bluuebunny/crossref_metadata_2025_split huggingface dataset:
The taxonomic status ofFarlowella colombiensisRetzer & Page 1997 with comments on species of theF. acusspecies group (Loricariidae: Loricariinae)
Authors: Melo-Ortiz Omar Eduardo , Retzer Michael E. , Prada-Pedreros Saúl , Ballen Gustavo A. 
Published: November 2024

AbstractThe genusFarlowellahas been historically challenging, in part due to the difficulty in defining diagnostic characters which allow to clearly set apart and identify the species.Farlowella colombiensisRetzer & Page 1997 is one of such examples, whose diagnostic characters were based on caudal-fin colour pattern, body cover ventral pattern, and details of the head. We herein reassess the taxonomic status of this species against congeners of theF. acusspecies group (F. acus,F. martini,F. mitoupibo,F. venezuelensis, andF. vittata). We found no significant differences betweenF. colombiensisandF. acusin morphometric, meristic, and discrete characters, therefore renderingFarlowella colombiensisa junior synonym ofFarlowella acus. We provide remarks on different species of theF. acusgroup in Colombia, as well as description of sexual dimorphism in the genital papilla for the first time in the subfamily. We also provide a key to the species of theF. acusspecies group in Colombia.
Direct thin-layer agar for bedaquiline-susceptibility testing ofMycobacterium tuberculosisat BSL2 level yields high accuracy in 15 days from sputum processing
Authors: Martin I. Cuella , Runyambo D. , De Bock S. , Diels M. , Niyompano H. , Hakizayezu F. , Keysers J. , De Rijk W.B. , Habimana Y. M. , Gahamanyi N. , Ardizzoni E. , Muvunyi C.M. , de Jong B.C. , Ngabonziza J.C.S. , Rigouts L. 
Published: November 2024

AbstractThis study evaluated thin-layer agar (TLA) as a faster alternative for both indirect MIC determination of bedaquiline (BDQ) from culture isolates and direct drug-susceptibility testing (DST) from sputum samples. Indirect BDQ-MIC results from TLA were compared to the established 7H11 solid DST. Direct-TLA-DST performance was assessed using 143 baseline sputum samples from rifampicin-resistant TB cases. Direct-TLA tested susceptibility to rifampicin, isoniazid, levofloxacin, and BDQ, with results compared to Löwenstein-Jensen (LJ) and MGIT.For indirect BDQ-MIC determination, TLA demonstrated high accuracy, with MIC values for H37Rv falling within the WHO control range (0.015-0.12μg/ml). The incubation conditions (5-10% CO2, standard) and reading time (day 7, 14) significantly affected results, with D7 readings in standard incubator providing optimal accuracy. Direct-TLA-DST detected MTB in 53.8% of samples, compared to 55.9% on LJ and 69.4% in MGIT. Uninterpretable results due to contamination or medium drying were low (4.9%). Median time to result was 15 days for smear-positive and 22 days for smear-negative samples, faster than WHO endorsed methods. Sensitivity was 100% for rifampicin and 87.8% for isoniazid, with a specificity of 100% for all drugs except isoniazid (96.2%). No BDQ nor levofloxacin resistance was detected, thus direct TLA sensitivity could not be assessed.In conclusion, direct-TLA-DST offers a reliable and faster alternative to conventional DST methods for BDQ and other anti-TB drugs. Essentially, this technique can be operated at BioSafety Level 2, allowing decentralization of pDST for managing drug-resistant TB in settings with limited laboratory infrastructure.ImportanceThis paper addresses the critical need for faster direct drug-susceptibility testing (DST) on sputum, especially for bedaquiline (BDQ), which is a key drug in treating drug-resistant TB. Currently, there is a lack of rapid, reliable methods for direct BDQ testing from sputum samples, limiting timely and accurate treatment decisions and monitoring. By demonstrating the potential of thin-layer agar (TLA) for direct BDQ-MIC determination, this study offers a promising solution that could significantly improve patient care.
Activation of IL1A/IRAK1 axis and downstream proinflammatory signaling in healthy adult and neonatal African American skin
Authors: Trubetskoy Dimitri , Grudzien Patrick , Klopot Anna , Tsoi Lam C , Kundu Roopal V , White Bethany E Perez , Budunova Irina 
Published: November 2024

