bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvements in viral gene annotation using large language models and soft alignments
Authors: Harrigan William L. , Ferrell Barbra D. , Wommack K. Eric , Polson Shawn W. , Schreiber Zachary D. , Belcaid Mahdi 
Published: April 2024

Abstract
Background
The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known proteins when using alignment, k-mer, or profile-based homology search approaches. A novel methodology employing Large Language Models (LLMs) addresses this methodological challenge by annotating protein sequences based on embeddings.

Results
Central to our contribution is the soft alignment algorithm, drawing from traditional protein alignment but leveraging embedding similarity at the amino acid level to bypass the need for conventional scoring matrices. This method not only surpasses pooled embedding-based models in efficiency but also in interpretability, enabling users to easily trace homologous amino acids and delve deeper into the alignments. Far from being a black box, our approach provides transparent, BLAST-like alignment visualizations, combining traditional biological research with AI advancements to elevate protein annotation through embedding-based analysis while ensuring interpretability. Tests using the Virus Orthologous Groups and ViralZone protein databases indicated that the novel soft alignment approach recognized and annotated sequences that both blastp and pooling-based methods, which are commonly used for sequence annotation, failed to detect.

Conclusion
The embeddings approach shows the great potential of LLMs for enhancing protein sequence annotation, especially in viral genomics. These findings present a promising avenue for more efficient and accurate protein function inference in molecular biology.
Germline genetic regulation of the colorectal tumor immune microenvironment
Authors: Schmit Stephanie L. , Tsai Ya-Yu , Bonner Joseph D. , Sanz-Pamplona Rebeca , Joshi Amit D. , Ugai Tomotaka , Lindsey Sidney S. , Melas Marilena , McDonnell Kevin J. , Idos Gregory E. , Walker Christopher P. , Qu Chenxu , Kast W. Martin , Da Silva Diane M. , Glickman Jonathan N. , Chan Andrew T. , Giannakis Marios , Nowak Jonathan A. , Rennert Hedy S. , Robins Harlan S. , Ogino Shuji , Greenson Joel K. , Moreno Victor , Rennert Gad , Gruber Stephen B. 
Published: April 2024

Abstract
Objective
To evaluate the contribution of germline genetics to regulating the briskness and diversity of T cell responses in CRC, we conducted a genome-wide association study to examine the associations between germline genetic variation and quantitative measures of T cell landscapes in 2,876 colorectal tumors from participants in the Molecular Epidemiology of Colorectal Cancer Study (MECC).

Methods
Germline DNA samples were genotyped and imputed using genome-wide arrays. Tumor DNA samples were extracted from paraffin blocks, and T cell receptor clonality and abundance were quantified by immunoSEQ (Adaptive Biotechnologies, Seattle, WA). Tumor infiltrating lymphocytes per high powered field (TILs/hpf) were scored by a gastrointestinal pathologist. Regression models were used to evaluate the associations between each variant and the three T-cell features, adjusting for sex, age, genotyping platform, and global ancestry. Three independent datasets were used for replication.

Results
We identified a SNP (rs4918567) near RBM20 associated with clonality at a genome-wide significant threshold of 5 × 10− 8, with a consistent direction of association in both discovery and replication datasets. Expression quantitative trait (eQTL) analyses and in silico functional annotation for these loci provided insights into potential functional roles, including a statistically significant eQTL between the T allele at rs4918567 and higher expression of ADRA2A (P = 0.012) in healthy colon mucosa.

Conclusions
Our study suggests that germline genetic variation is associated with the quantity and diversity of adaptive immune responses in CRC. Further studies are warranted to replicate these findings in additional samples and to investigate functional genomic mechanisms.
Genome composition and GC content influence loci distribution in reduced representation genomic studies
Authors: Galià-Camps Carles , Pegueroles Cinta , Turon Xavier , Carreras Carlos , Pascual Marta 
Published: April 2024

Abstract
Background
Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored.

Results
Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected.

Conclusions
Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.
Circadian rhythm response and its effect on photosynthetic characteristics of the Lhcb family genes in tea plant
Authors: Hu Zhi-Hang , Zhang Nan , Qin Zhi-Yuan , Li Jing-Wen , Tao Jian-Ping , Yang Ni , Chen Yi , Kong Jie-Yu , Luo Wei , Chen Xuan , Li Xing-Hui , Xiong Ai-Sheng , Zhuang Jing 
Published: April 2024

Abstract
Background
The circadian clock, also known as the circadian rhythm, is responsible for predicting daily and seasonal changes in the environment, and adjusting various physiological and developmental processes to the appropriate times during plant growth and development. The circadian clock controls the expression of the Lhcb gene, which encodes the chlorophyll a/b binding protein. However, the roles of the Lhcb gene in tea plant remain unclear.

