bluuebunny/crossref_metadata_2025_split huggingface dataset:
A scoring system derived from electronic health records to identify patients at high risk for noninvasive ventilation failure
Authors: Stefan Mihaela S. , Priya Aruna , Pekow Penelope S. , Steingrub Jay S. , Hill Nicholas S. , Lagu Tara , Raghunathan Karthik , Bhat Anusha G. , Lindenauer Peter K. 
Published: February 2021

AbstractObjectiveTo develop and validate a clinical risk prediction score for noninvasive ventilation (NIV) failure defined as intubation after a trial of NIV in non-surgical patients.DesignRetrospective cohort study of a multihospital electronic health record database.PatientsNon-surgical adult patients receiving NIV as the first method of ventilation within two days of hospitalization.MeasurementPrimary outcome was intubation after a trial of NIV. We used a non-random split of the cohort based on year of admission for model development and validation. We included subjects admitted in years 2010–2014 to develop a risk prediction model and built a parsimonious risk scoring model using multivariable logistic regression. We validated the model in the cohort of subjects hospitalized in 2015 and 2016.Main resultsOf all the 47,749 patients started on NIV, 11.7% were intubated. Compared with NIV success, those who were intubated had worse mortality (25.2% vs. 8.9%). Strongest independent predictors for intubation were organ failure, principal diagnosis group (substance abuse/psychosis, neurological conditions, pneumonia, and sepsis), use of invasive ventilation in the prior year, low body mass index, and tachypnea. The c-statistic was 0.81, 0.80 and 0.81 respectively, in the derivation, validation and full cohorts. We constructed three risk categories of the scoring system built on the full cohort; the median and interquartile range of risk of intubation was: 2.3% [1.9%–2.8%] for low risk group; 9.3% [6.3%–13.5%] for intermediate risk category; and 35.7% [31.0%–45.8%] for high risk category.ConclusionsIn patients started on NIV, we found that in addition to factors known to be associated with intubation, neurological, substance abuse, or psychiatric diagnoses were highly predictive for intubation. The prognostic score that we have developed may provide quantitative guidance for decision-making in patients who are started on NIV.
Stratified care integrated with eHealth versus usual primary care physiotherapy in patients with neck and/or shoulder complaints: protocol for a cluster randomized controlled trial
Authors: van Tilburg Mark L. , Kloek Corelien J. J. , Pisters Martijn F. , Staal J. Bart , van Dongen Johanna M. , de Weerd Marjolein , Ostelo Raymond W. J. G. , Foster Nadine E. , Veenhof Cindy 
Published: February 2021

AbstractBackgroundNeck and shoulder complaints are common in primary care physiotherapy. These patients experience pain and disability, resulting in high societal costs due to, for example, healthcare use and work absence. Content and intensity of physiotherapy care can be matched to a patient’s risk of persistent disabling pain. Mode of care delivery can be matched to the patient’s suitability for blended care (integrating eHealth with physiotherapy sessions). It is hypothesized that combining these two approaches to stratified care (referred to from this point as Stratified Blended Approach) will improve the effectiveness and cost-effectiveness of physiotherapy for patients with neck and/or shoulder complaints compared to usual physiotherapy.MethodsThis paper presents the protocol of a multicenter, pragmatic, two-arm, parallel-group, cluster randomized controlled trial. A total of 92 physiotherapists will be recruited from Dutch primary care physiotherapy practices. Physiotherapy practices will be randomized to the Stratified Blended Approach arm or usual physiotherapy arm by a computer-generated random sequence table using SPSS (1:1 allocation). Number of physiotherapists (1 or > 1) will be used as a stratification variable. A total of 238 adults consulting with neck and/or shoulder complaints will be recruited to the trial by the physiotherapy practices. In the Stratified Blended Approach arm, physiotherapists will match I) the content and intensity of physiotherapy care to the patient’s risk of persistent disabling pain, categorized as low, medium or high (using the Keele STarT MSK Tool) and II) the mode of care delivery to the patient’s suitability and willingness to receive blended care. The control arm will receive physiotherapy as usual. Neither physiotherapists nor patients in the control arm will be informed about the Stratified Blended Approach arm. The primary outcome is region-specific pain and disability (combined score of Shoulder Pain and Disability Index & Neck Pain and Disability Scale) over 9 months. Effectiveness will be compared using linear mixed models. An economic evaluation will be performed from the societal and healthcare perspective.DiscussionThe trial will be the first to provide evidence on the effectiveness and cost-effectiveness of the Stratified Blended Approach compared with usual physiotherapy in patients with neck and/or shoulder complaints.Trial registrationNetherlands Trial Register:NL8249. Officially registered since 27 December 2019. Date of first enrollment: 30 September 2020. Study status: ongoing, data collection.
Evidence to support a drain-free strategy in kidney transplantation using a retrospective comparison of 500 consecutively transplanted cases at a single center
Authors: Farag Ahmed , Gaynor Jeffrey J. , Serena Giuseppe , Ciancio Gaetano 
Published: February 2021

