bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference-free transcriptome signatures for prostate cancer prognosis
Authors: Nguyen Ha T.N. , Xue Haoliang , Firlej Virginie , Ponty Yann , Gallopin Melina , Gautheret Daniel 
Published: April 2021

Abstract
Background
RNA-seq data are increasingly used to derive prognostic signatures for cancer outcome prediction. A limitation of current predictors is their reliance on reference gene annotations, which amounts to ignoring large numbers of non-canonical RNAs produced in disease tissues. A recently introduced kind of transcriptome classifier operates entirely in a reference-free manner, relying on k-mers extracted from patient RNA-seq data.

Methods
In this paper, we set out to compare conventional and reference-free signatures in risk and relapse prediction of prostate cancer. To compare the two approaches as fairly as possible, we set up a common procedure that takes as input either a k-mer count matrix or a gene expression matrix, extracts a signature and evaluates this signature in an independent dataset.

Results
We find that both gene-based and k-mer based classifiers had similarly high performances for risk prediction and a markedly lower performance for relapse prediction. Interestingly, the reference-free signatures included a set of sequences mapping to novel lncRNAs or variable regions of cancer driver genes that were not part of gene-based signatures.

Conclusions
Reference-free classifiers are thus a promising strategy for the identification of novel prognostic RNA biomarkers.
When lockdown policies amplify social inequalities in COVID-19 infections: evidence from a cross-sectional population-based survey in France
Authors:   for the SAPRIS study group, Bajos Nathalie , Jusot Florence , Pailhé Ariane , Spire Alexis , Martin Claude , Meyer Laurence , Lydié Nathalie , Franck Jeanna-Eve , Zins Marie , Carrat Fabrice 
Published: April 2021

AbstractBackgroundSignificant differences in COVID-19 incidence by gender, class and race/ethnicity are recorded in many countries in the world. Lockdown measures, shown to be effective in reducing the number of new cases, may not have been effective in the same way for all, failing to protect the most vulnerable populations. This survey aims to assess social inequalities in the trends in COVID-19 infections following lockdown.MethodsA cross-sectional survey conducted among the general population in France in April 2020, during COVID-19 lockdown.Ten thousand one hundred one participants aged 18–64, from a national cohort who lived in the three metropolitan French regions most affected by the first wave of COVID-19.The main outcome was occurrence of possible COVID-19 symptoms, defined as the occurrence of sudden onset of cough, fever, dyspnea, ageusia and/or anosmia, that lasted more than 3 days in the 15 days before the survey. We used multinomial regression models to identify social and health factors related to possible COVID-19 before and during the lockdown.ResultsIn all, 1304 (13.0%; 95% CI: 12.0–14.0%) reported cases of possible COVID-19. The effect of lockdown on the occurrence of possible COVID-19 was different across social hierarchies. The most privileged class individuals saw a significant decline in possible COVID-19 infections between the period prior to lockdown and during the lockdown (from 8.8 to 4.3%,P = 0.0001) while the decline was less pronounced among working class individuals (6.9% before lockdown and 5.5% during lockdown,P = 0.03). This differential effect of lockdown remained significant after adjusting for other factors including history of chronic disease. The odds of being infected during lockdown as opposed to the prior period increased by 57% among working class individuals (OR = 1.57; 95% CI: 1.00–2.48). The same was true for those engaged in in-person professional activities during lockdown (OR = 1.53; 95% CI: 1.03–2.29).ConclusionsLockdown was associated with social inequalities in the decline in COVID-19 infections, calling for the adoption of preventive policies to account for living and working conditions. Such adoptions are critical to reduce social inequalities related to COVID-19, as working-class individuals also have the highest COVID-19 related mortality, due to higher prevalence of comorbidities.
Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada
Authors: Papst Irena , Li Michael , Champredon David , Bolker Benjamin M. , Dushoff Jonathan , D. Earn David J. 
Published: April 2021

Abstract
Background
Patient age is one of the most salient clinical indicators of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for many regions. Less attention has been given to the age distributions of serious medical interventions administered to COVID-19 patients, which could reveal sources of potential pressure on the healthcare system should SARS-CoV-2 prevalence increase, and could inform mass vaccination strategies. The aim of this study is to quantify the relationship between COVID-19 patient age and serious outcomes of the disease, beyond fatalities alone.

