bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-study analyses of microbial abundance using generalized common factor methods
Authors: Hayes Molly G. , Langille Morgan G. I. , Gu Hong 
Published: October 2023

Abstract
Background
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.

Results
We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.

Conclusions
By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.
Systematic dissection of genomic features determining the vast diversity of conotoxins
Authors: Zheng Jian-Wei , Lu Yang , Yang Yu-Feng , Huang Dan , Li Da-Wei , Wang Xiang , Gao Yang , Yang Wei-Dong , Guan Yuanfang , Li Hong-Ye 
Published: October 2023

Abstract
Background
Conus, a highly diverse species of venomous predators, has attracted significant attention in neuroscience and new drug development due to their rich collection of neuroactive peptides called conotoxins. Recent advancements in transcriptome, proteome, and genome analyses have facilitated the identification of conotoxins within Conus’ venom glands, providing insights into the genetic features and evolutionary patterns of conotoxin genes. However, the underlying mechanism behind the extraordinary hypervariability of conotoxins remains largely unknown.

Results
We analyzed the transcriptomes of 34 Conus species, examining various tissues such as the venom duct, venom bulb, and salivary gland, leading to the identification of conotoxin genes. Genetic variation analysis revealed that a subset of these genes (15.78% of the total) in Conus species underwent positive selection (Ka/Ks > 1, p < 0.01). Additionally, we reassembled and annotated the genome of C. betulinus, uncovering 221 conotoxin-encoding genes. These genes primarily consisted of three exons, with a significant portion showing high transcriptional activity in the venom ducts. Importantly, the flanking regions and adjacent introns of conotoxin genes exhibited a higher prevalence of transposon elements, suggesting their potential contribution to the extensive variability observed in conotoxins. Furthermore, we detected genome duplication in C. betulinus, which likely contributed to the expansion of conotoxin gene numbers. Interestingly, our study also provided evidence of introgression among Conus species, indicating that interspecies hybridization may have played a role in shaping the evolution of diverse conotoxin genes.

Conclusions
This study highlights the impact of adaptive evolution and introgressive hybridization on the genetic diversity of conotoxin genes and the evolution of Conus. We also propose a hypothesis suggesting that transposable elements might significantly contribute to the remarkable diversity observed in conotoxins. These findings not only enhance our understanding of peptide genetic diversity but also present a novel approach for peptide bioengineering.
Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant
Authors: Fu Yafen , Yi Langbo , Li Fu , Rao Jing , Yang Xiai , Wang Yanzhou , Liu Chan , Liu Touming , Zhu Siyuan 
Published: October 2023

Abstract
Background
MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the two main types of non-coding RNAs that play crucial roles in plant growth and development. However, their specific roles in the fiber growth of ramie plant (Boehmeria nivea L. Gaud) remain largely unknown.

Methods
In this study, we performed miRNA and whole-transcriptome sequencing of two stem bark sections exhibiting different fiber growth stages to determine the expression profiles of miRNAs, lncRNAs, and protein-encoding genes.

Results
Among the identified 378 miRNAs and 6,839 lncRNAs, 88 miRNAs and 1,288 lncRNAs exhibited differential expression. Bioinformatics analysis revealed that 29 and 228 differentially expressed protein-encoding genes were targeted by differentially expressed miRNAs and lncRNAs, respectively, constituting eight putative competing endogenous RNA networks. lncR00022274 exhibited downregulated expression in barks with growing fibers. It also had an antisense overlap with the MYB gene, BntWG10016451, whose overexpression drastically increased the xylem fiber number and secondary wall thickness of fibers in the stems of transgenic Arabidopsis, suggesting the potential association of lncR00022274-BntWG10016451 expression with fiber growth.

