tbuckley/cabot-search huggingface dataset:
TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies
Authors: Pixu Shi, Cameron Martino, Rungang Han, Stefan Janssen, Gregory Buck, Myrna Serrano, Kouros Owzar, Rob Knight, Liat Shenhav, Anru R. Zhang
Journal: Genome biology (2024)

Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treats time as a continuous variable, effectively characterizing temporal information and handling varying temporal sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data. In simulations, it achieves 90% accuracy in phenotype classification, significantly outperforming existing methods. In real data, TEMPTED identifies vaginal microbial markers linked to term and preterm births, demonstrating robust performance across datasets and sequencing platforms.
Differential diagnosis and comparison of diagnostic algorithms in children and adolescents with autoimmune encephalitis in Spain: a prospective cohort study and retrospective analysis
Authors: Gemma Olivé-Cirera, Elianet Fonseca, Li-Wen Chen, Anna Fetta, Eugenia Martínez-Hernández, Mar Guasp, Veronica González-Álvarez, Verónica Delgadillo, Verónica Cantarín-Extremera, María Jiménez-Legido, Lorena Monge-Galindo, Ana Felipe, Beatriz Beseler, Eulàlia Turón-Viñas, Joaquín Fernández-Ramos, Maria J Martínez-González, Maria Vázquez-López, Luisa Arrabal Fernandez, Mireia Alvarez-Molinero, Beatriz Muñoz-Cabello, Ana Camacho, Noemí Nuñez-Enamorado, Marianna Spatola, Lídia Sabater, Yolanda Blanco, Albert Saiz, Francesc Graus, Josep Dalmau, Thaís Armangué
Journal: The Lancet Neurology (2024)
Prophylactic Clip Closure in Preventing Delayed Bleeding After Colorectal Endoscopic Submucosal Dissection on anticoagulants: A multicenter retrospective cohort study in Japan
Authors: Kazunori Takada, Naohisa Yoshida, Yoshikazu Hayashi, Daichi Togo, Shiro Oka, Shusei Fukunaga, Yoshinori Morita, Takemasa Hayashi, Kazunori Kozuka, Yosuke Tsuji, Takashi Murakami, Takeshi Yamamura, Yoriaki Komeda, Yoji Takeuchi, Kensuke Shinmura, Hiroko Fukuda, Shinji Yoshii, Shouko Ono, Shinichi Katsuki, Kazumasa Kawashima, Daiki Nemoto, Hiroyuki Yamamoto, Yutaka Saito, Naoto Tamai, Aya Tamura
Journal: Endoscopy (2024)

Prophylactic clip closure after colorectal endoscopic submucosal dissection (ESD) among patients on anticoagulants is of uncertain effectiveness in reducing delayed bleeding (DB) risk. We aimed to assess the effect of prophylactic clip closure in preventing DB after colorectal ESD among patients on anticoagulants.
Maternal and fetal responses to acute high-intensity resistance exercise during pregnancy
Authors: Amy N Moolyk, Megan K Wilson, Brittany A Matenchuk, Gyanjot Bains, Matthew J Gervais, Jenna B Wowdzia, Margie H Davenport
Journal: British Journal of Sports Medicine (2024)

To examine maternal and fetal cardiovascular responses to high-intensity resistance exercise in pregnancy.
Concurrent symptom domains and associations with recovery timelines among collegiate athletes with sport-related concussion
Authors: Bernadette A D'Alonzo, Andrea LC Schneider, Ian J Barnett, Christina L Master, Roy H Hamilton, Douglas J Wiebe
Journal: British Journal of Sports Medicine (2024)

Concussion symptoms can be clustered into domains and understanding how multiple symptom domains present clinically may guide more accurate interventions. We investigate the associations between concurrent symptom domains and clinical recovery outcomes, as well as the role of sex in these relationships.
