tbuckley/cabot-search huggingface dataset:
Genomic anatomy of homozygous XX females and YY males reveals early evolutionary trajectory of sex-determining gene and sex chromosomes in <i>Silurus</i> fishes
Authors: Tao Wang, Gaorui Gong, Zhi Li, Jun-Sheng Niu, Wen-Xuan Du, Zhong-Wei Wang, Yang Wang, Li Zhou, Xiao-Juan Zhang, Zong-Qiang Lian, Jie Mei, Jian-Fang Gui, Xi-Yin Li
Journal: Molecular Biology and Evolution (2024)

Abstract Sex chromosomes display remarkable diversity and variability among vertebrates. Compared with research on the X/Y and Z/W chromosomes, which have long evolutionary histories in mammals and birds, studies on the sex chromosomes at early evolutionary stages are limited. Here, we precisely assembled the genomes of homozygous XX female and YY male Lanzhou catfish (Silurus lanzhouensis) derived from an artificial gynogenetic family and a self-fertilized family, respectively. Chromosome 24 (Chr24) was identified as the sex chromosome based on resequencing data. Comparative analysis of the X and Y chromosomes showed an approximate 320 kb Y-specific region with a Y-specific duplicate of anti-Mullerian hormone type II receptor (amhr2y), which is consistent with findings in 2 other Silurus species but on different chromosomes (Chr24 of Silurus meridionalis and Chr5 of Silurus asotus). Deficiency of amhr2y resulted in male-to-female sex reversal, indicating that amhr2y plays a male-determining role in S. lanzhouensis. Phylogenetic analysis and comparative genomics revealed that the common sex-determining gene amhr2y was initially translocated to Chr24 of the Silurus ancestor along with the expansion of transposable elements. Chr24 was maintained as the sex chromosome in S. meridionalis and S. lanzhouensis, whereas a sex-determining region transition triggered sex chromosome turnover from Chr24 to Chr5 in S. asotus. Additionally, gene duplication, translocation, and degeneration were observed in the Y-specific regions of Silurus species. These findings present a clear case for the early evolutionary trajectory of sex chromosomes, including sex-determining gene origin, repeat sequence expansion, gene gathering and degeneration in sex-determining region, and sex chromosome turnover.
Single-cell RNA sequencing comparison of CD4+, CD8+ and TCR-γδ+ cutaneous T-cell lymphomas reveals subset-specific molecular phenotypes
Authors: Sumanth Chennareddy, Katharina Rindler, John R Ruggiero, Natalia Alkon, Emry R Cohenour, Sophia Tran, Wolfgang Weninger, Johannes Griss, Constanze Jonak, Patrick M Brunner
Journal: British Journal of Dermatology (2024)

Malignant clones of primary cutaneous T-cell lymphomas (CTCL) can show a CD4, CD8 or TCR-γδ phenotype, but their individual impact on tumor biology and skin lesion formation remains ill-defined.
Acute Kidney Injury in Hospitalized Patients With Exertional Rhabdomyolysis
Authors: Amir H. Sabouri, Brian Yurgionas, Sara Khorasani, Edward J. Durant, Jafar Kafaie, Yun-Yi Hung, Jeffery G. Klingman, Siamack Nemazie
Journal: JAMA Network Open (2024)