Abstract
Introduction
Routine placement of surgical drains at the time of kidney transplant has been debated in terms of its prognostic value.

Objectives
To determine whether the placement of a surgical drain affects the incidence rate of developing wound complications and other clinical outcomes, particularly after controlling for other prognostic factors.

Methods
Retrospective analysis of 500 consecutive renal transplant cases who did not (Drain-free, DF) vs. did (Drain, D) receive a drain at the time of transplant was performed. The primary outcome was the development of any wound complication (superficial or deep) during the first 12 months post-transplant. Secondary outcomes included the development of superficial wound complications, deep wound complications, DGF, and graft loss during the first 12 months post-transplant.

Results
388 and 112 recipients had DF/D, respectively. DF-recipients were significantly more likely to be younger, not have pre-transplant diabetes, receive a living donor kidney, receive a kidney-alone transplant, have a shorter duration of dialysis, shorter mean cold-ischemia-time, and greater pre-transplant use of anticoagulants/antiplatelets. Wound complications were 4.6% (18/388) vs. 5.4% (6/112) in DF vs. D groups, respectively (P = 0.75). Superficial wound complications were observed in 0.8% (3/388) vs. 0.0% (0/112) in DF vs. D groups, respectively (P = 0.35). Deep wound complications were observed in 4.1% (16/388) vs. 5.4% ((6/112) in DF vs. D groups, respectively (P = 0.57). Higher recipient body mass index and ≥ 1 year of pre-transplant dialysis were associated in multivariable analysis with an increased incidence of wound complications. Once the prognostic influence of these 2 factors were controlled, there was still no notable effect of drain use (yes/no). The lack of prognostic effect of drain use was similarly observed for the other clinical outcomes.

Conclusions
In a relatively large cohort of renal transplant recipients, routine surgical drain use appears to offer no distinct prognostic advantage.
Evaluation of antioxidant and anticancer activity of crude extract and different fractions of Chlorella vulgaris axenic culture grown under various concentrations of copper ions
Authors: El-fayoumy Eman A. , Shanab Sanaa M. M. , Gaballa Hanan S. , Tantawy Mohamed A. , Shalaby Emad A. 
Published: February 2021

Abstract
Background
Chlorella vulgaris is a microalga potentially used for pharmaceutical, animal feed, food supplement, aquaculture and cosmetics. The current study aims to study the antioxidant and prooxidant effect of Chlorella vulgaris cultivated under various conc. of copper ions.

Methods
The axenic green microalgal culture of Chlorella vulgaris was subjected to copper stress conditions (0.00, 0.079, 0.158, 0.316 and 0.632 mg/L). The growth rate was measured at OD680 nm and by dry weight (DW). Moreover, the Antioxidant activity against DPPH and ABTS radical, pigments and phytochemical compounds of the crude extracts (methylene chloride: Methanol, 1:1) were evaluated. The promising Cu crude extract (0.316 mg/L) further fractionated into twenty-one fractions by silica gel column chromatography using hexane, chloroform and ethyl acetate as a mobile phase.

