bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Mortality Surveillance through Notification of Death at Mbale Regional Referral Hospital, Uganda, October 2023–April 2024
Authors: Ssemanda Innocent , Namulondo Edith , Naziri Carol , Obbo Stephen , Kwesiga Benon , Migisha Richard , Bulage Lilian , Morukileng Job , Ario Alex Riolexus 
Published: December 2024

AbstractBackgroundAccurate mortality reporting is crucial for monitoring population health, detecting disease outbreaks, and informing health policies. However, the implementation of medical certification of cause of death remains low in Uganda, with only 3.2% of health facility deaths being notified to the Ministry of Health. Using a quality improvement approach, we aimed to improve mortality reporting through medical certification of cause of death at Mbale Regional Referral Hospital (MRRH) in Uganda from 1% to 80% within 6 months.MethodsWe purposively selected MRRH as one of five regional referral hospitals with the lowest death notifications (0%-20%) during 2022 and 2023. We adopted the existing quality improvement team, which includes medical and non-medical personnel. Focus group discussions identified challenges that informed the root cause analysis. Using the Plan-Do-Study-Act (PDSA) cycle, we generated change ideas (interventions) to address these bottlenecks. We monitored the progress of the interventions with process indicators (number of mentorship sessions conducted, number of review meetings held) and an outcome indicator (proportion of deaths occurring in the hospital notified through the District Health Information System version 2 (DHIS2)) for 6 months. We tracked notifications monthly and analyzed the trend at six months using the Mann-Kendall test.ResultsWe conducted 4/6 (67%) mentorship sessions and 7/19 (38%) review meetings and trained 32/50 (64%) nurses. The qualitative findings highlighted key challenges, including lack of knowledge and training, competing priorities and workload, resource constraints, undervaluing the importance of mortality reporting, failure to follow guidelines, and heavy workloads. The interventions included training and mentorship sessions for the staff on properly completing the death notification form, adopting a standardized process for form completion, and conducting bi-monthly review meetings. The proportion of deaths notified through DHIS2 from November 2023 to April 2024 increased from 17% to 65% (p=0.01).ConclusionTraining of staff, adoption of a standard protocol on notification, and routine review meetings could facilitate death notification and improve mortality surveillance in Uganda enabling more accurate resource allocation for mortality prevention. The target was not met probably because all the staff were not trained, and the review meetings were sub-optimal.
Relaxation-selective Intravoxel Incoherent Motion Imaging of Microvascular Perfusion and Fluid Compartments in the Human Choroid Plexus
Authors: Li Chenyang , Sun Zhe , Zhang Jiangyang , Ge Yulin 
Published: December 2024

AbstractThe choroid plexus (ChP) plays an important role in the glymphatic system of the human brain as the primary source of the cerebrospinal fluid (CSF) production. Development of a non-invasive imaging technique is crucial for studying its function and age-related neurofluid dynamics. This study developed a relaxation-selective intravoxel incoherent motion (IVIM) technique to assess tissue and fluid compartments in the ChP in a prospective cross-sectional study involving 83 middle-aged to elderly participants (age: 61.5 ± 17.1 years old) and 15 young controls (age: 30.7 ± 2.9 years old). Using a 3T MRI scanner, IVIM, FLAIR-IVIM, LongTE-IVIM, and VASO-LongTE-IVIM were employed to measure diffusivity and volume fractions of fluid compartments and evaluate aging effects on microvascular perfusion and interstitial fluid (ISF). FLAIR-IVIM identified an additional ISF compartment with free-water-like diffusivity (2.4 ± 0.9 x10-3mm2/s). Older adults exhibited increased ChP volume (2320 ± 812 mm3vs 1470 ± 403 mm³, p=0.0017), reduced perfusion (6.5 ± 4.7 vs 3.6 ± 2.9 x10⁻³ mm²/s, p=0.0088), decreased ISF volume fraction (0.58 ± 0.09 vs 0.67 ± 0.06, p=0.0042), and lower tissue diffusivity (1.16 ± 0.14 vs 1.29 ± 0.17 x10-3mm²/s, p=0.031) compared to younger adults. Relaxation-selective IVIM may offers enhanced specificity for characterizing age-related changes in ChP structure and fluid dynamics.
Differential control of mycobacteria among COVID-19 patients is associated with CD28+ CD8+ T cells
Authors: Llibre Alba , Siddiqui Henna , Pillaye Jamie , Burel Julie G , Jones Charlotte , Hill Harriet , Faustini Sian E , Windle Ella , Karim Hanfa , Sherry Emma , Green Christopher A , Dedicoat Martin , Stamataki Zania , Cunningham Adam F , O’Shea Matthew K 
Published: December 2024

