bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated genomic analysis revealed a dominant role of transcriptional regulation during the evolution of C4 photosynthesis in Flaveria species
Authors: Zhu Xin-Guang , Lyu Ming-Ju , Du Huilong , Yao Hongyan , zhang zhiguo , Chen Genyun , Huang Yuhui , Ni Xiaoxiang , Chen Faming , Zhao Yong-Yao , Tang Qiming , Miao Fenfen , Wang Yanjie , Zhao Yuhui , Lu Hongwei , Fang Lu , Gao Qiang , Qi Yiying , Zhang Qing , Zhang Jisen , Yang Tao , Cui Xuean , Liang Chengzhi , Lu Tiegang 
Published: April 2024

Abstract

C4 photosynthesis represents a remarkable example of convergent evolution of complex traits. In this study, we present an integrated genomic analysis of the genus Flaveria, which includes species at different evolutionary stages from C3 to C4 photosynthesis. The chromosome-scale genome sequences of five Flaveria species, representing C3, intermediate, and C4 types, reveal a gradual increase in genome size attributed to the expansion of transposable elements (TEs). Through a combination of gene phylogeny and transcript abundance analysis, we systematically identified genes encoding C4 enzymes and transporters. We further found that C4 species acquired additional copies of genes encoding three C4 enzymes through retrotranspositions. Moreover, we observed an increased abundance of ERF cis-regulatory elements and ERF transcriptional factors associated with the regulation of C4 genes in C4 species compared to non-C4 species. Notably, C4 genes exhibited elevated both RNA and protein levels but decreased protein-to-RNA ratios in C4 species. Additionally, codon usage patterns are conserved among the five Flaveria species. All these results suggest a predominant role of transcriptional regulation in the evolution of C4 photosynthesis. Our comprehensive dataset also provides valuable resources to study the evolution and regulatory mechanisms underlying C4 photosynthesis.
Impact of a Longitudinal Mentorship Intervention on the Documentation of Maternal Vital Signs in Blantyre District, Malawi
Authors: Mitchell Ashley , Mwale Nelson Ntemang'ombe , Simwinga Luseshelo , Jana Oveka , Rouse Miranda , Baltzell Kimberly , Blair Alden Hooper 
Published: April 2024

Abstract
Background
Staff shortages, insufficient training and support, and high patient caseloads limit maternal quality of care (QoC) and influence poor documentation of vital signs and labor progress in Malawi. Aware that this limits providers’ ability to anticipate or manage complications, we explored the impact of a longitudinal multipronged intervention on the documentation of maternal vital signs at key clinical times during childbirth to identify targeted opportunities for improvement.
Methods
We conducted a retrospective quantitative analysis of maternal charts from two primary health centres in Blantyre district in Malawi to assess for differences in the documentation of vital signs established in the WHO Safe Childbirth Checklist (SCC). The intervention consisted of short course training followed by 12 months of bedside mentorship. Bivariate and multivariate analyses assessed differences in the recording of each vital sign both pre- and post-intervention as well as according to availability of the appropriate device for that vital sign.
Results
A total of 271 maternal charts—96 from the pre-intervention period and 175 from the post-intervention period—were analyzed and found to have recorded between 2% and 52% of key maternal vital signs at the SCC-designated times. Post-intervention charts showed a statistically significant (p < 0.05) increase in the documentation of heart rate/pulse and blood pressure both upon admission and immediately postpartum, though not at the time of active childbirth. Additionally, while few maternal charts included all vital signs, there was a significant increase in the number of vital signs recorded between the pre- and post-intervention periods. A sub-analysis explored the impact of the availability of key medical devices on documentation during the post-intervention period and found that the recorded availability of thermometers and blood pressure cuffs were not significantly associated with whether temperature or blood pressure was recorded, respectively. However, at admission, significantly more vital signs were recorded when all a centre’s medical devices were consistently available.
Conclusion
A deeper exploration into which strategies are most effective for vital sign measurement and how it affects QoC indicators is warranted. Meanwhile, continuing and expanding training followed by supportive mentorship will be key to making sustainable maternal QoC improvement.
COVID-19 Preventive behaviors based on social cognitive integrative model among medical students
Authors: Mirzaie Arman , Gholamnia-Shirvani Zeinab , Jahani Mohammad- Ali , Nikbakht Hossein-Ali , Pakpour Amir 
Published: April 2024

