bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nurses’ perception of workplace discrimination
Authors: ZareKhafri Fatemeh , Torabizadeh Camellia , Jaberi Azita 
Published: February 2022

Background: Discrimination and injustice are big obstacles in nurses’ way to socialization and are among the major clinical challenges faced by nurses. Workplace discrimination is associated with such negative consequences as stress, fatigue, demoralization, loss of professional commitment, tension and conflicts at work, and resignation. A review of literature shows that not much research has been dedicated to workplace discrimination in nursing. Objective: This study aims to investigate nurses’ perception of workplace discrimination. Method: This cross-sectional study was conducted in the hospitals affiliated with a university of medical sciences in the largest city in the south of Iran in 2019. The participants consisted of 597 nurses who were selected through stratified random sampling. Data were collected using a researcher-made workplace discrimination questionnaire and analyzed in SPSS v. 21. Findings: The mean of the nurses’ workplace discrimination scores was found to be 102.57 ± 14.5, which is considered as moderate. The nurses’ mean scores for the dimensions of vertical and horizontal discrimination (44.53 ± 6.8), consequences of discrimination (20.52 ± 5.55), and unfair promotion (12.38 ± 2.44) were moderate. As for the two other dimensions of workplace discrimination, namely, gender discrimination (14.41 ± 3.28) and cultural-organizational discrimination (11.88 ± 2.99), the participants’ mean scores were low. There was a significant relationship between the nurses’ workplace discrimination mean score on the one hand and their employment status (p = 0.016) and work experience (p = 0.002) on the other. However, the nurses’ workplace discrimination mean score was not found to correlate with their level of education (p = 0.65), marital status (p = 0.274), and gender (p = 0.479). Ethical consideration: This study has been approved by the ethics committee of the university. All the participants had signed the written informed consent form before participation. Conclusion: Hospital managers should take measures to reduce discrimination and establish organizational justice to raise nurses’ morale and improve the quality of their performance as caregivers.
Nimotuzumab as Additional Therapy for GLIOMA in Pediatric and Adolescent: A Systematic Review
Authors: Parenrengi Muhammad A , Suryaningtyas Wihasto , Al Fauzi Asra , Hafid Bajamal Abdul , Kusumastuti Kurnia , Utomo Budi , Muslim Hidayat Thamrin Ahmad , Sulistiono Bagus 
Published: February 2022

Introduction Pediatric gliomas represent the most common brain tumor in children and its higher grades are associated with higher recurrence and low survival rate. All therapeutic modalities are reported to be insufficient to achieve satisfactory result, with follow-up treatment such as adjuvant radiotherapy and chemotherapy recommended to increase survival and hinder tumor progression. Nimotuzumab is a monoclonal antibody that acts as an inhibitor of epidermal growth factor receptor found on the surface of glioma cells and had been studied for its usage in pediatric gliomas in recent years. Methods A systematic review is performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. A through literature search was conducted on PubMed, Scopus, Cochrane, and clinicaltrials.gov database. Articles were selected systematically based on the PRISMA protocol and reviewed completely. The relevant data were summarized and discussed. We measured overall survival, progression-free survival, and adverse Events (AE) for nimotuzumab usage as an adjunct therapy in pediatric glioma population. Result From 5 studies included for qualitative analysis, 151 patients are included with overall survival (OS) that vary from 3.2–22.8 mo, progression-free survival (PFS) from 1.7–21.6 mo, and relatively low serious adverse events (0–21) are recorded. Follow-up ranged from 2.4–66 mo with four studies reporting diffuse intrinsic pontine glioma (DIPG) patients and only one study reporting nimotuzumab usage in pediatric high-grade glioma (HGG) patients with better outcome in HGG patients than DIPG. Conclusion There are no significant differences in the PFS and OS of nimotuzumab as adjunct therapy for pediatric compared to result of standard therapy in majority of previous studies. There were also no differences in the AE of nimotuzumab for pediatric glioma between studies, and low event of serious adverse events indicating its safety. But still there is an evidence of possible benefit of nimotuzumab as adjuvant therapy in pediatric glioma. We recommend further studies with larger number of patients that may lead to possibly different results. There should also be more studies with better level of evidence to further validate the effect of nimozutumab on pediatric glioma.
Nonoperative Management of Humerus Fractures in Patients With Ispilateral Hemiparesis or Hemiplegia
Authors: Patel Raahil S. , Bartoletta John J. , Munaretto Nicholas F. , Tagliero Adam J. , Rhee Peter C. 
Published: February 2022

