bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative splicing plays key roles in response to stress across different stages of fighting in the fish Betta splendens
Authors: Vu Trieu-Duc , Oshima Kenshiro , Matsumura Kenya , Iwasaki Yuki , Chiu Ming-Tzu , Nikaido Masato , Okada Norihiro 
Published: May 2022

Abstract
Background
Aggression is an evolutionarily conserved behavior critical for animal survival. In the fish Betta splendens, across different stages of fighting interactions, fighting opponents suffer from various stressors, especially from the great demand for oxygen. Using RNA sequencing, we profiled differential alternative splicing (DAS) events in the brains of fish collected before fighting, during fighting, and after fighting to study the involvement of alternative splicing (AS) in the response to stress during the fight.

Results
We found that fighting interactions induced the greatest increase in AS in the ‘during-fighting’ fish, followed by that of the ‘after-fighting’ fish. Intron retention (IR) was the most enriched type among all the basic AS events. DAS genes were mainly associated with synapse assembly, ion transport, and regulation of protein secretion. We further observed that IR events significantly differentiated between winners and losers for 19 genes, which were associated with messenger RNA biogenesis, DNA repair, and transcription machinery. These genes share many common features, including shorter intron length and higher GC content.

Conclusions
This study is the first comprehensive view of AS induced by fighting interactions in a fish species across different stages of those interactions, especially with respect to IR events in winners and losers. Together, these findings facilitate future investigations into transcriptome complexity and AS regulation in response to stress under the context of aggression in vertebrates.
Maternal dietary methionine restriction alters the expression of energy metabolism genes in the duckling liver
Authors: Sécula Aurélie , Chapuis Hervé , Collin Anne , Bluy Lisa E. , Bonnet Agnès , Bodin Loys , Gress Laure , Cornuez Alexis , Martin Xavier , Bonnefont Cécile M. D. , Morisson Mireille 
Published: May 2022

AbstractBackgroundIn mammals, the nutritional status experienced during embryonic development shapes key metabolic pathways and influences the health and phenotype of the future individual, a phenomenon known as nutritional programming. In farmed birds as well, the quantity and quality of feed offered to the dam can impact the phenotype of the offspring. We have previously reported that a 38% reduction in the intake of the methyl donor methionine in the diet of 30 female ducks during the growing and laying periods - from 10 to 51 weeks of age - reduced the body weight of their 180 mule ducklings compared to that of 190 ducklings from 30 control females. The maternal dietary methionine restriction also altered the hepatic energy metabolism studied in 30 of their ducklings. Thus, their plasma glucose and triglyceride concentrations were higher while their plasma free fatty acid level was lower than those measured in the plasma of 30 ducklings from the control group. The objective of this new study was to better understand how maternal dietary methionine restriction affected the livers of their newly hatched male and female ducklings by investigating the hepatic expression levels of 100 genes primarily targeting energy metabolism, amino acid transport, oxidative stress, apoptotic activity and susceptibility to liver injury.ResultsSixteen of the genes studied were differentially expressed between the ducklings from the two groups. Maternal dietary methionine restriction affected the mRNA levels of genes involved in different pathways related to energy metabolism such as glycolysis, lipogenesis or electron transport. Moreover, the mRNA levels of the nuclear receptors PPARGC1B, PPARG and RXRA were also affected.ConclusionsOur results show that the 38% reduction in methionine intake in the diet of female ducks during the growing and egg-laying periods impacted the liver transcriptome of their offspring, which may explain the previously observed differences in their liver energy metabolism. These changes in mRNA levels, together with the observed phenotypic data, suggest an early modulation in the establishment of metabolic pathways.
Effects of different water conditions on the biomass, root morphology and aerenchyma formation in bermudagrass (Cynodon dactylon (L.) Pers)
Authors: Yuan Zhongxun , Ni Xilu , Chen Chunhua , Zhang Songlin , Chen Xuemei , Yang Zhihua , Li Changxiao 
Published: May 2022

Abstract
Background

The bermudagrass (Cynodon dactylon (L.) Pers) roots responded differently in terms of morphological and anatomical characteristics under diverse submergence conditions, and they developed aerenchyma under non-flooding condition. In order to understand these mechanisms, bermudagrass cuttings were used as experimental material to examine their biomass, root morphology, and aerenchyma formation under three different water treatments, including control (CK), shallow submergence (SS), and deep submergence (DS).