ABSTRACTDiseases caused by SARS-CoV-2 andMycobacterium tuberculosis(M.tb) represent two public health emergencies. In severe disease, both pathogens may share a biological niche in the lower respiratory tract. There is significant potential for SARS-CoV-2 andM.tbinfections to be co-present within individuals and enhance or moderate the respective outcomes of either infection. Here, we investigated how whole blood samples, as well as CD4+ and CD8+ T cells, from individuals hospitalised with acute COVID-19 disease respond to mycobacterial challenge. To do this, samples were assessed byex vivomycobacterial growth inhibition assays, immune cell phenotyping by mass cytometry, and whole blood cytokine responses to mycobacterial antigens assessed by flow cytometry. These studies identified a subgroup of COVID-19 patients whose blood had an enhanced capacity to inhibit mycobacterial growth. The ability to control mycobacterial growth was associated with the presence of a nonM.tb-specific CD28+ CD8+ T cell population, with a particular activation status and migratory phenotype. This work improves our understanding of factors involved in mycobacterial control, and may contribute to the design of novel therapies for TB.
L2G: Repurposing Language Models for Genomics Tasks
Authors: Cheng Wenduo , Shen Junhong , Khodak Mikhail , Ma Jian , Talwalkar Ameet 
Published: December 2024

AbstractPre-trained language models have transformed the field of natural language processing (NLP), and their success has inspired efforts in genomics to develop domain-specific foundation models (FMs). However, creating high-quality genomic FMs from scratch is resource-intensive, requiring significant computational power and high-quality pre-training data. The success of large language models (LLMs) in NLP has largely been driven by industrial-scale efforts leveraging vast, diverse corpora and massive computing infrastructure. In this work, we aim to bypass the data and computational bottlenecks of creating genomic FMs from scratch and instead propose repurposing existing LLMs for genomics tasks. Inspired by the recently observed ‘cross-modal transfer’ phenomenon – where transformers pre-trained on natural language can generalize to other modalities – we introduce L2G, which adapts a pre-trained LLM architecture for genomics using neural architecture search (NAS) and a novel three-stage training procedure. Remarkably, without requiring extensive pre-training on DNA sequence data, L2G achieves superior performance to fine-tuned genomic FMs and task-specific models on more than half of tasks across multiple genomics benchmarks. In an enhancer activity prediction task, L2G further demonstrates its capacity to identify significant transcription factor motifs. Our work not only highlights the generalizability and efficacy of language models in out-of-domain tasks such as genomics, but also opens new avenues for more efficient and less resource-intensive methodologies in genomic research.
Comparable neural and behavioural performance in dominant and non-dominant hands during grasping tasks
Authors: Eswari Balasubramanian , Balasubramanian Sivakumar , Varadhan SKM 
Published: December 2024

