bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune-response 3′UTR alternative polyadenylation quantitative trait loci contribute to variation in human complex traits and diseases
Authors: Li Lei , Ma Xuelian , Cui Ya , Rotival Maxime , Chen Wenyan , Zou Xudong , Ding Ruofan , Qin Yangmei , Wang Qixuan , Quintana-Murci Lluis , Li Wei 
Published: December 2023

AbstractGenome-wide association studies (GWASs) have identified thousands of non-coding variants that are associated with human complex traits and diseases. The analysis of such GWAS variants in different contexts and physiological states is essential for deciphering the regulatory mechanisms underlying human disease. Alternative polyadenylation (APA) is a key post-transcriptional modification for most human genes that substantially impacts upon cell behavior. Here, we mapped 9,493 3′-untranslated region APA quantitative trait loci in 18 human immune baseline cell types and 8 stimulation conditions (immune 3′aQTLs). Through the comparison between baseline and stimulation data, we observed the high responsiveness of 3′aQTLs to immune stimulation (response 3′aQTLs). Co-localization and mendelian randomization analyses of immune 3′aQTLs identified 678 genes where 3′aQTL are associated with variation in complex traits, 27.3% of which were derived from response 3′aQTLs. Overall, these analyses reveal the role of immune 3′aQTLs in the determination of complex traits, providing new insights into the regulatory mechanisms underlying disease etiologies.
Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata)
Authors: Liu Detuan , Tian Xiaoling , Shao Shicheng , Ma Yongpeng , Zhang Rengang 
Published: December 2023

AbstractMicrocos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.
Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)
Authors: Lan Linjing , Zhang Xin , Yang Shanxiu , Li Lingjie , Mao Xiuguang 
Published: December 2023

AbstractStoliczka’s Asian trident bat (Aselliscus stoliczkanus) is a small-bodied species and very sensitive to climate change. Here, we presented a chromosome-level genome assembly of A. stoliczkanus by combining Illumina sequencing, Nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) sequencing technology. The genome assembly was 2.18 Gb in size with 98.26% of the genome sequences anchored onto 14 autosomes and two sex chromosomes (X and Y). The quality of the genome assembly is very high with a contig and scaffold N50 of 72.98 and 162 Mb, respectively, Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 96.6%, and the consensus quality value (QV) of 47.44. A total of 20,567 genes were predicted and 98.8% of these genes were functionally annotated. Syntenic blocks between A. stoliczkanus and Homo sapiens, together with previous comparative cytogenetic studies, provide valuable foundations for further comparative genomic and cytogenetic studies in mammals. The reference-quality genome of A. stoliczkanus contributes an important resource for conservative genomics and landscape genomics in predicting adaptation and vulnerability to climate change.
Variations of the trapezius branch of the accessory nerve: an anatomic study
Authors: Lin Matthew E. , Kim Celeste , Howard Adam , Kokot Niels 
Published: December 2023

AbstractAlthough modified radical neck dissections have increased in popularity to reduce morbidity secondary to intraoperative accessory nerve damage, inadvertent injury still often occurs. As this phenomenon is thought to be due to anatomic variation in the trapezius branch of the accessory nerve, it is imperative to better understand the nuances of these anatomic variations to better inform surgical decision-making. A total of 24 accessory nerves were dissected, exposed, and traced in 15 cadavers. Three aspects of the accessory nerve were identified and recorded: the course of the trapezius branch in relation to the sternocleidomastoid, the number of trapezius branches at muscle insertion, and the number of cervical rootlet contributions. Four different anatomic patterns for the trapezius branch were identified, with the most common being where the trapezius branch separates from the main accessory nerve just medial to the sternocleidomastoid and courses deep to the sternocleidomastoid (58.3%). Most (75%) trapezius branches entered the muscle as a single nerve, whereas some (21%) were inserted as two separate nerves. The number of cervical rootlet contributions for each trapezius branch varied from zero to three. Bilateral anatomic variations were also noted. Even when the accessory nerve and its branches are thought to be spared during neck dissection, patients may postoperatively present with different degrees of accessory nerve damage. There may be unrecognized anatomic pathways that the nerve takes that may confer a higher risk of unintentional damage, especially those that have greater exposure within the anterior triangle unprotected by the sternocleidomastoid.
Economic burden of multidrug-resistant tuberculosis on patients and households: a global systematic review and meta-analysis
Authors: Akalu Temesgen Yihunie , Clements Archie C. A. , Wolde Haileab Fekadu , Alene Kefyalew Addis 
Published: December 2023