Menopause: a global health and wellbeing issue that needs urgent attention
Authors: Gayathri Delanerolle, Peter Phiri, Sohier Elneil, Vikram Talaulikar, George U Eleje, Rabia Kareem, Ashish Shetty, Lucky Saraswath, Om Kurmi, Cristina Laguna Benetti-Pinto, Ifran Muhammad, Nirmala Rathnayake, Teck-Hock Toh, Ieera Madan Aggarwal, Jian Qing Shi, Julie Taylor, Kathleen Riach, Kristina Potocnik, Ian Litchfield, Helen Felicity Kemp, Paula Briggs
Journal: The Lancet Global Health (2024)
Safety and efficacy of intrathecal antibodies to Nogo-A in patients with acute cervical spinal cord injury: a randomised, double-blind, multicentre, placebo-controlled, phase 2b trial
Authors: Norbert Weidner, Rainer Abel, Doris Maier, Klaus Röhl, Frank Röhrich, Michael Baumberger, Margret Hund-Georgiadis, Marion Saur, Jesús Benito, Kerstin Rehahn, Mirko Aach, Andreas Badke, Jiri Kriz, Katalin Barkovits, Tim Killeen, Lynn Farner, Maryam Seif, Michèle Hubli, Katrin Marcus, Michael A Maurer, Bérénice Robert, Rüdiger Rupp, Paulina S Scheuren, Martin Schubert, Christian Schuld, Christina Sina, Bettina Steiner, Tanja Weis, Andreas Hug, Marc Bolliger, Nikolaus Weiskopf, Patrick Freund, Torsten Hothorn, Martin E Schwab, Armin Curt
Journal: The Lancet Neurology (2024)
Cardiovascular events in patients with gout initiating urate-lowering therapy with or without colchicine for flare prophylaxis: a retrospective new-user cohort study using linked primary care, hospitalisation, and mortality data
Authors: Edoardo Cipolletta, Georgina Nakafero, Natalie McCormick, Chio Yokose, Anthony J Avery, Mamas A Mamas, Hyon K Choi, Laila J Tata, Abhishek Abhishek
Journal: The Lancet Rheumatology (2024)
An innovative Community Mobilisation and Community Incentivisation for child health in rural Pakistan (CoMIC): a cluster-randomised, controlled trial
Authors: Jai K Das, Rehana A Salam, Zahra Ali Padhani, Arjumand Rizvi, Mushtaq Mirani, Muhammad Khan Jamali, Imran Ahmed Chauhadry, Imtiaz Sheikh, Sana Khatoon, Khan Muhammad, Rasool Bux, Anjum Naqvi, Fariha Shaheen, Rafey Ali, Sajid Muhammad, Simon Cousens, Zulfiqar A Bhutta
Journal: The Lancet Global Health (2024)
Safety, tolerability, pharmacokinetics, and antimalarial activity of MMV533: a phase 1a first-in-human, randomised, ascending dose and food effect study, and a phase 1b Plasmodium falciparum volunteer infection study
Authors: Benoit Bestgen, Sam Jones, Vandana Thathy, Andrea Kuemmerle, Catalina Barcelo, Amina Haouala, Denis Gossen, Michael W Marx, Ilaria Di Resta, Maja Szramowska, Rebecca A Webster, Stacey Llewellyn, Dominic A Ritacco, Tomas Yeo, Didier Leroy, Bridget E Barber, David A Fidock, Paul Griffin, Jason Lickliter, Stephan Chalon
Journal: The Lancet Infectious Diseases (2024)
Global burden of tuberculous meningitis in children aged 0–14 years in 2019: a mathematical modelling study
Authors: Karen du Preez, Helen E Jenkins, Leonardo Martinez, Silvia S Chiang, Sicelo S Dlamini, Mariia Dolynska, Andrii Aleksandrin, Julia Kobe, Stephen M Graham, Anneke C Hesseling, Jeffrey R Starke, James A Seddon, Peter J Dodd
Journal: The Lancet Global Health (2024)
Rates and risk factors for relapse among children recovered from severe acute malnutrition in Mali, South Sudan, and Somalia: a prospective cohort study
Authors: Sarah King, Anastasia Marshak, Lauren D'Mello-Guyett, Ellyn Yakowenko, Sherifath Mama Chabi, Salimata Samake, Magloire Bunkembo, Samou Diarra, Feysal Abdisalan Mohamud, Mohamed Sheikh Omar, Nancy Grace Lamwaka, Mesfin Gose, Khamisa Ayoub, Ahmed Hersi Olad, Aliou Bagayoko, Indi Trehan, Oliver Cumming, Heather Stobaugh
Journal: The Lancet Global Health (2024)
Association of current Schistosoma mansoni, Schistosoma japonicum, and Schistosoma mekongi infection status and intensity with periportal fibrosis: a systematic review and meta-analysis