Background: Patients with upper limb dysfunction from a brain injury often have different goals of treatment and expectations following a fracture of the upper extremity. This study retrospectively reviewed outcomes of nonoperative management of acute humerus fractures in patients with severe ipsilateral hemiparesis or hemiplegia. Methods: Patients who had sustained an acute humerus fracture managed nonoperatively, greater than 1 year following an upper motor neuron (UMN) injury resulting in ipsilateral severe hemiparesis or hemiplegia at a single tertiary care center from 1988 to 2019, were reviewed. Fractures were classified using the AO-Müller/Orthopaedic Trauma Association and/or Neer classifications. Primary outcome measures included House classification level of function, pain, achievement of and time to radiographic union, and the need for subsequent surgical procedures. Results: Ten distinct nonoperatively managed humerus fractures—3 proximal (11A23), 5 mid-shaft (12A2b = 1, 12A2c = 2, 12A3a = 1, 12A2b = 1), and 2 distal (13A2 = 1, 13 C1 = 1)—were identified in 8 patients (6 women and 2 men) with ipsilateral hemiparesis or hemiplegia. The median radiographic follow-up was 20 months (range: 78 days to 12 years). The median clinical follow-up was 33.5 months (range: 100 days to 12 years). All patients presented with severe pain that was absent at final follow-up. Radiographic union was achieved in all patients with a mean time to union of 90.9 ± 39.3 days (range: 35-185 days). No patients required operative management. Conclusions: Nonoperative management of humerus fractures in patients with an ipsilateral UMN injury might result in reliable pain relief and union without the need for further surgical intervention. Management of humerus fractures in this patient population should be individualized toward their goals of care.
Effect of the COVID-19 Pandemic on Sports-Related Injuries Evaluated in US Emergency Departments
Authors: Sabbagh Ramsey S. , Shah Nihar S. , Kanhere Arun P. , Hoge Connor G. , Thomson Cameron G. , Grawe Brian M. 
Published: February 2022

Background: Organized athletics are undergoing a gradual resumption after a prolonged hiatus in 2020 because of the coronavirus disease 2019 (COVID-19) pandemic. Purpose/Hypothesis: The purpose of this study was to evaluate the effect of the 2020 COVID-19 period on emergency department (ED) visits for sports-related injuries in the United States. It was hypothesized that such visits decreased in response to the pandemic conditions. Study Design: Descriptive epidemiology study. Methods: A selection of sports (baseball, basketball, softball, soccer, American football, weightlifting, track and field, martial arts, boxing, golf, personal fitness, cycling, tennis, and ice hockey) were classified as being an organized team, organized individual, or nonorganized sport. The National Electronic Injury Surveillance System database was then queried for ED visits for sports-related injuries between January 1, 2018, and December 31, 2020, and we compared weighted national injury estimates and injury characteristics from athletes presenting to EDs in 2018 and 2019 versus those from the 2020 COVID-19 pandemic period and between March 1 and May 31, 2020 (government-imposed lockdown period). Bivariate comparisons between variables were conducted using chi-square analysis, with strength of association assessed using odds ratios. Results: The 164,151 unweighted cases obtained from the query resulted in a weighted national estimate of 5,664,795 sports-related injuries during the study period. Overall, there was a 34.6% decrease in sports-related ED visits in 2020 compared with the yearly average between 2018 and 2019 (baseline). The number of ED visits in 2020 decreased by 53.9% versus baseline for injuries incurred by participation in an organized team sport and by 34.9% for injuries incurred by participation in an organized individual sport. The number of ED visits during the 2020 lockdown period decreased by 76.9% versus baseline for injuries incurred by participation in an organized team sport and by 65.8% for injuries incurred by participation in an organized individual sport. Injuries sustained while participating in a nonorganized sport remained relatively unaffected and decreased by only 8.1% in 2020. Conclusion: ED visits in the United States for injuries sustained while participating in an organized team or individual sport underwent a decrease after the beginning of the COVID-19 pandemic in 2020, especially during the lockdown period.
Impact of DHCWs’ Safety Perception on Vaccine Acceptance and Adoption of Risk Mitigation Strategies
Authors: Coker M.O. , Subramanian G. , Davidow A. , Fredericks-Younger J. , Gennaro M.L. , Fine D.H. , Feldman C.A. 
Published: February 2022