AbstractMultidrug-resistant tuberculosis (MDR-TB) is a major health threat worldwide, causing a significant economic burden to patients and their families. Due to the longer duration of treatment and expensive second-line medicine, the economic burden of MDR-TB is assumed to be higher than drug-susceptible TB. However, the costs associated with MDR-TB are yet to be comprehensively quantified. We conducted this systematic review and meta-analysis to determine the global burden of catastrophic costs associated with MDR-TB on patients and their households. We systematically searched five databases (CINHAL, MEDLINE, Embase, Scopus, and Web of Science) from inception to 2 September 2022 for studies reporting catastrophic costs on patients and affected families of MDR-TB. The primary outcome of our study was the proportion of patients and households with catastrophic costs. Costs were considered catastrophic when a patient spends 20% or more of their annual household income on their MDR-TB diagnosis and care. The pooled proportion of catastrophic cost was determined using a random-effects meta-analysis. Publication bias was assessed using visualization of the funnel plots and the Egger regression test. Heterogeneity was assessed using I2, and sub-group analysis was conducted using study covariates as stratification variables. Finally, we used the Preferred Reporting Items for Reporting Systematic Review and Meta-Analysis-20 (PRISMA-20). The research protocol was registered in PROSPERO (CRD42021250909). Our search identified 6635 studies, of which 11 were included after the screening. MDR-TB patients incurred total costs ranging from $USD 650 to $USD 8266 during treatment. The mean direct cost and indirect cost incurred by MDR-TB patients were $USD 1936.25 (SD ± $USD 1897.03) and $USD 1200.35 (SD ± $USD 489.76), respectively. The overall burden of catastrophic cost among MDR-TB patients and households was 81.58% (95% Confidence Interval (CI) 74.13–89.04%). The catastrophic costs incurred by MDR-TB patients were significantly higher than previously reported for DS-TB patients. MDR-TB patients incurred more expenditure for direct costs than indirect costs. Social protection and financial support for patients and affected families are needed to mitigate the catastrophic economic consequences of MDR-TB.
OPEFB pretreatment using the low-cost N,N,N-dimethylbutylammonium hydrogen sulfate ionic liquid under varying conditions
Authors: Shikh Zahari S. M. Shahrul Nizan , Liu Yichen , Yao Putian , Ideris Mahfuzah Samirah , Azman Hazeeq Hazwan , Hallett Jason P. 
Published: December 2023

Abstract
This study investigates the effects of temperature and period on the pretreatment of OPEFB using the low-cost N,N,N-dimethylbutylammonium hydrogen sulfate ionic liquid ([DMBA][HSO4] IL) with 20 wt% of water. The results demonstrate that higher pretreatment temperatures (120, 150, and 170 °C) and longer periods (0.5, 1, and 2 h) enhanced lignin recovery, resulting in increased purity of the recovered pulp and subsequently enhanced glucose released during enzymatic hydrolysis. However, at 170 °C, prolonging the period led to cellulose degradation and the formation of pseudo-lignin deposited on the pulps, resulting in a decreasing-trend in glucose released. Finally, the analysis of extracted lignin reveals that increasing pretreatment severity intensified lignin depolymerisation and condensation, leading to a decrease in number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index (Đ) values.
Mathematical models of apparent viscosity as a function of water–cement/binder ratio and superplasticizer in cement pastes
Authors: Yuan Yong , Wang Xiaoyun , Chen Xi , Xiao Peng , Koenders Eduardus , Dai Ying 
Published: December 2023

AbstractThe water–cement/binder ratio and the admixture of water-reducing agents strongly affect the rheological properties of cement pastes. This study develops mathematical models to predict the apparent viscosity of cement pastes with varying water-cement/binder ratios and polycarboxylate-based superplasticizer content by introducing the power law shear stress-shear strain relation of non-Newtonian fluids into the Navier–Stokes motion equations. The developed models are compared with the results of rheological experiments and verified for their accuracy in simulating the apparent viscosity of cement pastes. These models provide insight into the rheological behaviour of cement pastes and could have practical applications in the construction industry.
Changes in plasma endocan level are related to circulatory but not respiratory failure in critically ill patients with COVID-19
Authors: Lipińska-Gediga Małgorzata , Lemańska-Perek Anna , Gozdzik Waldemar , Adamik Barbara 
Published: December 2023

