bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of plant assemblages dampens the variability of the growing season phenology in wetland landscapes
Authors: Rheault Guillaume , Lévesque Esther , Proulx Raphaël 
Published: May 2021

Abstract
Background
The functioning of ecosystems is highly variable through space and time. Climatic and edaphic factors are forcing ecological communities to converge, whereas the diversity of plant assemblages dampens these effects by allowing communities’ dynamics to diverge. This study evaluated whether the growing season phenology of wetland plant communities within landscapes is determined by the climatic/edaphic factors of contrasted regions, by the species richness of plant communities, or by the diversity of plant assemblages. From 2013 to 2016, we monitored the phenology and floristic composition of 118 wetland plant communities across five landscapes distributed along a gradient of edaphic and climatic conditions in the Province of Québec, Canada.

Results
The growing season phenology of wetlands was driven by differences among plant assemblage within landscapes, and not by the species richness of each individual community (< 1% of the explained variation). Variation in the growing season length of wetlands reflected the destabilizing effect of climatic and edaphic factors on green-up dates, which is opposed to the dampening effect of plant assemblage diversity on green-down dates.

Conclusions
The latter dampening effect may be particularly important in the context of increasing anthropogenic activities, which are predicted to impair the ability of wetlands to adapt to fluctuating environmental conditions. Our findings suggest that stakeholders should not necessarily consider local species-poor plant communities of lower conservation value to the global functioning of wetland ecosystems.
Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Authors: Lloret-Villas Audald , Bhati Meenu , Kadri Naveen Kumar , Fries Ruedi , Pausch Hubert 
Published: May 2021

Abstract
Background
Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA_Angus_1).

Results
Read mapping accuracy did not differ notably between the ARS-UCD1.2 and UOA_Angus_1 assemblies. We discovered 22,744,517 and 22,559,675 high-quality variants from ARS-UCD1.2 and UOA_Angus_1, respectively. The concordance between sequence- and array-called genotypes was high and the number of variants deviating from Hardy-Weinberg proportions was low at segregating sites for both assemblies. More artefactual INDELs were genotyped from UOA_Angus_1 than ARS-UCD1.2 alignments. Using the composite likelihood ratio test, we detected 40 and 33 signatures of selection from ARS-UCD1.2 and UOA_Angus_1, respectively, but the overlap between both assemblies was low. Using the 161 sequenced Brown Swiss cattle as a reference panel, we imputed sequence variant genotypes into a mapping cohort of 30,499 cattle that had microarray-derived genotypes using a two-step imputation approach. The accuracy of imputation (Beagle R2) was very high (0.87) for both assemblies. Genome-wide association studies between imputed sequence variant genotypes and six dairy traits as well as stature produced almost identical results from both assemblies.

Conclusions
The ARS-UCD1.2 and UOA_Angus_1 assemblies are suitable for reference-guided genome analyses in Brown Swiss cattle. Although differences in read mapping and genotyping accuracy between both assemblies are negligible, the choice of the reference genome has a large impact on detecting signatures of selection that already reached fixation using the composite likelihood ratio test. We developed a workflow that can be adapted and reused to compare the impact of reference genomes on genome analyses in various breeds, populations and species.
The potential and effects of saline-alkali alfalfa microbiota under salt stress on the fermentation quality and microbial
Authors: Sa Duo Wen , Lu Qiang , Wang Zhen , Ge Gentu , Sun Lin , Jia Yushan 
Published: May 2021

Abstract
Background
The objective of this study was to evaluate the chemical compositions and microbial communities of salt-tolerant alfalfa silage. Salt-tolerant alfalfa was ensiled with no additive control, and cellulase for 30 and 60 to 90 days. In this study, the dry matter (DM) content of the raw material was 29.9% DM, and the crude protein (CP) content of the alfalfa was 21.9% CP.