AbstractHand dominance has long been associated with differences in neural control and motor performance, with the dominant hand typically exhibiting better coordination in reaching tasks. However, the extent to which this dominance influences performance in finger force control remains unclear. This study aimed to examine the behavioural and neural features of the dominant and non-dominant hands during grasping and lifting tasks in healthy young adults, focusing on the synergy index, EEG band power, and EEG–EMG coherence as key measures. Twenty right-handed adults (mean age = 26.95, STD = 2.68) participated in this study. Participants engaged in an experimental task where they grasped a handle for the initial five seconds, followed by lifting and holding it for an additional five seconds. There were two task conditions: fixed (thumb platform secured) and free (thumb platform movable). They performed 25 trials with both the dominant and non-dominant hands in the two task conditions, with the order of trials and hands block randomized to eliminate potential order effects. Contrary to the dynamic dominance hypothesis, we found statistical equivalence in the synergy index, EEG band power, and EEG–EMG coherence between the dominant and non-dominant hands across both fixed and free task conditions. These findings suggest that both hands are capable of achieving similar levels of performance in tasks emphasizing steady-state force maintenance, despite the typical advantages of the dominant hand in other motor tasks. While task-dependent modulations in behavioural and neural features were observed due to changes in friction, these adjustments were non-different between the dominant and non-dominant hands.
MDSGene update and expansion: Clinical and genetic spectrum ofLRRK2variants in Parkinson’s disease
Authors: Krüger Clara , Lim Shen-Yang , Buhrmann Alissa , Fahrig Fenja L. , Gabbert Carolin , Bahr Natascha , Madoev Harutyun , Marras Connie , Klein Christine , Lohmann Katja 
Published: December 2024

ABSTRACTPathogenic variants in theLRRK2gene are one of the most commonly identifiable monogenic causes of Parkinsońs disease (PD, PARK-LRRK2). This systematic MDSGene literature review comprehensively summarizes published demographic, clinical, and genetic findings related to potentially pathogenicLRRK2variants (https://www.mdsgene.org/). Recent insights on LRRK2’s kinase activity have been incorporated for pathogenicity scoring.Data on 7,885 individuals with 292 different variants were curated, including 3,296 patients with PD carrying 205 different potentially disease-causingLRRK2variants. The initial MDSGene review covered only 724 patients carrying 23 differentLRRK2variants. Missingness of phenotypic data in the literature was high, hampering the identification of detailed genotype-phenotype correlations. Notably, the median age at onset in the patients with available information was 56 years, with approximately one-third having PD onset <50 years. Tremor was the most frequently reported initial symptom and more frequent than reported in other dominantly inherited forms of PD. Of the 205 potentially disease-causing variants, 14 (6.8%) were classified as pathogenic, 8 (3.9%) as likely pathogenic, and the remaining 183 (89.3%) as variants of uncertain significance (VUS). The pathogenic p.G2019S variant was the most frequent pathogenic variant, followed by p.R1441G and p.R1441C, accounting for >80% of patients, with Tunisia, Spain, and Italy contributing about half of patients.This systematic review represents the largest database on PARK-LRRK2 to date and provides an important resource to improve precision medicine. Given their high frequency, a better interpretation of the pathogenicity of VUS is needed for selection and stratification of patients in clinical trials.
Lineage-associated Human Divergently-Paired Genes (DPGs) Exhibit Regulatory Characteristics and Evolutionary Trends
Authors: Duan Guangya , Zhang Sisi , Tang Bixia , Xiao Jingfa , Zhang Zhang , Cui Peng , Yu Jun , Zhao Wenming 
Published: December 2024