Objectives: To estimate the association between safety perception on vaccine acceptance and adoptions of risk mitigation strategies among dental health care workers (DHCWs). Methods: A survey was emailed to DHCWs in the New Jersey area from December 2020 to January 2021. Perceived safety from regular SARS-CoV-2 testing of self, coworkers, and patients and its association with vaccine hesitancy and risk mitigation were ascertained. Risk Mitigation Strategy (RiMS) scores were computed from groupings of office measures: 1) physical distancing (reduced occupancy, traffic flow, donning of masks, minimal room crowding), 2) personal protective equipment (fitted for N95; donning N95 masks; use of face shields; coverings for head, body, and feet), and 3) environmental disinfection (suction, air filtration, ultraviolet, surface wiping). Results: SARS-CoV-2 testing of dental professionals, coworkers, and patients were perceived to provide safety at 49%, 55%, and 68%, respectively. While dentists were least likely to feel safe with regular self-testing for SARS-CoV-2 (P < 0.001) as compared with hygienists and assistants, they were more willing than hygienists (P = 0.004; odds ratio, 1.79 [95% CI, 1.21 to 2.66]) and assistants (P < 0.001; odds ratio, 3.32 [95% CI, 1.93 to 5.71]) to receive the vaccine. RiMS scores ranged from 0 to 19 for 467 participants (mean [SD], 10.9 [2.9]). RiMS scores did not significantly differ among groups of DHCWs; however, mean RiMS scores were higher among those who received or planned to receive the COVID-19 vaccine than those with who did not (P = 0.004). DHCWs who felt safer with regular testing had greater RiMS scores than those who did not (11.0 vs. 10.3, P = 0.01). Conclusions: Understanding DHCWs’ perception of risk and safety is crucial, as it likely influences attitudes toward testing and implementation of office risk mitigation policies. Clinical studies that correlate risk perception and RiMS with SARS-CoV-2 testing are needed to demonstrate the effectiveness of RiMS in dental care settings. Knowledge Transfer Statement: Educators, clinicians, and policy makers can use the results of this study when improving attitudes toward testing and implementation of risk mitigation policies within dental offices, for current and future pandemics.
Patterns of comorbidity and multimorbidity among middle-aged and elderly women in peri-urban Tanzania
Authors: Stieglitz Laura-Marie , Bärnighausen Till , Leyna Germana H. , Kazonda Patrick , Killewo Japhet , Rohr Julia K. , Kohler Stefan 
Published: February 2022

