bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of genomic predictors of radiation sensitivity using preclinical data
Authors: Manem Venkata S. K. 
Published: August 2021

Abstract
Background
Radiation therapy is among the most effective and commonly used therapeutic modalities of cancer treatments in current clinical practice. The fundamental paradigm that has guided radiotherapeutic regimens are ‘one-size-fits-all’, which are not in line with the dogma of precision medicine. While there were efforts to build radioresponse signatures using OMICS data, their ability to accurately predict in patients is still limited.

Methods
We proposed to integrate two large-scale radiogenomics datasets consisting of 511 with 23 tissues and 60 cancer cell lines with 9 tissues to build and validate radiation response biomarkers. We used intrinsic radiation sensitivity, i.e., surviving fraction of cells (SF2) as the radiation response indicator. Gene set enrichment analysis was used to examine the biological determinants driving SF2. Using SF2 as a continuous variable, we used five different approaches, univariate, rank gene ensemble, rank gene multivariate, mRMR and elasticNet to build genomic predictors of radiation response through a cross-validation framework.

Results
Through the pathway analysis, we found 159 pathways to be statistically significant, out of which 54 and 105 were positively and negatively enriched with SF2. More importantly, we found cell cycle and repair pathways to be enriched with SF2, which are inline with the fundamental aspects of radiation biology. With regards to the radiation response gene signature, we found that all multivariate models outperformed the univariate model with a ranking based approach performing well compared to other models, indicating complex biological processes underpinning radiation response.

Conclusion
To summarize, we found biological processes underpinning SF2 and systematically compared different machine learning approaches to develop and validate predictors of radiation response. With more patient data available in the future, the clinical value of these biomarkers can be assessed that would allow for personalization of radiotherapy.
The effect of depressive symptoms on pain in a substance-using population with persistent pain: a cross-sectional cohort study
Authors: Voon Pauline , Choi Jin Cheol , Hayashi Kanna , Milloy M-J , Buxton Jane , Kerr Thomas 
Published: August 2021

Abstract
Background
In light of the ongoing opioid overdose crisis, there is an urgent need for research on the impacts of mental health among people presenting with concurrent pain and substance use. This study examined the effect of depressive symptoms on pain severity and functional interference among people who use drugs (PWUD) during a community-wide overdose crisis.

Methods
From December 1st 2016 to December 31st 2018, 288 participants in two cohort studies of PWUD in Vancouver, Canada completed interviewer-administered questionnaires that included the Brief Pain Inventory and PROMIS Emotional Distress–Depression instruments. Generalized linear regression modelling (GLM) was used to examine the cross-sectional effect of depressive symptoms and other confounding factors on pain severity and interference.

Results
Moderate to severe depressive symptoms were significantly associated with greater pain-related functional interference (adjusted β = 1.24, 95% confidence interval [CI] = 0.33–2.15), but not significantly associated with greater average pain severity (adjusted β = 0.22, 95% CI = − 0.3 – 0.82), when controlling for confounding variables. Reported daily heroin use (adjusted β = 1.26, 95% CI = 0.47–2.05) and non-fatal overdose (adjusted β = 1.02, 95% CI = 0.08–1.96) were also significantly associated with greater pain-related functional interference.

Conclusions
In a substance-using population, greater pain-related functional interference was positively associated with depressive symptoms as well as overdose and daily heroin use. These findings emphasize the need to address the functional impact of pain, mental health comorbidity, and high-risk substance use that may contribute to overdose and other harms.
E- Learning experience of the medical profession’s college students during COVID-19 pandemic in Saudi Arabia
Authors: Al Zahrani Eidan M. , Al Naam Yaser A. , AlRabeeah Saad M. , Aldossary Deemah N. , Al-Jamea Lamiaa H. , Woodman Alexander , Shawaheen Mohammad , Altiti Osama , Quiambao Jenifer V. , Arulanantham Zechariah J. , Elsafi Salah H. 
Published: August 2021

