bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infection control practices and challenges in Pakistan during the COVID-19 pandemic: a multicentre cross-sectional study
Authors: Abbas Salma , Sultan Faisal 
Published: June 2021

Background: Patient and staff safety at healthcare facilities during outbreaks hinges on a prompt infection prevention and control response. Physicians leading these programmes have encountered numerous obstacles during the pandemic. Aim/objective: The aim of this study was to evaluate infection prevention and control practices and explore the challenges in Pakistan during the coronavirus disease 2019 pandemic. Methods: We conducted a cross-sectional study and administered a survey to physicians leading infection prevention and control programmes at 18 hospitals in Pakistan. Results: All participants implemented universal masking, limited the intake of patients and designated separate triage areas, wards and intensive care units for coronavirus disease 2019 patients at their hospitals. Eleven (61%) physicians reported personal protective equipment shortages. Staff at three (17%) hospitals worked without the appropriate personal protective equipment due to limited supplies. All participants felt overworked and 17 (94%) reported stress. Physicians identified the lack of negative pressure rooms, fear and anxiety among hospital staff, rapidly evolving guidelines, personal protective equipment shortages and opposition from hospital staff regarding the choice of recommended personal protective equipment as major challenges during the pandemic. Discussion: The results of this study highlight the challenges faced by physicians leading infection prevention and control programmes in Pakistan. It is essential to support infection prevention and control personnel and bridge the identified gaps to ensure patient and staff safety at healthcare facilities.
Associations of loneliness and social isolation with physical and mental health among adolescents and young adults
Authors: Christiansen J , Qualter P , Friis K , Pedersen SS , Lund R , Andersen CM , Bekker-Jeppesen M , Lasgaard M 
Published: June 2021

Aims: The present study investigates whether loneliness and social isolation are associated with poor physical and mental health among adolescents and young adults, and whether age and gender play a role in the associations of loneliness and social isolation with mental and physical health. Methods: This study used cross-sectional self-report data from the 2017 Danish Health and Morbidity Surveys titled ‘How are you?’ ( N = 19,890, M = 22.6 years). Results: Logistic regression analyses showed that loneliness and social isolation were independently associated with poor physical and mental health. Loneliness was associated with increased odds of asthma, migraine, osteoarthritis, rheumatoid arthritis, hypertension, slipped disc/back pain, tinnitus, long-term mental illness, depressive symptomatology, anxiety symptomatology and alcohol problems. Social isolation was associated with decreased odds of having migraine, osteoarthritis and alcohol problems, and an increased risk of long-term mental illness and depressive symptomatology. Small age and gender differences were detected. Conclusions: In adolescents and young adults, loneliness and social isolation were associated with poor mental health and loneliness with poor physical health. These findings highlight the need for targeted prevention and intervention initiatives to alleviate loneliness and social isolation.
Rehabilitation Variability Following Femoral Condyle and Patellofemoral Microfracture Surgery of the Knee
Authors: Crowley Stephen G. , Swindell Hasani W. , Saltzman Bryan M. , Ahmad Christopher S. , Popkin Charles A. , Trofa David P. 
Published: June 2021

