bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel genetic variants data for adaptation to hypoxia in native chickens
Authors: Moradi Atieh , Kharrati-Koopaee Hamed , Fardi Morteza , Farahmandzadeh Mehdi , Nowroozi Fatemeh 
Published: September 2023

Abstract
Objective
The genomic response and the role of genetic variants in hypoxia condition are always interesting issues about adaption pathways at genomic level. Herein, we carried out a comparative genomic study between highland and lowland native chickens, in order to identify the adaptive variants in hypoxia condition. We generated more than 20 million genetic variants in highland and lowland chickens. Finally, 3877 SNVs including the mtDNA ones, were discovered as novel adaptive genetic variants. The generated data set can provide new insight about mechanism of adaptation to hypoxia at genomic level.

Data description
To investigate the role of genetic variants in adaptation to hypoxia, 10 whole-genome sequencing data sets associated to highland and lowland native chickens were provided. DNA was extracted by salting-out protocol. Paired-end 125 bp short reads were sequenced by Illumina Hiseq 2000. Variants calling of highland and lowland native chickens were performed by fix ploidy algorithm in CLC Genomic Workbench. Total genetic variants of highland chickens were compared to lowland chickens in order to identify the differential genetic variants (DGVs) between highland and lowland chickens. In this way, 3877 novel SNVs (VCF format) including the mtDNA ones, were deposited at EBI database (https://identifiers.org/ena.embl:ERZ491574) for the first time.
Restrictive versus conventional ward fluid therapy in non-cardiac surgery patients and the effect on postoperative complications: a meta-analysis
Authors: Bosboom Joachim J. , Wijnberge Marije , Geerts Bart F. , Kerstens Martijn , Mythen Michael G. , Vlaar Alexander P. J. , Hollmann Markus W. , Veelo Denise P. 
Published: September 2023

Abstract
Background
Diligent fluid management is an instrumental part of Enhanced Recovery After Surgery. However, the effect of a ward regimen to limit intravenous fluid administration on outcome remains unclear. We performed a meta-analysis investigating the effect of a restrictive versus a conventional fluid regimen on complications in patients after non-cardiac surgery in the postoperative period on the clinical ward.

Study design
We performed a systematic search in MEDLINE, Embase, Cochrane Library, and CINAHL databases, from the start of indexing until June 2022, with constraints for English language and adult human study participants. Data were combined using classic methods of meta-analyses and were expressed as weighted pooled risk ratio (RR) or odds ratio (OR) with 95% confidence interval (CI). Quality assessment and risk of bias analyses was performed according to PRISMA guidelines.

Results
Seven records, three randomized controlled trials, and four non-randomized studies were included with a total of 883 patients. A restrictive fluid regimen was associated with a reduction in overall complication rate in the RCTs (RR 0.46, 95% CI 0.23 to 0.95; P < .03; I2 = 35%). This reduction in overall complication rate was not consistent in the non-randomized studies (RR 0.74, 95% CI 0.53 to 1.03; P 0.07; I2 = 45%). No significant association was found for mortality using a restrictive fluid regimen (RCTs OR 0.51, 95% CI 0.05 to 4.90; P = 0.56; I2 = 0%, non-randomized studies OR 0.30, 95% CI 0.06 to 1.46; P = 0.14; I2 = 0%). A restrictive fluid regimen is significantly associated with a reduction in postoperative length of stay in the non-randomized studies (MD − 1.81 days, 95% CI − 3.27 to − 0.35; P = 0.01; I2 = 0%) but not in the RCTs (MD 0.60 days, 95% CI − 0.75 to 1.95; P = 0.38). Risk of bias was moderate to high. Methodological quality was very low to moderate.

Conclusion
This meta-analysis suggests restrictive fluid therapy on the ward may be associated with an effect on postoperative complication rate. However, the quality of evidence was moderate to low, the sample size was small, and the data came from both RCTs and non-randomized studies.
Development and validation of a competitive risk model in patients with rectal cancer: based on SEER database
Authors: Hu Ruobing , Li Xiuling , Zhou Xiaomin , Ding Songze 
Published: September 2023

Abstract
Background
Rectal cancer is one of the most common malignancies. To predict the specific mortality risk of rectal cancer patients, we constructed a predictive nomogram based on a competing risk model.

Methods
The information on rectal cancer patients was extracted from the SEER database. Traditional survival analysis and specific death analysis were performed separately on the data.

