bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transitioning to Teaching Online During the COVID-19 Pandemic
Authors: Wilson Jessica L. , Hensley Angie , Culp-Roche Amanda , Hampton Debra , Hardin-Fanning Fran , Thaxton-Wiggins Amanda 
Published: June 2021

Background During the COVID-19 pandemic many nursing educators have been required to abruptly convert to an online delivery model. Faculty need resources and support to transition face to face courses into an online format. Purpose The purpose of this article is to highlight nursing faculty perceptions of the effectiveness of resources, support, and methodologies for online teaching during the COVID-19 Pandemic. Methods A cross-sectional descriptive survey design was used to collect data about nursing faculty resources, support and methodologies used to transition at least one undergraduate or graduate degree nursing course to an online format during the COVID-19 pandemic. Results Eighty-four faculty who taught in ten university colleges of nursing used varied teaching methodologies in online courses, but included some consistent methods such as websites and web based tools. The student engagement strategies that faculty were most satisfied with were journal writing and projects. Most faculty reported having information technology support and access to instructional design resources. Conclusion Nursing faculty were resourceful, adaptive, and willing to use both novel and existing resources and methodologies to meet their teaching objectives and engage students. They were also, overall, satisfied with the administrative support they received from their respective institutions. Many of these resources, methodologies, and supports will continue to be used by faculty as likely more programs and courses will continue to be managed online.
Estimating age-specific COVID-19 fatality risk and time to death by comparing population diagnosis and death patterns: Australian data
Authors: Marschner Ian C. 
Published: June 2021

AbstractBackgroundMortality is a key component of the natural history of COVID-19 infection. Surveillance data on COVID-19 deaths and case diagnoses are widely available in the public domain, but they are not used to model time to death because they typically do not link diagnosis and death at an individual level. This paper demonstrates that by comparing the unlinked patterns of new diagnoses and deaths over age and time, age-specific mortality and time to death may be estimated using a statistical method called deconvolution.MethodsAge-specific data were analysed on 816 deaths among 6235 cases over age 50 years in Victoria, Australia, from the period January through December 2020. Deconvolution was applied assuming logistic dependence of case fatality risk (CFR) on age and a gamma time to death distribution. Non-parametric deconvolution analyses stratified into separate age groups were used to assess the model assumptions.ResultsIt was found that age-specific CFR rose from 2.9% at age 65 years (95% CI:2.2 – 3.5) to 40.0% at age 95 years (CI: 36.6 – 43.6). The estimated mean time between diagnosis and death was 18.1 days (CI: 16.9 – 19.3) and showed no evidence of varying by age (heterogeneity P = 0.97). The estimated 90% percentile of time to death was 33.3 days (CI: 30.4 – 36.3; heterogeneity P = 0.85). The final age-specific model provided a good fit to the observed age-stratified mortality patterns.ConclusionsDeconvolution was demonstrated to be a powerful analysis method that could be applied to extensive data sources worldwide. Such analyses can inform transmission dynamics models and CFR assessment in emerging outbreaks. Based on these Australian data it is concluded that death from COVID-19 occurs within three weeks of diagnosis on average but takes five weeks in 10% of fatal cases. Fatality risk is negligible in the young but rises above 40% in the elderly, while time to death does not seem to vary by age.
A steep increase in healthcare seeking behaviour in the last months before colorectal cancer diagnosis
Authors: Kuiper Josephina G. , van Herk-Sukel Myrthe P. P. , Lemmens Valery E. P. P. , Kuipers Ernst J. , Herings Ron M. C. 
Published: June 2021

Abstract
Background
Timely recognition of colorectal cancer related symptoms is essential to reduce time to diagnosis. This study aims to investigate the primary healthcare use preceding a colorectal cancer diagnosis.

Methods
From a cohort of linked cancer and primary care data, patients diagnosed with primary colorectal cancer in the period 2007–2014 were selected and matched to cancer-free controls on gender, birth year, GP practice and follow-up period. Primary healthcare use among colorectal cancer cases before diagnosis was compared with matched cancer-free controls. Mean monthly number of GP consultations and newly prescribed medication was assessed in the year before index date (diagnosis date for cases). Results were stratified by colorectal cancer site: proximal colon cancer, distal colon cancer and rectal cancer.

