bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on Long-Term Exposure to Carbon Emissions and Lung Cancer Incidence Rate in China
Authors: He Fengdie , Lin Yongqing , Wang Baohua , Dong Shaoxia
Published: September 2021

Background: This study has shown the incidence of lung cancer in association with exposure to air pollution. We investigated the relationship, focusing on long-term exposure to carbon emissions (CE) and lung cancer incidence rate (LIR) in China.Methods: We collected the incidence rate of lung cancer from 2013 to 2015, and the data of carbon emissions from 1997 to 2015. We modeled the panel data of 30 provinces and cities in China from 2013 to 2015 and applied a spatial Durbin model (SDM) to explore the spatial effect of CE on the LIR. Pearson test to determine the long-term impact of CE on LIR.Findings: The results showed that the direct effect coefficient of CE and UR were 0.132 and 0.425, respectively, both significant at a 1% level, which showed that CE and UR had an obvious positive effect on LIR. The value of Moran’s I indicated that there was a positive spatial correlation between the LIR and CE in China from 2013 to 2015, while the indirect effect coefficient of all the variables was nonsignificant at a 10% level, which indicated that CE had not impact on the LIR of its surrounding areas. on the whole, the effect cofficient of CE is 0.005 ,which is significant at a 1% level, which points out that the average effect of a change in CE in a certain region on LIR in all regions. Therefore, the research results indicated that there were geographical differences in carbon emissions but there is no spatial spillover effects. In the time fixed effects, the coefficients of CE were positive at the 10% significance level, which pointed out that CE exposure had a long-term impact on LIR from 2013 to 2015. Besides, the Pearson test implied that CE in the period had the greatest impact on the LIR in 2015 in China, and the lag period was about 17 years.Interpretation: The impact of CE on LIR had geographical distribution differences and long-term effects in China. We recommend that adopting policies to reduce carbon emission will have a positive health impact.
Barriers To Participation in Research As Perceived By Undergraduate Medical Students: A Cross-Sectional Study From Qassim
Authors: Elmannan Abeer Abuzeid Atta , Alrebish Saleh A , Alqarzai Rahaf Khalid , Alshubrmi Atheen Ahmad , Alammar Abdulrahman Yousef , Alsaeed Hammad Saleh
Published: September 2021

Background
It is vital for healthcare practitioners to have the necessary skills and competence to review the literature and critically appraise research evidence. However, medical students` engagement in research activities continues to be below the expectation. In this study we aimed to investigate students` views about research, and to identify the barriers preventing them from participation in research projects.
Methods
A cross-sectional study was carried out in the College of Medicine in Qassim University. A total of 230 students were included. Data were collected online through a self- administered questionnaire .The perceptions of students were assessed using a 16-item questionnaire organized as ; Students` attitudes towards research, Students` perception of research benefits, Students` willingness to participate in research, and Students` perception of research barriers. The mean scores of these four subscales were compared between students using Mann-Whitney test .Factors associated with students` perception of research barriers were analyzed using four separate logistic regression models.
Results
The overall response rate was 89.4%. The results indicate that the students generally possess a moderately positive attitude towards research with a mean score of 14.8 ± 2.7 (range: 5–25). A substantial number of participants reported their willingness to take part in any research-related task (77.0%). However, the participants highly agreed that lack of time (70.4%), lack of supervision and guidance (72.6%), lack of research training and support (73.9%), and lack of research exposure and opportunities (75.2%) were major barriers to their participation in research .We found that students having lower CGPA ranks are almost three times more likely to indicate lack of time as a challenge (AOR: 2.94; 95% CI: 1.09,7.94; p.value = 0.033). Overall, female students were more likely to report concerns about research training and availability of research opportunities, while male students were more likely to indicate lack of time and lack of supervision as research barriers.
Conclusions
The barriers addressed in the current study —both discretely and cumulatively—are highly demotivating for students, and negatively affect their participation in research. Efforts should be invested to shift the focus from providing superficial research exposure to incorporating more in-depth and effective research training for undergraduate students
How Do Simulated Interviews Increase the Self-efficacy of Medical Students? - Quasi-experimental Research-
Authors: Aoki Shuntaro , Shikama Yayoi , Yasui Kiyotaka , Moroi Yoko , Sakamoto Nobuo , Suenaga Hiroki , Tang Zunyi , Yasuda Megumi , Chiba Yasuko , Stanyon Maham , Otani Koji
Published: September 2021

Background Self-efficacy is crucial in improving medical student communication skills. This study aims to clarify whether the self-efficacy of medical students conducting medical interviews increased after simulated interviews or after feedback discussions. Methods A total of 162 medical students (109 men, 53 women) in their fourth or fifth year at a university in Japan participated in this study. The degree of self-efficacy in medical interviewing was measured before and after a medical interview with a simulated patient, and after the subsequent feedback session. Results ANOVA analysis revealed that self-efficacy for medical interviews was higher after both the interview and the feedback session than before the interview. Self-efficacy was highest after the feedback session among all three time points. Conclusions Feedback following a simulated interview with a simulated patient is important to improve the self-efficacy of medical students learning medical interviewing skills.
RETRACTED: Dioxomolybdenum (VI) and Oxomolybdenum (IV) Complexes With N, O, and S Bidentate Ligands, Spectral Characterization, and DFT Studies
Authors: Alajrawy Othman Ibrahim , Almhmdi Ayad A.
Published: September 2021

