bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient synthesis of 3D MR images for schizophrenia diagnosis classification with generative adversarial networks
Authors: King Sebastian , Hollenbenders Yasmin , Reichenbach Alexandra 
Published: June 2024

AbstractSchizophrenia and other psychiatric disorders can greatly benefit from objective decision support in diagnosis and therapy. Machine learning approaches based on neuroimaging, e.g. magnetic resonance imaging (MRI), have the potential to serve this purpose. However, the medical data sets these algorithms can be trained on are often rather small, leading to overfit, and the resulting models can therewith not be transferred into a clinical setting. The generation of synthetic images from real data is a promising approach to overcome this shortcoming. Due to the small data set size and the size and complexity of medical images, i.e. their three-dimensional nature, those algorithms are challenged on several levels. We develop four generative adversarial network (GAN) architectures that tackle these challenges and evaluate them systematically with a data set of 193 MR images of schizophrenia patients and healthy controls. The best architecture, a GAN with spectral normalization regulation and an additional encoder (α-SN-GAN), is then extended with an auxiliary classifier into an ensemble of networks capable of generating distinct image sets for the two diagnostic categories. The synthetic images increase the accuracy of a diagnostic classifier from a baseline accuracy of around 61% to 79%. This novel end-to-end pipeline for schizophrenia diagnosis demonstrates a data and memory efficient approach to support clinical decision-making that can also be transferred to support other psychiatric disorders.
Prevalence and Predictors of Preterm Delivery among Mothers at the Tamale Teaching Hospital in the Tamale Metropolis of Ghana
Authors: Agyemang George Sarpong , Gmanyami Jonathan Mawutor , Appiah Elvis Angelo , Bosoka Samuel Adolf , Gohoho Mawuli , Alorwu James , Sorengmen Amos Ziema , Haruna Umar , Amoakoh Michael Yaw , Kweku Margaret 
Published: June 2024

AbstractBackgroundPreterm delivery (PTD) remains a global public health challenge. It is estimated that 15 million babies are born prematurely. Developing countries account for 18.3% of PTD. This study assessed the prevalence and risk factors associated with PTD deliveries in the Tamale Metropolis.MethodsA cross-sectional study accessed the birth records and interviewed 318 participants who delivered at the Tamale Teaching Hospital between January to December 2021. Univariate and multivariate regression models predicted the risk factors of PTD.ResultsThe prevalence of preterm delivery was 18.5%. Women with multiple pregnancies who had a caesarean section and large household size were 4.28, 7.31 and 6.88, times more likely to have preterm delivery [AOR = 4.28 (95% CI: 1.75-24.23)], [AOR = 7.31 (95% CI: 2.59-36.14)] and [AOR = 6.88 (95% CI: 1.56-30.38)] respectively. Women who had normal haemoglobin concentration levels at 36 weeks and those who had pipe-borne water as the source of drinking water were 90% and 78% less likely to have preterm delivery [AOR = 0.10 (95% CI: 0.03-0.33)] and [AOR = 0.22 (95% CI: 0.06-0.78)] respectively.ConclusionThere is a high prevalence of preterm delivery in the Tamale Metropolis. Having multiple pregnancies, caesarean sections and large household size are risk factors of preterm birth. Whilst maintaining a normal haemoglobin at 36 weeks and drinking pipe-borne water are protective factors against preterm delivery in the Tamale metropolis.
Prompting is all you need: LLMs for systematic review screening
Authors: Cao Christian , Sang Jason , Arora Rohit , Kloosterman Robbie , Cecere Matt , Gorla Jaswanth , Saleh Richard , Chen David , Drennan Ian , Teja Bijan , Fehlings Michael , Ronksley Paul , Leung Alexander A , Weisz Dany E , Ware Harriet , Whelan Mairead , Emerson David B , Arora Rahul , Bobrovitz Niklas 
Published: June 2024