Importance An association between serum creatine kinase (CK) levels and the risk of kidney failure in patients with exertional rhabdomyolysis (ERM) has been suggested. However, the actual incidence of AKI in hospitalized patients with ERM along with the contributing cofactors that may increase the risk of AKI have rarely been investigated. Objectives To examine the incidence of kidney injury in hospitalized patients with ERM and to identify additional cofactors that might contribute to the development of kidney injury in patients with ERM. Design, Setting, and Participants This retrospective cohort study was conducted in a diverse community population of patients 18 years or older with ERM who were hospitalized across Kaiser Permanente Northern California between January 1, 2009, and December 31, 2019. Patients were initially identified through electronic screening for all-cause rhabdomyolysis admissions, followed by manual medical record reviews to verify their eligibility for the study. The diagnosis of AKI and chronic kidney disease (CKD) was determined using KDIGO (Kidney Disease Improving Global Outcomes) criteria and confirmed by medical record review. Data analysis was performed from October 1, 2023, to January 31, 2024. Exposures History of strenuous physical exercise before hospitalization for ERM. Main Outcome and Measures Development of AKI, CKD, and compartment syndrome and number of deaths. Results Among 3790 patients hospitalized for rhabdomyolysis between 2009 and 2019 in Kaiser Permanente Northern California, 200 (mean [SD] age, 30.5 [8.5] years; 145 [72.5%] male) were confirmed to have ERM via medical record review. Seventeen patients (8.5%) developed AKI, none developed CKD, 1 (0.5%) developed compartment syndrome, and there were no fatalities. There was no association between serum CK levels and the risk of AKI. However, the risk of AKI was significantly higher in patients with ERM who used nonsteroidal anti-inflammatory drugs (NSAIDs) before admission (11 of 17 with AKI [64.7%] vs 40 of 183 without AKI [21.9%], P &amp;amp;lt; .001) or experienced dehydration (9 of 183 without AKI [52.9%] vs 9 of 17 with AKI [4.9%], P &amp;amp;lt; .001). This analysis suggests that eliminating preadmission NSAID use and dehydration could reduce the risk of potential AKI in patients with ERM by 92.6% (95% CI, 85.7%-96.1%) in this population. Conclusions and Relevance The findings of this cohort study of hospitalized patients with ERM suggest that serum CK elevation alone is insufficient as an indicator of AKI in patients with ERM. Concurrent risk factors, such as NSAID use or dehydration, may be associated with AKI development in patients with ERM.
Disease activity and therapeutic response to pegcetacoplan for geographic atrophy identified by deep learning-based analysis of OCT
Authors: Ursula Schmidt-Erfurth, Julia Mai, Gregor S Reiter, Sophie Riedl, Wolf-Dieter Vogl, Amir Sadeghipour, Alex McKeown, Emma Foos, Lukas Scheibler, Hrvoje Bogunovic
Journal: Ophthalmology (2024)
Radiological predictors of visual outcome in myelin oligodendrocyte glycoprotein-related optic neuritis
Authors: Armin Handzic, Jim Shenchu Xie, Nanthaya Tisavipat, Roisin Maire O’Cearbhaill, Deena A. Tajfirouz, Kevin D. Chodnicki, Eoin P. Flanagan, John J. Chen, Jonathan Micieli, Edward Margolin
Journal: Ophthalmology (2024)

This study aimed to determine whether magnetic resonance imaging (MRI) biomarkers are associated with visual prognosis in myelin oligodendrocyte protein (MOG)-associated optic neuritis (ON).
Use of peroral cholangiopancreatoscopy-assisted endoscopic mucosal resection for biliopancreatic intraductal lesions
Authors: Wengang Zhang, Yaqi Zhai, Bozong Shao, Jiafeng Wang, Qingzhen Wu, Ningli Chai, Enqiang Linghu
Journal: Endoscopy (2024)

Abstract Background This study aimed to assess the feasibility and safety of performing cholangiopancreatoscopy-assisted endoscopic mucosal resection (CA-EMR) for biliopancreatic intraductal lesions. Methods Special electrocautery snares and injection needles that can pass through the working channel of a single-operator cholangiopancreatoscope were developed. Between November 2023 and April 2024, we performed CA-EMR for two patients with gallbladder polyps, one patient with a neoplastic lesion in the common bile duct (CBD), and one patient with a neoplastic lesion in the main pancreatic duct. The technical success rate and adverse events were recorded. Results All four CA-EMR procedures were performed successfully. Postoperative pathology revealed inflammatory gallbladder polyps in two patients, low grade intraepithelial neoplasia of the CBD in one patient, and intraductal papillary mucinous neoplasm (IPMN) in one patient. The patient with IPMN experienced mild postoperative pancreatitis and recovered after conservative treatment. No adverse events were encountered in the other three CA-EMR procedures. Conclusion This study preliminarily confirmed the feasibility and safety of CA-EMR for treating biliopancreatic intraductal lesions.
The role of generative language systems in increasing patient awareness of colon cancer screening.
Authors: Marcello Maida, Daryl Ramai, Yuichi Mori, Mário Dinis-Ribeiro, Antonio Facciorusso, Cesare Hassan
Journal: Endoscopy (2024)