Results
After 30 days of fermentation, the DM content with the cellulase treatment was reduced by 3.6%, and the CP content was reduced by 12.7%. After 60 days of fermentation, compared with alfalfa raw material, the DM content in the control group (CK) was reduced by 1%, the CP content was reduced by 9.5%, and the WSC (water-soluble carbohydrates) content was reduced by 22.6%. With the cellulase, the lactic acid content of the 30- and 60-day silages was 2.66% DM and 3.48% DM. The content of Firmicutes in salinized alfalfa raw material was less than 0.1% of the total bacterial content. Before and after ensiling, the microbes had similar composition at the phylum level, and were composed of Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria. The abundance of Pantoea was dominant in fresh alfalfa. In the absence of additives, after 30 days and 60 days of silage, the dominant lactic acid bacteria species became Lactococcus and Enterococcus.

Conclusions
The results showed that LAB (Lactobacillus, Lactococcus, Enterococcus, and Pediococcus) played a major role in the fermentation of saline alfalfa silage. It also can better preserve the nutrients of saline alfalfa silage. The use of cellulase enhances the reproduction of Lactobacillus. The fermentation time would also change the microbial community of silage fermentation.
Association between fatality rate of COVID-19 and selenium deficiency in China
Authors: Zhang Hai-Yang , Zhang An-Ran , Lu Qing-Bin , Zhang Xiao-Ai , Zhang Zhi-Jie , Guan Xiu-Gang , Che Tian-Le , Yang Yang , Li Hao , Liu Wei , Fang Li-Qun 
Published: May 2021

Abstract
Background
COVID-19 has impacted populations around the world, with the fatality rate varying dramatically across countries. Selenium, as one of the important micronutrients implicated in viral infections, was suggested to play roles.

Methods
An ecological study was performed to assess the association between the COVID-19 related fatality and the selenium content both from crops and topsoil, in China.

Results
Totally, 14,045 COVID-19 cases were reported from 147 cities during 8 December 2019–13 December 2020 were included. Based on selenium content in crops, the case fatality rates (CFRs) gradually increased from 1.17% in non-selenium-deficient areas, to 1.28% in moderate-selenium-deficient areas, and further to 3.16% in severe-selenium-deficient areas (P = 0.002). Based on selenium content in topsoil, the CFRs gradually increased from 0.76% in non-selenium-deficient areas, to 1.70% in moderate-selenium-deficient areas, and further to 1.85% in severe-selenium-deficient areas (P < 0.001). The zero-inflated negative binomial regression model showed a significantly higher fatality risk in cities with severe-selenium-deficient selenium content in crops than non-selenium-deficient cities, with incidence rate ratio (IRR) of 3.88 (95% CIs: 1.21–12.52), which was further confirmed by regression fitting the association between CFR of COVID-19 and selenium content in topsoil, with the IRR of 2.38 (95% CIs: 1.14–4.98) for moderate-selenium-deficient cities and 3.06 (1.49–6.27) for severe-selenium-deficient cities.

Conclusions
Regional selenium deficiency might be related to an increased CFR of COVID-19. Future studies are needed to explore the associations between selenium status and disease outcome at individual-level.
Two-stage prediction model for in-hospital mortality of patients with influenza infection
Authors: Cheong Chan-Wa , Chen Chien-Lin , Li Chih-Huang , Seak Chen-June , Tseng Hsiao-Jung , Hsu Kuang-Hung , Ng Chip-Jin , Chien Cheng-Yu 
Published: May 2021

Abstract
Background
Infleunza is a challenging issue in public health. The mortality and morbidity associated with epidemic and pandemic influenza puts a heavy burden on health care system. Most patients with influenza can be treated on an outpatient basis but some required critical care. It is crucial for frontline physicians to stratify influenza patients by level of risk. Therefore, this study aimed to create a prediction model for critical care and in-hospital mortality.

Methods
This retrospective cohort study extracted data from the Chang Gung Research Database. This study included the patients who were diagnosed with influenza between 2010 and 2016. The primary outcome of this study was critical illness. The secondary analysis was to predict in-hospital mortality. A two-stage-modeling method was developed to predict hospital mortality. We constructed a multiple logistic regression model to predict the outcome of critical illness in the first stage, then S1 score were calculated. In the second stage, we used the S1 score and other data to construct a backward multiple logistic regression model. The area under the receiver operating curve was used to assess the predictive value of the model.