Results
A total of 6,087 colorectal cancer cases could be matched to four cancer-free controls (N = 24,348). While mean monthly number of GP consultation were stable through the year among cancer-free controls, a statistical significant increase was seen among colorectal cancer cases in the last 4–8 months before diagnosis. Proximal colon cancer cases showed the longest time interval of increased mean monthly number of GP consultations. This increase was largely driven by a consultation for malignant neoplasm colon/rectum. The number patients receiving a newly prescribed medication was stable around 120 per 1,000 persons per month until 8 months before index date for proximal colon cancer cases, 4 months before index date for distal colon cancer cases and 3 months for rectal cancer cases. This increase was mainly driven by the prescription of laxatives drugs.

Conclusion
An increase in the healthcare seeking behaviour of colorectal cancer patients prior to diagnosis was seen. The longest period of increased GP consultations and newly prescribed medication was seen among patients diagnosed with proximal colon cancer. This can be explained by the difficultly to diagnose proximal colon cancer given the more subtle signs compared to distal colon cancer and rectal cancer. Therefore, faster diagnosis for this specific tumour subtype may only be possible when clear clinical signs and symptoms are present.
The association between nutritional status and functional limitations among centenarians: a cross-sectional study
Authors: Song Yang , Liu Miao , Jia Wang-ping , Han Ke , Wang Sheng-shu , He Yao 
Published: June 2021

Abstract
Background
Although there have been studies on the association between nutritional status and functional limitations, there were few studies on Asian centenarians in community. Therefore, this study aims to identify associations between nutritional status and functional limitations among centenarians in China.

Methods
This cross-sectional study was conducted with the data from the China Hainan Centenarian Cohort Study. These data ultimately included basic characteristics, hematologic indicators, and chronic disease status for 1,002 centenarians. The nutritional status was evaluated using the Mini Nutritional Assessment Short-Form scale. The functional limitations were assessed using the activities of daily living (ADL) scale, namely Barthel Index and Lawton Scale. The association between nutritional status and ADL was assessed using multivariate logistic regression models.

Results
In this study, the prevalence of malnutrition was 20.8 % among centenarians, basic ADL (BADL) limitation was 28.6 %, and instrumental ADL (IADL) limitation was 64.7 %. As the nutritional status deteriorated, the risk of ADL limitations increased in total population (BADL limitation: OR = 17.060, 95 % CI: 8.093-35.964; IADL limitation: OR = 11.221, 95 % CI: 5.853-21.511; p for trend < 0.001). Similar results were found in both men and women after stratifying sex but were more prominent in women.

Conclusions
Malnutrition is associated with functional limitations among centenarians in China and more pronounced among women.
Feasibility of and barriers to thalassemia screening in migrant populations: a cross-sectional study of Myanmar and Cambodian migrants in Thailand
Authors: Xu Julia Z. , Tanongsaksakul Wilaslak , Suksangpleng Thidarat , Ekwattanakit Supachai , Riolueang Suchada , Telen Marilyn J. , Viprakasit Vip 
Published: June 2021

Abstract
Background
Thalassemia, an inherited hemoglobin disorder, has become a global public health problem due to population migration. Evidence-based strategies for thalassemia prevention in migrants are lacking. We characterized barriers to thalassemia screening and the burden of thalassemia in migrant workers in Thailand.

Methods
Multilingual demographic and KAP surveys were completed by 197 Thai, 119 Myanmar, and 176 Cambodian adults residing in Thailand. Thalassemia awareness, socio-demographic predictors, and knowledge and attitude scores were compared between migrant and Thai subjects. Comprehensive thalassemia testing was performed for migrants.

Results
Migrants had extremely poor thalassemia awareness (4.1%) compared to Thai subjects (79.6%) and had lower thalassemia knowledge scores but similar attitude scores. Surveys identified differing sociodemographic factors predicting awareness in Thai and migrant subjects, as well as key misconceptions likely to hinder thalassemia screening uptake. Nearly all migrants consented to thalassemia testing. We identified abnormal hemoglobin profiles in 52.7% of migrants and a higher projected rate of severe thalassemia births in migrants.