Results
The total root length, root volume, root surface area, and biomass of bermudagrass were largest in CK, followed by SS and DS. However, the average root diameter was greater in each of DS and SS than that in CK. Root aerenchyma formation was observed in CK, and submergence boosted the aerenchyma formation and the root cavity rate. Furthermore, our study found that the process of aerenchyma formation began with the increase of cell volume and cell separation to form a narrow space, and these cells gradually died to form matured aerenchyma cavity, which belongs to schizo-lysigenous aerenchyma. Meanwhile, typical biomarkers of programmed cell death were also observed.

Conclusion
Overall, these results suggested that submergence inhibited the accumulation of biomass and root growth, but facilitated aerenchyma formation by increasing root diameter.
The outcome of intravenous and inhalation anesthesia after pancreatic cancer resection: a retrospective study
Authors: Ren Jie , Wang Junli , Chen Jingwen , Ma Yue , Yang Yutong , Wei Ming , Wang Yu , Wang Liping 
Published: May 2022

Abstract
Background
Different types of anesthesia may affect cancer patient’s outcomes, we compared the overall survival (OS) and disease-free survival (DFS) of patients with pancreatic cancer under total intravenous and inhalation anesthesia.

Methods
The authors collected the electronic medical records of patients who had accepted at a pancreatectomy from January 1, 2010 to December 31, 2016. Patients respectively received total intravenous anesthesia (TIVA) or inhalational anesthesia (INHA). Stabilized inverse probability of treatment weighting (SIPTW)was used to minimize differences. Kaplan–Meier survival was established to analyze the influence of sort of anesthesia on disease-free and overall survival. We compare the effects of each sort of anesthesia on cancer recurrence or metastasis and all-cause mortality.

Results
A total of 463 patients who had undergone pancreatic cancer resection were collected in this study, of which 421 patients were available (TIVA group, n = 114 INHA group, n = 307). After SIPTW there were no significant differences between the two groups in disease-free survival (hazard ratio, 1.01, 95%CI, 0.78 to 1.29, P = 0.959) or overall survival (hazard ratio, 1.11, 95%CI, 0.87 to 1.42, P = 0.405).

Conclusions
In conclusion, the present study showed no significant difference in overall survival and disease-free survival between total intravenous anesthesia and volatile anesthesia.
Effects of head-elevated position on tracheal intubation using a McGrath MAC videolaryngoscope in patients with a simulated difficult airway: a prospective randomized crossover study
Authors: Chun Eun Hee , Chung Mi Hwa , Kim Jung Eun , Kim Kyung Mi , Lee Hye Sun , Son Jung Mo , Park Jiho , Jun Joo Hyun 
Published: May 2022

Abstract
Background
The head-elevated laryngoscopy position has been described to be optimal for intubation, particularly in obese patients and those with anticipated difficult airways. Horizontal alignment of the external auditory meatus and sternal notch (AM-S) can be used as endpoints for optimal positioning. Thus, we aligned the head-elevated position with the AM-S in the horizontal plane and evaluated its effect on laryngeal visualization and ease of intubation using a McGrath MAC videolaryngoscope in patients with a simulated difficult airway.

Methods
Sixty-four patients were included in this prospective, crossover, randomized controlled trial. A cervical collar was used to restrict neck movement and mouth opening. The head-elevated position was achieved by raising the back section of the operation room table and ensuring that the end point was horizontally aligned with the AM-S (table-ramp method). The laryngeal view was randomly assessed in both head-flat and head-elevated positions based on the percentage of glottic opening (POGO) score and modified Cormack–Lehane (MCL) grade. External laryngeal manipulation was not permitted when laryngeal visualization was scored. The trachea was intubated only once (in the second position). The ease of intubation was assessed based on the need for optimization maneuvers, intubation difficulty scale (IDS) scores and time to intubation.

Results
The mean table-ramp angle required to achieve the horizontal alignment of AM-S was 17.5 ± 4.1°. The mean POGO score improved significantly in the head-elevated position (59.4 ± 23.8%) when compared with the head-flat position (37.5 ± 24%) (P <  0.0001). MCL grade 1 or 2a was achieved in 56 (85.9%) and 28 (43.7%) of patients in the head-elevated and head-flat positions, respectively (P <  0.0001). Optimization maneuvers for intubation were required in 7 (21.9%) and 17 (53.1%) patients in the head-elevated and head-flat positions, respectively (P <  0.0001). The IDS scores and time to intubation did not differ significantly between the two positions.

Conclusion
In the head-elevated position, aligning the AM-S in the horizontal plane consistently improved laryngeal visualization without worsening the view when the McGrath MAC videolaryngoscope was used in patients with simulated difficult airways. It also improved the ease of intubation, which reduced the need for optimization maneuvers.