AbstractSystematic reviews (SRs) are the highest standard of evidence, shaping clinical practice guidelines, policy decisions, and research priorities. However, their labor-intensive nature, including an initial rigorous article screen by at least two investigators, delays access to reliable information synthesis. Here, we demonstrate that large language models (LLMs) with intentional prompting can match human screening performance. We introduce Framework Chain-of-Thought, a novel prompting approach that directs LLMs to systematically reason against predefined frameworks. We evaluated our prompts across ten SRs covering four common types of SR questions (i.e., prevalence, intervention benefits, diagnostic test accuracy, prognosis), achieving a mean accuracy of 93.6% (range: 83.3-99.6%) and sensitivity of 97.5% (89.7-100%) in full-text screening. Compared to experienced reviewers (mean accuracy 92.4% [76.8-97.8%], mean sensitivity 75.1% [44.1-100%]), our full-text prompt demonstrated significantly higher sensitivity in four reviews (p<0.05), significantly higher accuracy in one review (p<0.05), and comparable accuracy in two of five reviews (p>0.05). While traditional human screening for an SR of 7000 articles required 530 hours and $10,000 USD, our approach completed screening in one day for $430 USD. Our results establish that LLMs can perform SR screening with performance matching human experts, setting the foundation for end-to-end automated SRs.
Race-dependent variability in the human tumor mycobiome
Authors: Coster Dan , Margalit Thomy , Boursi Ben , Shamir Ron 
Published: June 2024

AbstractIntroductionRecently, Narunsky-Haziza et. al. showed that fungi species identified in a variety of cancer types may have prognostic and diagnostic signficane. We used that data in order to better understand the effects of demographic factors (age, sex, BMI, and race) on the intratumor mycobiome composition.Materials and MethodsWe first tested the data in view of recent critiques of microbiome data processing procedures, and concluded that the batch correction and transformation used on it may produce false signals. Instead, we explored 14 combinations of data transformation and batch correction methods on data of 224 fungal species across 13 cancer types. Propensity scores were utilized to adjust for potential confounders such as histological type and tumor stage. To minimize false outcomes, we identified as positive results only those fungi species that showed significant difference in abundance across a demographic factor within a particular cancer type, using data normalized according to all 14 combinations.Results and DiscussionWe observed significant differences in fungal species abundance within tumors for certain demographic characteristics. Most differences were among races in specific cancers. The findings indicate that there are intricate interactions among the mycobiome, cancer types, and patient demographics. Our study highlights the need for accounting for potential confounders in order to further understanding of the mycobiome’s role in cancer, and underscores the importance of data processing techniques.
The safety and efficacy of using age-adjusted D-dimers in hospitalised patients in a diverse urban centre: a real-world data study
Authors: Gallier S. , Evison F. , Hodson J. , Khosla R. , Ranasinghe T. , Rickard L. , Atkin C. , Reddy-Kolanu V. , Nirantharakumar K. , Lester W. , Holloway B. , Sapey E. 
Published: June 2024

AbstractObjectiveDespite recommendations, age adjusted thresholds (AAT) for D Dimers are not routinely used as part of venous thromboembolism (VTE) screening in many healthcare settings due to concerns about missing cases, especially in older and co-morbid adults. The National Institute for Health and Care Excellence in the UK has highlighted that evidence to support AAT is not plentiful. This study assessed the real-world use of AAT D-dimers for VTE in a large cohort of acutely hospitalised patients.MethodsThis retrospective data study included all adult patients attending a large hospital with a suspected VTE between January 2017 to December 2021. The predictive accuracy of D-dimer was assessed against gold standard imaging. Outcomes of false negative (with AAT) and false positives (with standard thresholds) cases were assessed.Results27,526 suspected VTE attendances were included, with a 4.3% confirmed VTE diagnosis rate. The ST D-dimer exhibited high sensitivity (91.1%) but modest specificity (65.2%). The AAT demonstrated slightly lower sensitivity (87.0%) but higher specificity (71.7%, p<0.001). The performance of ST thresholds declined with age, with false positive rates increasing from 17.4% to 80.0% in people aged < 50 years and > 90 years respectively. The AAT accurately identified 1,700 true negatives misclassified as false positives by the ST. 14 patients in this group were admitted with a bleed within 30 days. AAT misdiagnosed 24 cases as false negatives, with most being small sub-segmental pulmonary emboli or non-occlusive DVTs. Using AAT thresholds could have avoided 64 scans per 1,000 attendances, saving approximately £235,310 of imaging costs in this cohort.ConclusionThe age-adjusted D-dimer threshold enhances diagnostic precision and could decrease unnecessary imaging and anticoagulation, reducing investigations with time and cost savings with no significant safety signal.
Association of sexual orientation with substance use in Colombian adults experiencing homelessness
Authors: Campo-Arias Adalberto , Pineda-Roa Carlos Alejandro , Herazo Edwin 
Published: June 2024