Conclusions
The high burden of thalassemia and tremendous knowledge gap in migrants needs urgent attention. Thalassemia screening was feasible and acceptable in our migrant population. Sociocultural and structural barriers merit further attention when designing thalassemia screening and prevention policies for migrants in Thailand and globally.
Use of magnetic nanotrap particles in capturing Yersinia pestis virulence factors, nucleic acids and bacteria
Authors: Ii Alexandra N. , Lin Shih-Chao , Lepene Benjamin , Zhou Weidong , Kehn-Hall Kylene , van Hoek Monique L. 
Published: June 2021

Abstract
Background
Many pathogens, including Yersinia pestis, cannot be consistently and reliably cultured from blood. New approaches are needed to facilitate the detection of proteins, nucleic acid and microorganisms in whole blood samples to improve downstream assay performance. Detection of biomarkers in whole blood is difficult due to the presence of host proteins that obscure standard detection mechanisms. Nanotrap® particles are micron-sized hydrogel structures containing a dye molecule as the affinity bait and used to detect host biomarkers, viral nucleic acids and proteins as well as some bacterial markers. Nanotraps have been shown to bind and enrich a wide variety of biomarkers and viruses in clinically relevant matrices such as urine and plasma. Our objective was to characterize the binding ability of Nanotrap particle type CN3080 to Y. pestis bacteria, bacterial proteins and nucleic acids from whole human blood in order to potentially improve detection and diagnosis.

Results
CN3080 Nanotraps bind tightly to Yersinia bacteria, even after washing, and we were able to visualize the co-localized Nanotraps and bacteria by electron microscopy. These magnetic hydrogel Nanotraps were able to bind Yersinia DNA, supporting the utility of Nanotraps for enhancing nucleic acid-based detection methods. Nanotraps were capable of increasing Y. pestis nucleic acid yield by fourfold from whole human blood compared to standard nucleic acid extraction. Interestingly, we found CN3080 Nanotraps to have a high affinity for multiple components of the Yersinia type III secretion system (T3SS), including chaperone proteins, Yop effector proteins and virulence factor protein LcrV (V). Using Nanotraps as a rapid upstream sample-prep tool, we were able to detect LcrV in human blood by western blotting with minimal blood interference in contrast to direct western blotting of blood samples in which LcrV was obscured. We were able to computationally model the interaction of LcrV with the CN3080 Nanotrap dye and found that it had a low delta-G, suggesting high affinity. Importantly, Nanotraps were also able to enhance detection of secreted Yersinia proteins by mass spectrometry.

Conclusion
Upstream use of magnetic CN3080 Nanotrap particles may improve the downstream workflow though binding and enrichment of biomarkers and speed of processing. Utilization of Nanotrap particles can improve detection of Yersinia pestis proteins and nucleic acid from whole human blood and contribute to downstream assays and diagnostics including molecular methods such as sequencing and PCR and protein-based methods.

Graphic Abstract
Disk compression of k-mer sets
Authors: Rahman Amatur , Chikhi Rayan , Medvedev Paul 
Published: June 2021

AbstractK-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such large datasets is a detriment to tool developers, tool users, and reproducibility efforts. General purpose compressors like gzip, or those designed for read data, are sub-optimal because they do not take into account the specific redundancy pattern in k-mer sets. In our earlier work (Rahman and Medvedev, RECOMB 2020), we presented an algorithm UST-Compress that uses a spectrum-preserving string set representation to compress a set of k-mers to disk. In this paper, we present two improved methods for disk compression of k-mer sets, called ESS-Compress and ESS-Tip-Compress. They use a more relaxed notion of string set representation to further remove redundancy from the representation of UST-Compress. We explore their behavior both theoretically and on real data. We show that they improve the compression sizes achieved by UST-Compress by up to 27 percent, across a breadth of datasets. We also derive lower bounds on how well this type of compression strategy can hope to do.
ERCC1 rs11615 polymorphism and chemosensitivity to platinum drugs in patients with ovarian cancer: a systematic review and meta-analysis
Authors: Zhang Yuqiang , Cao Sufen , Zhuang Chunyu , Chen Jiacheng , Chen Xiaojing , Sun Hong , Lin Shengying , Lin Bailang 
Published: June 2021