Objective: To assess the variability of postoperative rehabilitation protocols used by orthopedic surgery residency programs for microfracture of femoral condyle and patellofemoral lesions of the knee. Design: Online postoperative microfracture rehabilitation protocols from US orthopedic programs and the scientific literature were reviewed. A custom scoring rubric was developed to analyze each protocol for the presence of discrete rehabilitation modalities and the timing of each intervention. Results: A total of 18 programs (11.6%) from 155 US academic orthopedic programs’ published online protocols and a total of 44 protocols were analyzed. Seventeen protocols (56.7%) recommended immediate postoperative bracing for femoral condyle lesions and 17 (89.5%) recommended immediate postoperative bracing for patellofemoral lesions. The average time to permitting weight-bearing as tolerated (WBAT) was 6.1 weeks (range, 0-8) for femoral condyle lesions and 3.7 weeks (range, 0-8 weeks) for patellofemoral lesions. There was considerable variation in the inclusion and timing of strength, proprioception, agility, and pivoting exercises. For femoral condyle lesions, 10 protocols (33.3%) recommended functional testing prior to return to sport at an average of 23.3 weeks postoperatively (range, 12-32 weeks). For patellofemoral lesions, 4 protocols (20.0%) recommended functional testing for return to sport at an average of 21.0 weeks postoperatively (range, 12-32 weeks). Conclusion: A minority of US academic orthopedic programs publish microfracture rehabilitation protocols online. Among the protocols currently available, there is significant variability in the inclusion of specific rehabilitation components and timing of many modalities. Evidence-based standardization of elements of postoperative rehabilitation may help improve patient care and subsequent outcomes.
Total Femoral Replacement- A Case Report
Authors: Guerra Jose , Chaghouri Patrick , Guerra Jose Andres , Peters Sophia Lorina 
Published: June 2021

Introduction: Total femoral replacement(TFR) is a well-recognized salvage procedure performed after multiple failed endoprosthetic replacements, which result in severely compromised bone stock and damaged structural integrity. TFR is performed as an alternative to lower limb amputation, restoring femoral integrity and enabling patients to resume ambulation. TFR is expected to be performed more frequently as the worldwide rate of revision arthroplasty increases due to improved patient survival rates and their underlying diseases, exceeding the functional life of endoprosthetic arthroplasty. We present a 74-year-old, overweight woman with an extensive surgical history with respect to her right knee. Her right lower extremity x-rays showed a long-cemented stem knee tumour prosthesis and a Garden 4 subcapital fracture of the ipsilateral hip. Due to multiple surgeries of the knee and femur in the past, a total femoral replacement was required to be performed. The procedure was successful, and the expected outcome was met. A successful procedure performed by a skilled and experienced surgical team, a thorough rehabilitation program, and prompt post-operative management of complications, can overcome the high incidence of infection and dislocation to preserve the limb with improved functionality and reduce pain. TFR is a drastic operative intervention that can preserve the quality of life for most patients.
MiR-206 regulates the Th17/Treg ratio during osteoarthritis
Authors: Ye Xiguang , Lu Qilin , Yang Aofei , Rao Jun , Xie Wei , He Chengjian , Wang Weijun , Li Hao , Zhang Zhiwen 
Published: June 2021

Abstract
Background
The present study aimed to determine the functional role of miR-206 in T helper 17 (Th17)/regulatory T (Treg) cell differentiation during the development of osteoarthritis (OA).

Methods
Patients with OA and healthy controls were recruited for investigating the association between miR-206 and Th17/Treg ratio. Transfection experiments were conducted in CD4+ T cells to verify the mechanism of miR-206 on the balance of Treg/Th17. OA model was constructed to detect the clinical score, histopathological changes and Treg/Th17 ratio. OA model was induced in rats to verify the effect of miR-206 inhibition on Th17/Treg immunoregulation.

Results
High expression of miR-206 was positively correlated with peripheral Th17/Treg imbalance in patients with OA. The interactions between miR-206 and the 3′ untranslated regions (3'-UTR) of suppressor of cytokine signaling-3 (SOCS3) and fork head transcriptional factor 3 (Foxp3) were confirmed by luciferase reporter assays. MiR-206 disturbed the Th17/Treg balance by targeting SOCS3 and Foxp3. In vivo assay demonstrated that antagomiR directed against miR-206 restored Th17/Treg balance during the development of OA.