The authors have requested that this preprint be removed from Research Square. The authors' request does not imply errors or misconduct.
Long-term Effectiveness of Overnight Shiftwork Implementation on Pediatric Residents’ Wellness: A Cross-Sectional Survey
Authors: Nakao Hiro , Nomura Osamu , Kubota Mitsuru , Ishiguro Akira
Published: September 2021

BackgroundIn Japan, the “Work Style Reform Bill” was partially enacted in 2019. In 2011, an Overnight Call Shift (OCS) system was introduced for pediatric training at the National Center for Child Health and Development (NCCHD). A questionnaire survey was conducted twice during the introduction of this system, finding a decrease in working hours, but no change in the depressive tendency of the residents. We conducted a follow-up survey in 2019 to investigate the long-term effectiveness of the OCS system to improve the pediatric residents’ wellness at NCCHD.MethodsA questionnaire-based cross-sectional survey was conducted for pediatric residents in 2019, and the results were compared to those of the previous survey in 2012. The questionnaire includes demographic data, working conditions data, and wellness assessment by the Center for Epidemiologic Studies Depression scale (CES-D) and the Maslach Burnout Inventory (MBI).ResultsThe collection rate for the 2019 survey was 94.5% (37 participants/39 eligible). Compared to 2012, there were no significant changes in demographic data and working hours, a significant increase by about 30% in residents who took daytime off after night work, about 10% decrease in residents who scored 16 and above on the CES-D, and a significant decrease in the mean score for depersonalization (DP) in the MBI.ConclusionsThis survey demonstrated the long-term effectiveness of the implemented OCS system to improve pediatric residents’ wellness. This study provides evidence for the further initiative to improve pediatricians’ wellness for preparing for the government’s overtime regulations for physicians scheduled for 2024.
Uncertainties In The Effectiveness of Biological Control of Stem Borers Under Different Climate Change Scenarios In Eastern Africa
Authors: Jendritzki Ines Gwendolyn , Tonnang Henri E. Z. , Calatayud Paul-André , Borgemeister Christian , Johansson Tino , Biber-Freudenberger Lisa
Published: September 2021

Climate change (CC) is expected to significantly affect biodiversity and ecosystem services. Adverse impacts from CC in the Global South are likely to be exacerbated by limited capacities to take adequate adaptation measures and existing developmental challenges. Insect pests today are already causing considerable yield losses in agricultural crop production in East Africa. Studies have shown that insects are strongly responding to CC by proliferation, shift in distribution or by altering their phenology, which is why an impact on agriculture can also be expected. Biological control (BC) has been proposed as an alternative measure to sustainably contain insect pests but few studies predict its efficacy under future CC. Using the species distribution modelling approach Maxent, we predict the current and future distribution of three important lepidopteran stem borer pests of maize in eastern Africa, i.e., Busseola fusca (Fuller, 1901), Chilo partellus (Swinhoe, 1885) and Sesamia calamistis (Hampson, 1910), and two of their parasitoids that are currently used for BC, i.e., Cotesia flavipes (Cameron, 1891) and Cotesia sesamiae (Cameron, 1906) . Based on these potential distributions and data collected during household surveys with local farmers in Kenya and Tanzania, future maize yield losses are predicted for a business-as-usual scenario and a sustainable development scenario. Accordingly, we found that BC of the three stem borer pests by C. flavipes and C. sesamiae will be less effective under more severe CC resulting in a reduced ability to curb maize yield losses caused by the stem borers. These results highlight the need to adapt BC measures to future CC to maintain its potential for environmentally-friendly pest management strategies. The findings of this research are thus of particular relevance to policy makers, extension officers and farmers in the region and will aid the adaptation of smallholder agricultural practices to current and future impacts of CC.
Partial Upper Sternotomy for Extensive arch Repair in Older Acute type A Aortic Dissection Patients
Authors: Qiu Zhihuang , Xiao Jun , Wu Qingsong , Chai Tianci , Zhang Li , Li Yumei , chen Liangwan
Published: September 2021

Objectives: The partial upper sternotomy (PUS) approach is acceptable for aortic valve replacement, and even aortic root operation. However, the efficiency of PUS for extensive arch repair of acute type A aortic dissection (AAAD) in older adult patients has not been well investigated.Methods: Between January 2012 and December 2019, 222 older adult patients (≥65 years) diagnosed with AAAD went through extensive arch repair, among which 127 received PUS, and 95 underwent full sternotomy (FS). Logistic regression analysis was used to identify risk factors for early death, and negative binomial regression analysis was applied to explore risk factors related to post-operative ventilator-supporting time and intensive care unit stay time. Results: Total early mortality was 8.1% (18/222 patients). The PUS group had shorter Cardiopulmonary bypass time (133.0 vs.155.0 minutes, P<0.001), cross-clamp time (44.0 vs. 61.0 minutes, P<0.001) and shorter selective cerebral perfusion time (11.0 vs. 21.0 minutes, P<0.001) than the FS group. Left ventricle ejection fraction (LVEF)<50% (odds ratio [OR], 17.05; 95% confidence interval [CI] 1.87-155.63; P=0.012) and malperfusion syndromes (OR, 65.83; 95% CI 11.53-375.86; P<0.001) were related to early death. In the multivariate model, the PUS approach contributed to shorter ventilator-supporting time (incidence rate ratio [IRR], 0.76; 95% CI 0.64-0.91; P=0.003) , when compared with the FS group. Conclusions: The early results of emergency extensive arch repair of AAAD via PUS in older adult patients were satisfactory. However, the long-term results remain to be investigated.
Source Apportionment and Health Risk Assessment of Zn (II) Ions Based on Gridded Spatial Interpolation and Geochemical Equilibrium Simulation
Authors: Miao Fangfang , Zhang Yimei , Li Yu , Lin Qianguo
Published: September 2021