Background This study aimed to evaluate the effectiveness of ChatGPT (Chat Generative Pretrained Transformer) in answering patientsʼ questions about colorectal cancer (CRC) screening, with the ultimate goal of enhancing patients' awareness and adherence to national screening programs. Methods 15 questions on CRC screening were posed to ChatGPT4. The answers were rated by 20 gastroenterology experts and 20 nonexperts in three domains (accuracy, completeness, and comprehensibility), and by 100 patients in three dichotomic domains (completeness, comprehensibility, and trustability). Results According to expert rating, the mean (SD) accuracy score was 4.8 (1.1), on a scale ranging from 1 to 6. The mean (SD) scores for completeness and comprehensibility were 2.1 (0.7) and 2.8 (0.4), respectively, on scales ranging from 1 to 3. Overall, the mean (SD) accuracy (4.8 [1.1] vs. 5.6 [0.7]; P &lt; 0.001) and completeness scores (2.1 [0.7] vs. 2.7 [0.4]; P &lt; 0.001) were significantly lower for the experts than for the nonexperts, while comprehensibility was comparable among the two groups (2.8 [0.4] vs. 2.8 [0.3]; P = 0.55). Patients rated all questions as complete, comprehensible, and trustable in between 97 % and 100 % of cases. Conclusions ChatGPT shows good performance, with the potential to enhance awareness about CRC and improve screening outcomes. Generative language systems may be further improved after proper training in accordance with scientific evidence and current guidelines.
Potential impact of replacing the 13-valent pneumococcal conjugate vaccine with 15-valent or 20-valent pneumococcal conjugate vaccine in the 1 + 1 infant schedule in England: a modelling study
Authors: Yoon Hong Choi, Marta Bertran, David J Litt, Shamez N Ladhani, Elizabeth Miller
Journal: The Lancet Public Health (2024)

Paediatric pneumococcal conjugate vaccine (PCV) programmes in England using seven-valent PCV (PCV7) in 2006 and 13-valent PCV (PCV13) in 2010 have reduced vaccine-type invasive pneumococcal disease, but the overall effect has been reduced by an increase in invasive pneumococcal disease due to non-vaccine serotypes and serotype 3. We developed pneumococcal transmission models to investigate the potential effect on invasive pneumococcal disease of higher valency PCVs covering an additional two (ie, 15-valent PCV [PCV15]) or seven serotypes (ie, 20-valent PCV [PCV20]) in England.
Safety and immunogenicity of a next-generation live-attenuated yellow fever vaccine produced in a Vero cell line in the USA: a phase 1 randomised, observer-blind, active-controlled, dose-ranging clinical trial
Authors: Kayvon Modjarrad, Paul T Scott, Melanie McCauley, Brittany Ober-Shepherd, Erica Sondergaard, Mihret F Amare, Ajay P Parikh, Badryah Omar, Ada-Marie Minutello, Haritha Adhikarla, Yukun Wu, Andrey Rojas P, Valentine Delore, Nathalie Mantel, Meshell N Morrison, Kamila S Kourbanova, Melissa E Martinez, Ivelese Guzman, Melissa E Greenleaf, Janice M Darden, Michael A Koren, Melinda J Hamer, Christine E Lee, Jack N Hutter, Sheila A Peel, Merlin L Robb, Manuel Vangelisti, Emmanuel Feroldi
Journal: The Lancet Infectious Diseases (2024)
Improving effective coverage of medical-oxygen services for neonates and children in health facilities in Uganda: a before–after intervention study
Authors: Hamish R Graham, Freddy Eric Kitutu, Yewande Kamuntu, Blasio Kunihira, Santa Engol, Jasmine Miller, Absolom Zisanhi, Dorcas Kemigisha, Lorraine Nabbanja Kabunga, Charles Olaro, Harriet Ajilong, Freddie Ssengooba, Felix Lam
Journal: The Lancet Global Health (2024)