Abstract
Objective: The COVID-19 outbreak in Iran prompted the investigation of preventive behaviors in vulnerable and key groups. This descriptive and analytical cross-sectional study aimed to determine COVID-19 prevention behaviors among medical students using an integrated social cognition model and identified influencing factors.
Results: The results of the study of 650 medical students with a mean age of 24.37±3.78 years showed that the total score of the integrated social cognition model was at a medium level (85.44±8.70). The constructs of attitude (16.14±2.66), subjective norms (5.33±1.30), perceived behavioral control (8.18±1.76), action self-efficacy (8.60±1.66), maintenance self-efficacy (12.29±2.25), intention (8.05±1.55), action planning (8.00±1.62), coping planning (8.08±1.62), and COVID‐19 preventive behaviors (10.78±1.99) were at a medium level. There was a good correlation between the constructs of the integrated model (r = 0.42-0.64, p<0.001). Students who were older, unmarried, had a mother or father with a university education, were nondormitory, were native, at the basic science level obtained higher scores for the model constructs (p<0.001). These findings should be considered to improve health education interventions and encourage COVID-19 preventive behaviors in students.
Childhood dairy consumption is associated with lower age of menarche in a national representative sample of US women
Authors: Vernarelli Jacqueline Andrea , Szollosy Sara 
Published: April 2024

Abstract

Background and aims:
Breast cancer is the most prevalent cancer and leader in cancer-related deaths among women with a variety of established risk factors.
Methods
Data from a nationally representative sample of 5,574 women who participated in the 2015–2018 NHANES was used to evaluate the correlation of childhood and adolescent dairy milk consumption and age of menarche. Reproductive history was asked of women > 12y. Data regarding dairy consumption between the ages of 5–12 was available for women > 20y. Survey regression models were used to calculate adjusted age of menarche for categories of dairy consumption after adjusting for relevant confounders.
Results
Women who reported never or rarely consuming dairy milk were significantly older at age of menarche compared to those who reported more frequent milk consumption. Age of menarche is affected by consumption of dairy milk in childhood even when controlling for factors which have been consider as possible affecting agents.
Conclusions
With the known link between the age of menarche and increased risk in breast cancer, guidance regarding childhood milk consumption should be developed.
Rhomboid intercostal and sub serratus plane block for post-operative analgesia after laparoscopic cholecystectomy: a randomized control study
Authors: Elhouty Mohamed Gad , Elawady Mostafa Sayed , Elbahrawy Khaled 
Published: April 2024

Abstract

Background: The "Rhomboid intercostal and subserratus plane" block (RISS) is a relatively new block technique that proved its efficacy in different thoracic procedures. Nonetheless, its role in laparoscopic cholecystectomy is undervaluated. We conducted this study to evaluate the effectiveness of RISS block in providing and maintaining postoperative analgesia in patients undergoing laparoscopic cholecystectomy.
Methodology: This prospective trial included 90 patients who were randomly divided into two groups: the RISS group that received the block (n = 45) and the control group that received no block (n = 45).
Results: Baseline demographic parameters and the operative time did not differ between the two groups (P ˃ 0.05). The RISS group had a significantly better intraoperative hemodynamic profile, manifested by the decreased heart rate and arterial pressure measurements compared to controls (P ˂ 0.05). Lower pain scores were encountered in the RISS group during the initial 12 hours after the operation (P ˂ 0.05). Additionally, The RISS led to significant prolongation in the time to the first rescue analgesia (729.11 vs. 23.89 minutes, respectively) and Postoperative fentanyl consumption was markedly decreased (45.11 vs. 153.24 mcg, respectively) compared to controls (both P ˂ 0.05). Subsequently, patient satisfaction showed better improvement when the RISS was used (P ˂ 0.05).
Conclusion: Bilateral RISS block is an effective option to provide post-operative analgesia for patients undergoing laparoscopic cholecystectomy. It should be performed as a part of a multimodal analgesia.
Transcriptome analysis of the common moss Bryum pseudotriquetrum grown under Antarctic field conditions
Authors: Otani Masahiro , Kitamura Haruki , Kudoh Sakae , Imura Satoshi , Nakano Masaru 
Published: April 2024