Soil heavy metal pollution had become a global issue involving environmental safety and human health risks. A methodology was explored to quantify the sources of heavy metals in the soils and investigate the spatial distributions of heavy metals by the gridded spatial scale. The case study was implemented in the industrial waste sites in Suzhou city, Jiangsu province. Zinc (Zn) was screened out as the targeted metal (TM) through the potential ecological risk assessment, the species of which was simulated by the geochemical software PHREEQC. The aim of this research was to determine the dominant metal species of TM with potential hazardous health risk to local people to achieve key prevention and pollution control. Herein, according to the morphological evolution of metal species, the activity and concentration of the Zn species was calculated for both carcinogenic and non-carcinogenic health risk assessment. The evaluation of the optimized human health risk demonstrated that the associated health risk of Zn (II) depended predominantly on its metal speciation and was also affected by acidity and soil organic matter. Overall, the optimized carcinogenic and non-carcinogenic risk value of Zn2S32− for adults was 2.01E-04 and for children was 1.31 respectively, resulting in corresponding hazardous risk to human, which accounted for high risk level of 61.5% and 58.5%, respectively. This method could provide a reference for the decision-making of soil heavy metal pollution control and targeted hypotoxic convertion of metal species and remediation for certain heavy metal of polluted area.
Awareness and Perceptions Regarding Evidence Based Practice Among Nurses and Midwives in Two Ugandan National Referral Hospitals: A Cross-Sectional Study
Authors: Mwitende Francine , Muhindo Richard
Published: September 2021

Background: Integration of evidence-based practice (EBP) in nursing and midwifery increases patient satisfaction, patient safety and reduced length of hospital stay, which all contribute to better patient outcomes and improved quality of care. Little is known about awareness and perception regarding evidence-based practice among nurses and midwives in Uganda. Objective: This study sought to assess awareness and perceptions regarding evidence-based practice among nurses and midwives.Methods: A descriptive cross-sectional study using self-administered questionnaires was conducted among 384 nurses and midwives in Mulago and Kawempe National Referral Hospitals. The participants were recruited consecutively until when the desired sample size was obtained. Statistical Package for Social Sciences (SPSS) version 26 was used to analyze and summarize data using frequency and percentages. We performed Chi-square test to assess the factors association with awareness and perception. The independent variables with p-value <0.05 were significant. Results: Most of the participants were female (81.8%) and were practicing as nurses (76.2%). The results indicated that less than a half (46.2%, n=138) of participants were aware of EBP. Majority of the participants (96.3%- 97.7%) felt that EBP is highly important, necessary and an obligation in nursing and midwifery practice, although only 68.0% were routinely practicing it in their practice. Awareness was associated with level of education attained (p= 0.000), gender (0.001), going back to school after first qualification (p=0.000), access to learning resources at work place (p=0.000) and attendance of continuous medical education (p= 0.000), whereas, perception was associated with attendance of continuous medical education (0.017).Conclusion: Data show that nurses and midwives’ awareness regarding evidence-based practice was low in this study, however, they possessed positive perceptions regarding evidence-based practice. Moreover, only about two-thirds were practicing EBPs. Therefore, I recommend increased calls for interventions to sensitize nurses and midwives about EBP like continuous medical education (CME) and Continuous professional development (CPD) or refreshing training
Association Between Multimorbidity and Quality of Life Among Older Adults in Community-Dwelling of Uttar Pradesh, India
Authors: Himanshu Himanshu , Arokiasamy P. , Selvamani Y.
Published: September 2021