Conclusion
MiR-206 contributed to the progression of OA by modulating Th17/Treg imbalance, suggesting that miR-206 inhibition might be a promising therapeutic strategy for the treatment of OA.
Thalamo-cortical networks in subtypes of migraine with aura patients
Authors: Coppola Gianluca , Di Renzo Antonio , Tinelli Emanuele , Petolicchio Barbara , Parisi Vincenzo , Serrao Mariano , Porcaro Camillo , Fiorelli Marco , Caramia Francesca , Schoenen Jean , Di Piero Vittorio , Pierelli Francesco 
Published: June 2021

Abstract
Background
We searched for differences in resting-state functional connectivity (FC) between brain networks and its relationship with the microstructure of the thalamus between migraine with pure visual auras (MA), and migraine with complex neurological auras (MA+), i.e. with the addition of at least one of sensory or language symptom.

Methods
3T MRI data were obtained from 20 patients with MA and 15 with MA + and compared with those from 19 healthy controls (HCs). We collected resting state data among independent component networks. Diffusivity metrics of bilateral thalami were calculated and correlated with resting state ICs-Z-scores.

Results
As compared to HCs, both patients with MA and MA + disclosed disrupted FC between the default mode network (DMN) and the right dorsal attention system (DAS). The MA + subgroup had lower microstructural metrics than both HCs and the MA subgroup, which correlated negatively with the strength of DMN connectivity. Although the microstructural metrics of MA patients did not differ from those of HCs, these patients lacked the correlation with the strength of DAS connectivity found in HCs.

Conclusions
The present findings suggest that, as far as MRI profiles are concerned, the two clinical phenotypes of migraine with aura have both common and distinct morpho-functional features of nodes in the thalamo-cortical network.
The effect of cold waves on mortality in urban and rural areas of Madrid
Authors: López-Bueno José Antonio , Navas-Martín Miguel Ángel , Díaz Julio , Mirón Isidro Juan , Luna María Yolanda , Sánchez-Martínez Gerardo , Culqui Dante , Linares Cristina 
Published: June 2021

Abstract
Background
While many studies analyze the effect of extreme thermal events on health, little has been written about the effects of extreme cold on mortality. This scarcity of papers is particularly relevant when we search studies about extreme cold on the health of rural population. Therefore, we tried to analyze the effect of cold waves on urban areas and rural areas from Madrid and to test whether differentiated effects exist between both population classes. For this purpose, we analyzed data from the municipalities with over 10,000 inhabitants for the period from January 1, 2000 through December 31, 2013. Municipalities were classified as urban or rural (Eurostat), and they were grouped into similar climatological zones: Urban Metropolitan Centre (UMC), Rural Northern Mountains (RNM), Rural Centre (RC) and Southern Rural (SR). The dependent variable was the daily mortality rate due to natural causes per million inhabitants (CIE-X: A00-R99) that occurred between the months of November and March for the period. The independent variable was minimum daily temperature (ºC) (Tmin). Social and demographic contextual variables were used, including: population > age 64 (%), deprivation index and housing indicators. The analysis was carried out in three phases: (1) determination of the threshold temperature (Tthreshold) which defines the cold waves; (2) determination of the relative risk (RR) for cold waves using Poisson linear regression (GLM); and (3) using GLM of the binomial family, Odds Ratios (OR) were calculated to analyze the relationship between the frequency of the appearance of cold waves and the socioeconomic variables.

Results
The UMC zone experienced 585 extreme cold events related to attributable increases in the mortality rate. The average number of cold waves in the rural zones was 319. The primary risk factor was the percentage of population over age 64, and the primary protective factor was housing rehabilitation. As a whole, the period experienced more cold waves (1542) than heat waves (1130).

Conclusion
The UMC was more vulnerable than the rural areas. Furthermore, the results support the development of prevention policies, especially considering the fact that cold wave events were more frequent than heat waves.
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
Authors: Akbarinejad Shaya , Hadadian Nejad Yousefi Mostafa , Goudarzi Maziar 
Published: June 2021

Abstract
Background
Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data.