AbstractBackgroundWorldwide, most of educational institutions have moved to online electronic learning methods because of the COVID-19 pandemic. On March 8, 2020, the Saudi Ministry of Education announced remote learning for public and private schools and universities as a preventive and precautionary measure to curb the spread of the coronavirus. The objective of this study was to explore the e-learning experience of the students of the colleges of health sciences with regard to the technical preparedness, academic achievements, e-learning advantages and limitations. A well-structured and validated questionnaire on a five-point Likert scale and open-ended questions about their e-learning experience was distributed to a heterogeneous purposive sample of the health sciences students in Saudi Arabian universities.ResultsOf the 1288 respondents, of various demographical features a relatively higher proportion of 58.2 % agreed that they had enough information about the online learning. However, the proportion who reported receiving adequate guidance, technical support, and having satisfactory hardware and internet access to online learning were 48.1 %, 42, and 35.4 %, respectively. Of all participants, 40.8 % agreed that they had gained a good understanding of their courses learning outcomes. Only 30.0 % agreed that the quality of the online teaching was similar to traditional classes and 56.1 % agreed that the online learning is unsuitable for the medical sciences studies.E-learning advantages mentioned were the flexible accessibility of the learning materials, time, effort, and money saving, acquiring and improving technical and self-learning skills, health safety, interaction without shyness, and better academic accomplishment. On the other hand, disadvantages and difficulties included inadequate tools to facilitate online learning, poor internet connection, lack of technological skills by the educators and students. In addition, there was inadequate or lack of practical classes, lack of a unified clear policy for the conduct of online classes and exams and grade distribution, limited online exam time.ConclusionsThe sudden shift to e-learning without prior preparedness has revealed some pitfalls that need to be adjusted. The initial findings were considered satisfactory for such a new experience for both learners and students. However, there is a great chance for improving and expanding the e-learning process.
Untargeted metabolomic approach to study the serum metabolites in women with polycystic ovary syndrome
Authors: Yu Ying , Tan Panli , Zhuang Zhenchao , Wang Zhejiong , Zhu Linchao , Qiu Ruyi , Xu Huaxi 
Published: August 2021

Abstract
Background
Polycystic ovary syndrome (PCOS) is not only a kind of common endocrine syndrome but also a metabolic disorder, which harms the reproductive system and the whole body metabolism of the PCOS patients worldwide. In this study, we aimed to investigate the differences in serum metabolic profiles of the patients with PCOS compared to the healthy controls.

Material and methods
31 PCOS patients and 31 matched healthy female controls were recruited in this study, the clinical characteristics data were recorded, the laboratory biochemical data were detected. Then, we utilized the metabolomics approach by UPLC-HRMS technology to study the serum metabolic changes between PCOS and controls.

Results
The metabolomics analysis showed that there were 68 downregulated and 78 upregulated metabolites in PCOS patients serum compared to those in the controls. These metabolites mainly belong to triacylglycerols, glycerophosphocholines, acylcarnitines, diacylglycerols, peptides, amino acids, glycerophosphoethanolamines and fatty acid. Pathway analysis showed that these metabolites were enriched in pathways including glycerophospholipid metabolism, fatty acid degradation, fatty acid biosynthesis, ether lipid metabolism, etc. Diagnosis value assessed by ROC analysis showed that the changed metabolites, including Leu–Ala/Ile–Ala, 3-(4-Hydroxyphenyl) propionic acid, Ile–Val/Leu–Val, Gly–Val/Val–Gly, aspartic acid, DG(34:2)_DG(16:0/18:2), DG(34:1)_DG(16:0/18:1), Phe–Trp, DG(36:1)_DG(18:0/18:1), Leu–Leu/Leu–Ile, had higher AUC values, indicated a significant role in PCOS.

Conclusion
The present study characterized the difference of serum metabolites and related pathway profiles in PCOS patients, this finding hopes to provide potential metabolic markers for the prognosis and diagnosis of this disease.
Linkage of microbial living communities and residues to soil organic carbon accumulation along a forest restoration gradient in southern China
Authors: Zhang Shuo , Deng Qi , Wang Ying-Ping , Chen Ji , Yu Mengxiao , Fang Xi , He Hongbo , Chen Jinlei , Xu Pingping , Wang Shenhua , Yan Junhua 
Published: August 2021

Abstract
Background
Forest restoration has been considered an effective method to increase soil organic carbon (SOC), whereas it remains unclear whether long-term forest restoration will continuously increase SOC. Such large uncertainties may be mainly due to the limited knowledge on how soil microorganisms will contribute to SOC accumulation over time.