Background
The rise in life expectancy and the share of older population represents the most significant demographic transformation in the twenty-first century. Increasing longevity with the coexistence of chronic multimorbidity makes the elderly population vulnerable to functional limitation, disability and more frequent hospitalization, resulting deterioration in QoL. The present study aims to investigate the association between non-communicable disease (NCD) multimorbidity and QoL among the older population in Varanasi, India.
Methods
A cross-sectional data of 500 individuals in the Varanasi district aged 50 + years were collected, using a multistage simple random sampling procedure from November 2017 to May 2018. WHOQOL-BREF was utilised to assess the quality of life of the study participants, and the important covariates used in the analysis are; age, sex, marital status, place of residence, health factors, socioeconomic status, and behavioral risk factors. Descriptive analysis was performed to assess the mean QoL score pattern, whereas multivariate linear regression analysis examines the association between multimorbidity and QoL.
Results
The QoL scores decreased with age and was higher among females. Regression results show that demographic and lifestyle risk factors are closely associated with QoL. multimorbidity was significantly associated with reduced quality of life. Older adults with multimorbidity had 5 points lower quality of life than those with no chronic diseases.
Conclusions
Multimorbidity along with demographic and lifestyle factors are significantly associated with QoL. Healthcare programmes need to factor in multimorbidity while promoting a healthy and risk-free lifestyle to control modifiable risk factors. Government assistance is necessary for the most economically dependent older population for their day-to-day needs.
Heavy Metal -Induced Oxidative Stress And Alteration In Secretory Proteins In Yeast Isolates
Authors: Bhavya Gurulingaiah , Geetha Nagaraja , Hiremath Kavitha , JOGAIAH SUDISHA
Published: September 2021

In the recent years, yeasts have evolved as potent bioremediative candidates for the detoxification of xenobiotic compounds found in the natural environment. Candida sp. are well studied apart from Saccharomyces in heavy metal detoxification mechanisms. In the current study, Candida parapsilosis strain ODBG2, Candida sp. strain BANG3 and Candida viswanathii strain ODBG4 were isolated from industrial effluents and contaminated ground water were studied for their metal tolerance. Among these three isolates, the metal tolerance was found to be more towards Lead (Pb 2mM), followed by Cadmium (Cd 1.5mM) and Chromium (Cr(VI), 1mM). On further exploring the involvement of primary defensive enzymes in these isolates exhibited towards metal tolerance, the anti-oxidative enzyme Superoxide dismutase (SOD) was found to be prominently high as 25% during first 24h of metal-isolate interaction. In the Catalase (CAT) enzyme assay, it was observed that, the increased enzyme activity at 48h also triggered the activity of peroxidases (PO), which lead to the increase in reduced glutathione (GSH) in the organism by 0.87-1.9 folds, as a metal chelator and also as a second line of defensive molecule. The exoproteome profile showed the early involvement (exponential growth phase) of secreted proteins (low molecular weight) of about ~40-45kDa under Cd and Pb stress (0.5mM). The exoproteome profiling under heavy metal stress in Candida parapsilosis strain ODBG2 and Candida viswanathii strain ODBG4 is the first report.
DNA Methylation Status of RETN and ADIPOQ Genes in Sporadic Colon Cancer
Authors: Al-Harithy Rowyda , abdulsalam Eman Al
Published: September 2021

Background: Colon cancer develops through a complex process that involves epigenetic alterations. Compelling evidence has been achieved that adipocytokines link obesity with colon cancer progression Therefore, understanding the epigenetic modifications in adipokine genes might help in clarifying their role in colon cancer pathogenesis. The aim of the present project was to study the DNA methylation status of RETN and ADIPOQ genes in sporadic colon cancer patients. Methods: 70 cancerous colon tissue and adjacent paired non-cancerous tissue was used to determine the DNA methylation status using methylation-specific polymerase chain reaction (MS-PCR) assay. Quantitative real-time PCR (qRT-PCR) was used to determine the expression level of RETN and ADIPOQ genes. Results: In colon cancer tissues, the CpG sites in the three selected promoter regions of ADIPOQ and RETN were hypermethylated in all samples. DNA methylation level at the CpG sites in exon one of the RETN gene exhibited a lower level in the non-cancerous tissue compared to the cancerous tissue and paired blood samples. The RETN mRNA was upregulated. Conclusion: We postulate that DNA methylation status at the CpG sites in exon one of the RETN gene might help uncover cancer signatures in sporadic colon cancer and may be used as a biomarker. The upregulation of the RETN mRNA level might play a role in sporadic colon cancer tumorigenesis.
mTOR Inhibitor PP242 Increases Antitumor Activity of Sulforaphane by Blocking Akt/mTOR Pathway in Esophageal Squamous Cell Carcinoma
Authors: Lu Zhaoming , Zhang Yalin , Xu Yujia , Wei Huiyun , Zhao Wen , Wang Pengju , Li Yan , Hou Guiqin
Published: September 2021

This study aims to explore the anti-tumor activity of Sulforaphane (SFN) alone and combined with Akt/mTOR pathway inhibitors as well as the potential molecular mechanism in esophageal squamous cell carcinoma (ESCC). MTT assay, clone formation experiment, wound healing assays, flow cytometry, Western blot and xenograft experiment were used to test the effects and molecular mechanism of SFN alone or combined with Akt/mTOR inhibitors on proliferation, migration, cell cycle phase, apoptosis of ESCC cells and tumor growth, respectively. The results showed that SFN significantly inhibited the viability and induced apoptosis of ECa109 and EC9706 cells in a dose-dependent manner by increasing the expression of the apoptotic proteins Cleaved-caspase 9. SFN combined with PP242, but not MK2206 and RAD001, had synergetic inhibition effects on the proliferation of ESCC cells. Moreover, the combination of SFN and PP242 had better inhibiting efficiency on clone formation, migratory, cell cycle phase and the growth of xenografts of ESCC cells, as well as the more powerful apoptosis-inducing effects on ESCC cells. Results of protein expression showed that PP242 abrogated the promotion effects of SFN on p-p70S6K (Thr389) and p-Akt (Ser473). These foundings demonstrated PP242 enhances the anti-tumor activity of SFN by blocking the activation of Akt/mTOR pathway by SFN in ESCC.
Effect of Short- and Long-term Melatonin Treatments on the Reproductive Activity of the Tropical Damselfish Chrysiptera Cyanea
Authors: Imamura Satoshi , Hur Sung-Pyo , Takeuchi Yuki , Badruzzaman Md. , Mahardini Angka , Rizky Dinda , Takemura Akihiro
Published: September 2021

