inhibition of p38 MAPK activity and resensitization to BRAFi therapies. Moreover, this activity was recapitulated by the p38 MAPK inhibitor BIRB 796. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial for patients with BRAFi-resistant melanoma.
A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology
Authors: Zhangming Pei, Yufei Liu, Yutao Chen, Tong Pan, Xihao Sun, Hongchao Wang, R. Paul Ross, Wenwei Lu, Wei Chen
Journal: Gut Microbes (2024)

Prophages, which are an existing form of temperate phages that integrate into host genomes, have been found extensively present in diverse bacterial species. The human gut microbiome, characterized by its complexity, dynamism, and interconnectivity among multiple species, remains inadequately understood in terms of the global landscape of bacterial prophages. Here, we analyzed 43,942 human gut-derived bacterial genomes (439 species of 12 phyla) and identified 105,613 prophage regions in ~ 92% of them. 16254 complete prophages were distributed in ~ 24% of bacteria, indicating an extremely uneven prophage distribution across various species within the human gut. Among all identified prophages, ~4% possessed cross-genera (2-20 genera) integration capacity, while ~ 17% displayed broad infection host ranges (targeting 2-35 genera). Functional gene annotation revealed that antibiotic-resistance genes and toxin-related genes were detected in ~ 2.5% and ~ 5.8% of all prophages, respectively. Furthermore, through sequence alignments between our obtained prophages and publicly available human gut phageome contigs, we have observed that ~ 72% of non-redundant prophages are previously unreported genomes, and they illuminate ~ 6.5-9.5% of the individual intestinal "viral dark matter". Our study represents the first comprehensive depiction of human gut-derived prophages, provides a substantial collection of reference sequences for forthcoming human gut phageome-related investigations, and potentially enables better risk assessment of prophage dissemination.
Atypia detected during breast screening and subsequent development of cancer: observational analysis of the Sloane atypia prospective cohort in England
Authors: Karoline Freeman, David Jenkinson, Karen Clements, Matthew G Wallis, Sarah E Pinder, Elena Provenzano, Hilary Stobart, Nigel Stallard, Olive Kearins, Nisha Sharma, Abeer Shaaban, Cliona Clare Kirwan, Bridget Hilton, Alastair M Thompson, Sian Taylor-Phillips
Journal: BMJ (2024)

Abstract Objective To explore how the number and type of breast cancers developed after screen detected atypia compare with the anticipated 11.3 cancers detected per 1000 women screened within one three year screening round in the United Kingdom. Design Observational analysis of the Sloane atypia prospective cohort in England. Setting Atypia diagnoses through the English NHS breast screening programme reported to the Sloane cohort study. This cohort is linked to the English Cancer Registry and the Mortality and Birth Information System for information on subsequent breast cancer and mortality. Participants 3238 women diagnosed as having epithelial atypia between 1 April 2003 and 30 June 2018. Main outcome measures Number and type of invasive breast cancers detected at one, three, and six years after atypia diagnosis by atypia type, age, and year of diagnosis. Results There was a fourfold increase in detection of atypia after the introduction of digital mammography between 2010 (n=119) and 2015 (n=502). During 19 088 person years of follow-up after atypia diagnosis (until December 2018), 141 women developed breast cancer. Cumulative incidence of cancer per 1000 women with atypia was 0.95 (95% confidence interval 0.28 to 2.69), 14.2 (10.3 to 19.1), and 45.0 (36.3 to 55.1) at one, three, and six years after atypia diagnosis, respectively. Women with atypia detected more recently have lower rates of subsequent cancers detected within three years (6.0 invasive cancers per 1000 women (95% confidence interval 3.1 to 10.9) in 2013-18 v 24.3 (13.7 to 40.1) in 2003-07, and 24.6 (14.9 to 38.3) in 2008-12). Grade, size, and nodal involvement of subsequent invasive cancers were similar to those of cancers detected in the general screening population, with equal numbers of ipsilateral and contralateral cancers. Conclusions Many atypia could represent risk factors rather than precursors of invasive cancer requiring surgery in the short term. Women with atypia detected more recently have lower rates of subsequent cancers detected, which might be associated with changes to mammography and biopsy techniques identifying forms of atypia that are more likely to represent overdiagnosis. Annual mammography in the short term after atypia diagnosis might not be beneficial. More evidence is needed about longer term risks.
Immune subtyping of melanoma whole slide images using multiple instance learning
Authors: Lucy Godson, Navid Alemi, Jérémie Nsengimana, Graham P. Cook, Emily L. Clarke, Darren Treanor, D. Timothy Bishop, Julia Newton-Bishop, Ali Gooya, Derek Magee
Journal: Medical Image Analysis (2024)