Medical oxygen services are essential for the care of acutely unwell patients. We aimed to assess the effects of a multilevel, multicomponent health-system intervention on hypoxaemia detection, oxygen therapy, and mortality among neonates and children attending level IV health centres and hospitals in Uganda.
Pregnancy outcome predictors in systemic lupus erythematosus: a systematic review and meta-analysis
Authors: Merlijn Wind, Juan J Fierro, Kitty W M Bloemenkamp, Karina de Leeuw, A Titia Lely, Maarten Limper, Marieke Sueters, Y K Onno Teng, Isabel J Walter, Judith Kooiman
Journal: The Lancet Rheumatology (2024)
Polyp detection with colonoscopy assisted by the GI Genius artificial intelligence endoscopy module compared with standard colonoscopy in routine colonoscopy practice (COLO-DETECT): a multicentre, open-label, parallel-arm, pragmatic randomised controlled trial
Authors: Alexander Seager, Linda Sharp, Laura J Neilson, Andrew Brand, James S Hampton, Tom J W Lee, Rachel Evans, Luke Vale, John Whelpton, Nathania Bestwick, Colin J Rees
Journal: The Lancet. Gastroenterology & hepatology (2024)
Experiences of an Israeli hospital in the management of repatriated civilian hostages
Authors: Amir Nutman, Liron Yosha Orpaz, Shirly Oren, Yasmin Maor, Adam Lee Goldstein, Giulia Barda, Anat Levy, Zehavit Shpitzer, Liron Levinberg, Yakov Nassimov, Iliya Galbert, Michal Noah, Orna Zvi, Yaniv Fogel, Adi Shilo Kaftori, Uri Feinstein, Anat Engel
Journal: The Lancet Global Health (2024)
Long-term effect of pneumococcal conjugate vaccines on invasive pneumococcal disease incidence among people of all ages from national, active, laboratory-based surveillance in South Africa, 2005–19: a cohort observational study
Authors: Anne von Gottberg, Jackie Kleynhans, Linda de Gouveia, Stefano Tempia, Susan Meiring, Vanessa Quan, Mignon du Plessis, Claire von Mollendorf, Penny Crowther-Gibson, Theunis Avenant, Nicolette du Plessis, Ranmini Kularatne, Vindana Chibabhai, Shabir A Madhi, Keith P Klugman, Cynthia G Whitney, Cheryl Cohen
Journal: The Lancet Global Health (2024)

In South Africa, 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in 2009 and 13-valent PCV (PCV13) was introduced in 2011, both in a two plus one schedule. We evaluated the ongoing effects of PCV on the prevention of invasive pneumococcal disease (IPD) over 15 years of sustained surveillance in South Africa before the COVID-19 pandemic.
Re-evaluating the impact and cost-effectiveness of pneumococcal conjugate vaccine introduction in 112 low-income and middle-income countries in children younger than 5 years: a modelling study
Authors: Cynthia Chen, Gregory Ang, Katika Akksilp, Jemima Koh, J Anthony G Scott, Andrew Clark, Mark Jit
Journal: The Lancet Global Health (2024)

Streptococcus pneumoniae has been estimated to cause 9·18 million cases of pneumococcal pneumonia, meningitis, and invasive non-pneumonia non-meningitis disease and 318 000 deaths among children younger than 5 years in 2015. We estimated the potential impact and cost-effectiveness of pneumococcal conjugate vaccine (PCV) introduction.
The effect on HIV transmission and cost-effectiveness of programmes for female sex workers in East, Central, and Southern Africa: a modelling study
Authors: Loveleen Bansi-Matharu, Paul Revill, Issac Taramusi, Richard Steen, Sungai T Chabata, Joanna Busza, Collin Mangenah, Sithembile Musemburi, Fortunate Machingura, Nicola Desmond, Primrose Matambanadzo, Maryam Shahmanesh, Raymond Yekeye, Owen Mugurungi, Frances M Cowan, James R Hargreaves, Andrew N Phillips
Journal: The Lancet Global Health (2024)