Results
In the present study, 1680 patients met the inclusion criteria. The overall ICU admission and in-hospital mortality was 10.36% (174 patients) and 4.29% (72 patients), respectively. In stage I analysis, hypothermia (OR = 1.92), tachypnea (OR = 4.94), lower systolic blood pressure (OR = 2.35), diabetes mellitus (OR = 1.87), leukocytosis (OR = 2.22), leukopenia (OR = 2.70), and a high percentage of segmented neutrophils (OR = 2.10) were associated with ICU admission. Bandemia had the highest odds ratio in the Stage I model (OR = 5.43). In stage II analysis, C-reactive protein (OR = 1.01), blood urea nitrogen (OR = 1.02) and stage I model’s S1 score were assocaited with in-hospital mortality. The area under the curve for the stage I and II model was 0.889 and 0.766, respectively.

Conclusions
The two-stage model is a efficient risk-stratification tool for predicting critical illness and mortailty. The model may be an optional tool other than qSOFA and SIRS criteria.
Association between time to stent dysfunction and the anti-tumour effect of systemic chemotherapy following stent placement in patients with pancreaticobiliary cancers and malignant gastric outlet obstruction: a retrospective cohort study
Authors: Kobayashi Satoshi , Ueno Makoto , Nagashima Shuhei , Sano Yusuke , Kawano Kuniyuki , Fukushima Taito , Asama Hiroyuki , Tezuka Shun , Morimoto Manabu 
Published: May 2021

Abstract
Background
Malignant gastric outlet obstruction (MGOO) occasionally occurs due to pancreaticobiliary cancer. Endoscopic duodenal stenting (DS) is a common treatment for MGOO. However, it has been reported that DS does not have sufficient patency time for it to be used in patients who have a potentially increased lifespan. Nowadays, systemic chemotherapy for pancreaticobiliary cancer has developed, and its anti-tumour effect would make time to stent dysfunction longer.
Therefore, we retrospectively evaluated the association between objective response to systemic chemotherapy, followed by DS and time to stent dysfunction in patients with advanced pancreaticobiliary cancer.

Methods
This retrospective study included 109 patients with advanced pancreaticobiliary cancer who received systemic chemotherapy after DS. Patients who showed complete or partial response were defined as responders. The rest were defined as non-responders. Time to stent dysfunction was compared between responders and non-responders using the landmark analysis at 2 months after DS. Death without recurrence of MGOO was considered as a competing risk for time to stent dysfunction.

Results
Combination and monotherapy regimens were adopted for 46 and 63 patients, respectively. Median progression-free survival and overall survival were 3.2 months (95% confidence interval [CI], 2.4–4.0) and 6.0 months (95% CI, 4.6–7.3). Objective response was observed in 21 patients (19.3%). Median time to stent dysfunction was 12.5 months (95% CI, 8.4–16.5) in the entire cohort. In 89 patients, responders had a lower cumulative incidence of stent dysfunction than non-responders: 9.5 and 19.1% at 6 months, and 19.0 and 27.9% at 1-year, respectively. There was difference of time to stent dysfunction between responders and non-responders among patients who received combination regimen as the first-line treatment with p-value of 0.009: cumulative incidence was 0 and 42.9% at 6 months, and 9.3 and 57.1% at 1-year, respectively.

Conclusions
Longer time to stent dysfunction is expected when systemic chemotherapy following DS suppresses tumour progression; DS is slated to be a standard treatment for MGOO even in patients with pancreaticobiliary cancer and a long lifespan.
Pediatric dentists’ perspectives of children with special health care needs in Japan: developmental disabilities, phobia, maltreatment, and multidisciplinary collaboration
Authors: Ide-Okochi Ayako , Funayama Hiromi , Asada Yoshinobu 
Published: May 2021

Abstract
Background
The number of children diagnosed with developmental disabilities (DDs) or other chronic difficulties has risen. However, each professional’s awareness of children with developmental, emotional and behavioural difficulties may differ, allowing their special needs to be overlooked at child health checkups until secondary difficulties appear. Therefore, it is necessary to explore the multi-professional views of children with such chronic difficulties. This study investigates pediatric dentists’ perception of children with potential chronic difficulties.

Methods
Interviews were conducted with 21 pediatric dentists, and the transcripts were analyzed using grounded theory to develop categories for the theoretical assessment.

Results
Four themes emerged regarding the children with potential chronic difficulties: children exhibiting possible DDs with awkward social communication and interaction; severe rampant caries possibly derived from maltreatment; dental phobia possibly derived from mental health problems; a complicated home environment where their mothers exhibit poor oral health literacy.

Conclusions
This study’s findings imply that participants’ concept of children of concern included the risks of poor oral health and mental health problems that other healthcare professionals might overlook. It is recommended that multidisciplinary professionals engaging in child health checkups be aware of children’s oral and mental health status as well as potential DDs and child maltreatment.
Minimum acceptable diet among children aged 6–23 months in South Kivu, Democratic Republic of Congo: a community-based cross-sectional study
Authors: Kambale Richard Mbusa , Ngaboyeka Gaylord Amani , Kasengi Joe Bwija , Niyitegeka Sarah , Cinkenye Boss Rutakaza , Baruti Armand , Mutuga Kizito Chentwali , Van der Linden Dimitri 
Published: May 2021

Abstract
Background
Suboptimal child nutrition remains the main factor underlying child undernutrition in Democratic Republic of Congo (DRC). This study aimed to assess the prevalence of minimum acceptable diet and associated factors among children aged 6–23 months old.

Methods
Community-based cross-sectional study including 742 mothers with children aged 6–23 months old was conducted in 2 Health Zones of South Kivu, Eastern DRC. WHO indicators of Infant and Young Child Feeding (IYCF) regarding complementary feeding practices were used. Logistic regression analysis was used to quantify the association between sociodemographic indicators and adequate minimum acceptable diet for both univariate and multivariate analysis.

Results
Overall, 33% of infants had minimum acceptable diet. After controlling for a wide range of covariates, residence urban area (AOR 2.39; 95% CI 1.43, 3.85), attendance postnatal care (AOR 1.68; 95% CI 1.12, 2.97), education status of mother (AOR 1.83; 95% CI 1.20, 2.77) and household socioeconomic status (AOR 1.72; 95% CI 1.14, 2.59) were factors positively associated with minimum acceptable diet.

Conclusion
Actions targeting these factors are expected to improve infant feeding practices in South Kivu.
Awareness and acceptability of HIV pre-exposure prophylaxis (PrEP) among students at two historically Black universities (HBCU): a cross-sectional survey
Authors: Okeke Nwora Lance , McLaurin Tony , Gilliam-Phillips Ruth , Wagner David H. , Barnwell Valerie J. , Johnson Yolanda M. , James Osaffo , Webb Padonda B. , Parker Sharon D. , Hill Bendu , McKellar Mehri S. , Mitchell John T. 
Published: May 2021

Abstract
Background
Despite young African American adults (ages 18–24) being among the highest risk groups for HIV infection, little is known about their awareness of HIV pre-exposure prophylaxis (PrEP) – a once daily pill shown to be > 90% effective in preventing HIV. To explore awareness and acceptability of PrEP among college students in this demographic, we conducted a survey of attendees at two large historically Black universities (HBCU) in North Carolina.

Methods
We administered a 14-item questionnaire to students at two HBCUs in North Carolina between February and April 2018. Questions were formatted in a yes/no or multiple choice format. Questionnaire items specifically addressed PrEP awareness and acceptability. Surveys were administered to students at a campus health fair and while transiting the campus student union via iPad. Response to all questions was optional. We fit a logistic regression model to determine association of key demographic determinants with PrEP acceptability and awareness. Statistical analyses were conducted using SAS 9.4 (SAS, Cary, NC).

Results
Overall, 210 students participated in the survey, of which 60 completed all survey items as presented. The survey cohort was 75% female, 89% heterosexual and 39% freshmen. The mean age of respondents was 19.8 years (SD: 1.8). Fifty-two percent of survey respondents reported that they were aware of PrEP prior to the time of survey administration. Only 3% of respondents reported that they were on PrEP. The most common sources of information on PrEP were campus health services (24%) and non-social media advertising (15%). Of respondents who were aware of PrEP, 61% reported that they had heard about in the 6 months prior to survey administration, while only 19% say they were aware of it for more than a year. Regarding acceptability of PrEP, 58% of respondents reported that they would take a once a day pill for HIV if they were at risk. Our logistic regression analysis found no statistically significant associations between key demographic factors and PrEP awareness. However, persons who perceived themselves to be at risk for HIV acquisition were more likely to find once daily oral PrEP (relative risk 2.66 (95% CI 1.31–5.42)) as an acceptable prevention strategy than the rest of the survey cohort.

Conclusions
African American HBCU students are becoming aware of PrEP, and generally perceive the intervention as acceptable and worth consideration.
The risk factors and care measures of surgical site infection after cesarean section in China: a retrospective analysis
Authors: Li Lijun , Cui Hongyan 
Published: May 2021

Abstract
Background
Surgical site infections after cesarean section are very common clinically, it is necessary to evaluate the risk factors of surgical site infections after cesarean section, to provide evidences for the treatment and nursing care of cesarean section.

Methods
This study was a retrospective cohort study design. Patients undergone cesarean section in a tertiary hospital of China from May 2017 to May 2020 were identified, we collected the clinical data of the included patients, and we analyzed the infection rate, etiological characteristics and related risk factors of surgical site infection after caesarean section.

Results
A total of 206 patients with cesarean section were included, and the incidence of surgical site infection in patients with cesarean section was 23.30%. A total of 62 cases of pathogens were identified, Enterococcus faecalis (33.87%) and Escherichia coli (29.03%) were the most common pathogens. Both Enterococcus faecalis and Escherichia coli were highly sensitive to Cefoperazone, Meropenem, and Levofloxacin. Logistic regression analyses indicated that Age ≥ 30y (OR 4.18, 95%CI: 1.23–7.09), BMI ≥ 24 (OR 2.39, 95%CI: 1.02–4.55), duration of cesarean section ≥ 1.5 h (OR 3.90, 95%CI: 1.28–5.42), estimated blood loss ≥ 400 ml (OR 2.35, 95%CI: 1.10–4.37) and the duration of urinary catheter ≥ 24 h (OR 3.18, 95% CI: 1.21–5.71) were the independent risk factors of surgical site infection after cesarean section (all p < 0.05).

Conclusions
Age, BMI, duration of surgery, blood loss and urinary catheter use were associated with higher risk of the surgical site infection after cesarean section. Clinical preventions and interventions are warranted for those population to reduce the occurrence of surgical site infection.
Qualitative exploration of medical student experiences during the Covid-19 pandemic: implications for medical education
Authors: Nolan Helen , Owen Katherine 
Published: May 2021

Abstract
Background
During the Covid-19 pandemic medical students were offered paid roles as medical student healthcare assistants. Anecdotal reports suggested that students found this experience rich for learning. Previous studies have explored alternative models of student service, however this defined medical student support role is novel.

Methods
Individual semi-structured interviews were recorded with 20 medical students at a UK medical school exploring their experiences of placement learning and experiences of working as healthcare assistants. Responses were analysed qualitatively using a framework approach. The framework was developed into a model describing key findings and their relationships.

Results
Interviews yielded data that broadly covered aspects of (1) Medical students’ experiences of clinical placement learning (2) Medical students’ experiences of working as medical student healthcare assistants (3) Learning resulting from working as a healthcare assistant (4) Hierarchies and professional barriers in the clinical environment (5) Influences on professional identity.
Participants described barriers and facilitators of clinical learning and how assuming a healthcare assistant role impacted on learning and socialisation within the multidisciplinary team. Students became increasingly socialised within the healthcare team, contributing directly to patient care; the resulting social capital opened new opportunities for learning, team working and enhanced students’ interprofessional identity. Students described the impact of these experiences on their aspirations for their future practice.

Conclusions
Changes to work patterns in healthcare and delivery models of medical education have eroded opportunities for students to contribute to healthcare delivery and be embedded within a team. This is impacting negatively on student learning and socialisation and we suggest that medical curricula have much to learn from nursing and allied health professional training. Longitudinal embedment with a multidisciplinary team, where students have a defined role and work directly with patients may not only add value to clinical service, but also overcome current barriers to effective placement learning and interprofessional identity formation for medical students.