Abstract
Mosses are distributed all over the world including Antarctica. Although Antarctic mosses show active growth in a short summer season under harsh environments such as low temperature, drought and high levels of UV radiation, survival mechanisms for such multiple environmental stresses of Antarctic mosses have not yet been clarified. In the present study, transcriptome analyses were performed using one of the common mosses Bryum pseudotriquetrum grown under Antarctic field and artificial cultivation conditions. Totally 88,205 contigs were generated by de novo assembly, among which 1,377 and 435 genes were significantly up- and down-regulated, respectively, under Antarctic field conditions compared with artificial cultivation condition. Among the up-regulated genes, a number of lipid metabolism-related and oil body formation-related genes were identified. Consistent with these results, B. pseudotriquetrum grown under Antarctic field conditions contained large amounts of fatty acids, especially α-linolenic acid, linolenic acid and arachidonic acid. In addition, proportion of unsaturated fatty acids to the total fatty acids was also higher. Since lipid accumulation and unsaturation of fatty acids are generally important factors for acquisition of various environmental stress tolerance in plants, these intracellular physiological and metabolic changes may be responsible for survival of B. pseudotriquetrum under Antarctic harsh environments.
Optimal content of bio-fibers in structural ice
Authors: Fantilli Alessandro Pasquale , Frigo Barbara , Dehkordi Farmehr M. 
Published: April 2024

Abstract

The use of ice as structural material has two main concerns: the low strength and the brittle failure of the structures. With the aim of finding a solution to these problems, an experimental campaign, performed on fiber-reinforced ice (FRI) samples, made with plain water and bio-fibers, is presented in this paper. In total, 12 ice prisms were cast at -18°C with a different content of fibers, and then tested in three-point bending and uniaxial compression. Test results indicate that the presence of a reinforcement increases both flexural and compressive strength with respect to plain ice. Moreover, FRI is a tougher material, as multiple cracking and deflection hardening behavior can be observed in the flexural tests. However, the mechanical performances of plain ice are not always enhanced by the fiber-reinforcement. Therefore, an empirical model, capable of predicting the optimal content of bio-fibers, is also proposed.
A retrospective study of efficacy of tofacitinib combined with bDMARDs in the treatment of rheumatoid arthritis patients with inadequate response to bDMARDs
Authors: Chang Jie , Wang Gang 
Published: April 2024

Abstract

Introduction: Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by synovial inflammation, joint swelling, and pain involving multiple joints. While biologic disease-modifying antirheumatic drugs(bDMARDs) and targeted synthetic DMARDs(tsDMARDs) are popular treatments for RA, there is limited research on their combined use. This study examined a cohort of RA patients who demonstrated inadequate response to bDMARDs and subsequently initiated combination therapy with tofacitinib and bDMARDs, assessing both the efficacy and safety profile of this therapeutic approach.
Methods: In this study, we retrospectively collected the electronic medical records (EMR) of 56 adult patients with RA who were admitted to the Fourth Affiliated Hospital Zhejiang University School of Medicine between August 2018 to December 2022. All patients had received at least one bDMARD treatment for more than three months and still exhibited moderate to high disease activity. Tofacitinib 5mg bid was added to their original biological treatment in 28 cases, and other 28 cases switched to another bDMARD or tsDMARD as control group. Treatment was continued for 60weeks following the initiation of combination therapy. Changes in DAS28-CRP and ACR20 response rate at week 60 were collected and analyzed from baseline, while changes in C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) at weeks 4, 8, 12 followed by subsequent assessments every 12 weeks until the completion of the 60-week study period were also collected and analyzed.
Results: After 60 weeks of treatment, the DAS28-CRP score in combined treatment group decreased significantly from a baseline of 5.16±0.91 (3.86~8.21) to 2.64±0.85 (1.39~5.13), with remission achieved by 19 patients (67.9%) and low disease activity achieved by 5 patients (17.9%). The DAS28-CRP in the control group exhibited a decrease from 5.20±0.79 (3.88~7.21) at baseline to 3.23±1.27 (1.53~5.59). 10 patients (35.7%) achieved remission, while another 10 patients (35.7%) achieved low disease activity. The ACR20 response rate was 85.71% in the combined treatment group, whereas it was 71.43% in the control group. Additionally, both ESR and CRP levels decreased significantly during the course of treatment without any reported adverse events leading to discontinuation.
Conclusion: Our findings offer some evidence, supporting the effectiveness and safety of combining bDMARD with JAKi tofacitinib in RA patients who have an inadequate response to bDMARD monotherapy. This combination effectively manages disease activity while maintaining a relatively low and manageable incidence of adverse events.Further prospective randomized controlled trials with large sample sizes are anticipated to provide evidence-based medical support.
Diverse Database and Machine Learning Model to Narrow the Generalization Gap in RNA Structure Prediction
Authors: Rouskin Silvi , de Lajart Alberic , des Taillades Yves Martin , Kalicki Colin , Wightman Federico Fuchs , Aruda Justin , Salazar Dragui , Allan Matthew , L’Esperance-Kerckhoff Casper , Kashi Alex , Jossinet Fabrice 
Published: April 2024

Abstract

Understanding macromolecular structures of proteins and nucleic acids is critical for discerning their functions and biological roles. Advanced techniques—crystallography, NMR, and CryoEM—have facilitated the determination of over 180,000 protein structures, all cataloged in the Protein Data Bank (PDB). This comprehensive repository has been pivotal in developing deep learning algorithms for predicting protein structures directly from sequences. In contrast, RNA structure prediction has lagged, and suffers from a scarcity of structural data. Here, we present the secondary structure models of 1098 pri-miRNAs and 1456 human mRNA regions determined through chemical probing. We develop a novel deep learning architecture, inspired from the Evoformer model of Alphafold and traditional architectures for secondary structure prediction. This new model, eFold, was trained on our newly generated database and over 300,000 secondary structures across multiple sources. We benchmark eFold on two new test sets of long and diverse RNA structures and show that our dataset and new architecture contribute to increasing the prediction performance, compared to similar state-of-the-art methods. All together, our results reveal that merely expanding the database size is insufficient for generalization across families, whereas incorporating a greater diversity and complexity of RNAs structures allows for enhanced model performance.
Isolation, genetic and biological characterization of human adenovirus type 55 positive isolates from Wuhan, China
Authors: Xie Jing , Wang Yan , Li Huan , Tan Bingxiu , Yu Zhengying , Li Lizhong , Zhang Wei , Song Hongbin , Jia Leili 
Published: April 2024

Abstract

Background
Human adenovirus (HAdV) infection causes acute respiratory diseases in immunocompetent individuals worldwide. Infections by HAdV-55, one of the most important pathogen leading to respiratory tract infections, often develop into pneumonia and are frequently associated with outbreaks in military camps and schools.
Methods
We studied 186 HAdV-55-positive nasopharyngeal swab samples that were collected from patients with respiratory infection in Wuhan, China, from 2018 and 2019. Fifteen samples with high viral loads were selected for viral isolation and cultured with MRC-5 cells. These strains were then whole-genome sequenced to investigate their genetic characteristics by phylogenetic analyses. We then selected three HAdV-55 strains to quantify viral replication and further assessed the pathogenic characteristics of one strain in Syrian hamsters and BALB/c nude mice.
Results
HAdV-55-174 exhibited the highest replication ability in cultured cells compared to other strains, so this strain was selected for further investigation. Although both the hamsters and mice were not so susceptible to HAdV-55-174 infection, viral loads were detected in the lungs and tracheas of the murine models, and persistent HAdV-55-174 replication was only observed in BALB/c nude mice. Histopathological lesions, including a widened alveolar septum and inflammatory cell infiltration, were observed in the lungs and tracheas of HAdV-55-174 infected animals.
Conclusion
In summary, we isolated and characterized the HAdV-55 strains circulating in Wuhan from 2018 to 2019, which may be meaningful for further studies on HAdV-55 infection and pathogenesis.
Differential Multiplant Monopoly on a Freight Network
Authors: Friesz Terry 
Published: April 2024