Results
In this study, a total of 16 CsLhcb genes were identified based on the tea plant genome, which were distributed on 8 chromosomes of the tea plant. The promoter regions of CsLhcb genes have a variety of cis-acting elements including hormonal, abiotic stress responses and light response elements. The CsLhcb family genes are involved in the light response process in tea plant. The photosynthetic parameter of tea leaves showed rhythmic changes during the two photoperiod periods (48 h). Stomata are basically open during the day and closed at night. Real-time quantitative PCR results showed that most of the CsLhcb family genes were highly expressed during the day, but were less expressed at night.

Conclusions
Results indicated that CsLhcb genes were involved in the circadian clock process of tea plant, it also provided potential references for further understanding of the function of CsLhcb gene family in tea plant.
In silico analysis of the wheat BBX gene family and identification of candidate genes for seed dormancy and germination
Authors: Cheng Xinran , Lei Shuying , Li Jin , Tian Bingbing , Li Chunxiu , Cao Jiajia , Lu Jie , Ma Chuanxi , Chang Cheng , Zhang Haiping 
Published: April 2024

Abstract
Background
B-box (BBX) proteins are a type of zinc finger proteins containing one or two B-box domains. They play important roles in development and diverse stress responses of plants, yet their roles in wheat remain unclear.

Results
In this study, 96 BBX genes were identified in the wheat genome and classified into five subfamilies. Subcellular localization prediction results showed that 68 TaBBXs were localized in the nucleus. Protein interaction prediction analysis indicated that interaction was one way that these proteins exerted their functions. Promoter analysis indicated that TaBBXs may play important roles in light signal, hormone, and stress responses. qRT-PCR analysis revealed that 14 TaBBXs were highly expressed in seeds compared with other tissues. These were probably involved in seed dormancy and germination, and their expression patterns were investigated during dormancy acquisition and release in the seeds of wheat varieties Jing 411 and Hongmangchun 21, showing significant differences in seed dormancy and germination phenotypes. Subcellular localization analysis confirmed that the three candidates TaBBX2-2 A, TaBBX4-2 A, and TaBBX11-2D were nuclear proteins. Transcriptional self-activation experiments further demonstrated that TaBBX4-2A was transcriptionally active, but TaBBX2-2A and TaBBX11-2D were not. Protein interaction analysis revealed that TaBBX2-2A, TaBBX4-2A, and TaBBX11-2D had no interaction with each other, while TaBBX2-2A and TaBBX11-2D interacted with each other, indicating that TaBBX4-2A may regulate seed dormancy and germination by transcriptional regulation, and TaBBX2-2A and TaBBX11-2D may regulate seed dormancy and germination by forming a homologous complex.

Conclusions
In this study, the wheat BBX gene family was identified and characterized at the genomic level by bioinformatics analysis. These observations provide a theoretical basis for future studies on the functions of BBXs in wheat and other species.
Influencing factors, gender differences and the decomposition of inequalities in cognitive function in Chinese older adults: a population-based cohort study
Authors: Yang Ciran , Mao Zongfu , Wu Shaotang , Yin Shicheng , Sun Yu , Cui Dan 
Published: April 2024

Abstract
Background
Evidence remains limited and inconsistent for assessing cognitive function in Chinese older adults (CFCOA) and inequalities in cognitive function in Chinese older adults (ICFCOA) and exploring their influencing factors and gender differences. This study aimed to identify influencing factors and inequality in CFCOA to empirically explore the existence and sources of gender differences in such inequality and analyse their heterogeneous effects.

Methods
Based on data from the China Health and Retirement Longitudinal Study (CHARLS) for three periods from 2011 to 2015, recentered influence function unconditional quantile regression (RIF-UQR) and recentered influence function ordinary least squares (RIF-OLS) regression were applied to assess influencing factors of CFCOA, while grouped treatment effect estimation, Oaxaca-Blinder decomposition, and propensity score matching (PSM) methods were conducted to identify gender differences in ICFCOA and influencing factors, respectively.

Results
The results showed heterogeneous effects of gender, age, low BMI, subjective health, smoking, education, social interactions, physical activity, and household registration on CFCOA. Additionally, on average, ICFCOA was about 19.2–36.0% higher among elderly females than among elderly males, mainly due to differences in characteristic effects and coefficient effects of factors such as marital status and education.