Results
The present study included 23,680 patients, with 16,580 in the training set and 7100 in the validation set. The specific mortality rate calculated by the competing risk model was lower than that of the traditional survival analysis. Age, Marriage, Race, Sex, ICD-O-3Hist/Behav, Grade, AJCC stage, T stage, N stage, Surgery, Examined LN, RX SUMM-SURG OTH, Chemotherapy, CEA, Deposits, Regional nodes positive, Brain, Bone, Liver, Lung, Tumor size, and Malignant were independent influencing factors of specific death. The overall C statistic of the model in the training set was 0.821 (Se = 0.001), and the areas under the ROC curve for cancer-specific survival (CSS) at 1, 3, and 5 years were 0.842, 0.830, and 0.812, respectively. The overall C statistic of the model in the validation set was 0.829 (Se = 0.002), and the areas under the ROC curve for CSS at 1, 3, and 5 years were 0.851, 0.836, and 0.813, respectively.

Conclusions
The predictive nomogram based on a competing risk model for time-specific mortality in patients with rectal cancer has very desirable accuracy. Thus, the application of the predictive nomogram in clinical practice can help physicians make clinical decisions and follow-up strategies.
CYFIP2 serves as a prognostic biomarker and correlates with tumor immune microenvironment in human cancers
Authors: Peng Qiliang , Ren Bixin , Xin Kedao , Liu Weihui , Alam Md Shahin , Yang Yinyin , Gu Xuhao , Zhu Yaqun , Tian Ye 
Published: September 2023

Abstract
Background
The mechanisms whereby CYFIP2 acts in tumor development and drives immune infiltration have been poorly explored. Thus, this study aimed to identifying the role of CYFIP2 in tumors and immune response.

Methods
In this study, we first explored expression patterns, diagnostic role and prognostic value of CYFIP2 in cancers, particularly in lung adenocarcinoma (LUAD). Then, we performed functional enrichment, genetic alterations, DNA methylation analysis, and immune cell infiltration analysis of CYFIP2 to uncover its potential mechanisms involved in immune microenvironment.

Results
We found that CYFIP2 significantly differentially expressed in different tumors including LUAD compared with normal tissues. Furthermore, CYFIP2 was found to be significantly correlated with clinical parameters in LUAD. According to the diagnostic and survival analysis, CYFIP2 may be employed as a potential diagnostic and prognostic biomarker. Moreover, genetic alterations revealed that mutation of CYFIP2 was the main types of alterations in different cancers. DNA methylation analysis indicated that CYFIP2 mRNA expression correlated with hypomethylation. Afterwards, functional enrichment analysis uncovered that CYFIP2 was involved in tumor-associated and immune-related pathways. Immune infiltration analysis indicated that CYFIP2 was significantly correlated with immune cells infiltration. In particular, CYFIP2 was strongly linked with immune microenvironment scores. Additionally, CYFIP2 exhibited a significant relationship with immune regulators and immune-related genes including chemokines, chemokines receptors, and MHC genes.

Conclusion
Our results suggested that CYFIP2 may serve as a prognostic cancer biomarker for determining prognosis and might be a promising therapeutic strategy for tumor immunotherapy.
Ameliorative effect of hesperidin against high dose sildenafil-induced liver and testicular oxidative stress and altered gene expression in male rats
Authors: Laila Ibrahim M. Ibrahim , Kassem Samar HassabAllah , Diab Marwa Salah ElDin Mohamed 
Published: September 2023

Abstract
Background
The clinical use of sildenafil citrate (Viagra), a drug used to treat erectile dysfunction, is limited because of its many side effects on tissues. In this context, we aimed to investigate the protective effects of hesperidin, a citrus flavonoid, on hepatic and testicular damage induced by a high dose of sildenafil citrate in male rats. Rats were randomly divided into four groups. The first group was used as the control group. The second group was orally administered sildenafil citrate at a high dose of 75 mg/kg thrice a week. In the third group, hesperidin was administered orally at a dose of 50 mg/kg/day. The fourth group was administered 75 mg/kg sildenafil citrate three times a week with 50 mg/kg hesperidin daily. The experiment lasted for 28 days.