AbstractObjectiveTo explore the relationship between ERCC1 rs11615 polymorphism and chemosensitivity to platinum drugs in ovarian cancer by the method of meta-analysis.MethodsPubmed, Web of Science, EMBASE, Cochrane Library, China National Knowledge Infrastructure (CNKI), and China Wanfang databases were comprehensively searched up to September 2020, to identify the relationship between ERCC1 rs11615 polymorphism and chemosensitivity of ovarian cancer. The data was analyzed by Stata 15.0 statistic software.ResultsA total of 10 published papers were included, including 1866 patients with ovarian cancer. The results showed that compared allele C at ERCC1 rs11615 locus with allele T, the pooled OR was 0.92 (95%CI:0.68 ~ 1.24,P > 0.05). There were no significant differences in recessive, dominant, homozygous, and heterozygous models. In accordance with a subgroup analysis of Ethnicity, all genotypes were statistically significant in the Asian population. In the allelic, dominant, recessive, homozygous and heterozygous models, the OR was 0.70 (95%CI:0.51 ~ 0.95), 0.20 (95%CI:0.07 ~ 0.56), 0.79 (95%CI:0.63 ~ 1.00), 0.21 (95%CI:0.07 ~ 0.59), 0.19 (95%CI:0.07 ~ 0.54), respectively, while in the Caucasian population, no statistically significant genotype was found.ConclusionThe ERCC1 rs11615 polymorphism is associated with chemosensitivity in patients with ovarian cancer, especially in the Asian population, but not in the Caucasian population.
Effectiveness of a psychological online training to promote physical activity among students: protocol of a randomized-controlled trial
Authors: Krämer Lena Violetta , Eschrig Nadine , Keinhorst Lena , Schöchlin Luisa , Stephan Lisa , Stiene Malin , Bengel Jürgen 
Published: June 2021

Abstract
Background
Many students in Germany do not meet recommended amounts of physical activity. In order to promote physical activity in students, web-based interventions are increasingly implemented. Yet, data on effectiveness of web-based interventions in university students is low. Our study aims at investigating a web-based intervention for students. The intervention is based on the Health Action Process Approach (HAPA), which discriminates between processes of intention formation (motivational processes) and processes of intention implementation (volitional processes). Primary outcome is change in physical activity; secondary outcomes are motivational and volitional variables as proposed by the HAPA as well as quality of life and depressive symptoms.

Methods
A two-armed randomized controlled trial (RCT) of parallel design is conducted. Participants are recruited via the internet platform StudiCare (www.studicare.com). After the baseline assessment (t1), participants are randomized to either intervention group (immediate access to web-based intervention) or control group (access only after follow-up assessment). Four weeks later, post-assessment (t2) is performed in both groups followed by a follow-up assessment (t3) 3 months later. Assessments take place online. Main outcome analyses will follow an intention-to-treat principle by including all randomized participants into the analyses. Outcomes will be analysed using a linear mixed model, assuming data are missing at random. The mixed model will include group, time, and the interaction of group and time as fixed effects and participant and university as random effect.

Discussion
This study is a high-quality RCT with three assessment points and intention-to-treat analysis meeting the state-of-the-art of effectiveness studies. Recruitment covers almost 20 universities in three countries, leading to high external validity. The results of this study will be of great relevance for student health campaigns, as they reflect the effectiveness of self-help interventions for young adults with regard to behaviour change as well as motivational and volitional determinants. From a lifespan perspective, it is important to help students find their way into regular physical activity.

Trial registration
The German clinical trials register (DRKS) DRKS00016889. Registered on 28 February 2019
The effect of a 24-week training focused on activities of daily living, muscle strengthening, and stability in idiopathic inflammatory myopathies: a monocentric controlled study with follow-up
Authors: Špiritović Maja , Heřmánková Barbora , Oreská Sabína , Štorkánová Hana , Růžičková Olga , Vernerová Lucia , Klein Martin , Kubínová Kateřina , Šmucrová Hana , Rathouská Adéla , Česák Petr , Komarc Martin , Bunc Václav , Pavelka Karel , Šenolt Ladislav , Mann Heřman , Vencovský Jiří , Tomčík Michal 
Published: June 2021