Results
The obtained results reported that nine out of these fractions exhibited more than 50% antioxidant activity and anticancer activity against Hela cancer cell lines. Based on IC50, fraction No. 7 was found to be the most effective fraction possessing a significant increase in both antioxidant and anticancer potency. Separation of active compound (s) in fraction No 7 was performed using precoated silica gel plates (TLC F254) with ethyl acetate: hexane (9:1 v/v) as mobile phase. Confirmation of active compound separation was achieved by two-dimensional TLC and visualization of the separated compound by UV lamp. The complete identification of the separated active compound was performed by UV- Vis- spectrophotometric absorption, IR, MS, H1-NMRT C13-NMR. The isolated compound ((2E,7R,11R)-3,7,11,15-Tetramethyl-2-hexadecenol) have high antioxidant activity with IC50 (10.59 μg/ml) against DPPH radical assay and comparable to the capacities of the positive controls, Butylated hydroxy toluene [BHT] (IC50 11.2 μg/ml) and Vitamin C (IC50 12.9 μg/ml). Furthermore, pure isolated compound exhibited a potent anticancer activity against Hela cell line with IC50 (4.38 μg/ml) compared to Doxorubicin (DOX) as synthetic drug (13.3 μg/ml). In addition, the interaction of the pure compound with Hela cancer cell line and gene expression were evaluated.

Conclusions
The authors recommend cultivation of Chlorella vulgaris in large scale under various stress conditions for use the crude extracts and semi purified fractions for making a pharmaco-economic value in Egypt and other countries.
A policy analysis of the national phenylketonuria screening program in Iran
Authors: Heidari Alireza , Arab Mohammad , Damari Behzad 
Published: February 2021

Abstract
Background
Phenylketonuria (PKU) screening is a public health measure taken to diagnose and treat the patients with PKU to prevent severe neurological disorders in them. The present study was aimed at analyzing the policies of the national PKU screening (NaPS) program in Iran.

Methods
PKU screening program policies were analyzed in compliance with the policy triangle model. Document review and 38 semi-structured interviews were used for data collection. Document review data were analyzed using content analysis, and interview data were analyzed using framework analysis.

Results
The national PKU screening (NaPS) program was a decision made at the genetics department of Ministry of Health and Medical Education (MOHME) in Iran. Many internal and external stakeholders were involved in it and valid evidence was used to formulate the policies. Despite some opposition and insufficient support, the program was implemented due to the continuous persistence of parents, interested executives, formulated valid content and a top-down approach. The main barriers included rapid substitution of managers, shortage of Phe-free milk, little awareness of patients’ families, social stigma, and inadequate co-operation of some hospital administrators.

Conclusions
The policy triangle framework contributed to explaining the different components of the PKU screening program. A successful PKU screening program requires more stability of senior managers in MOHME, enough human resources and Phe-free milk, educating patients’ families, and commitment of hospitals administrators. Meanwhile, all the stakeholders need to be involved in the program effectively.
The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories
Authors:   CMMID COVID-19 Working Group, Liu Yang , Morgenstern Christian , Kelly James , Lowe Rachel , Jit Mark 
Published: February 2021