Photoperiod plays a role in controlling the initiation and termination of reproduction in fish. Melatonin is an internal transducer of environmental photoperiod and is involved in regulating reproduction. The present study aimed to examine how melatonin impacts the transcript levels of kisspeptin ( kiss1 and kiss2 ), gonadotropin-releasing hormones ( gnrh1 ), and the β -subunit of gonadotropins ( fshβ and lhβ ) in the brain of the sapphire devil, a tropical damselfish with long photoperiod preference. Feeding mature females with melatonin-containing pellets inhibited increases in the transcript levels of kiss1 , gnrh1 , and lhβ within 3 h. Continuous melatonin treatment for 1 week resulted in oocyte regression and downregulation of kiss2 , gnrh1 , fshβ , and lhβ . When the transcript levels of kiss1 and gnrh1 were measured at 4-h intervals in the brain of sapphire devil, a day–low/night–high fluctuation was observed. The hypothalamic– pituitary–gonadal (HPG) axis may be influenced by melatonin, exerting a negative effect at night because the transcript levels of aralkylamine N -acetyltransferase ( aanat2 ) increased during the scotophase. The expression of aanat2 was higher under short-day than long-day conditions, suggesting that there is a seasonal change in melatonin levels at night. It was concluded that change in photoperiod becomes a proximal factor for controlling the hormone synthesis in the HPG axis through melatonin.
Stability of Rice Mutant Lines By Linear Mixed Model And Suggestion A New Index Based For Yield Performance And Stability
Authors: Sharifi Peyman , Ebadi Ali Akbar , Hallajian Mohammad Taher
Published: September 2021

The authors have requested that this preprint be removed from Research Square.
Polygenic Risk for Coronary Artery Disease in the Scottish and English Population
Authors: Yang Chuhua , Starnecker Fabian , Pang Shichao , Chen Zhifen , Güldener Ulrich , Li Ling , Heinig Matthias , Schunkert Heribert
Published: September 2021

Background: Epidemiological studies have repeatedly observed a markedly higher risk for coronary artery disease (CAD) in Scotland as compared to England. Up to now, it is unclear whether environmental or genetic factors might explain this phenomenon. Methods: Studying UK Biobank we assessed CAD risk based on the Framingham risk score (FRS) and common genetic variants to explore the respective contribution to CAD prevalence in Scotland (n=31,963) and England (n=317,889). We calculated FRS based on sex, age, body mass index, total cholesterol, high density lipoprotein cholesterol, systolic blood pressure, antihypertensive medication, smoking status, and diabetes. We determined the allele frequency of published genome-wide significant risk CAD alleles and a weighted genetic risk score (wGRS) for quantifying genetic CAD risk.Results: Prevalence of CAD was 16% higher in Scotland as compared to England (8.98% vs. 7.68%, P<0.001). By contrast, the FRS predicted a less than 1% higher CAD risk in Scotland (12.5±10.5 vs.12.6±10.6, P=0.03). Likewise, the overall number genome-wide significant variants affecting CAD risk (157.6±7.7 and 157.5±7.7; P=0.12) and a wGRS for CAD (2.49±0.25 in both populations, P=0.14) were remarkably similar in the English and Scottish population. Interestingly, we observed substantial differences with respect to the allele frequencies of individual risk variants. Of the previously described 163 genome-wide significant variants studied here 35 had higher frequencies in Scotland whereas 37 had higher frequencies in England (P<0.001 each).Conclusions: Neither the traditional risk factors included in the FRS nor a GRS based on established common risk alleles explained the higher CAD prevalence in Scotland. However, we observed marked differences in the distribution of individual risk alleles which emphasizes that even geographically and ethnically closely related populations may display relevant differences in the genetic architecture of a common disease.
Large-Scale Protein-Protein Post-Translational Modification Extraction With Distant Supervision And Confidence Calibrated BioBERT
Authors: Elangovan Aparna , Li Yuan , Pires Douglas E.V. , Davis Melissa J. , Verspoor Karin
Published: September 2021