Results
In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads that takes raw reads as the input and detects structural variants of size larger than 50 bp. Our pipeline utilizes state-of-the-art long-read aligners, namely NGMLR and Minimap2, and structural variation callers, videlicet Sniffle and SVIM. We found that by using a neural network, we can extract features from Minimap2 output to detect a subset of reads that provide useful information for structural variation detection. By only mapping this subset with NGMLR, which is far slower than Minimap2 but better serves downstream structural variation detection, we can increase the sensitivity in an efficient way. As a result of using multiple tools intelligently, SVNN achieves up to 20 percentage points of sensitivity improvement in comparison with state-of-the-art methods and is three times faster than a naive combination of state-of-the-art tools to achieve almost the same accuracy.

Conclusion
Since prohibitive costs of using high-coverage data have impeded long-read applications, with SVNN, we provide the users with a much faster structural variation detection platform for PacBio reads with high precision and sensitivity in low-coverage scenarios.
Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
Authors: Ferraro Aileen R. , Ameri Abigail J. , Lu Zefu , Kamei Masayuki , Schmitz Robert J. , Lewis Zachary A. 
Published: June 2021

Abstract
Background
Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes have described accessible chromatin regions, but little work has been done in filamentous fungi.

Results
Here we present a genome-scale characterization of accessible chromatin regions in Neurospora crassa, which revealed characteristic molecular features of accessible and inaccessible chromatin. We present experimental evidence of inaccessibility within heterochromatin regions in Neurospora, and we examine features of both accessible and inaccessible chromatin, including the presence of histone modifications, types of transcription, transcription factor binding, and relative nucleosome turnover rates. Chromatin accessibility is not strictly correlated with expression level. Accessible chromatin regions in the model filamentous fungus Neurospora are characterized the presence of H3K27 acetylation and commonly associated with pervasive non-coding transcription. Conversely, methylation of H3 lysine-36 catalyzed by ASH1 is correlated with inaccessible chromatin within promoter regions. Conclusions: In N. crassa, H3K27 acetylation is the most predictive histone modification for open chromatin. Conversely, our data show that H3K36 methylation is a key marker of inaccessible chromatin in gene-rich regions of the genome. Our data are consistent with an expanded role for H3K36 methylation in intergenic regions of filamentous fungi compared to the model yeasts, S. cerevisiae and S. pombe, which lack homologs of the ASH1 methyltransferase.
Prevalence and molecular characteristics of drug-resistant Mycobacterium tuberculosis in Hainan, China: from 2014 to 2019
Authors: Liu Lin , Zhao Xiujuan , Wu Xingyong , Li Sijing , Liu Biao , Rajaofera Mamy Jayne Nelly , Zeng Yingfei , Dong Sufang , Bei Zheng , Pei Hua , Xia Qianfeng 
Published: June 2021

Abstract
Background
The emergence of antimicrobial resistance against Mycobacterium tuberculosis (M. tuberculosis) has become the major concern in global tuberculosis control due to its limited therapy options and high mortality. However, the clinical and molecular characteristics of drug-resistant strains vary in different geographical areas. Hainan Island located in southern China, is a high drug-resistant tuberculosis burden area. This study aimed to determine the dynamic changes of drug-resistance patterns and drug-related gene mutation types of M. tuberculosis in Hainan from 2014 to 2019.

Results
A total of 1484 culture-confirmed M. tuberculosis were included in this study. It was found that the proportions of drug resistance to isoniazid and rifampin were 31.3 and 31.1% respectively. Overall the proportion of multidrug resistant M. tuberculosis was 24.9%. Multivariate logistic regression analysis showed that age and the treatment history were independent influencing factors of drug resistant tuberculosis. The proportions of drug-resistant tuberculosis in retreatment patients were considerably higher than those in new patients. The most common mutation types of isoniazid were Ser315 → Thr (66.3%), and the most common mutation types of rifampin were Ser531 → Leu (41.5%).