AbstractThe study’s objective was to quantify the association of sexual orientation with substance use among Colombian adults experiencing homelessness. A secondary analysis of the Census of Street Inhabitants - CHC-2020 was completed. Three thousand five hundred forty-seven participants between 18 and 75 years participated, and 3.16% reported lesbian, gay, or bisexual (LGB) sexual orientation. LGB sexual orientation was associated with alcohol consumption (OR = 2.14, 95%CI 1.46 - 3.14]), cigarettes (OR = 1.70, 95%CI 1.12 - 2.56), cannabis (OR = 1.58, 95%CI 1.07 - 2.33), cocaine (OR = 2.13, 95%CI 1.30 - 3.50) and benzodiazepines (OR = 2.15, 95%CI 1.19-3.89). In conclusion, Colombian adults experiencing homelessness with gay or lesbian sexual orientation have twice the risk of consuming alcohol, cigarettes, cannabis, cocaine, and benzodiazepines than heterosexuals. More studies are needed on this population.
Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak
Authors: Napit Rajindra , Ngono Annie Elong , Mihindukulasuriya Kathie A. , Pradhan Aunji , Khadka Binod , Shrestha Smita , Droit Lindsay , Paredes Anne , Karki Lata , Khatiwada Ravindra , Tamang Mamata , Chalise Bimal Sharma , Rawal Manisha , Jha Bimlesh , Wang David , Handley Scott A. , Shresta Sujan , Manandhar Krishna Das 
Published: June 2024

AbstractBackgroundThe 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies.Methods and ResultsDuring the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+participants by RT-PCR and identified DENV1, 2, and 3 – with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018.ConclusionThese findings highlight DENV’s geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.
TGFβ determines morphology and key cellular processes of activated CD4+T cells
Authors: Eizenberg-Magar Inbal , Rimer Jacob , Miller Stav , Elyahu Yehezqel , Mark Michal , Porat Ziv , Reich-Zeliger Shlomit , Monsonego Alon , Antebi Yaron E , Friedman Nir 
Published: June 2024

AbstractDuring an immune response, cells are simultaneously exposed to multiple cytokine signals that collectively determine their phenotype. Transforming growth factor β (TGFβ) is a pleiotropic cytokine acting as a key regulator of T-cell differentiation with activating and suppressive effects on their immune function. Here we identify and analyze the cellular responses of CD4+T cells to TGFβ across signaling contexts by analyzing the responses of T cells to multiple cytokine mixtures in the presence or absence of TGFβ. We found that TGFβ had a profound dominant effect independent of the presence of other cytokines, modulating the expression of more than 4,000 genes. In the presence of TGFβ, cells exhibit lower expression of translation-related and apoptosis-related genes, accompanied by increased survival of activated T cells. Notably, cells cultured in the presence of TGFβ were smaller in size while preserving their proliferative ability. Accordingly, we identified a dense network of transcription factors that were modulated by TGFβ, suggesting a core gene set connecting TGFβ signaling to the regulation of T-cell size. We found N-Myc to be at the center of this network, and we directly show that TGFβ regulates its gene expression level, protein level, and nuclear localization. Our work provides a system to study cell size control and demonstrate the profound effect of TGFβ in the modulation and regulation of T-cell properties, expanding its role beyond guiding their phenotype.
P-cadherin mechanoactivates tumor–mesothelium metabolic coupling to promote ovarian cancer metastasis
Authors: Ma Jing , To Sally K. Y. , Fung Katie S. W. , Wang Kun , Zhang Jiangwen , Ngan Alfonso H. W. , Yung Susan , Chan Tak-Mao , Wong Carmen C. L. , Ip Philip P. C. , Peng Ling , Guo Hong-Yan , Chan Chi Bun , Wong Alice S.T. 
Published: June 2024