AbstractThe aim of this prospective, observational study was to assess whether changes in the level of endocan, a marker of endothelial damage, may be an indicator of clinical deterioration and mortality in critically ill COVID-19 patients. Endocan and clinical parameters were evaluated in 40 patients with acute respiratory failure on days 1–5 after admission to the intensive care unit. Endocan levels were not related to the degree of respiratory failure, but to the presence of cardiovascular failure. In patients with cardiovascular failure, the level of endocan increased over the first 5 days (1.63, 2.50, 2.68, 2.77, 3.31 ng/mL, p = 0.016), while in patients without failure it decreased (1.51, 1.50, 1.56, 1.42, 1.13 ng/mL, p = 0.046). In addition, mortality was more than twice as high in patients with acute cardiovascular failure compared to those without failure (68% vs. 32%, p = 0.035). Baseline endocan levels were lower in viral than in bacterial infections (1.57 ng/mL vs. 5.25 ng/mL, p < 0.001), with a good discrimination between infections of different etiologies (AUC of 0.914, p < 0.001). In conclusion, endocan levels are associated with the occurrence of cardiovascular failure in COVID-19 and depend on the etiology of the infection, with higher values for bacterial than for viral sepsis.
Face coverings increase apparent honesty and cooperativeness
Authors: Lobmaier Janek S. , Knoch Daria 
Published: December 2023

AbstractPeople readily make inferences about trait-like characteristics of another person’s face. Since the recent global COVID-19 pandemic, the widespread use of hygienic face masks has led to large proportions of the face being covered. We investigated the effect of face masks on the inference of prosocially relevant characteristics, namely cooperativeness and honesty. Portraits of participants of previous studies from which we knew their “true” prosocial tendencies served as stimuli. These facial stimuli were presented once with and once without a hygienic face mask to 60 naïve participants who rated the faces for cooperativeness and honesty. Results revealed that wearing face masks made people generally appear more cooperative and more honest than without a mask, but that these ratings were unrelated to the true prosocial tendencies of these people. Together, these findings have important implications for social interactions, particularly in contexts where nonverbal communication is essential, such as in healthcare settings, job interviews, and social gatherings.
Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009–2018 influenza seasons
Authors: Owuor D. Collins , de Laurent Zaydah R. , Nyawanda Bryan O. , Emukule Gideon O. , Kondor Rebecca , Barnes John R. , Nokes D. James , Agoti Charles N. , Chaves Sandra S. 
Published: December 2023

AbstractInfluenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines.
The effect of donor against recipient one-way HLA mismatch on liver transplantation outcomes from a multicenter registry analysis
Authors: Park Sunghae , Choi Young Rok , Joo Dong Jin , You Young Kyoung , Kim Bong-Wan , Nah Yang Won , Cho Jai Young , Kim Tae-Seok , Hong Geun , Ju Man Ki , Suh Suk-Won , Yang Jae Do , Park Pyoung Jae , Jeong Jaehong , Moon Ju Ik , Kim Dong-Sik , Rhu Jinsoo ,   The Korean Organ Transplantation Registry Study Group
Published: December 2023

AbstractDonor against recipient one-way Human leukocyte antigen (HLA) mismatch (D → R one-way HLA MM) seemed strongly associated with graft-versus-host disease (GVHD). The aim of this study is to investigate the relevance of D → R one-way HLA MM in outcome of liver transplantation (LT). We retrospectively analyzed 2670 patients in Korean Organ Transplantation Registry database between April 2014 and December 2020. The patients were categorized into two groups whether D → R one-way HLA MM or not and evaluated the outcomes of LT between the two groups. 18 patients were found to be D → R one-way HLA MM. The incidence of GVHD (0.3% vs. 22.2%, p < 0.001) and mortality rate (11.6% vs. 38.9%, p = 0.003) was much higher in D → R one-way HLA MM group. D → R one-way HLA MM at 3 loci was seemed to be strongly associated with the incidence of GVHD (OR 163.3, p < 0.001), and found to be the strongest risk factor for patient death (HR 12.75, p < 0.001). Patients with D → R one-way HLA MM at 3 loci showed significantly lower overall survival (p < 0.001) but there were no significant differences in rejection-free survival and death-censored graft survival. D → R one-way HLA MM at 3 loci not only affects the overall survival of LT patients but also the incidence of GVHD.
Comparative analysis of neutrophil-to-lymphocyte ratio and remnant cholesterol in predicting cardiovascular events and mortality in general adult population
Authors: Wang Qian-Chen , Wang Zhen-Yu 
Published: December 2023