Authors: Adanna Ewuzie, Lauren Wilburn, Dixa B Thakrar, Huike Cheng, Fabian Reitzug, Nia Roberts, Reem Malouf, Goylette F Chami
Journal: The Lancet Global Health (2024)
Progress in reducing socioeconomic inequalities in the use of modern contraceptives in 48 focus countries as part of the FP2030 initiative between 1990 and 2020: a population-based analysis
Authors: Carolina Cardona, Jean Christophe Rusatira, Carolina Salmeron, Michelle Martinez-Baack, Jose G Rimon, Philip Anglewicz, Saifuddin Ahmed
Journal: The Lancet Global Health (2024)
Safety and immunogenicity of an acellular pertussis vaccine containing genetically detoxified pertussis toxin administered to pregnant women living with and without HIV and their newborns (WoMANPOWER): a randomised controlled trial in Uganda
Authors: Eve Nakabembe, Melanie Greenland, Kyle Amaral, Bahaa Abu-Raya, Alexander Amone, Nick Andrews, Liberty Cantrell, Elodie Lesne, Andrew Gorringe, Rachel Halkerston, Nikki Mcstraw, Louisa Dixon, Olivia F Hunter, Paul T Heath, Esther Imede, Mary Kyohere, Philippa Musoke, Annettee Nakimuli, Musa Sekikubo, Stephen Taylor, Valerie Tusubira, Manish Sadarangani, Kirsty Le Doare
Journal: The Lancet Global Health (2024)
Effectiveness and acceptability of a 24-h interval versus a 48-h interval between mifepristone intake and misoprostol administration for in-hospital abortion at 9–20 gestational weeks: an international, open-label, randomised, controlled, non-inferiority trial
Authors: Margit Endler, Unnop Jaisamrarn, Suneeta Mittal, Phutrakool Phanupong, Du Van Du, Toan Anh Ngo, Hans Vemer, A Metin Gülmezoglu, Kristina Gemzell-Danielsson
Journal: The Lancet Global Health (2024)
Integrating cancer into crisis: a global vision for action from WHO and partners
Authors: Raffaella Casolino, Richard Sullivan, Kiran Jobanputra, May Abdel-Wahab, Miljana Grbic, Nazik Hammad, Tezer Kutluk, Nelya Melnitchouk, Alexandra Mueller, Roberta Ortiz, Diana Paez, Omar Shamieh, Gevorg Tamamyan, Horia Vulpe, Bente Mikkelsen, Andrè Ilbawi, Slim Slama
Journal: The Lancet Oncology (2024)
Autocrine TGF-β1 drives tissue-specific differentiation and function of resident NK cells
Authors: Colin Sparano, Darío Solís-Sayago, Nathan Sébastien Zangger, Lukas Rindlisbacher, Hannah Van Hove, Marijne Vermeer, Frederike Westermann, Caroline Mussak, Elisa Rallo, Stanislav Dergun, Gioana Litscher, Yishu Xu, Mitchell Bijnen, Christin Friedrich, Melanie Greter, Vanda Juranić Lisnić, Burkhard Becher, Georg Gasteiger, Annette Oxenius, Sonia Tugues
Journal: The Journal of Experimental Medicine (2024)

Group 1 innate lymphoid cells (ILCs) encompass NK cells and ILC1s, which have non-redundant roles in host protection against pathogens and cancer. Despite their circulating nature, NK cells can establish residency in selected tissues during ontogeny, forming a distinct functional subset. The mechanisms that initiate, maintain, and regulate the conversion of NK cells into tissue-resident NK (trNK) cells are currently not well understood. Here, we identify autocrine transforming growth factor-β (TGF-β) as a cell-autonomous driver for NK cell tissue residency across multiple glandular tissues during development. Cell-intrinsic production of TGF-β was continuously required for the maintenance of trNK cells and synergized with Hobit to enhance cytotoxic function. Whereas autocrine TGF-β was redundant in tumors, our study revealed that NK cell–derived TGF-β allowed the expansion of cytotoxic trNK cells during local infection with murine cytomegalovirus (MCMV) and contributed to viral control in the salivary gland. Collectively, our findings reveal tissue-specific regulation of trNK cell differentiation and function by autocrine TGF-β1, which is relevant for antiviral immunity.