HIV prevalence and incidence has declined in East, Central, and Southern Africa (ECSA), but remains high among female sex workers (FSWs). Sex worker programmes have the potential to considerably increase access to HIV testing, prevention, and treatment. We aimed to quantify these improvements by modelling the potential effect of sex worker programmes at two different intensities on HIV incidence and key health outcomes, and assessed the programmes' potential cost-effectiveness in order to help inform HIV policy decisions.
Community-based strategies to increase coverage of intermittent preventive treatment of malaria in pregnancy with sulfadoxine–pyrimethamine in sub-Saharan Africa: a systematic review, meta-analysis, meta-ethnography, and economic assessment
Authors: Kadiatou Koita, Kassoum Kayentao, Eve Worrall, Anna Maria Van Eijk, Jenny Hill
Journal: The Lancet Global Health (2024)

Community-based approaches might increase uptake of intermittent preventive treatment of malaria in pregnancy with sulfadoxine-pyrimethamine (IPTp-SP). We assessed the effects of community-based approaches on IPTp-SP and antenatal care coverage, and barriers and facilitators to implementation in sub-Saharan Africa.
The global macroeconomic burden of Alzheimer's disease and other dementias: estimates and projections for 152 countries or territories
Authors: Simiao Chen, Zhong Cao, Arindam Nandi, Nathaniel Counts, Lirui Jiao, Klaus Prettner, Michael Kuhn, Benjamin Seligman, Daniel Tortorice, Daniel Vigo, Chen Wang, David E Bloom
Journal: The Lancet Global Health (2024)

Alzheimer's disease and other dementias (ADODs) severely threaten the wellbeing of older people, their families, and communities, especially with projected exponential growth. Understanding the macroeconomic implications of ADODs for policy making is essential but under-researched.
Paving the way for affordable and equitable liposomal amphotericin B access worldwide
Authors: Janice Soo Fern Lee, Rachel M Cohen, Rahela Ambaras Khan, Jessica Burry, Esther C Casas, Han Yang Chung, Luiz Henrique Costa, Nathan Ford, Diogo Lopes Nunes Galvao, Nora Giron, Joseph N Jarvis, Mousumi Mondal, Justine Jelagat Odionyi, Carmen Pérez Casas, Ajay Rangaraj, Joelle Rode, Carol Ruffell, Omar Sued, Isabela Ribeiro
Journal: The Lancet Global Health (2024)

Amphotericin B has long been crucial for treating many serious infectious diseases, such as invasive fungal infections and visceral leishmaniasis, particularly for patients who are immunocompromised, including those with advanced HIV infection. The conventional amphotericin B deoxycholate formulation has largely been replaced in high-income countries with liposomal amphotericin B (LAmB), which has many advantages, including lower rates of adverse events, such as nephrotoxicity and anaemia. Despite an evident need for LAmB in low-income and middle-income countries, where mortality from invasive fungal infections is still substantial, many low-income and middle-income countries still often use the amphotericin B deoxycholate formulation because of a small number of generic formulations and the high price of the originator LAmB. The pricing of LAmB is also highly variable between countries. Overcoming supply barriers through the availability of additional quality-assured, generic formulations of LAmB at accessible prices would substantially facilitate equitable access and have a substantial effect on mortality attributable to deadly fungal infections.
Prevalence of syphilis among adults and adolescents in five sub-Saharan African countries: findings from Population-based HIV Impact Assessment surveys
Authors: Mansoor Farahani, Rose Killian, Giles A Reid, Godfrey Musuka, Owen Mugurungi, Wilford Kirungi, Harriet Nuwagaba-Biribonwoha, Wafaa M El-Sadr, Jessica Justman
Journal: The Lancet Global Health (2024)