Results
In the sildenafil-treated groups, blood indices were altered, liver function tests were deranged, and serum testosterone levels were reduced. In the liver and testicular tissue, sildenafil citrate treatment resulted in significant reductions in catalase and total antioxidant capacity; as well as increased malondialdehyde, reactive oxygen species, and nitrous oxide levels. In addition, sildenafil citrate treatment caused abnormal histopathological patterns in both the liver and the testes. Liver vascular endothelial growth factor and testicular steroidogenic acute regulatory protein gene expression were upregulated.

Conclusions
Hesperidin attenuated the harmful effects of intensive sildenafil citrate treatment on liver and testicular functions, alleviated oxidative stress and normalized blood indices. Therefore, hesperidin could be protective against sildenafil citrate-induced oxidative damage that may develop over the long term.
Impact of the COVID-19 pandemic on self-harm and self-harm/suicide ideation: population-wide data linkage study and time series analysis
Authors: Paterson Euan Neil , Kent Lisa , O'Reilly Dermot , O'Hagan Denise , O'Neill Siobhan M. , Maguire Aideen 
Published: September 2023

BackgroundThe COVID-19 pandemic and associated lockdowns were predicted to have a major impact on suicidal behaviour, including self-harm. However, current studies have produced contradictory findings with limited trend data.AimsNine years of linked individual-level administrative data were utilised to examine changes in hospital-presenting self-harm and ideation (thoughts of self-harm or suicide) before and during the pandemic.MethodNational self-harm registry data were linked to demographic and socioeconomic indicators from healthcare registration records (n = 1 899 437). Monthly presentations of self-harm or ideation were split (pre-COVID-19 restrictions: April 2012 to February 2020; and during restrictions: March to September 2020). Auto-regressive integrated moving average (ARIMA) models were trained in R taking into consideration trends and seasonal effects. Forecast (‘expected’) monthly values were compared with ‘actual’ values, stratified by demographic factors and method of harm.ResultsThe number of individuals presenting with self-harm or ideation dropped significantly at the beginning of the pandemic (March–May 2020), before returning mostly to expected trends from June 2020. Stratified analysis showed similar presentation trends across most demographic subgroups except for those aged over 65 years, living alone or in affluent areas, where presentations remained unaffected, and those aged under 16 years, where numbers presenting with self-harm or ideation increased above expected levels.ConclusionsAlthough population trends show an overall drop in presentations before a return to ‘normal’ from June 2020, the demographic profile of those presenting with self-harm or ideation varied significantly, with increases in children under the age of 16 years. This highlights important potential target groups who may have been most negatively affected by the pandemic.
Arterial Hyperoxemia During Cardiopulmonary Bypass Was Not Associated With Worse Postoperative Pulmonary Function: A Retrospective Cohort Study
Authors: Kelava Marta , Milam Adam J. , Mi Junhui , Alfirevic Andrej , Grady Patrick , Unai Shinya , Elgharably Haytham , McCurry Kenneth , Koprivanac Marijan , Duncan Andra 
Published: September 2023

BACKGROUND:
Arterial hyperoxemia may cause end-organ damage secondary to the increased formation of free oxygen radicals. The clinical evidence on postoperative lung toxicity from arterial hyperoxemia during cardiopulmonary bypass (CPB) is scarce, and the effect of arterial partial pressure of oxygen (Pao
2) during cardiac surgery on lung injury has been underinvestigated. Thus, we aimed to examine the relationship between Pao
2 during CPB and postoperative lung injury. Secondarily, we examined the relationship between Pao
2 and global (lactate), and regional tissue malperfusion (acute kidney injury). We further explored the association with regional tissue malperfusion by examining markers of cardiac (troponin) and liver injury (bilirubin).

METHODS:
This was a retrospective cohort study including patients who underwent elective cardiac surgeries (coronary artery bypass, valve, aortic, or combined) requiring CPB between April 2015 and December 2021 at a large quaternary medical center. The primary outcome was postoperative lung function defined as the ratio of Pao
2 to fractional inspired oxygen concentration (Fio
2); P/F ratio 6 hours following surgery or before extubation. The association between CPB in-line sample monitor Pao
2 and primary, secondary, and exploratory outcomes was evaluated using linear or logistic regression models adjusting for available baseline confounders.