Methods
We simultaneously documented SOC, total phospholipid fatty acids (PLFAs), and amino sugars (AS) content across a forest restoration gradient with average stand ages of 14, 49, 70, and > 90 years in southern China.

Results
The SOC and AS continuously increased with stand age. The ratio of fungal PLFAs to bacterial PLFAs showed no change with stand age, while the ratio of fungal AS to bacterial AS significantly increased. The total microbial residue-carbon (AS-C) accounted for 0.95–1.66 % in SOC across all forest restoration stages, with significantly higher in fungal residue-C (0.68–1.19 %) than bacterial residue-C (0.05–0.11 %). Furthermore, the contribution of total AS-C to SOC was positively correlated with clay content at 0–10 cm soil layer but negatively related to clay content at 10–20 cm soil layer.

Conclusions
These findings highlight the significant contribution of AS-C to SOC accumulation along forest restoration stages, with divergent contributions from fungal residues and bacterial residues. Soil clay content with stand age significantly affects the divergent contributions of AS-C to SOC at two different soil layers.
Landslide Susceptibility Mapping of Urban Areas: Logistic Regression and Sensitivity Analysis applied to Quito, Ecuador
Authors: Puente-Sotomayor Fernando , Mustafa Ahmed , Teller Jacques 
Published: August 2021

AbstractAlthough the Andean region is one of the most landslide-susceptible areas in the world, limited attention has been devoted to the topic in this context in terms of research, risk reduction practice, and urban policy. Based on the collection of landslides data of the Andean city of Quito, Ecuador, this article aims to explore the predictive power of a binary logistic regression model (LOGIT) to test secondary data and an official multicriteria evaluation model for landslide susceptibility in this urban area. Cell size resampling scenarios were explored as a parameter, as the inclusion of new “urban” factors. Furthermore, two types of sensitivity analysis (SA), univariate and Monte Carlo methods, were applied to improve the calibration of the LOGIT model. A Kolmogorov–Smirnov (K-S) test was included to measure the classification power of the models. Charts of the three SA methods helped to visualize the sensitivity of factors in the models. The Area Under the Curve (AUC) was a common metric for validation in this research. Among the ten factors included in the model to help explain landslide susceptibility in the context of Quito, results showed that population and street/road density, as novel “urban factors”, have relevant predicting power for landslide susceptibility in urban areas when adopting data standardization based on weights assigned by experts. The LOGIT was validated with an AUC of 0.79. Sensitivity analyses suggested that calibrations of the best-performance reference model would improve its AUC by up to 0.53%. Further experimentation regarding other methods of data pre-processing and a finer level of disaggregation of input data are suggested. In terms of policy design, the LOGIT model coefficient values suggest the need for a deep analysis of the impacts of urban features, such as population, road density, building footprint, and floor area, at a household scale, on the generation of landslide susceptibility in Andean cities such as Quito. This would help improve the zoning for landslide risk reduction, considering the safety, social and economic impacts that this practice may produce.
A systematic review of qualitative literature on antimicrobial stewardship in Sub-Saharan Africa
Authors: Porter George James , Owens Stephen , Breckons Matthew 
Published: August 2021

Abstract
Background
Antibiotic resistance is a major problem in every region of the globe and Sub-Saharan Africa (SSA) is no exception. Several systematic reviews have addressed the prevalence of resistant organisms but few have examined the underlying causes in this region. This systematic review of qualitative literature aims to highlight barriers and facilitators to antimicrobial stewardship in SSA.

Methods
A literature search of Embase and MEDLINE(R) was carried out. Studies were included if they were in English, conducted in SSA, and reported qualitative data on the barriers and facilitators of antimicrobial stewardship or on attitudes towards resistance promoting behaviours. Studies were screened with a simple critical appraisal tool. Secondary constructs were extracted and coded into concepts, which were then reviewed and grouped into themes in light of the complete dataset.