Conclusions
Different factors have heterogeneous and gender-differenced effects on CFCOA and ICFCOA, while the formation and exacerbation of ICFCOA were allied to marital status and education. Considering the severe ageing and the increasing incidence of cognitive decline, there is an urgent need for the government and society to adopt a comprehensive approach to practically work for promoting CFCOA and reducing ICFCOA.
Effects of Square Stepping Exercise on cognitive, physical, psychological, and group functioning in sedentary older adults: A center-based hybrid trial
Authors: Kawabata Masato , Gan Su Ren , Shen-Hsing Annabel Chen 
Published: April 2024

Abstract
Background
The Square Stepping Exercise (SSE) is an exercise training program that integrates physical exercise and cognitive elements and can be conducted in a group setting. The potential of SSE in delaying cognitive decline in older adults is promising. However, the coronavirus pandemic has made it more difficult for older adults worldwide to exercise together in person. To address this issue, this study conducted a wholistic evaluation of the effects of a center-based hybrid SSE trial on cognitive, physical, psychological, and group functioning in sedentary older adults.

Methods
A total of 93 older adults (19 men, 74 women) participated in the study. Fifty-eight participants (9 men, 49 women) completed center-based hybrid SSE sessions over 12 weeks under coronavirus pandemic circumstances, whereas other 35 participants in the control group maintained their current level of daily activities. Cognitive functions focused on executive functions assessed by the Stroop Color-Word Test (inhibition) and the Trail Marking Test (TMT) (set-shifting). Psychological and group functioning were assessed by the Subjective Vitality Scale and the Physical Activity Group Environment Questionnaire. Physical function was evaluated by measuring gait speeds. A repeated ANOVA was conducted on the measured variables separately for the intervention and control groups to focus on the change of participant’s performance over data collection points.

Results
Outcomes of the Stroop Color-Word Test and the TMT revealed that the hybrid SSE was highly effective in improving executive function. Stroop performance (correct trials) was significantly improved in the incongruent condition, as well as both TMT-A and -B over the intervention period in the intervention group. The hybrid SSE was also beneficial to improve physical (gait speed at usual pace and at the maximum pace) as well as psychological functioning (subjective vitality). Furthermore, SSE participants reported increased engagement with the SSE task, social communication, and increased bonding and closeness with their group members through the hybrid SSE.

Conclusions
In this study, hybrid SSE was found to be effective in enhancing cognitive, physical, psychological, and group functioning in sedentary older adults. The findings of this study are crucial to provide older adults with a safer and efficient option to exercise.
Guillain–Barre syndrome following scrub typhus: a case report and literature review
Authors: Hu Shijun , lin Zhichuan , Liu Tao , Huang Shixiong , Liang Hui 
Published: April 2024

Abstract
Background
Scrub typhus is an acute infectious disease caused by Orientia tsutsugamushi. Guillain–Barre syndrome (GBS) is an autoimmune-mediated peripheral neuropathy with a frequent history of prodromal infections, but GBS associated with scrub typhus is very rare.

Case presentation
We report a 51-year-old male patient who developed dysarthria and peripheral facial paralysis following the cure of scfrub typhus. CSF examination and electrophysiological findings suggested a diagnosis of GBS. After treatment with intravenous immunoglobulin, the patient’s neurological condition improved rapidly.

Conclusions
Scrub typhus infection is likely to be a potential predisposing factor in GBS, while scrub typhus-associated GBS has a favorable prognosis.
A population-based estimation of maternal mortality in Lagos State, Nigeria using the indirect sisterhood method
Authors: Wright Kikelomo Ololade , Fagbemi Temiloluwa , Omoera Victoria , Johnson Taiwo , Aderibigbe Adedayo Ayodele , Baruwa Basit , Oludara Folashade , Ogboye Olusegun , Imosemi Donald , Omololu Olufemi , Odugbemi Babatunde , Adeyemi Oluwatoni , Omosun Adenike , Akinola Ibironke , Akinyinka Modupe , Balogun Mobolanle , Abe John , Sadiku Bamidele , Banke-Thomas Aduragbemi , Fabamwo Adetokunbo O. 
Published: April 2024

Abstract
Background
Pregnancy and delivery deaths represent a risk to women, particularly those living in low- and middle-income countries (LMICs). This population-based survey was conducted to provide estimates of the maternal mortality ratio (MMR) in Lagos Nigeria.

Methods
A community-based, cross-sectional study was conducted in mapped Wards and Enumeration Areas (EA) of all Local Government Areas (LGAs) in Lagos, among 9,986 women of reproductive age (15–49 years) from April to August 2022 using a 2-stage cluster sampling technique. A semi-structured, pre-tested questionnaire adapted from nationally representative surveys was administered using REDCap by trained field assistants for data collection on socio-demographics, reproductive health, fertility, and maternal mortality. Data were analysed using SPSS and MMR was estimated using the indirect sisterhood method. Ethical approval was obtained from the Lagos State University Teaching Hospital Health Research and Ethics Committee.