Conclusions
These findings provide insights into the roles of ncRNAs in the regulation of fiber growth in ramie, which can be used for the biotechnological improvement of its fiber yield and quality in the future.
Reduced glutathione and raffinose lengthens postharvest storage of cassava root tubers by improving antioxidant capacity and antibiosis
Authors: Fu Haitian , Zhao Ying , Huang Jianqi , Luo Yanchun , Wei Zusheng , Yu Benchi , Wen Feng 
Published: October 2023

AbstractCassava is an ideal food security crop in marginal and drought environment. However, the post-harvest storage of cassava is urgent problem to be resolved. In this study, the storage tolerant and non-tolerant cassava were screened by measuring the change of Peroxidase (POD), Superoxide dismutase (SOD), Catalase (CAT) and Malondialdehyde (MDA) in seven cultivars of cassava. Compared with other cultivars, the cultivar of SC14 showed the highest level of SOD, MDA and POD respectively at 0 day, 12 day and 9 day postharvest while exhibited lowest level of CAT at 0 day postharvest, indicating the strongest antioxidant capability and storage tolerance. In contrast, GR15231, termed as storage non-tolerance cultivars, showed lowest SOD and POD at 12 day and kept a relative high level of CAT at 12 day post-harvest. In addition, SC14 has higher level of starch and dry substance than GR15231. Mass spectrum was performed for SC14 and GR15231 to explore the key metabolites regulating the storage tolerance of cassava. The results showed that the expression of glutathione (reduced) and raffinose was significantly decreased at 12 day post-harvest both in tolerant SC14 and non-tolerant GR15231. Compared with GR15231, SC14 showed higher level of raffinose both at 0 and 12 day post-harvest, indicating that raffinose may be the potential metabolites protecting SC14 cultivar from deterioration post-harvest. Additionally, raffinose ratio of SC14a/SC14b was five times less than that of GR15231a/GR15231b, reflecting the slower degradation of raffinose in SC14 cultivar compared with GR15231 cultivar. In conclusion, the antioxidant microenvironment induced by reduced glutathione and higher level of raffinose in SC14 cultivar might be the promising metabolites to improve its antioxidant capacity and antibiosis and thus maintained the quality of Cassava root tubers.
Effects of PmaIAA27 and PmaARF15 genes on drought stress tolerance in pinus massoniana
Authors: Li Liangliang , Li Yan , Quan Wenxuan , Ding Guijie 
Published: October 2023

Abstract
Background
Auxin plays an important role in plant resistance to abiotic stress. The modulation of gene expression by Auxin response factors (ARFs) and the inhibition of auxin/indole-3-acetic acid (Aux/IAA) proteins play crucial regulatory roles in plant auxin signal transduction. However, whether the stress resistance of Masson pine (Pinus massoniana), as a representative pioneer species, is related to Aux/IAA and ARF genes has not been thoroughly studied and explored.

Results
The present study provides preliminary evidence for the regulatory role of the PmaIAA27 gene in abiotic stress response in Masson pine. We investigated the effects of drought and hormone treatments on Masson pine by examining the expression patterns of PmaIAA27 and PmaARF15 genes. Subsequently, we conducted gene cloning, functional testing using transgenic tobacco, and explored gene interactions. Exogenous auxin irrigation significantly downregulated the expression of PmaIAA27 while upregulating PmaARF15 in Masson pine seedlings. Moreover, transgenic tobacco with the PmaIAA27 gene exhibited a significant decrease in auxin content compared to control plants, accompanied by an increase in proline content - a known indicator of plant drought resistance. These findings suggest that overexpression of the PmaIAA27 gene may enhance drought resistance in Masson pine. To further investigate the interaction between PmaIAA27 and PmaARF15 genes, we performed bioinformatics analysis and yeast two-hybrid experiments which revealed interactions between PB1 structural region of PmaARF15 and PmaIAA27.

Conclusion
The present study provides new insights into the regulatory functions of Aux/IAA and ARF genes in Masson pine. Overexpression of PmaIAA gene may have negative effects on the growth of Masson pine, but may improve the drought resistance. Therefore, this study has great application prospects.
Association of infraclavicular axillary vein diameter and collapsibility index with general anesthesia-induced hypotension in elderly patients undergoing gastrointestinal surgery: an observational study
Authors: Chen Huijuan , Zhang Xianlong , Wang Lei , Zheng Cuijuan , Cai Shenquan , Cheng Wei 
Published: October 2023

Abstract
Background
The collapse index of inferior Vena Cava (IVC) and its diameter are important predictive tools for fluid responsiveness in patients, especially critically ones. The collapsibility of infraclavicular axillary vein (AXV) can be used as an alternative to the collapsibility of IVC (IVC-CI) to assess the patient’s blood volume.