Results
The literature search yielded 169 results, of which 14 studies from 11 countries were included in the final analysis. No studies were excluded as a result of the critical appraisal. Eight concepts emerged from initial coding, which were consolidated into five major themes: ineffective regulation, health system factors, clinical governance, patient factors and lack of resources. The ineffective regulation theme highlighted the balance between tightening drugstore regulation, reducing over-the-counter sale of antibiotics, and maintaining access to medicines for rural communities. Meanwhile, health system factors explored the tension between antimicrobial stewardship and the need of pharmacy workers to maintain profitable businesses. Additionally, a lack of resources, actions by patients and the day-to-day challenges of providing healthcare were shown to directly impede antimicrobial stewardship and exacerbate other factors which promote resistance.

Conclusion
Antibiotic resistance in SSA is a multi-faceted issue and while limited resources contribute to the problem they should be viewed in the context of other factors. We identify several contextual factors that affect resistance and stewardship that should be considered by policy makers when planning interventions. This literature base is also incomplete, with only 11 nations accounted for and many studies being confined to regions within countries, so more research is needed. Specifically, further studies on implementing stewardship interventions, successful or not, would be beneficial to inform future efforts.
Are we withholding the most effective treatment for severe depression from our patients?
Authors: McGilloway Angela 
Published: August 2021

SUMMARYIn response to an article on recent advances in the use of ECT for depression, this commentary supports earlier and more extensive use of the treatment. It challenges the belief that ECT is associated with a higher risk of cognitive deficits and mortality and points out its rapid effect compared with antidepressant medication. It calls for clinicians to remain up to date regarding ECT and consider its opportune use in severe depression.
Augmenting Real-World Data Through Modeling Key Clinical Trial Eligibility Criteria: An Example of Patients With Non–small-Cell Lung Cancer Treated With Pembrolizumab
Authors: Jemielita Thomas , Li Xiaoyun (Nicole) , Burke Thomas , Liaw Kai-Li , Zhou Wei , Chen Cong 
Published: August 2021

PURPOSE To compare and characterize baseline characteristics and overall survival (OS) differences by key oncology eligibility criteria for real-world patients from the Flatiron Health database with advanced non–small-cell lung cancer (NSCLC) who received pembrolizumab monotherapy. METHODS Real world data (RWD) were from the Flatiron Health advanced NSCLC database and include patients who initiated pembrolizumab monotherapy (first, second, or third line of therapy) by November 30, 2019. At the data cutoff (May 31, 2020), the median survival follow-up time was 8.4 months. Eligible patients satisfy the criteria of Eastern Cooperative Oncology Group performance status of 0/1 and laboratory values indicative of adequate organ function. RWD were analyzed for all patients and patients with a programmed cell death ligand-1 tumor proportion score ≥ 1%. Patients were divided into three categories: ineligible, eligible, and unknown (who satisfy all observed criteria, with at least one missing). An augmented population was also formed, which combines the latter two groups through a propensity-based adjustment. RESULTS At the data cutoff, N = 3,877 patients with NSCLC received pembrolizumab monotherapy (1L = 2,682, 2L = 946, and 3L = 249). OS was consistently lower for the ineligible with similar survival for the eligible and augmented. Among all patients, the median OS in months (95% CI) was 8.2 (7.5 to 9.6), 16.3 (14.5 to 18.4), 16.4 (15.1 to 19.3), and 16.8 (15.6 to 18.5) for the ineligible (47%, n = 1,827), unknown (27%, n = 1,045), eligible (26%, n = 1,005), and augmented, respectively. The results were similar for patients with a programmed cell death ligand-1 tumor proportion score ≥ 1%. CONCLUSION Real-world patients who received pembrolizumab monotherapy and meet key clinical eligibility criteria exhibited similar baseline characteristics and OS profiles as the unknown and augmented patient groups. Population augmentation is a feasible approach for improving the power of RWD analysis.
Online Platform to Assess Complex Social Relationships and Patient-Reported Outcomes Among Adolescent and Young Adult Cancer Survivors
Authors: Poudel Pragya G. , Bauer Hailey E. , Srivastava D. Kumar , Krull Kevin R. , Hudson Melissa M. , Robison Leslie L. , Wang Zhaoming , Huang I-Chan 
Published: August 2021