Trial registration
This trial was registered with www.clinicaltrials.gov, NCT04716218, on 20/01/2021.
A multistate competing risks framework for preconception prediction of pregnancy outcomes
Authors: Cook Kaitlyn , Perkins Neil J. , Schisterman Enrique , Haneuse Sebastien 
Published: May 2022

Abstract
Background
Preconception pregnancy risk profiles—characterizing the likelihood that a pregnancy attempt results in a full-term birth, preterm birth, clinical pregnancy loss, or failure to conceive—can provide critical information during the early stages of a pregnancy attempt, when obstetricians are best positioned to intervene to improve the chances of successful conception and full-term live birth. Yet the task of constructing and validating risk assessment tools for this earlier intervention window is complicated by several statistical features: the final outcome of the pregnancy attempt is multinomial in nature, and it summarizes the results of two intermediate stages, conception and gestation, whose outcomes are subject to competing risks, measured on different time scales, and governed by different biological processes. In light of this complexity, existing pregnancy risk assessment tools largely focus on predicting a single adverse pregnancy outcome, and make these predictions at some later, post-conception time point.

Methods
We reframe the individual pregnancy attempt as a multistate model comprised of two nested multinomial prediction tasks: one corresponding to conception and the other to the subsequent outcome of that pregnancy. We discuss the estimation of this model in the presence of multiple stages of outcome missingness and then introduce an inverse-probability-weighted Hypervolume Under the Manifold statistic to validate the resulting multivariate risk scores. Finally, we use data from the Effects of Aspirin in Gestation and Reproduction (EAGeR) trial to illustrate how this multistate competing risks framework might be utilized in practice to construct and validate a preconception pregnancy risk assessment tool.

Results
In the EAGeR study population, the resulting risk profiles are able to meaningfully discriminate between the four pregnancy attempt outcomes of interest and represent a significant improvement over classification by random chance.

Conclusions
As illustrated in our analysis of the EAGeR data, our proposed prediction framework expands the pregnancy risk assessment task in two key ways—by considering a broader array of pregnancy outcomes and by providing the predictions at an earlier, preconception intervention window—providing obstetricians and their patients with more information and opportunities to successfully guide pregnancy attempts.
Estimating risk ratio from any standard epidemiological design by doubling the cases
Authors: Ning Yilin , Lam Anastasia , Reilly Marie 
Published: May 2022

Abstract
Background
Despite the ease of interpretation and communication of a risk ratio (RR), and several other advantages in specific settings, the odds ratio (OR) is more commonly reported in epidemiological and clinical research. This is due to the familiarity of the logistic regression model for estimating adjusted ORs from data gathered in a cross-sectional, cohort or case-control design. The preservation of the OR (but not RR) in case-control samples has contributed to the perception that it is the only valid measure of relative risk from case-control samples. For cohort or cross-sectional data, a method known as ‘doubling-the-cases’ provides valid estimates of RR and an expression for a robust standard error has been derived, but is not available in statistical software packages.

Methods
In this paper, we first describe the doubling-of-cases approach in the cohort setting and then extend its application to case-control studies by incorporating sampling weights and deriving an expression for a robust standard error. The performance of the estimator is evaluated using simulated data, and its application illustrated in a study of neonatal jaundice. We provide an R package that implements the method for any standard design.

Results
Our work illustrates that the doubling-of-cases approach for estimating an adjusted RR from cross-sectional or cohort data can also yield valid RR estimates from case-control data. The approach is straightforward to apply, involving simple modification of the data followed by logistic regression analysis. The method performed well for case-control data from simulated cohorts with a range of prevalence rates. In the application to neonatal jaundice, the RR estimates were similar to those from relative risk regression, whereas the OR from naive logistic regression overestimated the RR despite the low prevalence of the outcome.

Conclusions
By providing an R package that estimates an adjusted RR from cohort, cross-sectional or case-control studies, we have enabled the method to be easily implemented with familiar software, so that investigators are not limited to reporting an OR and can examine the RR when it is of interest.
Prediction models for functional status in community dwelling older adults: a systematic review
Authors: Van Grootven Bastiaan , van Achterberg Theo 
Published: May 2022

Abstract
Background
Disability poses a burden for older persons, and is associated with poor outcomes and high societal costs. Prediction models could potentially identify persons who are at risk for disability. An up to date review of such models is missing.

Objective
To identify models developed for the prediction of functional status in community dwelling older persons.

Methods
A systematic review was performed including studies of older persons that developed and/or validated prediction models for the outcome functional status. Medline and EMBASE were searched, and reference lists and prospective citations were screened for additional references. Risk of bias was assessed using the PROBAST-tool. The performance of models was described and summarized, and the use of predictors was collated using the bag-of-words text mining procedure.