AbstractPeritoneal metastasis exacerbates the prognosis of ovarian cancer patients. Adhesion of cancer cells to mesothelium is a rate-limiting prerequisite for this process. How metastatic cells sense and respond to the dynamic biomechanical microenvironment at the mesothelial niche to initiate metastatic lesions remains unclear. Here, the study demonstrates that highly metastatic (HM), but not non-metastatic (NM) ovarian cancer cells, selectively activate the peritoneal mesothelium. Atomic force microscopy reveals that HM cells exert increased adhesive force on mesothelial cells via P-cadherin, a cell-cell adhesion molecule abundant in late-stage tumors. Transcriptomic and molecular analyses show that mechanical induction of P-cadherin enhances lipogenic gene expression and lipid content in HM cells by SREBP1. P-cadherin activation does not affect lipogenic activity but induces glycolysis in the interacting mesothelium. Targeted lipidomic analysis reveals that lactate produced by the glycolytic mesothelium facilitates metastatic outgrowth as a direct substrate forde novolipogenesis. Inhibiting lactate shuttling via nanodelivery of siRNA targeting P-cadherin or MCT1/4 transporters significantly suppresses metastasis in mice. The association of high fatty acid synthase in patient metastatic samples and increased P-cadherin expression supports enhancedde novolipogenesis in the metastatic niche. The study reveals P-cadherin-mediated mechano-metabolic coupling as a promising target to restrain peritoneal metastasis.
Antibiotic self-medication in Otuke district, northern Uganda: Prevalence and associated factors
Authors: Adoko Denis Diko , Nakaziba Rebecca 
Published: June 2024

AbstractAntibiotic self-medication is a form of irrational drug use that contributes to antimicrobial resistance, which results in increasing health care costs and morbidity and mortality rates in the population. The misuse of antimicrobial agents is highly linked with the growing problem of antimicrobial resistance within the population globally. Unless addressed, antibiotic self-medication will drive the world back to the pre-antibiotic era, with people dying helplessly due to infectious diseases. This study aimed to investigate the prevalence of antibiotic self-medication and its associated factors in the Otuke District, Northern Uganda. A community-based cross-sectional study was conducted in the Otuke Town Council, Otuke district. The data of adults aged 18 years and above were collected using a semi-structured questionnaire, and the data were coded and entered into SPSS software version 26. The data were descriptively analyzed for frequencies and percentages. Bivariant and multivariant analyses were performed to determine associations between the variables. Out of 385 participants, 68% self-medicated with antibiotics in the past 12 months. Freedom from drug use (AOR: 3.071; 95% CI: 1.203, 7.876) and unregulated use of antibiotics (AOR at 95% CI: 8.288 (2.815, 24.397)) were more likely to lead to ASM (p value <0.001). Other significant factors included knowledge of antibiotics, previous symptom experience, previous successful treatment, long waiting hours and poor staff attitudes (p value <0.05). The most common self-medicated antibiotics were amoxicillin, Ampiclox and metronidazole.Antibiotic self-medication in the Otuke district is very high due to the availability of medicines and lack of functional drug use regulatory frameworks. The district and government of Uganda should design and implement measures to mitigate this widespread antimicrobial misuse to prevent the development of antimicrobial resistance.
Less is more: selection from a small set of options improves BCI velocity control
Authors: Alcolea Pedro , Ma Xuan , Bodkin Kevin , Miller Lee E. , Danziger Zachary C. 
Published: June 2024

AbstractWe designed the discrete direction selection (DDS) decoder for intracortical brain computer interface (iBCI) cursor control and showed that it outperformed currently used decoders in a human-operated real-time iBCI simulator and in monkey iBCI use. Unlike virtually all existing decoders that map between neural activity and continuous velocity commands, DDS uses neural activity to select among a small menu of preset cursor velocities. We compared closed-loop cursor control across four visits by each of 48 naïve, able-bodied human subjects using either DDS or one of three common continuous velocity decoders: direct regression with assist (an affine map from neural activity to cursor velocity), ReFIT, and the velocity Kalman Filter. DDS outperformed all three by a substantial margin. Subsequently, a monkey using an iBCI also had substantially better performance with DDS than with the Wiener filter decoder (direct regression decoder that includes time history). Discretizing the decoded velocity with DDS effectively traded high resolution velocity commands for less tortuous and lower noise trajectories, highlighting the potential benefits of simplifying online iBCI control.
PandemicVibrio parahaemolyticuswave succession by gene loss
Authors: Yang Chao , Qiu Hongling , Svensson Sarah L. , Ni Chengpei , Gao Song , Jia Zhizhou , Wen Huiqi , Xie Li , Xu Wenxuan , Qin Yujiao , Lin Shuzhu , Wang Jiancheng , Zhang Yiquan , Li Yinghui , Jiang Min , Shi Xiaolu , Hu Qinghua , Zhou Zhemin , Chao Yanjie , Yang Ruifu , Cui Yujun , Martinez-Urtaza Jaime , Wang Hui , Falush Daniel 
Published: June 2024