PURPOSE Social integration and relationship issues have been understudied among adolescent and young adult (AYA) cancer survivors. This study compared social relationships (social networks, support, and isolation) between AYA cancer survivors and noncancer controls, and identified social integration mechanisms through which the cancer experience influences patient-reported outcomes (PROs). MATERIALS AND METHODS One hundred two AYA cancer survivors and 102 age, sex, and race-matched noncancer controls from a national Internet panel completed an online survey to identify up to 25 of closest friends and relatives whom they have contacted within the past 2 years. Participants' interpersonal connections were used to create a social network index. The Duke-UNC Functional Social Support Questionnaire, UCLA Loneliness Scale, and PROMIS-29 Profile were used to measure social support, perceived isolation or loneliness, and PROs (physical functioning, pain interference, fatigue, anxiety, and depression domains), respectively. Path analysis tested effects of cancer experience on PROs using serial social relationship variables as mediators. RESULTS Compared with controls, survivors of lymphoma, leukemia, and solid tumor had better social networks; however, survivors of solid tumor and central nervous system malignancies had higher perceived loneliness (all P values < .05). Cancer experience was directly associated with poor PROs ( P values < .05 for all domains except fatigue) and indirectly associated through the social network-support-loneliness pathway (all P values < .05). Survivors with higher loneliness had lower physical functioning and higher pain interference, fatigue, anxiety, and depression versus controls with lower loneliness (all P values < .05). CONCLUSION Compared with controls, survivors were more socially connected but experienced greater loneliness, which was associated with poorer PROs. Screening social integration issues during follow-up care and providing appropriate interventions are warranted.
Impact of a short-time exposure to different temperatures on wakening time of Vertigo antivertigo (Draparnaud, 1801) (Gastropoda: Eupulmonata: Vertiginidae)
Authors: Książkiewicz-Parulska Zofia 
Published: August 2021

I checked experimentally how a short-time exposure to different temperatures: 1 °C, 24 °C and 34 °C in a high humidity affects wakening time of Vertigo antivertigo (Draparnaud). The snails were exposed to experimental conditions for 48 hours (each snail in a separate test tube, provided with food and a source of calcium). After that time, all the individuals were transferred to room temperature (24 °C) for counting the time needed for wakening. The shortest wakening time was noted for snails kept at 1 °C, the longest – for snails kept at room temperature of 24 °C.
Growth monitoring and mortality risk in low birthweight infants: a birth cohort study in Burkina Faso
Authors: Mwangome Martha , Ngari Moses , Bahwere Paluku , Kabore Patrick , McGrath Marie , Berkley James A. 
Published: August 2021

Background: Wasting and underweight in infancy is an increasingly recognised problem but consensus on optimum assessment is lacking. In particular, there is uncertainty on how to interpret anthropometry among low birth weight (LBW) infants who may be growing normally. This research aimed to determine growth of infants from birth to two months (around age of vaccination) and the mortality risk of underweight LBW infants compared to normal birth weight (NBW) infants at two and six months age. Methods: A secondary analysis of a birth cohort of 1103 infants in Burkina Faso was conducted. Anthropometry was performed monthly from 0 to 12 months. We assessed associations with mortality using Cox proportional hazards models and assessed discriminatory values using area under receiver operating characteristics curves. Results: Eighty-six (7.8%) children died by age one year, 26/86 (30%) and 51/86 (59%) within two and six months, respectively. At age two months, weight gain since birth did not better discriminate mortality risk than current weight-for-age (P=0.72) or mid-upper arm circumference (P=0.21). In total, 227 (21%) LBW infants had increased risk of mortality: adjusted hazards ratio (aHR) 3.30 (95%CI 2.09 to 4.90). Among infants who were underweight at two and six months, LBW infants (64% and 49%, respectively) were not at reduced risk of death compared to NBW infants (aHR 2.63 (95%CI 0.76 to 9.15) and 2.43 (95%CI 0.74 to 7.98), respectively). Conclusion: Assessing weight gain since birth does not offer advantages over immediate anthropometry for discriminating mortality risk. LBW infants who are later identified as underweight require care to help prevent mortality.