Heme promotes venetoclax resistance in multiple myeloma through MEK-ERK signaling and purine biosynthesis
Authors: Remya Nair, An Vu, Abigail K Freer, Karanpreet S Bhatia, Dongxue Wang, Milan R Savani, Shannon M Matulis, Sagar Lonial, David L Jaye, Lawrence H Boise, Seung-Yong Seo, Timothy William Corson, Ajay K. Nooka, Shruti Bhatt, Samuel K McBrayer, Vikas A Gupta, Xin Hu, Benjamin G Barwick, Amit R Reddi, Mala Shanmugam
Journal: Blood (2024)

We previously demonstrated that reduced intrinsic electron transport chain (ETC) activity predicts and promotes sensitivity to the BCL-2 antagonist, venetoclax (Ven) in multiple myeloma (MM). Heme, an iron-containing prosthetic group, and metabolite is fundamental to maintaining ETC activity. Interrogation of the CD2 subgroup of MM from the CoMMpass trial (NCT01454297), which can be used as a proxy for Ven-sensitive MM (VS MM), shows reduced expression of the conserved heme biosynthesis pathway gene signature. Consistent with this, we identified that VS MM exhibit reduced heme biosynthesis and curiously elevated hemin (oxidized heme) uptake. Supplementation with hemin or protoporphyrin IX (heme lacking iron) promotes Ven resistance while targeting ferrochetalase, the penultimate enzyme involved in heme biosynthesis, increases Ven sensitivity in cell lines and primary MM cells. Mechanistically, heme-mediated activation of pro-survival RAS-RAF-MEK signaling and metabolic rewiring, increasing de novo purine synthesis, were found to contribute to heme-induced Ven resistance. Co-targeting BCL-2 and MCL-1 suppresses heme-induced Ven resistance. Interrogation of the MMRF CoMMpass study of patients shows increased purine and pyrimidine biosynthesis to corelate with poor progression free survival and overall survival. Elevated heme and purine biosynthesis gene signatures were also observed in matched relapse refractory MM, underscoring the relevance of heme metabolism in therapy refractory MM. Overall, our findings reveal for the first time a role for extrinsic heme, a physiologically relevant metabolite, in modulating proximity to the apoptotic threshold with translational implications for BCL-2 antagonism in MM therapy.