Results
Forty-three studies were included and reported 167 evaluations of prediction models. The median c-statistic values for the multivariable development models ranged between 0.65 and 0.76 (minimum = 0.58, maximum = 0.90), and were consistently higher than the values of the validation models for which median c-statistic values ranged between 0.6 and 0.68 (minimum = 0.50, maximum = 0.81). A total of 559 predictors were used in the models. The five predictors most frequently used were gait speed (n = 47), age (n = 38), cognition (n = 27), frailty (n = 24), and gender (n = 22).

Conclusions
No model can be recommended for implementation in practice. However, frailty models appear to be the most promising, because frailty components (e.g. gait speed) and frailty indexes demonstrated good to excellent predictive performance. However, the risk of study bias was high. Substantial improvements can be made in the methodology.
Key gene network related to primary ciliary dyskinesia in hippocampus of patients with Alzheimer’s disease revealed by weighted gene co-expression network analysis
Authors: Xia Pengcheng , Chen Jing , Bai Xiaohui , Li Ming , Wang Le , Lu Zhiming 
Published: May 2022

AbstractBackgroundAlzheimer’s disease (AD) is closely related to aging, showing an increasing incidence rate for years. As one of the main brain regions involved in AD, hippocampus has been extensively studied due to its association with many human diseases. However, little is known about its association with primary ciliary dyskinesia (PCD).Material and MethodsThe microarray data of hippocampus on AD were retrieved from the Gene Expression Omnibus (GEO) database to construct the co-expression network by weighted gene co-expression network analysis (WGCNA). The gene network modules associated with AD screened with the common genes were further annotated based on Gene Ontology (GO) database and enriched based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The protein-protein interaction (PPI) network was constructed based on STRING database to identify the hub genes in the network.ResultsGenes involved in PCD were identified in the hippocampus of AD patients. Functional analysis revealed that these genes were mainly enriched in ciliary tissue, ciliary assembly, axoneme assembly, ciliary movement, microtubule based process, microtubule based movement, organelle assembly, axoneme dynamin complex, cell projection tissue, and microtubule cytoskeleton tissue. A total of 20 central genes, e.g.,DYNLRB2, ZMYND10, DRC1, DNAH5, WDR16, TTC25,andARMC4were identified as hub genes related to PCD in hippocampus of AD patients.ConclusionOur study demonstrated that AD and PCD have common metabolic pathways. These common pathways provide novel evidence for further investigation of the pathophysiological mechanism and the hub genes suggest new therapeutic targets for the diagnosis and treatment of AD and PCD.SubjectsBioinformatics, Cell Biology, Molecular Biology, Neurology.
Cystatin SN promotes epithelial-mesenchymal transition and serves as a prognostic biomarker in lung adenocarcinoma
Authors: Yang Jian , Luo Gaomeng , Li Chang , Zhao Zhunlin , Ju Sheng , Li Qifan , Chen Zhike , Ding Cheng , Tong Xin , Zhao Jun 
Published: May 2022

Abstract
Background
Cystatins are a class of proteins that can inhibit cysteine protease and are widely distributed in human bodily fluids and secretions. Cystatin SN (CST1), a member of the CST superfamily, is abnormally expressed in a variety of tumors. However, its effect on the occurrence and development of lung adenocarcinoma (LUAD) remains unclear.

Methods
We obtained transcriptome analysis data of CST1 from The Cancer Genome Atlas (TCGA) and GSE31210 databases. The association of CST1 expression with prognosis, gene mutations and tumor immune microenvironment was analyzed using public databases. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed to investigate the potential mechanisms of CST1.

Results
In this study, we found that CST1 was highly expressed in lung adenocarcinoma and was associated with prognosis and tumor immune microenvironment. Genetic mutations of CST1 were shown to be related to disease-free survival (DFS) by using the c-BioPortal tool. Potential proteins binding to CST1 were identified by constructing a protein-protein interaction (PPI) network. Gene set enrichment analysis (GSEA) of CST1 revealed that CST1 was notably enriched in epithelial-mesenchymal transition (EMT). Cell experiments confirmed that overexpression of CST1 promoted lung adenocarcinoma cells migration and invasion, while knockdown of CST1 significantly inhibited lung adenocarcinoma cells migration and invasion.

Conclusions
Our comprehensive bioinformatics analyses revealed that CST1 may be a novel prognostic biomarker in LUAD. Experiments confirmed that CST1 promotes epithelial-mesenchymal transition in LUAD cells. These findings will help to better understand the distinct role of CST1 in LUAD.