AbstractDivergently-paired genes (DPGs) represent one of the minimal co-transcriptional units (the rest include tandemly- and convergently-paired genes) of clustered genes; the former and the latter constitute greater than 10% and 75% of the total human genes, respectively. Our previous studies have shown that vertebrate DPGs are more conserved, both organizationally and functionally than invertebrates. Three critical questions remain to be addressed: (1) what are the conserved DPGs over vertebrate lineages, especially among mammals and primates? (2) being bidirectionally transcribed, to what extent do DPGs share their promoter sequences and how mechanistically and stringently are their co-expression regulated within the shared inter-TSS (transcription start site) sequence space? and (3) based on the recently released high-quality human genome assemblies, how do human-associated DPGs distribute over selected primate lineages and what are their possible functional consequences biologically? Our study begins by identifying 1399 human DPGs (12% of all human protein-coding genes), and presents findings from this analysis. First, 1136, 1118, 925, and 830 human DPGs are shared genetically with primates, mammals, avians, and fish, respectively. DPGs are not only functionally enriched toward direct protein-DNA interactions and cell cycle synchronization but also exhibit obvious lineage association, narrow in principle toward synchronization of certain core molecular mechanisms and cellular processes. Second, their inter-TSS distances and expression variables affect both co-expression strength and disparity between the two genes. Finally, our results based on a comparison among the primate DPGs reveal that the human-associated DPGs exhibit intensive diversification in co-expression, duplication, and definite involvement in neural development. Within humans, 55 and 357 DPGs are associated to the Chinese (YAO) and the European (CHM13) assemblies, respectively. Our results offer novel insights into comprehending the structure-function selection of gene clusters over evolutionary time scales, as well as a deeper understanding of the regulatory characteristics of co-expressed neighboring genes.
SegCSR: Weakly-Supervised Cortical Surfaces Reconstruction from Brain Ribbon Segmentations
Authors: Zheng Hao , Chen Xiaoyang , Li Hongming , Chen Tingting , Liang Peixian , Fan Yong 
Published: December 2024

AbstractDeep learning-based cortical surface reconstruction (CSR) methods heavily rely on pseudo ground truth (pGT) generated by conventional CSR pipelines as supervision, leading to dataset-specific challenges and lengthy training data preparation. We propose a new approach for reconstructing multiple cortical surfaces usingweak supervisionfrom brain MRI ribbon segmentations. Our approach initializes a midthickness surface and then deforms it inward and outward to form the inner (white matter) and outer (pial) cortical surfaces, respectively, by jointly learning diffeomorphic flows to align the surfaces with the boundaries of the cortical ribbon segmentation maps. Specifically, a boundary surface loss drives the initialization surface to the target inner and outer boundaries, and an inter-surface normal consistency loss regularizes the pial surface in challenging deep cortical sulci. Additional regularization terms are utilized to enforce surface smoothness and topology. Evaluated on two large-scale brain MRI datasets, our weakly-supervised method achieves comparable or superior CSR accuracy and regularity to existing supervised deep learning alternatives.
The antigenic landscape of N1 neuraminidase in human influenza A virus strains isolated between 2009 and 2020
Authors: Portela Catani João Paulo , Smet Anouk , Ysenbaert Tine , Amelinck Laura , Chan Yvonne , Tadmor Dan , Davidson Philip , Ray Satyajit , Camire Eric , Han Liqun , Zhang Jianxin , Cortés Guadalupe , Roebke Katherine , Baum Bianca , Hamberger John , Giel-Moloney Maryann , Saelens Xavier , Vogel Thorsten U. 
Published: December 2024

AbstractThe clinical burden caused by influenza can be mitigated by the prophylactic use of seasonal influenza vaccines. Their immunogen composition is revised biannually to optimally match the antigenic drift of the hemagglutinin of circulating influenza virus strains. Antibodies directed against the influenza neuraminidase also correlate with protection against influenza, yet the antigenic evolution of influenza neuraminidase remains underexplored. To evaluate the antigenic diversity of N1 neuraminidase, we generated a panel of immune sera directed against 17 N1 neuraminidases derived from human H1N1 strains that were isolated between 2009 and 2020 and determined its neuraminidase inhibition titers against a panel of 15 HxN1 viruses. The resulting neuraminidase inhibition pattern revealed two antigenic groups that circulated in this period. A machine learning method identified K432E and I321V as key determinants of N1 neuraminidase antigenicity.
Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein
Authors: Feng Ziqi , Huang Jiachen , Baboo Sabyasachi , Diedrich Jolene K. , Bangaru Sandhya , Paulson James C. , Yates John R. , Yuan Meng , Wilson Ian A. , Ward Andrew B. 
Published: December 2024