HIV and syphilis are common sexually transmitted infections in sub-Saharan Africa. We aimed to investigate the prevalence and distribution of active syphilis while considering HIV status, demographic characteristics, and behavioural characteristics.
Assessing the prevalence and impact of preserved ratio impaired spirometry in low-income and middle-income countries: a post-hoc cross-sectional analysis
Authors: Trishul Siddharthan, Kyle Grealis, Nicole M Robertson, Min Lu, Sibei Liu, Suzanne L Pollard, Shakir Hossen, Peter Jackson, Natalie A Rykiel, Adaeze C Wosu, Oscar Flores-Flores, Shumonta A Quaderi, Patricia Alupo, Bruce Kirenga, Federico Ricciardi, Julie A Barber, Ram K Chandyo, Arun K Sharma, Santa Kumar Das, Laxman Shresthra, J Jaime Miranda, William Checkley, John R Hurst
Journal: The Lancet Global Health (2024)

More than 90% of the morbidity and mortality from chronic respiratory disease occurs in low-income and middle-income countries (LMICs), with substantial economic impact. Preserved ratio impaired spirometry (PRISm) is a prevalent lung function abnormality associated with increased mortality in high-income countries. We aimed to conduct a post-hoc analysis of a cross-sectional study to assess the prevalence of, the risk factors for, and the impact of PRISm in three diverse LMIC settings.
Cost-effectiveness and health impact of screening and treatment of Mycobacterium tuberculosis infection among formerly incarcerated individuals in Brazil: a Markov modelling study
Authors: Ana van Lieshout Titan, Fayette Klaassen, Daniele Maria Pelissari, José Nildo de Barros Silva, Kleydson Alves, Layana Costa Alves, Mauro Sanchez, Patricia Bartholomay, Fernanda Dockhorn Costa Johansen, Julio Croda, Jason R Andrews, Marcia C Castro, Ted Cohen, Cornelis Vuik, Nicolas A Menzies
Journal: The Lancet Global Health (2024)

Individuals who were formerly incarcerated have high tuberculosis incidence, but are generally not considered among the risk groups eligible for tuberculosis prevention. We investigated the potential health impact and cost-effectiveness of Mycobacterium tuberculosis infection screening and tuberculosis preventive treatment (TPT) for individuals who were formerly incarcerated in Brazil. Using published evidence for Brazil, we constructed a Markov state transition model estimating tuberculosis-related health outcomes and costs among individuals who were formerly incarcerated, by simulating transitions between health states over time. The analysis compared tuberculosis infection screening and TPT, to no screening, considering a combination of M tuberculosis infection tests and TPT regimens. We quantified health effects as reductions in tuberculosis cases, tuberculosis deaths, and disability-adjusted life-years (DALYs). We assessed costs from a tuberculosis programme perspective. We report intervention cost-effectiveness as the incremental costs per DALY averted, and tested how results changed across subgroups of the target population. Compared with no intervention, an intervention incorporating tuberculin skin testing and treatment with 3 months of isoniazid and rifapentine would avert 31 (95% uncertainty interval 14-56) lifetime tuberculosis cases and 4·1 (1·4-5·8) lifetime tuberculosis deaths per 1000 individuals, and cost US$242 per DALY averted. All test and regimen combinations were cost-effective compared with no screening. Younger age, longer incarceration, and more recent prison release were each associated with significantly greater health benefits and more favourable cost-effectiveness ratios, although the intervention was cost-effective for all subgroups examined. M tuberculosis infection screening and TPT for individuals who were formerly incarcerated appears cost-effective, and would provide valuable health gains. National Institutes of Health. For the Portuguese translation of the abstract see Supplementary Materials section.
A risk-differentiated, community-led intervention to strengthen uptake and engagement with HIV prevention and care cascades among female sex workers in Zimbabwe (AMETHIST): a cluster randomised trial
Authors: Frances M Cowan, Fortunate Machingura, M Sanni Ali, Sungai T Chabata, Albert Takaruza, Jeffrey Dirawo, Memory Makamba, Tsitsi Hove, Loveleen Bansi-Matharu, Primrose Matambanadzo, Maryam Shahmanesh, Joanna Busza, Richard Steen, Raymond Yekeye, Amon Mpofu, Owen Mugurungi, Andrew N Phillips, James R Hargreaves
Journal: The Lancet Global Health (2024)

Female sex workers remain disproportionately affected by HIV. The aim of this study was to determine the effect of risk-differentiated, peer-led support for female sex workers in Zimbabwe on the risk of HIV acquisition and HIV transmission from sex among female sex workers.