AbstractThis study aimed to investigate the predictive value of neutrophil-to-lymphocyte ratio (NLR) and Remnant Cholesterol (Remnant-C) in relation to cardiovascular events and all-cause mortality in the general population. A population-based study. We conducted a retrospective cohort study analyzing data from the National Health and Nutrition Examination Survey (NHANES) spanning the years of 2011–2018, with follow-up for mortality status until December 31, 2019. Kaplan‒Meier and Cox proportional hazards regression analyses were used to evaluate the associations between NLR, Remnant-C, and cardiovascular events as well as all-cause mortality. Overall, 9409 individuals with both complete blood count and blood lipids were included in the analysis. Baseline NLR and Remnant-C were calculated. During the follow-up (median, 59.3 months), 177 cardiovascular events and 561 all-cause mortality occurred. In fully adjusted model, people with NLR > 2.26 were significantly associated with higher risk of cardiovascular events (HR 2.14, 95% CI 1.30–3.52, P < 0.001) and all-cause mortality (HR 1.66, 95% CI 1.30–2.12, P < 0.001). NLR exhibited a positive correlation with Remnant-C (r = 0.04, P < 0.001). Elevated NLR levels shown stronger association with cardiovascular events (HR 1.21, 95% CI 1.14–2.28, P < 0.001) compared with Remnant-C (HR 1.02, 95% CI 1.00–1.04, P = 0.020). Our findings suggest that NLR and Remnant-C are potential predictive markers for cardiovascular events in the general population. We observed a correlation between NLR and Remnant-C, and high NLR levels demonstrate a stronger association with the prediction of cardiovascular events and all-cause mortality compared with Remnant-C.
Comparing storm resolving models and climates via unsupervised machine learning
Authors: Mooers Griffin , Pritchard Mike , Beucler Tom , Srivastava Prakhar , Mangipudi Harshini , Peng Liran , Gentine Pierre , Mandt Stephan 
Published: December 2023

AbstractGlobal storm-resolving models (GSRMs) have gained widespread interest because of the unprecedented detail with which they resolve the global climate. However, it remains difficult to quantify objective differences in how GSRMs resolve complex atmospheric formations. This lack of comprehensive tools for comparing model similarities is a problem in many disparate fields that involve simulation tools for complex data. To address this challenge we develop methods to estimate distributional distances based on both nonlinear dimensionality reduction and vector quantization. Our approach automatically learns physically meaningful notions of similarity from low-dimensional latent data representations that the different models produce. This enables an intercomparison of nine GSRMs based on their high-dimensional simulation data (2D vertical velocity snapshots) and reveals that only six are similar in their representation of atmospheric dynamics. Furthermore, we uncover signatures of the convective response to global warming in a fully unsupervised way. Our study provides a path toward evaluating future high-resolution simulation data more objectively.
Usefulness of thalamic beta activity for closed-loop therapy in essential tremor
Authors: Guehl Dominique , Guillaud Etienne , Langbour Nicolas , Doat Emilie , Auzou Nicolas , Courtin Edouard , Branchard Olivier , Engelhardt Julien , Benazzouz Abdelhamid , Eusebio Alexandre , Cuny Emmanuel , Burbaud Pierre 
Published: December 2023

AbstractA partial loss of effectiveness of deep brain stimulation of the ventral intermediate nucleus of the thalamus (VIM) has been reported in some patients with essential tremor (ET), possibly due to habituation to permanent stimulation. This study focused on the evolution of VIM local-field potentials (LFPs) data over time to assess the long-term feasibility of closed-loop therapy based on thalamic activity. We performed recordings of thalamic LFPs in 10 patients with severe ET using the ACTIVA™ PC + S (Medtronic plc.) allowing both recordings and stimulation in the same region. Particular attention was paid to describing the evolution of LFPs over time from 3 to 24 months after surgery when the stimulation was Off. We demonstrated a significant decrease in high-beta LFPs amplitude during movements inducing tremor in comparison to the rest condition 3 months after surgery (1.91 ± 0.89 at rest vs. 1.27 ± 1.37 µV2/Hz during posture/action for N = 8/10 patients; p = 0.010), 12 months after surgery (2.92 ± 1.75 at rest vs. 2.12 ± 1.78 µV2/Hz during posture/action for N = 7/10 patients; p = 0.014) and 24 months after surgery (2.32 ± 0.35 at rest vs 0.75 ± 0.78 µV2/Hz during posture/action for 4/6 patients; p = 0.017). Among the patients who exhibited a significant decrease of high-beta LFP amplitude when stimulation was Off, this phenomenon was observed at least twice during the follow-up. Although the extent of this decrease in high-beta LFPs amplitude during movements inducing tremor may vary over time, this thalamic biomarker of movement could potentially be usable for closed-loop therapy in the long term.