Conclusions
Our data suggests that the prevalence of drug resistant TB remains high in Hainan, and the risks for developing drug resistance with diversified mutation types increased significantly in retreatment patients. These results contribute to the knowledge of the prevalence of drug resistance in Hainan Province and expand the molecular characteristics of drug resistance in China simultaneously.
Expressional diversity of grapevine 3-Hydroxy-3-methylglutaryl-CoA reductase (VvHMGR) in different grapes genotypes
Authors: Zheng Ting , Guan Lubin , Yu Kun , Haider Muhammad Salman , Nasim Maazullah , Liu Zhongjie , Li Teng , Zhang Kekun , Jiu Songtao , Jia Haifeng , Fang Jinggui 
Published: June 2021

AbstractBackground3-Hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a key enzyme in the mevalonate (MVA) pathway, which regulates the metabolism of terpenoids in the cytoplasm and determines the type and content of downstream terpenoid metabolites.ResultsResults showed that grapevine HMGR family has three members, such asVvHMGR1,VvHMGR2, andVvHMGR3. The expression ofVvHMGRsin 'Kyoho' has tissue specificity, for example,VvHMGR1keeps a higher expression,VvHMGR2is the lowest, andVvHMGR3gradually decreases as the fruit development.VvHMGR3is closely related toCsHMGR1andGmHMGR9and has collinearity withCsHMGR2andGmHMGR4. By the prediction of interaction protein, it can interact with HMG-CoA synthase, MVA kinase, FPP/GGPP synthase, diphosphate mevalonate decarboxylase, and participates in the synthesis and metabolism of terpenoids.VvHMGR3have similar trends in expression with some of the genes of carotenoid biosynthesis and MEP pathways.VvHMGR3responds to various environmental and phytohormone stimuli, especially salt stress and ultraviolet (UV) treatment. The expression level ofVvHMGRsis diverse in grapes of different colors and aroma.VvHMGRsare significantly higher in yellow varieties than that in red varieties, whereas rose-scented varieties showed significantly higher expression than that of strawberry aroma. The expression level is highest in yellow rose-scented varieties, and the lowest in red strawberry scent varieties, especially ‘Summer Black’ and ‘Fujiminori’.ConclusionThis study confirms the important role ofVvHMGR3in the process of grape fruit coloring and aroma formation, and provided a new idea to explain the loss of grape aroma and poor coloring during production. There may be an additive effect between color and aroma in the HMGR expression aspect.
Multimorbidity patterns in old adults and their associated multi-layered factors: a cross-sectional study
Authors: Lu Jiao , Wang Yuan , Hou Lihong , Zuo Zhenxing , Zhang Na , Wei Anle 
Published: June 2021

Abstract
Background
Influenced by various factors such as socio-demographic characteristics, behavioral lifestyles and socio-cultural environment, the multimorbidity patterns in old adults remain complex. This study aims to identify their characteristics and associated multi-layered factors based on health ecological model.

Methods
In 2019, we surveyed a total of 7480 participants aged 60+ by using a multi-stage random cluster sampling method in Shanxi province, China. Latent class analysis was used to discriminate the multimorbidity patterns in old adults, and hierarchical regression was performed to determine the multi-layered factors associated with their various multimorbidity patterns.

Results
The prevalence of multimorbidity was 34.70% among the old patients with chronic disease. Over half (60.59%) of the patients with multimorbidity had two co-existing chronic diseases. “Degenerative/digestive diseases”, “metabolic diseases” and “cardiovascular diseases” were three specific multimorbidity patterns. Behavioral lifestyles-layered factors had the most explanatory power for the three patterns, whose proportions of explanatory power were 54.00, 43.90 and 48.15% individually. But the contributions of other multi-layered factors were different in different patterns; balanced diet, medication adherence, the size of family and friendship network, and different types of basic medical insurance might have the opposite effect on the three multimorbidity patterns (p < 0.05).

Conclusions
In management of old patients with multimorbidity, we should prioritize both the “lifestyle change”-centered systematic management strategy and group-customized intervention programs.