ABSTRACTDifferences in prevalence of inflammatory skin diseases including atopic dermatitis and psoriasis in African American (AA) versus White Non-Hispanic (WNH) population are well recognized. However, the underlying mechanisms are largely unknown. We previously observed significant differences in healthy AA skin transcriptome with differentially expressed genes (DEG) enriched for inflammation and cornification processes. Here we analyzed proteome in skin biopsies from healthy AA and WNH volunteers usingOlink®Explore Inflammation384 biomarker panel. Among proteins with higher expression in AA skin were IRAK1, IL1A, IL4, IL22RA1. IL1A binding to IL1R1 receptor is known to result in recruitment of adapter molecules such as IRAK1, and activation of downstream NF-κB and MAPK signaling. We confirmed NF-κB and ERK1/2 activation in AA skin by Western blot analysis of their phosphorylation at specific activating sites. Importantly, we observed similar differences between AA and WNH neonatal foreskin and between AA and WNH 3D skin organoids. Further analysis of DEG promoters by Gene Transcription Regulation Database (GTRD) pointed to NF-κB and AP1 as key transcription factors involved in AA DEG regulation. Overall, proinflammatory signaling in healthy AA skin starting early in childhood may contribute to the increased risk of certain inflammatory skin diseases within the AA population.
Whole-Genome Sequencing of the Wild Barley Diversity Collection: A Resource for Identifying and Exploiting Genetic Variation for Cultivated Barley Improvement
Authors: Sallam Ahmad H. , Guo Yu , Jayakodi Murukarthick , Himmelbach Axel , Fiebig Anne , Simmons Jamie , Bethke Gerit , Lee Yoonjung , Spanner Rebecca , Badea Ana , Baum Michael , Belzile François , Ben-David Roi , Brueggeman Robert , Case Austin , Cattivelli Luigi , Davis Michael , Dockter Christoph , Doležel Jaroslav , Dreiseitl Antonin , Gavin Ryan , Glick Lior , Greiner Stephan , Hamilton Ruth , Hayes Patrick M. , Heisel Scott , Henson Cynthia , Kilian Benjamin , Komatsuda Takao , Li Chengdao , Liu Cheng , Mahalingam Ramamurthy , Maruschewski Maren , Matny Oadi , Maurer Andreas , Mayer Klaus F. X. , Mayrose Itay , Morrell Peter , Moscou Matthew , Muehlbauer Gary J. , Oono Youko , Ordon Frank , Özkan Hakan , Pecinka Ales , Perovic Dragan , Pillen Klaus , Pourkheirandish Mohammad , Russell Joanne , Šafář Jan , Salvi Silvio , Sanchez-Garcia Miguel , Sato Kazuhiro , Schmutzer Thomas , Scholz Uwe , Scott Jeness , Brar Gurcharn Singh , Smith Kevin P. , Sorrells Mark E. , Spannagl Manuel , Stein Nils , Tondelli Alessandro , Tuberosa Roberto , Tucker James , Turkington Thomas , Valkoun Jan , Verma Ramesh Pal Singh , Vinje Marcus A. , von Korff Schmising Maria , Walling Jason G. , Waugh Robbie , Wise Roger P. , Wulff Brande B. H. , Yang Shengming , Zhang Guoping , Mascher Martin , Steffenson Brian J. 
Published: November 2024

AbstractTo exploit allelic variation inHordeum vulgaresubsp.spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at ∼9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex V3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close toHvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.
Sensing the shape of a surface by intracellular filaments
Authors: Shi Handuo , Nguyen Jeffrey , Gitai Zemer , Shaevitz Joshua , Bratton Benjamin P. , Gopinathan Ajay , Grason Gregory , Huang Kerwyn Casey 
Published: November 2024

AbstractUnderstanding the mechanisms that dictate the localization of cytoskeletal filaments is crucial for elucidating cell shape regulation in prokaryotes. The actin homolog MreB plays a pivotal role in maintaining the shape of many rod-shaped bacteria such asEscherichia coliby directing cell-wall synthesis according to local curvature cues. However, the basis of MreB’s curvature-dependent localization has remained elusive. Here, we develop a biophysical model for the energetics of filament binding to a surface that integrates the complex interplay between filament twist and bending and the two-dimensional surface geometry. Our model predicts that the spatial localization of a filament like MreB with substantial intrinsic twist is governed by both the mean and Gaussian curvatures of the cell envelope, which strongly covary in rod-shaped cells. Using molecular dynamics simulations to estimate the mechanical properties of MreB filaments, we show that their thermodynamic preference for regions with lower mean and Gaussian curvatures matches experimental observations for physiologically relevant filament lengths of ∼50 nm. We find that the experimentally measured statistical curvature preference is maintained in the absence of filament motion and after a cycle of depolymerization, repolymerization, and membrane rebinding, indicating that equilibrium energetics can explain MreB localization. These findings provide critical insights into the physical principles underlying cytoskeletal filament localization, and suggest new design principles for synthetic shape sensing nanomaterials.Significance statementThe protein MreB, a homolog of eukaryotic actin, regulates the shape of bacteria likeEscherichia coliby guiding new cell-wall insertion based on local curvature cues. However, the mechanism by which a nanometer-scale MreB filament “senses” the micron-scale curvature of the cell wall has remained a mystery. We introduce a biophysical model of the energetics of twisted and bent filaments bound to curved surfaces, which predicts that localization of filaments like MreB is sensitive to both mean and Gaussian curvature. The model captures experimentally measured curvature enrichment patterns and explains how MreB naturally localizes to saddle-shaped regions without energy-consuming processes. Beyond cell shape regulation, our work suggests design principles for synthetic systems that can sense and respond to surface shape.
Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis
Authors: Xue Jin , Allaband Celeste , Zuffa Simone , Poulsen Orit , Meadows Jason , Zhou Dan , Dorrestein Pieter C. , Knight Rob , Haddad Gabriel G. 
Published: November 2024

AbstractBackgroundObstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis.ResultsAtherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF)ApoE-/-mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions. The fecal microbiota and metabolome were profiled using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry (LC-MS/MS) respectively. Phenotypic data showed that HFHC significantly increased atherosclerosis as compared to regular chow (RC) in both aorta and pulmonary artery (PA) of SPF mice. IHC exacerbated lesions in addition to HFHC. Differential abundance analysis of gut microbiota identified an enrichment of Akkermansiaceae and a depletion of Muribaculaceae (formerly S24-7) family members in the HFHC-IHC group. LC-MS/MS showed a dysregulation of bile acid profiles with taurocholic acid, taurodeoxycholic acid, and 12-ketodeoxycholic acid enriched in the HFHC-IHC group, long-chain N-acyl amides, and phosphatidylcholines. Interestingly, GFApoE-/-mice markedly reduced atherosclerotic formation relative to SPFApoE-/-mice in the aorta under HFHC/IHC conditions. In contrast, microbial colonization did not show a significant impact on the atherosclerotic progression in PA.ConclusionsIn summary, this research demonstrated that (1) IHC acts cooperatively with HFHC to induce atherosclerosis; (2) gut microbiota modulate atherogenesis, induced by HFHC/IHC, in the aorta not in PA; (3) different analytical methods suggest that a specific imbalance between Akkermansiaceae and Muribaculaceae bacterial families mediate OSA-induced atherosclerosis; and (4) derived bile acids, such as deoxycholic acid and lithocholic acid, regulate atherosclerosis in OSA. The knowledge obtained provides novel insights into the potential therapeutic approaches to prevent and treat OSA-induced atherosclerosis.
Rethinking cholera diagnostic test performance, interpretation and evaluation: a field-based latent-class analysis in Bangladesh
Authors: Perez-Saez Javier , Bhuiyan Taufiqur Rahman , Hegde Sonia T , Khan Ishtiakul Islam , Islam Md Taufiqul , Khan Zahid Hasan , Amin Mohammad Ashraful , Dent Hulse Juan , Ahmed Shakeel , Rashid Mamunur , Rashid Rumana , Hossain Md Zakir , Khan Ashraful Islam , Qadri Firdausi , Azman Andrew S 
Published: November 2024

AbstractBackgroundAccurate and reliable diagnostics, including rapid diagnostic tests (RDTs), are critical components of cholera control programs, though their performance has varied greatly across studies. While poorly understood, this variability may be due to the reference assay choice, patient-level and/or sampling characteristics, which hinder test result interpretation and performance evaluation.MethodsWe enrolled all suspected cholera cases seeking care at two healthcare facilities in Sitakunda, Bangladesh over 19 months. All stool samples were tested with the Cholkit RDT, and a subset by PCR and culture. Test performance was estimated using a latent-class Bayesian framework accounting for imperfect test performance, incomplete PCR and culture testing, and time-varying changes in cholera incidence. Patient-level (including age, antibiotic use) and sampling (season, testing delays) factor effects were estimated, and simulations were used to assess the bias in RDT performance estimates when using traditional reference assays.FindingsWe enrolled 3,744 suspected cases, 692 of whom were RDT-positive. Among the RDT-positives, 573 were PCR-positive and 450 culture-positive. For RDT, PCR and culture, we estimated a sensitivity of 93.5% (95% Credible Intervals, CrI: 91.3-95.4), 90.3% (88.4-92.1), and 73.7% (70.8-76.5), and a specificity of 97.3% (96.7-97.8), 97.2% (96.6-97.8), and 100% (culture specificity assumed perfect), respectively. We found that younger age (≤ 5), antibiotic use, and testing delays decreased culture sensitivity, but RDT performance remained relatively constant. The RDT positive predictive value ranged from <15% in children <5 years to >80% in adults, varying greatly across seasons. Simulations demonstrated underestimation of RDT sensitivity and specificity in low and high cholera prevalence settings, respectively, when evaluated against PCR or culture.InterpretationOur results shed light on the potential mechanisms leading to heterogeneous cholera RDT performance estimates in previous studies, including the use of culture as a reference assay. Across various patient and sampling characteristics, Cholkit RDT had high performance in this cholera-endemic setting, supporting its use for cholera surveillance and control. Accounting for epidemiologic context is crucial both for individual-level clinical test interpretation, and for the future evaluation of diagnostics like RDTs.FundingThe work was supported by the Bill & Melinda Gates Foundation (INV-021879).
Improved Data Alignment Between National HIV Reporting Systems, Mozambique, 2017–2023
Authors: Tiberi Orrin , Templin Lindsay , Ferreira Ferreira , Nhaguiombe Herminio , Couto Aleny , Lara Joe , Keating Ryan , Mizela Jose , Matsimbe Lucio , Magaia Helio , da Cunha Morais 
Published: November 2024

IntroductionData quality improvements have aimed to align national reporting systems for Ministry of Health (MISAU) and PEPFAR. For example, in 2019 the patient Master Card improved systematic data collection process and sites were selected for intensified support including data quality activities (AJUDA). This study aims to compare reported data between MISAU and PEPAFR to understand data alignment trends.MethodsThe annual number of PLHIV on ART, newly initiating ART and HIV status in first ANC visit as reported by MISAU and PEPFAR were compared for 2017-2023. The absolute difference was calculated as MISAU-reported number minus PEPFAR-reported number; proportional absolute difference as the absolute difference over the MISAU-reported number and assessed the slope of the difference over time.ResultsDuring 2017–2023, median absolute difference for PLHIV on ART was 104,940 (range = 154,901 [2018] to 1,598 [2020]), and median proportional difference was 5.0% (range = 0.1% [2020] to 12.8% [2018]), with a trend towards improved concordance. A similar trend was found in positive HIV status at first ANC (10.4% [2017] to 0.0% [2023]), as well as with newly initiated on ART (2.7% [2017] to 0.3% [2023]).ConclusionIn the three indicators analyzed, there were improvements in data alignment between the years of 2017 and 2023, with increased alignment in different years and for different reasons. Continued improvements will support programming and increase certainty for tracking progress toward the UNAIDS 95-95-95 goals to end HIV.
Segmentation and Measurements of Major Blood Vessels from CT Pulmonary Angiography Using Deep Learning
Authors: Kahraman Ali Teymur , Fröding Tomas , Toumpanakis Dimitris , Gustafsson Christian Jamtheim , Sjöblom Tobias 
Published: November 2024