Methods
A total of 188 elderly patients aged between 65 and 85 years were recruited for gastrointestinal surgery under general anesthesia. Ultrasound measurements AXV and IVC were performed before induction of general anesthesia. Patients were grouped in accordance to the hypotension after induction. ROC curves were used to analyze the predictive value of ultrasound measurements of AXV and IVC for hypotension after induction of anesthesia. Pearson linear correlation was used to assess the correlation of ultrasound measurements and decrease in mean arterial blood pressure (MAP).

Results
The maximum diameter of AXV(dAXVmax) and the maximum diameter of IVC (dIVCmax) were not related to the percentage decrease in MAP; the collapsibility of AXV (AXV-CI) and IVC-CI were positively correlated with MAP changes (correlation coefficients:0.475, 0.577, respectively, p < 0.001). The areas under the curve (AUC) was 0.824 (0.759–0.889) for AXV-CI, and 0.874 (0.820–0.928) for IVC-CI. The optimal threshold for AXV-CI was 31.25% (sensitivity 71.7%, specificity 90.1%), while for IVC-CI was 36.60% (sensitivity 85.9%, specificity 79.0%). Hypotension and down-regulation of MAP during induction can be accurately predicted by AXV-Cl after correction for confounding variables.

Conclusion
Infraclavicular axillary vein diameter has no significant correlation with postanesthesia hypotension, whereas AXV-CI may predict postanesthesia hypotension during gastrointestinal surgery of the elderly.

Trial registration
This study was registered in the Clinical Trial Registry of China on 05/06/2022 (ChiCTR2200060596).
Raring to go? A cross-sectional survey of student paramedics on how well they perceive their UK pre-registration course to be preparing them to manage suspected seizures
Authors: Noble Adam J. , Lees Carolyn , Hughes Kay , Almond Lucy , Ibrahim Hesham , Broadbent Cerys , Dixon Pete , Marson Anthony G. 
Published: October 2023

Abstract
Background
Paramedics convey a high proportion of seizure patients with no clinical need to emergency departments (EDs). In a landmark study, only 27% of UK paramedics reported being “Very…”/ “Extremely confident” making seizure conveyance decisions. Improved pre-registration education on seizures for paramedics is proposed. Clarity is needed on its potential given recent changes to how UK paramedics train (namely, degree, rather than brief vocational course). This study sought to describe UK student paramedics’ perceived readiness to manage seizures and educational needs; compare this to what they report for other presentations; and, explore subgroup differences.

Methods
Six hundred thirty-eight students, in year 2 or beyond of their pre-registration programme completed a cross-sectional survey. They rated perceived confidence, knowledge, ability to care for, and educational needs for seizures, breathing problems and, headache. Primary measure was conveyance decision confidence.

Results
For seizures, 45.3% (95% CI 41.4–49.2) said they were “Very…”/“Extremely confident” to make conveyance decisions. This was similar to breathing problems, but higher than for headache (25.9%, 95% CI 22.6–29.5). Two hundred and thirty-nine participants (37.9%, 95% CI 34.1–41.8) said more seizure education was required – lower than for headache, but higher than for breathing problems. Subgroup differences included students on university-based programmes reporting more confidence for conveyance decisions than those completing degree level apprenticeships.

Conclusions
Student paramedics report relatively high perceived readiness for managing seizures. Magnitude of benefit from enhancements to pre-registration education may be more limited than anticipated. Additional factors need attention if a sizeable reduction to unnecessary conveyances for seizures is to happen.
Non-alcoholic fatty liver disease and socioeconomic determinants in an Iranian cohort study
Authors: Sadeghianpour Zahra , Cheraghian Bahman , Farshchi Hamid Reza , Asadi-Lari Mohsen 
Published: October 2023

Abstract
Background
Non-alcoholic fatty liver disease (NAFLD) is widespread worldwide. On the other hand, social inequality and socioeconomic status (SES) can affect all aspects of health. Therefore, this study aimed to investigate the relationship between SES indicators and NAFLD.