Determining early-stage prognostic markers and stratifying patients for effective treatment are two key challenges for improving outcomes for melanoma patients. Previous studies have used tumour transcriptome data to stratify patients into immune subgroups, which were associated with differential melanoma specific survival and potential predictive biomarkers. However, acquiring transcriptome data is a time-consuming and costly process. Moreover, it is not routinely used in the current clinical workflow. Here, we attempt to overcome this by developing deep learning models to classify gigapixel haematoxylin and eosin (H&E) stained pathology slides, which are well established in clinical workflows, into these immune subgroups. We systematically assess six different multiple instance learning (MIL) frameworks, using five different image resolutions and three different feature extraction methods. We show that pathology-specific self-supervised models using 10x resolution patches generate superior representations for the classification of immune subtypes. In addition, in a primary melanoma dataset, we achieve a mean area under the receiver operating characteristic curve (AUC) of 0.80 for classifying histopathology images into 'high' or 'low immune' subgroups and a mean AUC of 0.82 in an independent TCGA melanoma dataset. Furthermore, we show that these models are able to stratify patients into 'high' and 'low immune' subgroups with significantly different melanoma specific survival outcomes (log rank test, P< 0.005). We anticipate that MIL methods will allow us to find new biomarkers of high importance, act as a tool for clinicians to infer the immune landscape of tumours and stratify patients, without needing to carry out additional expensive genetic tests.
Effects of breastfeeding on children’s gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru
Authors: Maya L. Nadimpalli, Luismarcelo Rojas Salvatierra, Subhra Chakraborty, Jenna M. Swarthout, Lilia Z. Cabrera, Amy J. Pickering, Maritza Calderon, Mayuko Saito, Robert H. Gilman, Monica J. Pajuelo
Journal: Gut Microbes (2024)

Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing
Comparison of patients with isolated cutaneous lupus erythematosus versus systemic lupus erythematosus with cutaneous lupus erythematosus as the sole clinical feature: A monocentric study of 149 patients
Authors: Clémence Masseran, Laura Perray, Quitterie Murat de Montai, Alexis Mathian, Alexandre Teboul, Camille Francès, Laurent Arnaud, Nathalie Costedoat-Chalumeau, Zahir Amoura, Delphine S. Courvoisier, Annick Barbaud, François Chasset
Journal: Journal of the American Academy of Dermatology (2024)
Platelet Count, Platelet Volume, and CKD
Authors: Hinpetch Daungsupawong, Viroj Wiwanitkit
Journal: Journal of the American Society of Nephrology (2024)

1Private Academic Consultant, Phonhong, Lao People's Democratic Republic 2Chandigarh University, Mohali, Punjab, India Correspondence: Dr. Hinpetch Daungsupawong, Private Academic Consultant, Lak52, Phonhong, Vientaine, 10000 Lao People's Democratic Republic. Email: [email protected] See related reply, "Authors' Reply: Platelet Count, Platelet Volume, and CKD," on pages 250–251, and original article, "Platelet Count and Platelet Volume in Patients with CKD," in Vol. 34, Iss. 11, 1772–1775.