AbstractWhile the importance of spontaneous mutation and gene acquisition in the emergence and adaptive evolution of microbial pathogens is well recognized, the role of gene loss remains underexplored. Here, by large-scale phylogenomic analysis of 8,684 global isolates, we reconstructed the origin and evolutionary dynamics of the pandemic clone (PC) ofVibrio parahaemolyticus, the leading cause of seafood-associated infections worldwide. As has also been observed for the pandemic lineage ofV. cholerae, there was an ‘explosive’ burst of gene and genomic island acquisition during the emergence of the clone followed by divergence into distinct, successive sublineages mediating independent waves of cross-country transmission. InV. parahaemolyticus,a recent global wave succession event has been driven by gene-loss in the putrescine utilization (Puu) pathway, which confers phenotypic advantages related to environmental adaptation (enhanced biofilms) and human transmission (increased cell adhesion and intestinal colonization, reduced virulence in an animal model and milder clinical symptoms in humans), aligning with the trade-off hypothesis of pathogen virulence evolution. We identify similar lineage-specific Puu-gene-loss across multiple bacterial genera, with effects on biofilm and adhesion replicated inV. choleraeandE. coli, suggesting convergent evolution and universal mechanisms across bacteria. Our findings provide a paradigm of adaptative evolution by gene loss in a pandemic pathogen.
Chemical signatures delineate heterogeneous amyloid plaque populations across the Alzheimer’s disease spectrum
Authors: Koutarapu Srinivas , Ge Junyue , Dulewicz Maciej , Srikrishna Meera , Szadziewska Alicja , Wood Jack , Blennow Kaj , Zetterberg Henrik , Michno Wojciech , Ryan Natalie S , Lashley Tammaryn , Savas Jeffrey , Schöll Michael , Hanrieder Jörg 
Published: June 2024

ABSTRACTAmyloid plaque deposition is recognized as the primary pathological hallmark of Alzheimer’s disease(AD) that precedes other pathological events and cognitive symptoms. Plaque pathology represents itself with an immense polymorphic variety comprising plaques with different stages of amyloid fibrillization ranging from diffuse to fibrillar, mature plaques. The association of polymorphic Aβ plaque pathology with AD pathogenesis, clinical symptoms and disease progression remains unclear. Advanced chemical imaging tools, such as functional amyloid microscopy combined with MALDI mass spectrometry imaging (MSI), are now enhanced by deep learning algorithms. This integration allows for precise delineation of polymorphic plaque structures and detailed identification of their associated Aβ compositions. We here set out to make use of these tools to interrogate heterogenic plaque types and their associated biochemical architecture. Our findings reveal distinct Aβ signatures that differentiate diffuse plaques from fibrilized ones, with the latter showing substantially higher levels of Aβx-40. Notably, within the fibrilized category, we identified a distinct subtype known as coarse-grain plaques. Both in sAD and fAD brain tissue, coarse grain plaques contained more Aβx-40 and less Aβx-42 compared with cored plaques. The coarse grain plaques in both sAD and fAD also showed higher levels of neuritic content including paired helical filaments (PHF-1)/phosphorylated phospho Tau-immunopositive neurites. Finally, the Aβ peptide content in coarse grain plaques resembled that of vascular Aβ deposits (CAA) though with relatively higher levels of Aβ1-42 and pyroglutamated Aβx-40 and Aβx-42 species in coarse grain plaques. This is the first of its kind study on spatialin situbiochemical characterization of different plaque morphotypes demonstrating the potential of the correlative imaging techniques used that further increase the understanding of heterogeneous AD pathology. Linking the biochemical characteristics of amyloid plaque polymorphisms with various AD etiologies and toxicity mechanisms is crucial. Understanding the connection between plaque structure and disease pathogenesis can enhance our insights. This knowledge is particularly valuable for developing and advancing novel, amyloid-targeting therapeutics.