Methods
We analysed 277,555 known SARS-CoV-2 infection records for Ontario, Canada, from 23 January 2020 to 16 February 2021 and estimated the age distributions of hospitalizations, Intensive Care Unit admissions, intubations, and ventilations. We quantified the probability of hospitalization given known SARS-CoV-2 infection, and of survival given COVID-19-related hospitalization.

Results
The distribution of hospitalizations peaks with a wide plateau covering ages 60–90, whereas deaths are concentrated in ages 80+. The estimated probability of hospitalization given known infection reaches a maximum of 27.8% at age 80 (95% CI 26.0%–29.7%). The probability of survival given hospitalization is nearly 100% for adults younger than 40, but declines substantially after this age; for example, a hospitalized 54-year-old patient has a 91.7% chance of surviving COVID-19 (95% CI 88.3%–94.4%).

Conclusions
Our study demonstrates a significant need for hospitalization in middle-aged individuals and young seniors. This need is not captured by the distribution of deaths, which is heavily concentrated in very old ages. The probability of survival given hospitalization for COVID-19 is lower than is generally perceived for patients over 40. If acute care capacity is exceeded due to an increase in COVID-19 prevalence, the distribution of deaths could expand toward younger ages. These results suggest that vaccine programs should aim to prevent infection not only in old seniors, but also in young seniors and middle-aged individuals, to protect them from serious illness and to limit stress on the healthcare system.
En bloc resection and reconstruction of a huge chondrosarcoma involving multilevel upper thoracic spine and chest wall: case report
Authors: Tang Xiaodong , Cai Zhenyu , Wang Ruifeng , Ji Tao , Guo Wei 
Published: April 2021

Abstract
Background
En bloc resection of malignant tumors involving upper thoracic spine is technically difficult. We surgically treated a patient with grade 2 chondrosarcoma involving T1–5, left upper thoracic cavity, and chest wall.

Case presentation
A 37 years old, male patient was referred to our hospital for a huge lump involved left shoulder and chest wall. In order to achieve satisfied surgical margins, anterior approach, posterior approach, and lateral approach were carried out sequentially. After en bloc tumor resection, the upper thoracic spine was reconstructed with a 3D-printed modular vertebral prosthesis, and the huge chest wall defect was repaired by a methyl methacrylate layer between 2 pieces of polypropylene mesh. Postoperatively, the patient suffered from pneumonia and neurological deterioration which fully recovered eventfully. At 24 months after operation, the vertebral prosthesis and internal fixation were intact; there was no tumor local recurrence, and the patient was alive with stable pulmonary metastases.

Conclusion
This case report describes resection of a huge chondrosarcoma involving not only multilevel upper thoracic spine, but also entire left upper thoracic cavity and chest wall. Although with complications, en bloc tumor resection with combined surgical approach and effective reconstructions could improve oncologic and functional prognosis in carefully selected spinal tumor patients.
Transforaminal epidural steroid injection combined with radio frequency for the treatment of lumbar disc herniation: a 2-year follow-up
Authors: Wei Wen-Bo , Dang Sha-Jie , Wei Ling , Liu Tian , Wang Jue 
Published: April 2021

Abstract
Background
To assess the therapeutic efficacy of transforaminal epidural steroid injection (TFESI) combined with radio frequency (RF) for the treatment of lumbar disc herniation (LDH).

Methods
A total of 230 patients participated in the study: TFESI (Group T, n = 110), TFESI combined with RF (Group TR, n = 120). Visual analogue scale (VAS), Oswestry disability index (ODI) and Global perceived effect (GPE) scale were measured pre-operation, 1, 3, 6, 12 and 24 months after the operation. Hospitalization time, treatment time, complications, and recurrence were compared between the two groups.

Results
The VAS and ODI at each observation point of the post-operation were significantly decreased compared with the pre-operation in both groups (P < 0.05). There was no statistically difference of VAS and ODI between the two groups at 1 and 3 months of the post-operation (P > 0.05). However, The VAS and ODI scores in Group TR were significantly lower than that in Group T at 6, 12 and 24 months of the post-operation (P < 0.05). The GPE in group TR was high in the early days, while that at 1 and 3 months after treatment was significantly higher than that in group T (P < 0.05). The recurrence rate in Group TR was lower than that in Group T (P = 0.002). There was no significant difference in hospitalization time, complications, VAS and ODI score at the pre-operation between the two groups (P > 0.05).

Conclusion
These findings suggest that TFESI combined with RF could effectively improve the pain and function, and had a long-term satisfactory effect for the treatment of LDH.
The use of BokaFlo™ instrument to measure salivary flow
Authors: Fallon Braden S. , Chase Trevor J. , Cooke Elaine M. , Ghazitabatabaei Amir , Naylor Nathan O. , Cutshall Jordan J. , Trump Bryan G. , Weller Melodie L. 
Published: April 2021

Abstract
Background
Dry mouth currently affects roughly 20% of the population and is a condition characterized by chronic hyposalivation and/or subjective reports of xerostomia. Low saliva flow can be indicative of other undiagnosed diseases, such as primary Sjogren’s syndrome, and may contribute to difficulty chewing, increased caries susceptibility and infection. The passive drool test (PDT) is the primary method used to evaluate patients for hyposalivation but it is time-consuming and inconvenient. New methodology is needed to facilitate increased testing for hyposalivation in the dental clinic. The aim of this study was to evaluate an alternative method to measure salivary flow in dental offices.

Methods
In this study, we tested a new biomedical device, the BokaFlo™, to measure salivary flow in subjects in comparison to the current PDT standard. Participants completed an oral health questionnaire and saliva flow was evaluated by the PDT and the BokaFlo™ system.

Results
Saliva flow as measured by the BokaFlo™ positively correlated with the saliva flow measured by the PDT methodology (r = 0.22, p < 0.05). The device predicted low saliva flow in subjects with a sensitivity of 0.76 and specificity of 0.84 for subjects with hyposalivation, defined as a saliva flow rate of ≤ 0.1 ml/min. A significant negative correlation between the total oral health questionnaire score and the likelihood of participant exhibiting low salivary flow was observed (r = − 0.31, p < 0.006).

Conclusion
The BokaFlo™ was effectively able to measure low saliva flow correlating with the PDT methodology and may provide more efficient testing of saliva flow in the dental office.
Stainless-steel crowns in children: Norwegian and Finnish dentists’ knowledge, practice and challenges
Authors: Uhlen M. M. , Tseveenjav B. , Wuollet E. , Furuholm J. , Ansteinsson V. , Mulic A. , Valen H. 
Published: April 2021

Abstract
Background
Stainless-steel crowns (SSCs) are recommended for restorative treatment of young teeth severely affected by caries, fractures or dental developmental disorders (DDDs). However, despite recommendations and clinical evidence, SSCs are not widely used by general dentists, who favour extraction and more conventional restorations. The present study aimed to investigate the views of and use of SSCs among Norwegian and Finnish dentists.

Methods
The present study was a cross-sectional survey among Norwegian and Finnish dentists. An electronic questionnaire was sent to Norwegian and Finnish dentists asking whether they used SSCs and on which indications. In addition, the questionnaire assessed reasons for non-use and dentists’ perceptions regarding advantages and challenges in the use of SSCs, as well as the need for additional training. Distributions of background characteristics, use of and views on SSCs were calculated, and statistical significance of the associations between respondents’ background and their answers were evaluated.

Results
Of the 574 Norwegian and 765 Finnish respondents, only 12.0% and 12.9% reported to use SSCs, respectively. The most frequently reported barrier reported by those who did not use SSCs was lack of practical training. The most frequent challenge reported by those using SSCs was difficulties in crown adjustment followed by aesthetic issues, and the most frequently reported advantage was that SSCs maintain the function and occlusion. The majority of respondents reported a need for more information and practical training in the use of SSCs, with hands-on course as their most frequently preferred education type.

Conclusion
Although the value of SSCs for restoring young molars is recognized by Norwegian and Finnish dentists, SSCs are rarely used by general dentists. The majority of the respondents reported lack of training and materials and was interested in receiving more information and education.
Hospice care providers experiences of grappling with medical assistance in dying in a hospice setting: a qualitative descriptive study
Authors: Freeman Shannon , Banner Davina , Ward Valerie 
Published: April 2021

Abstract
Background
Rapid implementation of Medical Assistance in Dying (MAiD) across care settings has challenged providers and organizations, including hospices, to develop and implement new modes of practice. The aim of this study was to examine the effects that legalization of MAiD has had on hospice care provider roles within the non-provider context.

Methods
Eight in-depth semi-structured interviews were conducted and a qualitative descriptive approach used to examine hospice care providers experiences in a small western Canadian city. In the study context, patients who choose MAiD are cared for until immediately prior to the procedure when they are transferred off-site to undergo MAiD. Inductive and thematic analyses were undertaken.

Results
Participants experienced practical, philosophical, and professional challenges. Despite the overwhelming desire to support patient autonomy and decision-making, some interpreted patient choice for MAiD as rejection of the natural death experience at the hospice. Patient choice for MAiD initiated a new and different pathway of end-of-life care. While participants felt uncertain how best to support patients undergoing MAiD, they shared mixed optimism on how their care provider roles were evolving as their level of experience broadened. While implementation of MAiD was rapid, the introduction of practical and professional supports has remained slow to materialize, leaving many providers to navigate their own personal and professional positions and practices.

Conclusion
Care providers require a multi-faceted range of clinical, legal, and logistical supports at the practice, organizational, and health system levels, to facilitate care delivery to those requesting and undergoing MAiD and to promote coordinated and holistic patient-centered care. The different pathway for those who chose MAiD may lead care providers to struggle with relational challenges and interpersonal unease. Further research may address how to support those undergoing MAiD within the hospice context.
An emergency care research course for healthcare career preparation
Authors: Miller Karen F. , Das Rishub K. , Majors Ciera D. , Paz Hadassah H. , Robinson Ayana N. , Hamilton Veronica F. , Jackson Brittney E. , Collins Sean P. , Storrow Alan B. 
Published: April 2021

Abstract
Background
University students have limited opportunities to gain healthcare clinical exposure within an academic curriculum. Furthermore, traditional pre-medical clinical experiences like shadowing lack active learning components. This may make it difficult for students to make an informed decision about pursuing biomedical professions. An academic university level research course with bedside experience provides students direct clinical participation in the healthcare setting.

Methods
Described is a research immersion course for senior university students (3rd to 5th year) interested in healthcare and reported study enrollment with final course evaluations. The setting was an adult, academic, urban, level 1 trauma center emergency department (ED) within a tertiary-care, 1000-bed, medical center. Our course, “Immersion in Emergency Care Research”, was offered as a university senior level class delivered consecutively over 16-weeks for students interested in healthcare careers. Faculty and staff from the Department of Emergency Medicine provided a classroom lecture program and extensive bedside, hands-on clinical research experience. Students enrolled patients in a survey study requiring informed consent, interviews, data abstraction and data entry. Additionally, they were required to write and present a mock emergency care research proposal inspired by their clinical experience. The course evaluations from students’ ordinal rankings and blinded text responses report possible career impact.

Results
Thirty-two students, completed the 16-week, 6–9 h per week, course from August to December in 1 of 4 years (2016 to 2019). Collectively, students enrolled 759 ED patients in the 4 survey studies and reported increased confidence in the clinical research process as each week progressed. Ranked evaluations were extremely positive, with many students describing how the course significantly impacted their career pathways and addressed an unmet need in biomedical education. Six students continued the research experience from the course through independent study using the survey data to develop 3 manuscripts for submission to peer-reviewed journals.

Conclusions
A bedside emergency care research course for students with pre-healthcare career aspirations can successfully provide early exposure to patients and emergency care, allow direct experience with clinical bedside research, research data collection, and may impact biomedical science career choices.
Validity evidence for a novel instrument assessing medical student attitudes toward instruction in implicit bias recognition and management
Authors: Gonzalez Cristina M. , Grochowalski Joseph H. , Garba Ramya J. , Bonner Shacelles , Marantz Paul R. 
Published: April 2021

Abstract
Background
Implicit bias instruction is becoming more prevalent in health professions education, with calls for skills-based curricula moving from awareness and recognition to management of implicit bias. Evidence suggests that health professionals and students learning about implicit bias (“learners”) have varying attitudes about instruction in implicit bias, including the concept of implicit bias itself. Assessing learner attitudes could inform curriculum development and enable instructional designs that optimize learner engagement. To date, there are no instruments with evidence for construct validity that assess learner attitudes about implicit bias instruction and its relevance to clinical care.

Methods
The authors developed a novel instrument, the Attitude Towards Implicit Bias Instrument (ATIBI) and gathered evidence for three types of construct validity- content, internal consistency, and relationship to other variables.

Results
Authors utilized a modified Delphi technique with an interprofessional team of experts, as well as cognitive interviews with medical students leading to item refinement to improve content validity. Seven cohorts of medical students, N = 1072 completed the ATIBI. Psychometric analysis demonstrated high internal consistency (α = 0.90). Exploratory factor analysis resulted in five factors. Analysis of a subset of 100 medical students demonstrated a moderate correlation with similar instruments, the Integrative Medicine Attitude Questionnaire (r = 0.63, 95% CI: [0.59, 0.66]) and the Internal Motivation to Respond Without Prejudice Scale (r = 0.36, 95% CI: [0.32, 0.40]), providing evidence for convergent validity. Scores on our instrument had low correlation to the External Motivation to Respond Without Prejudice Scale (r = 0.15, 95% CI: [0.09, 0.19]) and the Groningen Reflection Ability Scale (r = 0.12, 95% CI: [0.06, 0.17]) providing evidence for discriminant validity. Analysis resulted in eighteen items in the final instrument; it is easy to administer, both on paper form and online.

Conclusion
The Attitudes Toward Implicit Bias Instrument is a novel instrument that produces reliable and valid scores and may be used to measure medical student attitudes related to implicit bias recognition and management, including attitudes toward acceptance of bias in oneself, implicit bias instruction, and its relevance to clinical care.
Serial serum creatinine, SDMA and urinary acute kidney injury biomarker measurements in dogs envenomated by the European adder (Vipera berus)
Authors: Harjen Hannah J. , Nicolaysen Tove V. , Negard Tale , Lund Hege , Sævik Bente K. , Anfinsen Kristin P. , Moldal Elena R. , Zimmer Karin E. , Rørtveit Runa 
Published: April 2021

AbstractBackgroundAcute kidney injury (AKI) is associated with high morbidity and mortality in dogs, but diagnosis may be impaired due the insensitivity of routine renal function biomarkers to detect earlier or milder forms of injury. Snake envenomation is one of several causes of AKI in dogs and humans. Dogs are commonly envenomated by the European adder (Vipera berus) between April and October each year, but few studies exist examining serial serum creatinine (sCr) and symmetric dimethylarginine (SDMA) measurements and AKI biomarkers in these dogs. Novel urinary biomarkers could improve clinical outcome by allowing earlier diagnosis of and intervention in AKI. The aim of this study was to assess the presence of AKI in dogs envenomated byV. berusat 12, 24 and 36 h after bite, as well as 14 days later, using sCr, SDMA and a panel of urinary AKI biomarkers normalised to urine creatinine (uCr), compared to a group of healthy control dogs.ResultsThirty-five envenomated dogs and 35 control dogs were included. Serum creatinine did not exceed the upper reference limit at any time point in any dog after envenomation. Serum SDMA did not exceed 0.89 μmol/L in any dog. Compared to controls, urinary albumin/uCr, neutrophil gelatinase-associated lipocalin/uCr and monocyte chemotactic protein-1/uCr were significantly elevated 12 h (P <  0.0001,P <  0.0001,P = 0.01), 24 h (P <  0.001,P <  0.001,P = 0.002) and 36 h (P <  0.001,P <  0.001,P = 0.0008) after bite. Osteopontin/uCr was higher 24 and 36 h after bite (P < 0.0001), kidney injury molecule-1/uCr, interleukin-8/uCr and γ- glutamyl transferase/uCr were significantly higher 36 h after bite (P = 0.003,P = 0.0005,P = 0.001). Urinary cystatin C/uCr was not significantly different to controls at any timepoint. Biomarker/uCr ratios were not significantly different 14 days after envenomation compared to controls.ConclusionUrinary biomarker/Cr ratios are indicative of mild transient, non-azotaemic AKI in dogs envenomated byV. berus.