Results
Most of the respondents (28.7%) were aged 25–29 years. Out of 546 deceased sisters reported, 120 (22%) died from maternal causes. Sisters of the deceased aged 20–24 reported almost half of the deaths (46.7%) as due to maternal causes, while those aged 45–49 reported the highest number of deceased sisters who died from other causes (90.2%). The total fertility rate (TFR) was calculated as 3.807, the Lifetime Risk (LTR) of maternal death was 0.0196 or 1-in-51, and the MMR was 430 per 100,000 [95% CI: 360–510].

Conclusion
Our findings show that the maternal mortality rate for Lagos remains unacceptable and has not changed significantly over time in actual terms. There is need to develop and intensify community-based intervention strategies, programs for private hospitals, monitor MMR trends, identify and contextually address barriers at all levels of maternal care.
The impact of gestational weight gain on fetal and neonatal outcomes: the Araraquara Cohort Study
Authors: Victor Audêncio , de França da Silva Teles Laísla , Aires Isabel Oliveira , de Carvalho Leticia Falcão , Luzia Liania A. , Artes Rinaldo , Rondó Patrícia H. 
Published: April 2024

Abstract
Background
Gestational weight gain (GWG) is an important indicator for monitoring maternal and fetal health. Objective: To evaluate the effect of GWG outside the recommendations of the Institute of Medicine (IOM) on fetal and neonatal outcomes.

Study design
A prospective cohort study with 1642 pregnant women selected from 2017 to 2023, with gestational age ≤ 18 weeks and followed until delivery in the city of Araraquara, Southeast Brazil. The relationship between IOM-recommended GWG and fetal outcomes (abdominal subcutaneous tissue thickness, arm and thigh subcutaneous tissue area and intrauterine growth restriction) and neonatal outcomes (percentage of fat mass, fat-free mass, birth weight and length, ponderal index, weight adequateness for gestational age by the Intergrowth curve, prematurity, and Apgar score) were investigated. Generalized Estimating Equations were used.

Results
GWG below the IOM recommendations was associated with increased risks of intrauterine growth restriction (IUGR) (aOR 1.61; 95% CI: 1.14–2.27), low birth weight (aOR 2.44; 95% CI: 1.85–3.21), and prematurity (aOR 2.35; 95% CI: 1.81–3.05), and lower chance of being Large for Gestational Age (LGA) (aOR 0.38; 95% CI: 0.28–0.54), with smaller arm subcutaneous tissue area (AST) (-7.99 g; 95% CI: -8.97 to -7.02), birth length (-0.76 cm; 95% CI: -1.03 to -0.49), and neonatal fat mass percentage (-0.85%; 95% CI: -1.12 to -0.58). Conversely, exceeding GWG guidelines increased the likelihood of LGA (aOR 1.53; 95% CI: 1.20–1.96), with lower 5th-minute Apgar score (aOR 0.42; 95% CI: 0.20–0.87), and increased birth weight (90.14 g; 95% CI: 53.30 to 126.99).

Conclusion
Adherence to GWG recommendations is crucial, with deviations negatively impacting fetal health. Effective weight control strategies are imperative.
A retrospective study of cumulative absolute reduction in axial length after photobiomodulation therapy
Authors: Qiu Kaikai , David Coveney , Li Ying , Lei Zhou , Tong Liyang , Lin Wen 
Published: April 2024

Abstract
Background
To assess the age and timeline distribution of ocular axial length shortening among myopic children treated with photobiomodulation therapy in the real world situations.

Methods
Retrospective study of photobiomodulation therapy in Chinese children aged 4 to 13 years old where axial length measurements were recorded and assessed to determine effectiveness at two age groups (4 ∼ 8 years old group and 9 ∼ 13 years old group). Data was collected from myopic children who received photobiomodulation therapy for 6 ∼ 12 months. Effectiveness of myopia control was defined as any follow-up axial length ≤ baseline axial length, confirming a reduction in axial length. Independent t-test was used to compare the effectiveness of the younger group and the older group with SPSS 22.0.

Results
342 myopic children were included with mean age 8.64 ± 2.20 years and baseline mean axial length of 24.41 ± 1.17 mm. There were 85.40%, 46.30%, 71.20% and 58.30% children with axial length shortening recorded at follow-up for 1 month, 3 months, 6 months and 12 months, respectively. With respect to the axial length shortened eyes, the mean axial length difference (standard deviation) was − 0.039 (0.11) mm, -0.032 (0.11) mm, -0.037 (0.12) mm, -0.028 (0.57) mm at 1, 3, 6, and 12-month follow-up, respectively. Greater AL shortening was observed among the older group who had longer baseline axial lengths than the younger group (P < 0.001).

Conclusions
Overall myopia control effectiveness using photobiomodulation therapy was shown to be age and time related, with the maximum absolute reduction in axial elongation being cumulative.