Oral Inflammation and Microbiome Dysbiosis Exacerbate Chronic Graft-versus-host Disease
Authors: Yui Kambara, Hideaki Fujiwara, Akira Yamamoto, Kazuyoshi Gotoh, Shuma Tsuji, Mari Kunihiro, Tadashi Oyama, Toshiki Terao, Ayame Sato, Takehiro Tanaka, Daniel Peltier, Keisuke Seike, Hisakazu Nishimori, Noboru Asada, Daisuke Ennishi, Keiko Fujii, Nobuharu Fujii, Ken-ichi Matsuoka, Yoshihiko Soga, Pavan Reddy, Yoshinobu Maeda
Journal: Blood (2024)
Levofloxacin Preventive Treatment in Children Exposed to MDR Tuberculosis
Authors: Anneke C Hesseling, Susan E Purchase, Neil A Martinson, Lee Fairlie, H Simon Schaaf, Joanna Brigden, Suzanne Staples, Diana M Gibb, Anthony Garcia-Prats, Francesca Conradie, Charlotte McGowan, Charlotte Layton, Elize Batist, Anne-Marie Demers, Samukelisiwe Nyamathe, Lisa Frigati, Rebecca Turner, Trinh Duong, James A Seddon
Journal: New England Journal of Medicine (2024)

BackgroundWorldwide, approximately 2 million children younger than 15 years of age are infected with multidrug-resistant (MDR) Mycobacterium tuberculosis, with MDR tuberculosis developing in approximately 30,000 annually. Evidence from randomized, controlled trials on tuberculosis preventive treatment in persons exposed to MDR tuberculosis is lacking.MethodsIn this community-based, multisite, double-blind, cluster-randomized, placebo-controlled trial in South Africa, we assessed the efficacy and safety of levofloxacin as preventive treatment in children with household exposure to an adult with bacteriologically confirmed MDR pulmonary tuberculosis. Children younger than 5 years of age were eligible for inclusion regardless of interferon-γ release assay result or human immunodeficiency virus (HIV) status, and children 5 to 17 years of age were eligible if they had a positive interferon-γ release assay or HIV infection. Households were randomly assigned to a trial regimen, and children in the household received levofloxacin or placebo once daily for 24 weeks. The primary efficacy end point was incident tuberculosis, which included death from tuberculosis, by week 48 after randomization. The primary safety end point was any adverse event of grade 3 or higher during the treatment period that was at least possibly related to the trial regimen.Download a PDF of the Plain Language Summary.ResultsOf 922 participants from 497 households, 453 were assigned to receive levofloxacin and 469 to placebo; 91.0% of the participants were younger than 5 years of age. At least 80% of the assigned doses of levofloxacin or placebo were received by 86% of the participants in each trial group. By week 48, tuberculosis had developed in 5 participants (1.1%) in the levofloxacin group and in 12 participants (2.6%) in the placebo group (hazard ratio, 0.44; 95% confidence interval [CI], 0.15 to 1.25). The results of sensitivity analyses were consistent with those of the primary analysis. Grade 3 or higher adverse events during the treatment period that were considered to be at least possibly related to the trial regimen occurred in 4 participants in the levofloxacin group and in 8 participants in the placebo group (hazard ratio, 0.52; 95% CI, 0.16 to 1.71). Grade 2 tendonitis occurred in 1 child in the levofloxacin group.ConclusionsAlthough preventive treatment with levofloxacin led to a lower incidence of tuberculosis than placebo among children with household exposure to MDR tuberculosis, the difference was not significant. (Supported by Unitaid and others; TB-CHAMP ISRCTN Registry number, ISRCTN92634082.) Quick Take Preventive Levofloxacin in Children Exposed to Multidrug-Resistant TB 2m 1s
Levofloxacin for the Prevention of Multidrug-Resistant Tuberculosis in Vietnam
Authors: Greg J Fox, Nguyen Viet Nhung, Nguyen Cam Binh, Nguyen Binh Hoa, Frances L Garden, Andrea Benedetti, Pham Ngoc Yen, Nguyen Kim Cuong, Emily L MacLean, H Manisha Yapa, David W Dowdy, Nguyen Huu Lan, Elyse Guevara-Rattray, Pham Duc Cuong, Ori Solomon, Marcel A Behr, Ben J Marais, Steven M Graham, Dick Menzies, Nguyen Thu Anh, Guy B Marks