RESULTS:
A total of 9141 patients met inclusion and exclusion criteria, and 8429 (92.2%) patients had complete baseline variables available and were included in the analysis. The mean age of the sample was 64 (SD = 13), and 68% were men (n = 6208). The time-weighted average (TWA) of in-line sample monitor Pao
2 during CPB was weakly positively associated with the postoperative P/F ratio. With a 100-unit increase in Pao
2, the estimated increase in postoperative P/F ratio was 4.61 (95% CI, 0.71–8.50; P = .02). Our secondary analysis showed no significant association between Pao
2 with peak lactate 6 hours post CPB (geometric mean ratio [GMR], 1.01; 98.3% CI, 0.98–1.03; P = .55), average lactate 6 hours post CPB (GMR, 1.00; 98.3% CI, 0.97–1.03; P = .93), or acute kidney injury by Kidney Disease Improving Global Outcomes (KDIGO) criteria (odds ratio, 0.91; 98.3% CI, 0.75–1.10; P = .23).

CONCLUSIONS:
Our investigation found no clinically significant association between Pao
2 during CPB and postoperative lung function. Similarly, there was no association between Pao
2 during CPB and lactate levels, postoperative renal function, or other exploratory outcomes.
Translating Line Breaks: A View from Persian Poetics
Authors: Tahmasebian Kayvan , Gould Rebecca Ruth 
Published: September 2023

Abstract
Line breaks are arguably the defining feature of poetry, in the absence of which a text becomes prose. Consequently, the translation of line breaks is a decisive issue for every poetry translator. Classical and modern literary theorists have argued that the potential for enjambment, which we understand as the effect that makes line breaks possible in poetry, constitutes the difference between poetry and prose. Yet, the translation of line breaks is among the least studied areas of translation theory. This essay explores the challenge of translating classical and modernist line breaks through examples from Persian and European literary canons. From Shams-i Qays’s classic treatise on Persian prosody to Arthur Rimbaud and William Carlos Williams to modernist poet Bijan Elahi’s poetic rewriting of One Thousand and One Nights, we explore the options open to the translator-poet who seeks to create a new poem in and through translation.
Quantifying Patient-Initiated Upper Extremity Movement After Surgical Reconstruction for Adult Pan-Brachial Plexus Injury
Authors: Muhlestein Whitney E. , Chang Tommy Nai-Jen , Chang Kate W.-C. , Lu Johnny Chuieng-Yi , Chen Pei-Ju , Chung Kevin C. , Yang Lynda J.-S. , Brown Susan H. , Chuang David Chwei-Chin 
Published: September 2023

BACKGROUND AND OBJECTIVES:
Determining functional recovery in adult patients with traumatic pan-brachial plexus injury (pBPI) is hampered by the fact that most outcome measures are collected in the clinical setting and may not reflect arm use in the real world. This study's objectives were to demonstrate the feasibility of using wearable motion sensor technology to quantify spontaneous arm movement in adult patients with pBPI after surgical reconstruction and report the time and intensity with which the affected arm was used.

METHODS:
Twenty-nine patients with pBPI who underwent surgical reconstruction at least 2 years prior were included in this study. Study participants wore an accelerometer on bilateral arms for 7 days. The vector time (VT) and magnitude with which each arm moved were collected and divided by the same values collected from the uninjured arm to generate a ratio (VT and vector magnitude [VM], respectively) to quantify differences between the arms. Correlations between VT, VM, and patient demographic and physician-elicited clinical measures were calculated. Patients were enrolled at Chang Gung Memorial Hospital, Linkou Medical Center, Taiwan, and data analysis was performed at the University of Michigan.

RESULTS:
Twelve patients had pan-avulsion injuries, and 17 patients had C5 rupture with C6-T1 avulsion injuries. All underwent nerve reconstruction with contralateral C7 or ipsilateral C5 nerve roots as donors. At mean 7.3 years after surgery, the mean VT ratio was 0.54 ± 0.13 and the mean VM ratio was 0.30 ± 0.13. Both VT and VM ratios were significantly correlated with patient employment and movements at the elbow and forearm.

CONCLUSION:
Wearable motion detection technology can capture spontaneous, real-world movements of the arm in patients who have undergone surgical reconstruction for pBPI. Despite severe injuries, these patients are able to use their affected arm 50% of the time and with 30% of the intensity of their unaffected arm, which is positively correlated with return to work after injury. These data support the use of surgical reconstruction for pBPI.
Technology integration during teaching and learning: the COVID-19 context
Authors: Mudau Awelani V. , Sikhosana Lettah 
Published: September 2023

Background: The aim of this paper was to explore how the Fourth Industrial Revolution shapes teaching and learning during COVID-19 in some of the schools located in the Gauteng and Mpumalanga provinces, South Africa. This paper employed qualitative interpretative multiple case study design. Purposive sampling was used to sample our participants. Methods: We selected four teachers who separately taught at the early childhood development stage, intermediate phase, senior phase, and further education and training phases. Data was collected telephonically through semi-structured interviews with teachers from Limpopo, Gauteng and Mpumalanga provinces of South Africa. Data was collected from their experiences of COVID-19 from 2019 to 2021. Collected data was analysed using a typology approach whereby themes that derived from the literature reviewed and research questions were used. Results: We inferred from the results of the paper that teachers had challenges with teaching and availability of learning resources, such as limited access to internet and socio-economic backgrounds, which hindered the integration of the Fourth Industrial Revolution in the teaching and learning process. There were also challenges related to teachers’ background on the usage of the Fourth Industrial Revolution and the lack of school management teams support. The paper revealed that the integration of the Fourth Industrial Revolution in teaching and learning was affected negatively by the existence of the above-mentioned challenges, which needs to be addressed. Conclusions: Therefore, we recommended that the government and stakeholders within the education sector provide resources such as smart-boards, computers, and network access in schools lacking such facilities, as well as providing professional development interventions and training teachers to have an in-depth understanding of the Fourth Industrial Revolution within the teaching and learning context.
Results of a national survey of IBD nurses reported barriers and facilitators towards providing care to patients with microscopic colitis
Authors: Avery Pearl , Campbell Rachel 
Published: September 2023

Objective The authors developed a survey to understand the barriers and facilitators that might be present in providing care for patients with microscopic colitis (MC) in existing inflammatory bowel disease (IBD) nurse-led services. Methods A survey was developed using Google Forms to collect anonymous responses from IBD nurses across all four nations of the UK. Twitter and the IBD Royal College of Nurses IBD network Facebook page and email group were used to disseminate the survey. Analyses were carried out using descriptive statistics. Results Of the n=102, responses received showed that 89.2% (n=91) consider MC when they see patients with watery diarrhoea. No training had been received about MC by 58.8% (n=60) of the n=102, while 52% (n=53) of the same cohort felt they had enough knowledge/confidence to manage a patient diagnosed with microscopic colitis. Conclusions The survey results also indicate an interest among the IBD nursing community in MC and a desire to learn more about MC to support patients living with this condition.
Appraising causal risk and protective factors for rheumatoid arthritis
Authors: Gu Peng , Pu Bin , Liu Teng , Yue Dan , Xin Qiao , Li Hai-Shan , Yang Bai-Lin , Ke Dao-Ze , Zheng Xiao-Hui , Zeng Zhan-Peng , Zhang Zhi-Qiang 
Published: September 2023

AimsMendelian randomization (MR) is considered to overcome the bias of observational studies, but there is no current meta-analysis of MR studies on rheumatoid arthritis (RA). The purpose of this study was to summarize the relationship between potential pathogenic factors and RA risk based on existing MR studies.MethodsPubMed, Web of Science, and Embase were searched for MR studies on influencing factors in relation to RA up to October 2022. Meta-analyses of MR studies assessing correlations between various potential pathogenic factors and RA were conducted. Random-effect and fixed-effect models were used to synthesize the odds ratios of various pathogenic factors and RA. The quality of the study was assessed using the Strengthening the Reporting of Observational Studies in Epidemiology using Mendelian Randomization (STROBE-MR) guidelines.ResultsA total of 517 potentially relevant articles were screened, 35 studies were included in the systematic review, and 19 studies were eligible to be included in the meta-analysis. Pooled estimates of 19 included studies (causality between 15 different risk factors and RA) revealed that obesity, smoking, coffee intake, lower education attainment, and Graves’ disease (GD) were related to the increased risk of RA. In contrast, the causality contribution from serum mineral levels (calcium, iron, copper, zinc, magnesium, selenium), alcohol intake, and chronic periodontitis to RA is not significant.ConclusionObesity, smoking, education attainment, and GD have real causal effects on the occurrence and development of RA. These results may provide insights into the genetic susceptibility and potential biological pathways of RA.Cite this article: Bone Joint Res 2023;12(9):601–614.