AbstractBackgroundThe structural and functional changes of the skeletal muscles in idiopathic inflammatory myopathies (IIM) caused by inflammation and immune changes can be severely disabling. The objective of this study was to assess the effect of a 24-week program combining a supervised training of activities of daily living (ADL), resistance, and stability with home exercise for improving muscle function, compared to a daily home-based exercise representing the regular outpatient care.MethodsFifty-seven patients with IIM were consecutively and non-selectively enrolled in an intervention (IG,n= 30) or control (CG,n= 27) group. Both groups were provided a standard-of-care pharmacological treatment and follow-up. Only the IG underwent the supervised intervention twice a week for 1 h per session. At baseline, 12, 24, and 48 weeks, all patients were assessed by an assessor blinded to the intervention for primary outcomes: muscle strength (Manual Muscle Testing of eight muscle groups [MMT-8]) and endurance (Functional Index-2 [FI-2]), and secondary outcomes: stability and body composition. Secondary outcomes also included questionnaires evaluating disability (Health Assessment Questionnaire [HAQ]), quality of life (Short Form 36 [SF-36]), depression (Beck’s Depression Inventory-II [BDI-II]), and fatigue (Fatigue Impact Scale [FIS]), and analysis of the systemic and local inflammatory response and perceived exertion to assess the safety of the intervention.ResultsTwenty-seven patients in the IG and 23 in the CG completed the entire program and follow-up. At week 24, compared to deterioration in the CG, we found a significant improvement in the IG in muscle strength (mean % improvement compared to baseline by 26%), endurance (135%), disability (39%), depression (26%), stability (11%), and basal metabolism (2%) and a stabilization of fitness for physical exercise. The improvement was clinically meaningful (a 24-week change by >20%) in most outcomes in a substantial proportion of patients. Although the improvement was still present at 48 weeks, the effect was not sustained during follow-up. No significant increase in the systemic or local expression of inflammatory markers was found throughout the intervention.ConclusionsThis 24-week supervised intervention focused on ADL training proved to be safe and effective. It not only prevented the progressive deterioration, but also resulted in a significant improvement in muscle strength, endurance, stability, and disability, which was clinically meaningful in a substantial proportion of patients.Trial registrationISRCTN35925199(retrospectively registered on 22 May 2020).
Pulmonary artery thrombosis as the first presentation of Behçet’s syndrome: a case report and review of the literature
Authors: Alakkas Ziyad , Kazi Waad , Mattar Mohamed , Salem Eman Abdul Wahhab , Seleem Naglaa Fawzy 
Published: June 2021

Abstract
Background
Behçet’s syndrome is a type of systemic chronic vasculitis of unknown etiology, frequently characterized by recurrent oral and genital ulcers and uveitis. It is less commonly characterized by arthritis and skin, vascular, and gastrointestinal involvements. Behçet’s syndrome affects various sizes of vessels by perivascular infiltration and vasculitis. Unlike other classic types of vasculitis, Behçet’s syndrome patients can present with both arterial and venous involvement. Although vascular Behçet’s syndrome is found in only around 15% of Behçet’s syndrome patients, it is the major cause of morbidity and mortality among them. Furthermore, although deep venous thrombosis has high incidence in Behçet’s syndrome patients, pulmonary artery thrombosis is an uncommon complication. Combining the findings of this and previous case reports of pulmonary artery thrombosis in Behçet’s syndrome patients, we sought to determine the best treatment options for pulmonary artery thrombosis in Behçet’s syndrome patients.

Case presentation
We present the case of a 22-year-old Arabian male who was admitted to an emergency department with acute chest pain, dyspnea, and hemoptysis for 2 weeks. He gave a long history of recurrent oral and genital ulcers for the last 4 months but without seeking medical advice. Spiral computed tomography showed arterial filling defects with a pulmonary nodule for which the presence of a pulmonary artery aneurysm ruled out. The lung perfusion scan showed multiple pulmonary perfusion defects. After excluding common infectious diseases such as tuberculosis and brucellosis, a diagnosis of Behçet’s syndrome with pulmonary artery thrombosis was made. Steroids with enoxaparin were initiated. The patient was discharged later on prednisolone (tapering dose) with adalimumab and apixaban. He was on regular follow-up for the next 9 months.

Conclusions
Vascular involvement in Behçet’s syndrome is a major contributor to morbidity and mortality of Behçet’s syndrome patients. Consequently, early detection of vascular involvement has a major impact on the prognosis of patients with Behçet’s syndrome.