Journal: New England Journal of Medicine (2024)

BackgroundPrevention of drug-resistant tuberculosis is a global health priority. However, trials evaluating the effectiveness of treating Mycobacterium tuberculosis infection among contacts of persons with drug-resistant tuberculosis are lacking.MethodsWe conducted a double-blind, randomized, controlled trial comparing 6 months of daily levofloxacin (weight-based doses) with placebo to treat M. tuberculosis infection. The trial population comprised household contacts of persons with bacteriologically confirmed rifampicin-resistant or multidrug-resistant (MDR) tuberculosis in Vietnam. Contacts of any age with a positive tuberculin skin test or immunologic impairment were eligible. The primary end point was bacteriologically confirmed tuberculosis within 30 months. Secondary end points included grade 3 or 4 adverse events, death from any cause, and acquired drug resistance.Download a PDF of the Plain Language Summary.ResultsOf 3948 persons screened for eligibility, 61 (1.5%) had coprevalent tuberculosis (defined as active tuberculosis disease diagnosed before randomization) and 2041 underwent randomization. Of these 2041 participants, 1995 (97.7%) completed 30 months of follow-up, had a primary end-point event, or died. Confirmed tuberculosis occurred in 6 participants (0.6%) in the levofloxacin group and 11 (1.1%) in the placebo group (incidence rate ratio, 0.55; 95% confidence interval [CI], 0.19 to 1.62); this difference was not significant. There was little difference in grade 3 or 4 adverse events between the two groups (risk difference, 1.0 percentage point; 95% CI, −0.3 to 2.4). Adverse events of any grade were reported in 306 participants (31.9%) taking levofloxacin and 125 (13.0%) taking placebo (risk difference, 18.9 percentage points; 95% CI, 14.2 to 23.6). No acquired fluoroquinolone resistance was observed.ConclusionsAlthough the incidence of tuberculosis was lower in the levofloxacin group than in the placebo group at 30 months, the difference was not significant. (Funded by the National Health and Medical Research Council of Australia; VQUIN MDR Australia New Zealand Clinical Trials Registry number, ACTRN12616000215426.) Quick Take Levofloxacin and Preventing Multidrug-Resistant Tuberculosis 1m 49s
Ponsegromab for Cancer Cachexia — A New Dawn for an Old Condition?
Authors: Barry J A Laird, Richard J E Skipworth
Journal: New England Journal of Medicine (2024)

Hippocrates, the father of medicine (460 to 370 b.c.), described cachexia as a condition in which "the flesh is consumed and becomes water,…the abdomen fills with water, the feet and legs swell, and the shoulders, clavicles, chest, and thighs melt away." Nearly 2500 years later, we recognize that cachexia undermines the effectiveness of cancer therapy, diminishes the quality of life for patients and their loved ones, and reduces survival rates. Despite major advances in cancer care, no standard treatment has been developed for cancer cachexia, and, alarmingly, no approved therapy is available in North America or Europe. Considering that cachexia . . .
Chest Radiography for Presumed Pneumonia in Children
Authors: Julie R. Barzilay, Mark I. Neuman, Todd A. Florin
Journal: New England Journal of Medicine (2024)

This case vignette about a boy with cough, congestion, and fever is accompanied by two essays, one supporting empirical treatment with antibiotics for presumed bacterial pneumonia and the other recommending radiography to better characterize the diagnosis.
Mutations in AMBRA1 aggravate β-thalassemia by impairing autophagy-mediated clearance of free α-globin
Authors: Yong Long, Qianqian Zhang, Ling Ling, Yuan Zhuang, Xiaolei Wei, Haoyang Huang, Zhanping Lu, Yushan Huang, Xianming Chen, Yuhua Ye, Xiaoqin Feng, Haokun hao Zhang, Binbin Huang, Yueyan Huang, Yidan Liang, Mingyan Fang, Yukio Nakamura, Bin Lin, Xinhua Zhang, Daru Lu, Xin Jin, Xiangmin Xu
Journal: Blood (2024)