SummaryThe JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigated how mutations and a deletion in the KP.3.1.1 spike protein (S) affect ACE2 binding and antibody escape. Mass spectrometry revealed a new glycan site at residue N30 and altered glycoforms at neighboring N61. Cryo-EM structures showed that the N30 glycan and rearrangement of adjacent residues did not significantly change the overall spike structure, up-down ratio of the receptor-binding domains (RBDs), or ACE2 binding. Furthermore, a KP.3.1.1 S structure with hACE2 further confirmed an epistatic effect between F456L and Q493E on ACE2 binding. Our analysis shows SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.
Peristaltic pumping of viscoelastic fluid in a diverging channel: effects of magnetic field and surface roughness
Authors: Kumar Ashvani , Bhardwaj Anjali , Tripathi Dharmendra 
Published: December 2024

Purpose
Surface properties (smooth or roughness) play a critical role in controlling the wettability, surface area and other physical and chemical properties like fluid flow behaviour over the rough and smooth surfaces. It is reported that rough surfaces are offering more significant insights as compared to smooth surfaces. The purpose of this study is to examine the effects of surface roughness in the diverging channel on physiological fluid flows.

Design/methodology/approach
A mathematical formulation based on the conservation of mass and momentum equations is developed to derive exact solutions for the physical quantities under the assumption of low Reynolds numbers and long wavelengths, which are appropriate for biological transport scenarios.

Findings
The results reveal that an increase in surface roughness reduces axial velocity and volumetric flow rate while increasing pressure distribution and turbulence in skin friction.

Research limitations/implications
These findings offer valuable insights for biological flow analysis, highlighting the effects of surface roughness, non-uniformity of the channel and magnetic fields.

Practical implications
These findings are very much applicable for designing the pumping devices for transportation of the fluids in non-uniform channels.

Originality/value
This study examines the impact of surface roughness on the peristaltic pumping of viscoelastic (Jeffrey) fluids in diverging channels with transverse magnetic fields.
When to perform cloud seeding for maximum agricultural crop yields? A modeling study
Authors: Misra Arvind Kumar , Agrawal Gauri , Yadav Akash 
Published: December 2024

Purpose
Agricultural crops play a crucial role in food security and require commensurating environmental conditions, including adequate rainfall to ensure optimum growth. However, in the recent past, a reduction in the agriculture crop yield has been observed due to the deteriorating rainfall pattern. This paper aims to present a novel mathematical model to analyze the impact of rainfall on the growth of agriculture crops, as well as the impact of cloud seeding for promoting the rainfall, in case of less rainfall to ensure the optimum growth of agriculture crops.

Design/methodology/approach
The authors formulate a mathematical model assuming that the growth of agriculture crops wholly depends on rainfall. Also, agricultural crops can sustain and give optimal yields at a threshold of rainfall, after which rainfall negatively affects the growth rate of agriculture crops. Further, if the agriculture crops get insufficient rain to grow, the authors assume that cloud seeding agents are introduced in the regional atmosphere in proportion to the density of cloud droplets to increase rainfall.

Findings
This research shows that while cloud seeding agents boost crop yield, excessive rainfall poses significant risks on the yield. For any given value of π1 (conversion of cloud droplets into raindrops because of introduced cloud seeding agents), we have identified the threshold value of ϕ (introduction rate of cloud seeding agents into clouds) where crop yield can be maximized.

Research limitations/implications
This model highlights the delicate balance between rainfall and cloud seeding, offering policymakers valuable insights for maximizing agricultural crop yields.

Originality/value
This research provides strategies to mitigate crop loss due to unpredictable rainfall patterns.