Background Multimorbidity poses an increasing challenge to health care systems in Sub-Saharan Africa. We studied the extent of multimorbidity and patterns of comorbidity among women aged 40 years or older in a peri-urban area of Dar es Salaam, Tanzania. Methods We assessed 15 chronic conditions in 1528 women who participated in a cross-sectional survey that was conducted within the Dar es Salaam Urban Cohort Study (DUCS) from June 2017 to July 2018. Diagnoses of chronic conditions were based on body measurements, weight, blood testing, screening instruments, and self-report. Results The five most prevalent chronic conditions and most common comorbidities were hypertension (49.8%, 95% CI 47.2 to 52.3), obesity (39.9%, 95% CI 37.3 to 42.4), anemia (36.9%, 95% CI 33.3 to 40.5), signs of depression (32.5%, 95% CI 30.2 to 34.9), and diabetes (30.9%, 95% CI 27.6 to 34.2). The estimated prevalence of multimorbidity (2+ chronic conditions) was 73.8% (95% CI 71.2 to 76.3). Women aged 70 years or older were 4.1 (95% CI 1.5 to 10.9) times mores likely to be affected by multimorbidity and had 0.7 (95% CI 0.3 to 1.2) more chronic conditions than women aged 40 to 44 years. Worse childhood health, being widowed, not working, and higher food insecurity in the household were also associated with a higher multimorbidity risk and level. Conclusion A high prevalence of multimorbidity in the general population of middle-aged and elderly women suggests substantial need for multimorbidity care in Tanzania. Comorbidity patterns can guide multimorbidity screening and help identify health care and prevention needs.
Lasting shift in the gut microbiota in patients with acute myeloid leukemia
Authors: Rashidi Armin , Ebadi Maryam , Rehman Tauseef Ur , Elhusseini Heba , Halaweish Hossam Fathi , Kaiser Thomas , Holtan Shernan G. , Khoruts Alexander , Weisdorf Daniel J. , Staley Christopher 
Published: February 2022

AbstractPrevious studies have shown that the gut microbiota of patients with acute myeloid leukemia (AML) is disrupted during induction chemotherapy; however, the durability of microbiota changes is unknown. This is an important knowledge gap, because reduced microbiota diversity at the time of stem cell transplantation weeks to months after the initial chemotherapy has been associated with higher mortality after transplantation. By sequencing the gut microbiota in 410 longitudinal stool samples from 52 patients with AML, we found that, during inpatient chemotherapy, the gut microbiota is stressed beyond its ability to recover its original state. Despite major reductions in antibiotic pressure and other disturbances to the microbiota after hospital discharge, the trajectory of microbiota recovery yields new communities that are highly dissimilar to baseline. This lasting shift in the gut microbiota is relevant for subsequent phases of curative therapy and is a potential target for novel microbiota protective/restorative interventions. This trial was registered at www.clinicaltrials.gov as #NCT03316456.
Distance correlation application to gene co-expression network analysis
Authors: Hou Jie , Ye Xiufen , Feng Weixing , Zhang Qiaosheng , Han Yatong , Liu Yusong , Li Yu , Wei Yufen 
Published: February 2022

AbstractBackgroundTo construct gene co-expression networks, it is necessary to evaluate the correlation between different gene expression profiles. However, commonly used correlation metrics, including both linear (such as Pearson’s correlation) and monotonic (such as Spearman’s correlation) dependence metrics, are not enough to observe the nature of real biological systems. Hence, introducing a more informative correlation metric when constructing gene co-expression networks is still an interesting topic.ResultsIn this paper, we test distance correlation, a correlation metric integrating both linear and non-linear dependence, with other three typical metrics (Pearson’s correlation, Spearman’s correlation, and maximal information coefficient) on four different arrays (macrophage and liver) and RNA-seq (cervical cancer and pancreatic cancer) datasets. Among all the metrics, distance correlation is distribution free and can provide better performance on complex relationships and anti-outlier. Furthermore, distance correlation is applied to Weighted Gene Co-expression Network Analysis (WGCNA) for constructing a gene co-expression network analysis method which we named Distance Correlation-based Weighted Gene Co-expression Network Analysis (DC-WGCNA). Compared with traditional WGCNA, DC-WGCNA can enhance the result of enrichment analysis and improve the module stability.ConclusionsDistance correlation is better at revealing complex biological relationships between gene profiles compared with other correlation metrics, which contribute to more meaningful modules when analyzing gene co-expression networks. However, due to the high time complexity of distance correlation, the implementation requires more computer memory.
Genome-wide identification of MITE-derived microRNAs and their targets in bread wheat
Authors: Crescente Juan M. , Zavallo Diego , del Vas Mariana , Asurmendi Sebastián , Helguera Marcelo , Fernandez Elmer , Vanzetti Leonardo S. 
Published: February 2022