AbstractBackgroundMeasuring major blood vessels from CT pulmonary angiography examinations (CTPAs) to assess cardiovascular diseases has the potential to improve overall patient outcomes. However, this process is time-consuming and prone to errors. Deep learning (DL) approaches offer the potential to enhance accuracy, speed, and consistency.ObjectivesTo develop and train a deep learning-based algorithm capable of automatically and accurately segmenting and measuring major blood vessels in CTPAs.MethodsSeven hundred CTPAs from 652 patients were retrospectively collected at a single center. The dataset was split into two subsets, one for training and cross-validation (n = 490) and one for assessing model performance (n = 210). The segmentation masks for the descending aorta (DAo), ascending aorta (AAo), and pulmonary trunk (PT) were generated by our previously developed segmentation model and were quantitatively validated by two radiologists. These validated masks were subsequently used as ground truth for model training. An U-Net deep learning model was created using the nnU-Net framework and trained on 490 CTPAs with 5-fold cross-validation. Following the training, the model was applied to volumes of interest in the images to generate a pool of candidate regions containing potential vessels. A vessel detection algorithm was developed and used on the candidate pool to identify vessels followed by measurement. The final model was evaluated on 210 and 47 CTPAs from internal and external datasets, respectively.ResultsAssessing model segmentation performance on the internal evaluation set, the median Dice scores were 0.95 for the DAo, 0.96 for the AAo, and 0.95 for the PT. The model measurements showed a strong correlation with those made by the radiologist, with Pearson’s r values of 0.91 for image noise, 0.98 for intravenous contrast concentration in the PT, 0.93 for AAo diameter, and 0.55 for PT diameter (P< .001). Additionally, the AAo segmentation (median Dice score 0.94) and the PT diameter measurement (r = 0.77) were evaluated in two external datasets.ConclusionsThe fully automated, deep learning-based algorithm accurately segmented and measured major blood vessels in real-world CTPAs.
Efficacy and Safety of Transcranial Temporal Interference Stimulation for Treating Bipolar Disorder with Depressive Episodes
Authors: Zhou Hetong , Wang Minmin , Qi Shuangyu , Chen Qianfeng , Lai Jianbo , Wu Zhengping , Liu Ruobing , Wang Liang , Tang Junxian , Zhang Shaomin , Hu Shaohua 
Published: November 2024

AbstractBackgroundBipolar disorder (BD) presents significant challenges in clinical management, often characterized by persistent depressive symptoms and cognitive deficits. Transcranial temporal interference stimulation (tTIS) has shown promise in targeting deep brain structures with minimal invasiveness. This study aimed to assess the efficacy and safety of tTIS in newly diagnosed or medication-washout BD patients.MethodsWe conducted a single-arm clinical trial with 36 BD patients who underwent 10 sessions of tTIS targeting the left nucleus accumbens over one week, with two sessions per day. Each tTIS session lasted 20 minutes, utilizing a maximum current intensity of 2 mA and an envelope stimulation frequency of 40 Hz. Depressive symptoms were assessed pre- and post-intervention using validated scales, including HAMD, QIDS, MADRS, and HAMA, while cognitive functions were evaluated using standardized neuropsychological tests. Safety was monitored through adverse event reporting.ResultsAmong 36 participants, 25 completed the full intervention protocol. Significant reductions were observed in depressive symptom scores: HAMD decreased from 23.36 to 16.16 (P< 0.0001), QIDS from 13.52 to 9.68 (P< 0.001), MADRS from 39.12 to 31.28 (P< 0.01), and HAMA from 19.68 to 15.44 (P< 0.05). Cognitive evaluations demonstrated notable improvements in memory and executive function. Adverse events were mild, primarily limited to transient scalp discomfort.ConclusionsThis study provides preliminary evidence supporting the efficacy and safety of tTIS in alleviating depressive symptoms and improving cognitive function in BD patients.