Motivation: Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through post-translational modifications (PTM). However, only 4% of PPIs are annotated with PTMs in biological knowledge databases such as IntAct, mainly performed through manual curation, which is neither time- nor cost-effective. Here we aim to facilitate annotation by extracting PPIs along with their pairwise PTM from the literature by using distantly supervised training data using deep learning to aid human curation. We further assessed model generalisation in a real-world scenario, evaluating its performance on a randomly sampled subset of predictions from 18 million PubMed abstracts. Method: We use the IntAct PPI database to create a distant supervised dataset annotated with interacting protein pairs, their corresponding PTM type, and associated abstracts from the PubMed database. We train an ensemble of BioBERT models – dubbed PPI-BioBERT-x10 – to improve confidence calibration. We extend the use of ensemble average confidence approach with confidence variation to counteract the effects of class imbalance to extract high confidence predictions. Results and conclusion: The PPI-BioBERT-x10 model evaluated on the test set resulted in a modest F1-micro 41.3 (P=58.1, R=32.1). However, by combining high confidence and low variation to identify high quality predictions, tuning the predictions for precision, we retained 19% of the test predictions with 100% precision. We evaluated PPI-BioBERT-x10 on 18 million PubMed abstracts and extracted 1.6 million (546507 unique PTM-PPI triplets) PTM-PPI predictions, and filter ≈5,700 (4584 unique) high confidence predictions. Of the 5700, human evaluation on a small randomly sampled subset shows that the precision drops to 33.7% despite confidence calibration and highlights the challenges of generalisability beyond the test set even with confidence calibration. We circumvent the problem by only including predictions associated with multiple papers, improving the precision to 58.8%. In this work, we highlight the benefits and challenges of deep learning-based text mining in practice, and the need for increased emphasis on confidence calibration to facilitate human curation efforts.
Nitrogen-Doped Porous Carbon Derived From Bimetallic Zeolitic Imidazolate Frameworks For Electrochemical Li+/Na+ Storage
Authors: Dong Shuai , Cui Jiewu , Yu Dongbo , Cao Zhongnan , Yu Cuiping , Zhang Yong , Wu Yucheng
Published: September 2021

Porous carbon is regarded as one of the most promising anode candidates for Li-ion battery and Na-ion battery. We herein demonstrate a series of nitrogen-doped porous carbon (NPC) by simply carbonizing bimetallic ZnCo-containing zeolitic imidazolate frameworks (ZnCo-ZIFs). The nitrogen content, specific surface area, pore size distribution and microstructure of prepared NPC are balanced by adjusting Zn2+/Co2+ molar ratio of ZnCo-ZIFs and carbonization process parameters. It is found that the optimized ZnCo-ZIF-derived NPC shows promise for electrochemical Li+/Na+ storage, which could be attributed to the hierarchical porous structure, large specific surface area and relatively high N-doping content.
Association Study of the SLC1A2 (rs4354668), SLC6A9 (rs2486001) and SLC6A5 (rs2000959) Polymorphisms in Major Depressive Disorder
Authors: Rodek Patryk , Kowalczyk Małgorzata , Kowalski Jan , Owczarek Aleksander , Choręza Piotr , Kucia Krzysztof
Published: September 2021

Background: In recent years, a growing body of evidence highlights a causal link between glutamate and depression. The membrane excitatory amino acid transporter 2 (EAAT2), encoded by SLC1A2 is responsible for the uptake and redistribution of most of the synaptic glutamate. Glycine, an inhibitory neurotransmitter, acts as an obligatory co-agonist of N-methyl-D-aspartate (NMDA) receptors and modulates excitatory neurotransmission. The clearance of synaptic glycine is performed by glycine transporters encoded by SLC6A9 and SLC6A5. Higher synaptic glycine and glutamate levels could enhance the activation of NMDA receptors, therefore counteract the hypofunction of glutamate neurotransmission described in major depressive disorder (MDD). The aim of the study was to assess whether polymorphisms of SCL1A2, SCL6A5 and SCL6A9 play a role in the development of MDD and its clinical picture in the Polish population. Methods: The study group consisted of 161 unrelated Caucasian patients with MDD, and 462 healthy controls. Polymorphisms of SLC1A2, SLC6A5 and SLC6A9 were genotyped with PCR-RLFP and TaqMan assays. The relationship between the studied single nucleotide polymorphisms (SNPs) was assessed based on the comparison of genotype and allele distribution in the study and the control group. The research also evaluated the relationships between the studied polymorphisms and clinical variables such as age of disease onset, number of episodes, duration of depression or severity of symptoms.Results: We found a statistically significant association between SLC1A2 rs4354668 polymorphism and MDD development (the frequency of rs4354668 CC genotype and allele C was 2-fold higher in patients than in the control). Such associations were not detected for SLC6A5 and SLC6A9 polymorphisms. No statistically significant impact of the studied SNPs on clinical variables of MDD was also observed. Conclusions: The results of the current study indicate an association of rs4354668 polymorphism in SCL1A2 with depression development in Polish population. Further studies with larger samples should be performed in the future to clarify the current findings.
Transmission Risk of COVID-19 in High School and College Water Polo
Authors: Kreienkamp Raymond J. , Kreienkamp Christopher J. , Terrill Cindy , Halstead Mark E. , Newland Jason G.
Published: September 2021

Background: Concerns that athletes may be at a higher risk for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission has led to reduced participation in sports during the COVID-19 pandemic. We aimed to assess COVID-19 incidence and transmission during the spring 2021 high school and college water polo seasons across the United States. Methods: This prospective observational study enrolled 1,825 water polo athletes from 54 high schools and 36 colleges. Surveys were sent to coaches throughout the season, and survey data were collected and analyzed. Results: We identified 17 COVID-19 cases among 1,223 high school water polo athletes (1.4%) and 66 cases among 602 college athletes (11.0%). Of these cases, contact tracing suggested that 3 were water polo–associated in high school, and 0 were water polo–associated in college. Quarantine data suggest low transmission during water polo play as only 3 out of 232 (1.3%) high school athletes quarantined for a water polo–related exposure developed COVID-19. In college, 0 out of 54 athletes quarantined for exposure with an infected opponent contracted COVID-19. However, in both high school and college, despite the physical condition of water polo athletes, both high school (47%) and college athletes (21%) had prolonged return to play after contracting COVID-19, indicating the danger of COVID-19, even to athletes. Conclusions: While COVID-19 spread can occur during water polo play, few instances of spread occurred during the spring 2021 season, and transmission rates appear similar to those in other settings, such as school environments.
High-quality Chromosome-scale De Novo Assembly of the Paspalum Notatum ‘Flugge’ Genome
Authors: Yan Zhenfei , Liu Huancheng , Chen Yu , Sun Juan , Ma Lichao , Wang Aihua , Miao Fuhong , Cong Lili , Song Hui , Yin Xue , Wang Qi , Gong Yayun , Yang Guofeng , Wang Zengyu
Published: September 2021

Background: Paspalum notatum is a diploid multi-purpose subtropical herb native to South America. Its chromosome length is 2n=20XX and has a high ecological significance. It is currently widely planted in tropical and subtropical regions. Despite the gene pool of P. notatum being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in Paspalum have been reported. In this study, the complete genome information of P. notatum was established and annotated through sequencing and de novo assembly of its genome. Results: The latest PacBio third-generation HiFi assembly and sequencing revealed that the genome size of P. notatum is 541M. The assembly result is the highest index among the genomes of the gramineous family published so far, with a contig N50=52Mbp, scaffold N50=49Mbp, and BUSCOs=98.1%, accounting for 98.5% of the estimated genome. Genome annotation revealed 36511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research. A comparison of the genome annotation results of P. notatum with other closely related species revealed that it had a close relationship with Zea mays. An analysis of the expansion and contraction of gene families suggested that P. notatum contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits. Conclusion: This study is the first to report the high-quality chromosome-scale-based genome of P. notatum assembled using the latest PacBio third-generation HiFi sequencing reads. The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants. Keywords: Paspalum notatum ‘Flugge’, Genome, De novo assembly, Genome annotation
The Optimized Quantum Dots Mediated Thermometry Reveals the Efficiency of Myosin Extracted from Muscle Mini Bundles
Authors: Li Meishan , Coppo Lucia , Jena Bhanu P. , Larsson Lars
Published: September 2021

Background: The quantum dots (QD) has been investigated as thermometrical sensor in biological microenvironment and applied to measure the muscle efficiency with underlying mechanisms, i.e., a reduction in fluorescent intensity of QD reflects an increase in temperature caused by heat release during ATP hydrolysis, denoting the efficiency of the motor protein myosin. The aim of this study is to optimize the QD mediated thermometry for measuring the efficiency of freshly extracted myosin from muscle mini bundles rather than pre-purified myosin and test this approach in preparations with different myosin isoform.Methods: The protocol of myosin extraction used in the single muscle fiber in vitro motility assay was modified slightly for extracting myosin from the muscle mini bundles. Moreover, the quantitation of extracted myosin was calculated from the total extracted protein since the ratio of myosin to total protein was constant, performing through spectrophotometric measurement of UV absorbance at 280 nm. The change in fluorescence intensity of QD thermometry measurement of myosin ATPase enzymatic reaction was plotted over time, and the slope of the linear negative regression between time course and relatively decreased fluorescence intensity was used to reflect the efficiency of extracted myosin. Results: The optimized QD mediated thermometry is established for evaluating the efficiency of myosin extracted from muscle mini bundles. Moreover, myosin isoform specific differences in the myosin efficiency were observed in comparison between slow myosin and fast myosin, i.e., the low myosin has lower efficiency than fast myosin, evidenced by a higher heat release.Conclusions: The optimized QD mediated thermometric measure of myosin efficiency in muscle mini bundles provides a nanoscale approach to evaluate myosin function based on a minimal amount of muscle, which is essentially required in the muscle research.
SNP-based breeding for broiler resistance to ascites and evaluation of correlated production traits
Authors: Lee Katie P. , Anthony Nicholas B. , Orlowski Sara K. , Rhoads Douglas Duane
Published: September 2021

Background

The goal of this study was to evaluate marker-assisted selection (MAS) in broiler chickens using previously mapped gene regions associated with ascites syndrome incidence. The second-generation MAS products were assessed for impact on ascites phenotype and whether there were associated changes in important production traits. Previously, we used whole genome resequencing (WGR) to fine-map 28 chromosomal regions as associated with ascites phenotype in our experimental ascites broiler line (Relaxed, REL) based on a hypobaric chamber challenge. Genotypes for single nucleotide polymorphisms (SNPs) in mapped regions on chromosomes 2 and 22, were used for MAS in our REL line. After two generations, birds homozygous for the genotypes associated with resistance for both chromosomal regions were established. The MAS F2 generation was then compared to the REL line for ascites susceptibility and 25 production traits.

Results

Selection based on SNPs in the carboxypeptidase Q (CPQ, Gga2) and leucine rich repeat transmembrane neuronal 4 (LRRTM4, Gga22) gene regions resulted in a sex- and simulated altitude- dependent reduction of ascites incidence in two F2 cohorts of the MAS line. Comparisons of the F2 MAS and REL lines for production traits when reared at ambient pressure found no significant negative impacts for feed intake (FI), feed conversion ratio (FCR), or deboned part yields for either sex for two F2 cohorts. There were, however, improvements in the MAS for full-trial body weight gain (BWG), FCR, absolute and relative tender weights, and relative drumstick weight.

Conclusions

These results validate the mapping of the 28 chromosomal regions and demonstrate that fine mapping by WGR is an effective strategy for addressing a complex trait; it also stands as the first successful SNP-based selection program against a complex disease trait, such as ascites. The MAS line is comparable and, in some instances, superior, in growth performance to the REL control while being more resistant to ascites. This study indicates that MAS based on WGR can provide significant breeding potential in agricultural systems.
Brain microvascular endothelial cell dysfunction in an isogenic juvenile iPSC model of Huntington’s disease
Authors: Linville Raleigh , Nerenberg Renée , Grifno Gabrielle , Arevalo Diego , Guo Zhaobin , Searson Peter
Published: September 2021

Huntington’s disease (HD) is an inherited neurodegenerative disease caused by expansion of cytosine–adenine–guanine (CAG) repeats in the huntingtin gene, which leads to neuronal loss and decline in cognitive and motor function. Increasing evidence suggests that blood-brain barrier (BBB) dysfunction may contribute to progression of the disease. Studies in animal models, in vitro models, and post-mortem tissue suggest that disease progression is associated with increased microvascular density, altered cerebral blood flow, and loss of paracellular and transcellular barrier function. Here we report on changes in BBB phenotype due to expansion of CAG repeats using an isogenic pair of induced pluripotent stem cells (iPSCs) differentiated into brain microvascular endothelial-like cells (iBMECs). We show that CAG expansion alters the trajectory of iBMEC differentiation, producing cells with ~ 2-fold lower purity of adherent endothelial cells. CAG expansion is associated with lower transendothelial electrical resistance, lower tight junction protein expression, and unique gene expression profiles, but no significant changes in paracellular permeability. In addition, CAG expansion results in unique responses to pathological and therapeutic perturbations including angiogenic factors, oxidative stress, and osmotic stress. In a tissue-engineered BBB model, iBMECs show subtle changes in phenotype, including differences in cell turnover and immune cell adhesion. Our results further support that CAG expansion in BMECs may alter BBB phenotype during HD.
Preparation of Polyaniline Nanofibers And Experimental Study On Their Electrochemical Properties And Conductivity
Authors: chg Uihoa
Published: September 2021

Among nano polyaniline materials, polyaniline nanofibers are the most important. The low conductivity and poor processability have become the biggest obstacles to the application of polyaniline as a practical material. The excellent characteristics of new polyaniline nanofiber materials can just overcome the shortcomings of Polyaniline in forming and processing. In this study, a new polyaniline nanofiber was prepared by chemical oxidation, its structure was characterized, the mechanism of improving its conductivity was studied, and its superior electrocatalytic activity was evaluated by Electrochemical performance test. The results show that the diameter of polyaniline nanofibers is 20nm ~ 50nm and the fiber length is 2µm ~ 5µm. The structure is uniform and the conductivity can reach 13.5 S/cm. he electrocatalytic activity of polyaniline nanofibers for oxygen evolution and chlorine evolution was systematically tested. It was found that the electrocatalytic activity of polyaniline nanofibers for oxygen evolution was higher than that of polyaniline nanofibers. The electrocatalytic activity of carbon paper electrode prepared by β-PbO2 nano powder is superior to that of traditional chlorine evolution anode Ti/RuO2.
Defective endosome-TGN retrograde transport promotes NLRP3 inflammasome activation
Authors: Ricci Romeo , Zhang Zhirong , Ran Li , Venditti Rossella , Liu Zengzhen , Schürmann Annette , Bonifacino Juan , De Matteis Maria Antonietta
Published: September 2021

Inflammasome complexes are pivotal in the innate immune response to pathogens and other danger signals. The NLRP3 inflammasome is activated in response to a broad variety of cellular stressors. Most of the stimuli act in a potassium efflux-dependent manner but a primary and converging sensing mechanism by the NLRP3 receptor initiating inflammasome assembly remains ill-defined. Here we show that NLRP3 activators disrupt endosome-TGN retrograde transport (ETRT) and lead to localization of NLRP3 to endosomal vesicles. Genetic and pharmacologic perturbation of ETRT leads to accumulation of phosphoinositol-4-phosphate (PI4P) in endosomes to which NLRP3 is recruited. Disruption of ETRT potentiates NLRP3 inflammasome activation in murine and human macrophages in vitro. Mice with defects in ETRT in the myeloid compartment are more susceptible to LPS-induced sepsis showing enhanced mortality and IL-1β serum levels as compared to control animals. Our study thus uncovers that changes in endocytic trafficking mediate NLRP3-dependent inflammatory responses.