AbstractBackgroundPlant miRNAs are a class of small non-coding RNAs that can repress gene expression at the post-transcriptional level by targeting RNA degradation or promoting translational repression. There is increasing evidence that some miRNAs can derive from a group of non-autonomous class II transposable elements called Miniature Inverted-repeat Transposable Elements (MITEs).ResultsWe used public small RNA and degradome libraries fromTriticum aestivumto screen for microRNAs production and predict their cleavage target sites. In parallel, we also created a comprehensive wheat MITE database by identifying novel elements and compiling known ones. When comparing both data sets, we found high homology between MITEs and 14% of all the miRNAs production sites detected. Furthermore, we show that MITE-derived miRNAs have preference for targeting degradation sites with MITE insertions in the 3’ UTR regions of the transcripts.ConclusionsOur results revealed that MITE-derived miRNAs can underlay the origin of some miRNAs and potentially shape a regulatory gene network. Since MITEs are found in millions of insertions in the wheat genome and are closely linked to genic regions, this kind of regulatory network could have a significant impact on the post-transcriptional control of gene expression.
Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
Authors: Barbitoff Yury A. , Abasov Ruslan , Tvorogova Varvara E. , Glotov Andrey S. , Predeus Alexander V. 
Published: February 2022

AbstractBackgroundAccurate variant detection in the coding regions of the human genome is a key requirement for molecular diagnostics of Mendelian disorders. Efficiency of variant discovery from next-generation sequencing (NGS) data depends on multiple factors, including reproducible coverage biases of NGS methods and the performance of read alignment and variant calling software. Although variant caller benchmarks are published constantly, no previous publications have leveraged the full extent of available gold standard whole-genome (WGS) and whole-exome (WES) sequencing datasets.ResultsIn this work, we systematically evaluated the performance of 4 popular short read aligners (Bowtie2, BWA, Isaac, and Novoalign) and 9 novel and well-established variant calling and filtering methods (Clair3, DeepVariant, Octopus, GATK, FreeBayes, and Strelka2) using a set of 14 “gold standard” WES and WGS datasets available from Genome In A Bottle (GIAB) consortium. Additionally, we have indirectly evaluated each pipeline’s performance using a set of 6 non-GIAB samples of African and Russian ethnicity. In our benchmark, Bowtie2 performed significantly worse than other aligners, suggesting it should not be used for medical variant calling. When other aligners were considered, the accuracy of variant discovery mostly depended on the variant caller and not the read aligner. Among the tested variant callers, DeepVariant consistently showed the best performance and the highest robustness. Other actively developed tools, such as Clair3, Octopus, and Strelka2, also performed well, although their efficiency had greater dependence on the quality and type of the input data. We have also compared the consistency of variant calls in GIAB and non-GIAB samples. With few important caveats, best-performing tools have shown little evidence of overfitting.ConclusionsThe results show surprisingly large differences in the performance of cutting-edge tools even in high confidence regions of the coding genome. This highlights the importance of regular benchmarking of quickly evolving tools and pipelines. We also discuss the need for a more diverse set of gold standard genomes that would include samples of African, Hispanic, or mixed ancestry. Additionally, there is also a need for better variant caller assessment in the repetitive regions of the coding genome.
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization
Authors: Dudová Zdenka , Conte Nathalie , Mason Jeremy , Stuchlík Dalibor , Peša Radim , Halmagyi Csaba , Perova Zinaida , Mosaku Abayomi , Thorne Ross , Follette Alex , Pivarč Ľuboslav , Šašinka Radim , Usman Muhammad , Neuhauser Steven , Begley Dale A. , Krupke Debra M. , Frassà Massimiliano , Fiori Alessandro , Corsi Riccardo , Vezzadini Luca , Isella Claudio , Bertotti Andrea , Bult Carol , Parkinson Helen , Medico Enzo , Meehan Terrence , Křenek Aleš 
Published: February 2022

Abstract
Background
Patient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium.

Main body
In this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views.

(Short) Conclusion
EurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests.