bluuebunny/crossref_metadata_2025_split huggingface dataset:
A tool for analyzing and visualizing ribo-seq data at the isoform level
Authors: Wu Wei-Sheng , Tsao Yi-Hong , Shiue Sheng-Cian , Chen Ting-Yu , Tseng Yan-Yuan , Tseng Joseph T. 
Published: June 2021

Abstract
Background
Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo-seq, is a powerful experimental technique to study translational regulation. It can capture a snapshot of translation by deep sequencing of ribosome-protected mRNA fragments. Many ribosome profiling data processing tools have been developed. However, almost all tools analyze ribosome profiling data at the gene level. Since different isoforms of a gene may produce different proteins with distinct biological functions, it is advantageous to analyze ribosome profiling data at the isoform level. To meet this need, previously we developed a pipeline to analyze 610 public human ribosome profiling data at the isoform level and constructed HRPDviewer database.

Results
To allow other researchers to use our pipeline as well, here we implement our pipeline as an easy-to-use software tool called RPiso. Compared to Ribomap (a widely used tool which provides isoform-level ribosome profiling analyses), our RPiso (1) estimates isoform abundance more accurately, (2) supports analyses on more species, and (3) provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms.

Conclusions
In this study, we developed RPiso software tool (http://cosbi7.ee.ncku.edu.tw/RPiso/) to provide isoform-level ribosome profiling analyses. RPiso is very easy to install and execute. RPiso also provides a web-based viewer for interactively visualizing ribosome profiling data on the selected mRNA isoforms. We believe that RPiso is a useful tool for researchers to analyze and visualize their own ribosome profiling data at the isoform level.
Determinants for the implementation of person-centered tools for workers with chronic health conditions: a mixed-method study using the Tailored Implementation for Chronic Diseases checklist
Authors: Zipfel N. , Horreh B. , Hulshof C. T. J. , Suman A. , de Boer A. G. E. M. , van der Burg-Vermeulen S. J. 
Published: June 2021

Abstract
Background
The aim was to identify the most important determinants of practice for the implementation of person-centered tools which enhance work participation for patients with chronic health conditions.

Methods
A mixed-method study was conducted consisting of semi-structured interviews, a focus group and a survey. Various stakeholders were involved including (representatives of) workers with chronic health conditions, insurance physicians, occupational physicians, other healthcare professionals, researchers, employers, and policymakers. The semi-structured interviews were performed to identify implementation determinants, followed by a focus group to validate resulting determinants. To conclude, a survey was conducted to select the most important implementation determinants through prioritization by ranking the order of importance. The Tailored Implementation of Chronic Diseases checklist (TICD) was used as concept-driven coding frame for the qualitative analysis of the interviews and focus group. The self-developed survey was based on the domains of the TICD. The survey was analyzed by frequency count of first ranking of determinants per and between domains of the TICD.

Results
Various stakeholders participated (N = 27) in the interviews and focus group. The qualitative data retrieved yielded a list of determinants with additional in-depth themes according to the TICD. For the selection of the most important determinants, a survey with 101 respondents was conducted, consisting of occupational physicians, insurance physicians and workers with a chronic health condition. From the seven domains of the TICD, respondents emphasized the importance of taking into account the needs and factors associated with workers with a chronic health condition as this determinant ranked highest. Taking into account the individual needs and wishes of workers was mentioned to enable successful implementation, whereas stress of the workers was indicated to impede implementation. Other important determinants included ‘being able to work with the tools’ in terms of time and usability or ‘cognitions, beliefs and attitudes of occupational and insurance physicians’ to be able to use the tools.

Conclusion
This study identified the most important determinants from the perspective of various stakeholders involved in the implementation of client-centered tools in occupational health for workers with chronic health conditions. Furthermore, by prioritizing the most important determinants, targeted implementation strategies can be developed.
Predicting the incidence of COVID-19 using data mining
Authors: Ahouz Fatemeh , Golabpour Amin 
Published: June 2021

Abstract
Background
The high prevalence of COVID-19 has made it a new pandemic. Predicting both its prevalence and incidence throughout the world is crucial to help health professionals make key decisions. In this study, we aim to predict the incidence of COVID-19 within a two-week period to better manage the disease.

Methods
The COVID-19 datasets provided by Johns Hopkins University, contain information on COVID-19 cases in different geographic regions since January 22, 2020 and are updated daily. Data from 252 such regions were analyzed as of March 29, 2020, with 17,136 records and 4 variables, namely latitude, longitude, date, and records. In order to design the incidence pattern for each geographic region, the information was utilized on the region and its neighboring areas gathered 2 weeks prior to the designing. Then, a model was developed to predict the incidence rate for the coming 2 weeks via a Least-Square Boosting Classification algorithm.

Results
The model was presented for three groups based on the incidence rate: less than 200, between 200 and 1000, and above 1000. The mean absolute error of model evaluation were 4.71, 8.54, and 6.13%, respectively. Also, comparing the forecast results with the actual values in the period in question showed that the proposed model predicted the number of globally confirmed cases of COVID-19 with a very high accuracy of 98.45%.

Conclusion
Using data from different geographical regions within a country and discovering the pattern of prevalence in a region and its neighboring areas, our boosting-based model was able to accurately predict the incidence of COVID-19 within a two-week period.
Limited predictive value of illness perceptions for short-term poor recovery in musculoskeletal pain. A multi-center longitudinal study
Authors: de Raaij E. J. , Wittink H. , Maissan J. F. , Westers P. , Ostelo R. W. J. G. 
Published: June 2021

Abstract
Background
Musculoskeletal pain (MSP) is recognized worldwide as a major cause of increased years lived with disability. In addition to known generic prognostic factors, illness perceptions (IPs) may have predictive value for poor recovery in MSP. We were interested in the added predictive value of baseline IPs, over and above the known generic prognostic factors, on clinical recovery from MSP. Also, it is hypothesized there may be overlap between IPs and domains covered by the Four-Dimensional Symptom Questionnaire (4DSQ), measuring distress, depression, anxiety and somatization. The aim of this study is twofold; 1) to assess the added predictive value of IPs for poor recovery and 2) to assess differences in predictive value for poor recovery between the Brief Illness Perception Questionnaire - Dutch Language Version (Brief IPQ-DLV) and the 4DSQ.

Methods
An eligible sample of 251 patients with musculoskeletal pain attending outpatient physical therapy were included in a multi-center longitudinal cohort study. Pain intensity, physical functioning and Global Perceived Effect were the primary outcomes. Hierarchical logistic regression models were used to assess the added value of baseline IPs for predicting poor recovery. To investigate the performance of the models, the levels of calibration (Hosmer-Lemeshov test) and discrimination (Area under the Curve (AUC)) were assessed.

Results
Baseline ‘Treatment Control’ added little predictive value for poor recovery in pain intensity [Odds Ratio (OR) 0.80 (Confidence Interval (CI) 0.66–0.97), increase in AUC 2%] and global perceived effect [OR 0.78 (CI 0.65–0.93), increase in AUC 3%]. Baseline ‘Timeline’ added little predictive value for poor recovery in physical functioning [OR 1.16 (CI 1.03–1.30), increase in AUC 2%]. There was a non-significant difference between AUCs in predictive value for poor recovery between the Brief IPQ-DLV and the 4DSQ.

Conclusions
Based on the findings of this explorative study, assessing baseline IPs, over and above the known generic prognostic factors, does not result in a substantial improvement in the prediction of poor recovery.
Also, no recommendations can be given for preferring either the 4DSQ or the Brief IPQ-DLV to assess psychological factors.
Transplant-associated penile Kaposi sarcoma managed with single agent paclitaxel chemotherapy: a case report
Authors: Anderson Matthew A. , Ying Tracey , Wyburn Kate , Ferguson Peter M. , Strach Madeleine C. , Grimison Peter , Chadban Steve , Gracey David M. 
Published: June 2021

Abstract
Background
Kaposi’s sarcoma is an uncommon complication in renal transplant patients, and typically presents with cutaneous lesions on the lower extremities. Penile involvement has been reported only rarely. Management of cutaneous-limited disease is primarily reduction of immunosuppression and conversion to an mTOR-inhibitor, whereas the treatment of disseminated disease in transplant patients is more variable.

Case presentation
A 75-year-old male, originally from Somalia, received a deceased-donor kidney transplant for diabetic and hypertensive nephropathy. Seven months post-transplant he presented with lower limb lesions, oedema and bilateral deep vein thromboses. He then developed a fast-growing painful lesion on his penile shaft. A biopsy of this lesion confirmed KS, and a PET scan demonstrated disseminated disease in the lower extremities, penis and thoracic lymph nodes. His tacrolimus was converted to sirolimus, and his other immunosuppression was reduced. He was treated with single agent paclitaxel chemotherapy in view of his rapidly progressing, widespread disease. The penile lesion completely resolved, and the lower extremity lesions regressed significantly. His kidney allograft function remained stable throughout treatment.

Conclusion
This case illustrates a rare presentation of an uncommon post-transplant complication and highlights the need for a high index of suspicion of KS in transplant patients presenting with atypical cutaneous lesions. It serves to demonstrate that the use of single agent paclitaxel chemotherapy, switch to an mTORi and reduction in immunosuppression where possible produces excellent short-term outcomes, adding to the body of evidence for this management strategy in disseminated Kaposi’s sarcoma.
Frames and counter-frames giving meaning to palliative care and euthanasia in the Netherlands
Authors: Van Gorp Baldwin , Olthuis Gert , Vandekeybus Anneleen , van Gurp Jelle 
Published: June 2021

Abstract
Background
Based on the case of palliative care and euthanasia in the Netherlands, this paper presents an analysis of frames and counter-frames used in the ongoing public debate about these two intertwined topics. Each (counter)frame presents a cultural theme that can act as a prism to give meaning to palliative care and/or euthanasia. Each frame comprehends a different problem definition, consequences and policy options. Typical word choices and metaphors are identified that can evoke these frames and the underlying reasoning. The frames do not belong to a specific stakeholder but a pattern can be seen in their use that is related to interests and ideology.

Methods
An inductive framing analysis was conducted of 2,700 text fragments taken from various Dutch newspapers, websites of stakeholders and policy documents in the period 2016–2018. After an extensive process of thematic coding, axial coding, selective coding and peer review seven frames and seven counter-frames about palliative care and euthanasia were constructed. Fifteen experts in the field of palliative and/or end-of-life care commented on the overview during a member check.

Results
Two frames about palliative care were constructed: the Fear of death frame, which stresses the hopeless ‘terminality’ of palliative care and the Heavy burden frame, in which palliative care is too big a responsibility for the relatives of the patient. In addition, two counter-frames were constructed: palliative care as a contributor to Quality of life and Completion. With regard to euthanasia, five frames were identified that lead to a problematising definition: Thou shalt not kill, Slippery slope, Lack of willpower, I am not God, and Medical progress. Five counter-frames offer a non-problematising definition of euthanasia in the debate: Mercy, Prevention, Triumph of reason, Absolute autonomy, and Economic utility thinking.

Conclusions
The debate in the Netherlands on euthanasia and palliative care is characterized by a plurality of angles that goes beyond the bipolar distinction between the pros and cons of euthanasia and palliative care. Only with an overview of all potential frames in mind can an audience truly make informed decisions. The frame matrix is not only useful for policy makers to know all perspectives when joining public debate, but also to health care workers to get into meaningful conversations with their patients and families.
Phytochemical analysis and versatile in vitro evaluation of antimicrobial, cytotoxic and enzyme inhibition potential of different extracts of traditionally used Aquilegia pubiflora Wall. Ex Royle
Authors: Jan Hasnain , Usman Hazrat , Shah Muzamil , Zaman Gouhar , Mushtaq Sadaf , Drouet Samantha , Hano Christophe , Abbasi Bilal Haider 
Published: June 2021

AbstractBackgroundHimalayan Columbine (Aquilegia pubifloraWall. Ex Royle) is a medicinal plant and have been used as traditional treatments for various human diseases including skin burns, jaundice, hepatitis, wound healing, cardiovascular and circulatory diseases. Till now there is no report available on phytochemical investigation of Himalayan Columbine and to the best of our knowledge, through present study we have reported for the first time, the phytochemical analysis and pharmacological potentials of different leaf extracts ofAquilegia pubiflora.MethodsFour types of extracts were prepared using solvent of different polarities (Distilled water APDW, Methanol APM, Ethanol APEand Ethyl acetate APEA), and were evaluated to determine the best candidate for potent bioactivity. Phytochemical constituents in prepared extracts were quantified through HPLC analysis. Subsequently, all four types of leaf extracts were then evaluated for their potential bioactivities including antimicrobial, protein kinase inhibition, anti-inflammatory, anti-diabetic, antioxidant, anti-Alzheimer, anti-aging and cytotoxic effect.ResultsHPLC analysis demonstrated the presence of dvitexin, isovitexin, orientin, isoorientin, ferulic acid, sinapic acid and chlorogenic acid in varied proportions in all plant extracts. Antimicrobial studies showed that,K. pneumoniawas found to be most susceptible to inhibition zones of 11.2 ± 0.47, 13.9 ± 0.33, 12.7 ± 0.41, and 13.5 ± 0.62 measured at 5 mg/mL for APDW, APM, APEand APEArespectively.A. nigerwas the most susceptible strain in case of APDWwith the highest zone of inhibition 14.3 ± 0.32, 13.2 ± 0.41 in case of APM, 13.7 ± 0.39 for APEwhile 15.4 ± 0.43 zone of inhibition was recorded in case of APEAat 5 mg/mL. The highest antioxidant activity of 92.6 ± 1.8 μgAAE/mg, 89.2 ± 2.4 μgAAE/mg, 277.5 ± 2.9 μM, 289.9 ± 1.74 μM for TAC, TRP, ABTS and FRAP, respectively, was shown by APE. APM, APEand APEAextracts showed a significant % cell inhibition (above 40%) against HepG2 cells. The highest anti-inflammatory of the samples was shown by APE(52.5 ± 1.1) against sPLA2, (41.2 ± 0.8) against 15-LOX, followed by (38.5 ± 1.5) and (32.4 ± 0.8) against COX-1 and COX-2, respectively.ConclusionsStrong antimicrobial, Protein Kinase potency and considerable α-glucosidase, α-amylase, and cytotoxic potential were exhibited by plant samples. Significant anti-Alzheimer, anti-inflammatory, anti-aging, and kinase inhibitory potential of each plant sample thus aware us for further detailed research to determine novel drugs.
Factors associated with perceived stress of clinical practice among associate degree nursing students in Taiwan
Authors: Wu Chia-Shan , Rong Jiin-Ru , Huang Mei-Zen 
Published: June 2021

Abstract
Background
Clinical placements play an important role in helping nursing students to achieve clinical competence, but these placements can be highly challenging and stressful. It has been shown that stress can be either a trigger or aggravating factor for ill-health in general, but studies have seldom differentiated the impact of general health status on perceived stress.
This study examined factors associated with perceived stress of clinical practice among nursing students with a particular focus on the effect of general health status on stress.

Methods
This was a cross-sectional quantitative study conducted among 724 associate nursing degree students in Southern Taiwan.

Results
Health status scores varied from 28 to 139, with an average of 68.40 (SD = 25.75). Health status was reported to be ‘good’ (scores 28–55) in 35.5% of participants, moderate (scores 56–83) in 24.6%, and poor (Scores ≧ 84) in 39.9% of participants. Perceived stress scores ranged from 0 to 95 points with an average score of 36.65 (SD ± 15.95). The classification and regression tree (CART) analysis showed health status as the most important factor linked to perceived stress with a Normalized Importance value of 100%. Those who reported general health status (measured through General Health Questionnaire (GHQ)-28) score of ≤34.5 perceived mild stress and those with a score of > 34.5–< 84.5 perceived moderate stress. A score of 84.5 was found to be the point of transition to perceptions of severe stress. When health status score was greater than 84.5, perceived stress was at a severe or extremely severe level.

Conclusions
Our findings indicated health status as a potential measure to identify students who were most vulnerable to perceived stress. Given the cross-sectional design of this study and the bidirectional relationship between health and stress, more studies are needed to fully establish the predictive link between general health status and vulnerability to stress.
Evaluation of older persons’ medications: a critical incident technique study exploring healthcare professionals’ experiences and actions
Authors: Holmqvist Malin , Thor Johan , Ros Axel , Johansson Linda 
Published: June 2021

Abstract
Background
Older persons with polypharmacy are at increased risk of harm from medications. Therefore, it is important that physicians and nurses, together with the persons, evaluate medications to avoid hazardous polypharmacy. It remains unclear how healthcare professionals experience such evaluations. This study aimed to explore physicians’ and nurses’ experiences from evaluations of older persons’ medications, and their related actions to manage concerns related to the evaluations.

Method
Individual interview data from 29 physicians and nurses were collected and analysed according to the critical incident technique.

Results
The medication evaluation for older persons was influenced by the working conditions (e.g. healthcare professionals’ clinical knowledge, experiences, and situational conditions) and working in partnership (e.g. cooperating around and with the older person). Actions taken to manage these evaluations were related to working with a plan (e.g. performing day-to-day work and planning for continued treatment) and collaborative problem-solving (e.g. finding a solution, involving the older person, and communicating with colleagues).

Conclusion
Working conditions and cooperation with colleagues, the older persons and their formal or informal caregivers, emerged as important factors related to the medication evaluation. By adjusting their performance to variations in these conditions, healthcare professionals contributed to the resilience of the healthcare system by its capacity to prevent, notice and mitigate medication problems. Based on these findings, we hypothesize that a joint plan for continued treatment could facilitate such resilience, if it articulates what to observe, when to act, who should act and what actions to take in case of deviations from what is expected.
Organisational factors affecting emergency medical services’ performance in rural and urban areas of Saudi Arabia
Authors: Alanazy Ahmed Ramdan M , Fraser John , Wark Stuart 
Published: June 2021

Abstract
Background
There is a disparity in outcomes between rural and urban emergency medical services (EMS) around the world. However, there is a scarcity of research that directly asks EMS staff in both rural and urban areas how service delivery could be improved. The aim of the present study is to gain insights from frontline workers regarding organisational factors that may underpin discrepancies between rural and urban EMS performance.

Subject and methods
The study was undertaken in the Riyadh region of Saudi Arabia. Potential participants were currently employed by Saudi Red Crescent EMS as either a technician, paramedic or an EMS station manager, and had a minimum of five years experience with the EMS. Semi-structured interviews were undertaken between October 2019 and July 2020 with first respondents to a call for participants, and continued until data saturation was reached. All interviews were conducted in Arabic and transcribed verbatim. The Arabic transcript was shared with each participant, and they were asked to confirm their agreement with the transcription. The transcribed interviews were then translated into English; the English versions were shared with bi-lingual participants for validation, while independent certification of the translations were performed for data from participants not fluent in English. A thematic analysis methodological approach was used to examine the data.

Results
The final sample involved 20 participants (10 rural, 10 urban) from Saudi Red Crescent EMS. Data analyses identified key organisational factors that resulted in barriers and impediments for EMS staff. Differences and similarities were observed between rural and urban respondents, with identified issues including response and transportation time, service coordination, reason for call-out, as well as human and physical resourcing.

Conclusion
The findings identified key issues impacting on EMS performance across both rural and urban areas. In order to address these problems, three changes are recommended. These recommendations include a comprehensive review of rural EMS vehicles, with a particular focus on the age; incentives to improve the numbers of paramedics in rural areas and more localised specialist training opportunities for rurally-based personnel; and the implementation of national public education program focusing on the role of the EMS.