Abstract

In this paper we give a mathematical statement of a differential spatial monopoly wherein transactions are facilitated by a freight transportation network that is based on an underlying graph. The monopolist has a presence at every node, and freight services are available for paths connecting stipulated origin-destination (OD) pairs. The monopolist produces a single homogeneous product that may be manufactured and inventoried, as well as sold, at every node. The dynamics take the form of ordinary differential equations that describe flow conservation. We present the necessary conditions of the monopolist's optimal control problem and observe their interpretation is that marginal revenue equals marginal cost at each node for each instant of continuous time. Existence of an optimal solution to the monopolist's problem is proven and a numerical example solved using two algorithms: one implemented in discrete time and the other in continuous time.
The Interplay of Race, Ethnicity, and Language in Caregiver Health: Insights from the National Social Life, Health, and Aging Project
Authors: Piedra Lissette M. , Zhong Selena , Howe Melissa J. K. , Compernolle Ellen , Iveniuk James 
Published: April 2024

Abstract

Background: Recent socio-demographic shifts in the United States have underscored the growing importance of informal caregiving and raised concerns about caregivers' health and well-being. This study aims to deepen our understanding of the health dimensions of caregivers, considering their diverse backgrounds.
Objective: To examine five key health dimensions (physical, cognitive, mental, social, and sexual health) of caregivers, and to identify potential disparities based on ethnoracial and linguistic differences.
Methods: Using data from the National Social Life, Health, and Aging Project (NSHAP), this study explores the interconnections among the specified health dimensions of caregivers and their ethnoracial (Black, Hispanic, White, and others) and linguistic (Spanish, English) backgrounds, in addition to their social networks (N=1,309). Regression analysis was employed to discern the patterns and associations.
Results: The findings indicate that White caregivers generally report better physical, cognitive, and social health compared to their Black and Hispanic counterparts, but exhibit less favorable outcomes in sexual health than Hispanic caregivers. Spanish-speaking caregivers, while having lower cognitive and self-rated mental health than English-speaking caregivers, show stronger social health and greater relationship satisfaction. Notably, these correlations persist irrespective of the size of social networks, pointing to intrinsic links with health outcomes.
Conclusion: The study underscores the necessity of a comprehensive health evaluation for caregivers, acknowledging the intricate interplay between their health and various socio-demographic factors. It advocates for the development of targeted policies and interventions that address the complex health needs of caregivers, with an emphasis on their ethnoracial and linguistic contexts and social environments.
Enhancing Mental Workload Classification in Neuroscience: Deep Learning Approaches
Authors: Cakar Serenay , Yavuz Fulya Gokalp 
Published: April 2024

Abstract
This study aims to classify mental workload levels from n-back cognitive data by employing a diverse set of deep learning approaches capable of accommodating both dense and sparse features. The n-back task paradigm provides rich temporal data, capturing information on working memory and cognitive demand from the same subjects over time across different n-back conditions. By integrating deep learning techniques that leverage both dense and sparse features, this research introduces novel perspectives tailored to the data structure of the n-back task. Our findings highlight the effectiveness of the extreme Deep Factorization Machine model with stratified 5-fold cross-validation. Compared to the baseline model for the 0- vs 1-back classification task, this approach achieved significant improvements: 67.50% in accuracy, 68.74% in sensitivity, 66.24% in specificity, and 68.48% in F1-Score among the models in which dense features are the combinations of hemodynamic measures and experimental variable, and subject is considered as a sparse feature. Additionally, employing Principal Component Analysis (PCA) resulted in significant enhancements in performance metrics compared to the baseline Logistic Regression model. Specifically, the utilization of PCA led to remarkable improvements of 53.03% in accuracy, 98.03% in sensitivity, 24.14% in specificity, and 70.37% in F1-Score, as observed in the classification of the 0- vs 1-back condition when using the xDeepFM model. These results underscore the utility of deep learning methods in accurately discerning mental workload levels from complex n-back cognitive science data, offering valuable insights into cognitive functioning and workload assessment.