Methods
This was a cross-sectional study using data from the registration phase of the Hoveyzeh Cohort Study, which included 10,009 individuals aged 35–70 years from May 2016 to August 2018. Fatty liver disease was determined based on Fatty Liver Index (FLI). The crude and adjusted odds ratios were calculated by logistic regression analysis to estimate associations between the fatty liver index and SES after controlling the potential confounders.

Results
According to the FLI index, there were 2,006 people with fatty liver (28%) and 5,246 people without fatty liver (72%). Several 4496 people (62%) were women. The chi-square test showed significant relationships between the educational level and skill level (P < 0.001), the wealth index (P < 0.001), and Townsend Index (P < 0.001) with fatty liver index. In multivariable analysis, after adjustment for age, sex, physical activity, smoking, type of residence, calorie intake, dyslipidemia, skill level, and diabetes, the wealth index (p < 0.001) was positively associated with the fatty liver index. Besides, a reverse and significant association was seen between the Townsend index and the fatty liver index(p < 0.001). In contrast, no significant associations were seen between gender and educational level with the fatty liver index.

Conclusions
A more vulnerable SES is associated with NAFLD. Fatty liver index and socioeconomic indicators can be powerful monitoring tools to monitor health differences in diagnosing NAFLD.
Spanish version of the ICIQ-Bowel questionnaire among colorectal cancer patients: construct and criterion validity
Authors: Sacomori Cinara , Lorca Luz Alejandra , Martinez-Mardones Mónica , Pizarro-Hinojosa Marta Natalia , Rebolledo-Diaz Gonzalo Sebastián , Vivallos-González Jessica Andrea 
Published: October 2023

Abstract
Purpose
Bowel complaints are very common among patients with colorectal cancer. However, the most used questionnaires for colorectal cancer survivors do not comprehensively comprise bowel symptoms. This study aimed to examine construct and criterion validity, as well as internal consistency, of the Chilean Version of the International Consultation on Incontinence Questionnaire Bowel Module (ICIQ-B) among people with colorectal cancer.

Methods
Cross-sectional, validation study performed with 106 colorectal cancer patients from Hospital del Salvador, Chile. Bowel function was assessed with the ICIQ-B. Construct validity was assessed with confirmatory factor analysis and hypothesis testing. Specific items of a quality-of-life questionnaire (EORTC QLQ-CR29) were used to correlate with similar ICIQ-B items for criterion validity. For internal consistency, Cronbach’s alpha was computed.

Results
For construct validity, the confirmatory factor analysis showed that the three factors model did not fit our data. Meanwhile, hypothesis testing favored the construct validity of the instrument, considering that rectal cancer patients showed worse bowel pattern (p = 0.001), bowel control (p = 0.001) and quality of life (p < 0.001) scores compared to colon cancer patients. In addition, those patients assessed before surgery also presented worse scores bowel control (p = 0.023) and quality of life (p = 0.009) compared to post-surgical patients. Regarding criterion validity, the ICIQ-B items showed a significant correlation with similar QLQ-CR29 items. The internal reliability of the instrument was good (Cronbach’s α = 0.909).

Conclusion
Considering that this questionnaire appraises bowel function in more depth, it is recommended for use in clinical practice and research with colorectal cancer patients.
Classification of health needs: a cluster analysis of older adults in urban areas
Authors: Yang Liu , Zhou Quan , Wang Congzhi , Zhang Dongmei , Yuan Ting , Li Xiaoping , Lei Yunxiao , Zhang Lin 
Published: October 2023

AbstractBackgroundIn this study, a cross-sectional survey was used to understand and analyze the health status and health needs of the elderly in the community. The cluster analysis method was used to explore the relationship between health needs items and investigate the commonness among health demand items, to provide a reference for the development of health management of the elderly with chronic diseases.MethodsWe used convenience sampling to recruit the participants (aged 60 and above) from four urban community centers in Jinzhou City, Liaoning Province, China, in this study. This study uses the Medical Outcomes Study(MOS)36-Item Short-Form Health Survey. The self-designed questionnaire includes sociodemographic characteristics, chronic diseases, physical examination conditions, illness in the past two weeks, and a health needs questionnaire. SPSS 18.0 was used for data entry and analysis. Data analysis methods included descriptive statistical analysis, t-test, one-way analysis, cluster analysis, and linear multiple regression analysis.ResultsThe rate of health needs among the elderly in the community for various health services is 1.3–69.7%, of which the top three are: regular physical examination (69.7%), day Care Center (67.7%), the establishment of a Medical Alert Systems (66.1%). The health needs of the elderly in the community are divided into three categories: basic needs (24 items), health education (13 items), and first aid (2 items). The regression analysis found that the influencing factors of health status were age, revenue and expenditure, medical expenses, health education, basic needs, and first aid.ConclusionsThe community should strengthen the management of chronic diseases of the elderly and the publicity and education of related knowledge, and provide complementary health care services according to the health needs of the elderly, improve the health of the elderly, and improve the quality of life of the elderly.
The influence of Tai Chi exercise on the subjective well-being in the aged: the mediating role of physical fitness and cognitive function
Authors: Wang Heng , Liu Yangyang , Pei Zhengguo , Liang Jiafeng , Ding Xiaosheng 
Published: October 2023

AbstractThis study investigated the effects of Tai Chi exercise on subjective well-being in the aged. The participants were randomly assigned to an experimental group or a control group. The experimental group received 12-week Tai Chi exercise while the control group maintain their original living habits. The participants’ subjective well-being, physical fitness, self-control, and executive function were measured at baseline and after 12 weeks of Tai Chi exercise. Results: (1) Tai Chi exercise can positively affect the subjective well-being of the aged (F(1,78) = 37.699, p < 0.001); (2) Tai Chi exercise could affect the subjective well-being in the aged through the independent intermediary of physical fitness (95% CI=[0.115, 0.485]) and self-control (95% CI=[0.109, 0.433]); (3) Tai Chi exercise could indirectly affect the subjective well-being in the aged through the chain mediation of executive function and self-control (95% CI=[0.009, 0.104]). This study provides valuable insights into the potential benefits of Tai Chi exercise for subjective well-being in the aged.
The efficacy and safety of remdesivir alone and in combination with other drugs for the treatment of COVID-19: a systematic review and meta-analysis
Authors: Chen Chuizhe , Fang Junde , Chen Shu , Rajaofera Mamy Jayne Nelly , Li Xuemiao , Wang Bo , Xia Qianfeng 
Published: October 2023

Abstract
Background
Remdesivir is considered to be a specific drug for treating coronavirus disease 2019. This systematic review aims to evaluate the clinical efficacy and risk of remdesivir alone and in combination with other drugs.

Research design and methods
The PubMed, Embase, SCIE, Cochrane Library, and American Clinical trial Center databases were searched up to 1 April 2022 to identify. Randomized controlled trials (RCTs) and observational studies comparing the efficacy of remdesivir monotherapy and combination therapy with that of control drugs.

Results
Ten RCTs and 32 observational studies were included in the analysis. Regarding the primary outcome, remdesivir use reduced mortality in patients with severe COVID-19 (RR = 0.57, 95% CI (0.48,0.68)) and shortened the time to clinical improvement (MD = -2.51, 95% CI (-2.75, -2.28)). Regarding other clinical outcomes, remdesivir use was associated with improved clinical status (RR = 1.08, 95%CI (1.01, 1.17)). Regarding safety outcomes, remdesivir use did not cause liver or kidney damage (RR = 0.87, 95%CI (0.68, 1.11)) (RR = 0.88, 95%CI (0.70,1.10)). Compared with remdesivir alone, remdesivir combined with other drugs (e.g., steroids, favipiravir, and convalescent plasma) had no effect on mortality.

Conclusion
The use of remdesivir can help to reduce the mortality of patients with severe COVID-19 and shorten the time to clinical improvement. There was no benefit of remdesivir combination therapy for other clinical outcomes.

Trial registration
PROSPERO registration number: CRD42022322859.