AbstractBackgroundNon-pharmaceutical interventions (NPIs) are used to reduce transmission of SARS coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, empirical evidence of the effectiveness of specific NPIs has been inconsistent. We assessed the effectiveness of NPIs around internal containment and closure, international travel restrictions, economic measures, and health system actions on SARS-CoV-2 transmission in 130 countries and territories.MethodsWe used panel (longitudinal) regression to estimate the effectiveness of 13 categories of NPIs in reducing SARS-CoV-2 transmission using data from January to June 2020. First, we examined the temporal association between NPIs using hierarchical cluster analyses. We then regressed the time-varying reproduction number (Rt) of COVID-19 against different NPIs. We examined different model specifications to account for the temporal lag between NPIs and changes inRt, levels of NPI intensity, time-varying changes in NPI effect, and variable selection criteria. Results were interpreted taking into account both the range of model specifications and temporal clustering of NPIs.ResultsThere was strong evidence for an association between two NPIs (school closure, internal movement restrictions) and reducedRt. Another three NPIs (workplace closure, income support, and debt/contract relief) had strong evidence of effectiveness when ignoring their level of intensity, while two NPIs (public events cancellation, restriction on gatherings) had strong evidence of their effectiveness only when evaluating their implementation at maximum capacity (e.g. restrictions on 1000+ people gathering were not effective, restrictions on < 10 people gathering were). Evidence about the effectiveness of the remaining NPIs (stay-at-home requirements, public information campaigns, public transport closure, international travel controls, testing, contact tracing) was inconsistent and inconclusive. We found temporal clustering between many of the NPIs. Effect sizes varied depending on whether or not we included data after peak NPI intensity.ConclusionUnderstanding the impact that specific NPIs have had on SARS-CoV-2 transmission is complicated by temporal clustering, time-dependent variation in effects, and differences in NPI intensity. However, the effectiveness of school closure and internal movement restrictions appears robust across different model specifications, with some evidence that other NPIs may also be effective under particular conditions. This provides empirical evidence for the potential effectiveness of many, although not all, actions policy-makers are taking to respond to the COVID-19 pandemic.
Increasing adoption rates at animal shelters: a two-phase approach to predict length of stay and optimal shelter allocation
Authors: Bradley Janae , Rajendran Suchithra 
Published: February 2021

AbstractBackgroundAmong the 6–8 million animals that enter the rescue shelters every year, nearly 3–4 million (i.e., 50% of the incoming animals) are euthanized, and 10–25% of them are put to death specifically because of shelter overcrowding each year. The overall goal of this study is to increase the adoption rates at animal shelters. This involves predicting the length of stay of each animal at shelters considering key features such as animal type (dog, cat, etc.), age, gender, breed, animal size, and shelter location.ResultsLogistic regression, artificial neural network, gradient boosting, and the random forest algorithms were used to develop models to predict the length of stay. The performance of these models was determined using three performance metrics: precision, recall, and F1 score. The results demonstrated that the gradient boosting algorithm performed the best overall, with the highest precision, recall, and F1 score. Upon further observation of the results, it was found that age for dogs (puppy, super senior), multicolor, and large and small size were important predictor variables.ConclusionThe findings from this study can be utilized to predict and minimize the animal length of stay in a shelter and euthanization. Future studies involve determining which shelter location will most likely lead to the adoption of that animal. The proposed two-phased tool can be used by rescue shelters to achieve the best compromise solution by making a tradeoff between the adoption speed and relocation cost.
Preexisting respiratory diseases and clinical outcomes in COVID-19: a multihospital cohort study on predominantly African American population
Authors: Lohia Prateek , Sreeram Kalyan , Nguyen Paul , Choudhary Anita , Khicher Suman , Yarandi Hossein , Kapur Shweta , Badr M. Safwan 
Published: February 2021

Abstract
Background
Comorbidities play a key role in severe disease outcomes in COVID-19 patients. However, the literature on preexisting respiratory diseases and COVID-19, accounting for other possible confounders, is limited. The primary objective of this study was to determine the association between preexisting respiratory diseases and severe disease outcomes among COVID-19 patients. Secondary aim was to investigate any correlation between smoking and clinical outcomes in COVID-19 patients.

Methods
This is a multihospital retrospective cohort study on 1871 adult patients between March 10, 2020, and June 30, 2020, with laboratory confirmed COVID-19 diagnosis. The main outcomes of the study were severe disease outcomes i.e. mortality, need for mechanical ventilation, and intensive care unit (ICU) admission. During statistical analysis, possible confounders such as age, sex, race, BMI, and comorbidities including, hypertension, coronary artery disease, congestive heart failure, diabetes, any history of cancer and prior liver disease, chronic kidney disease, end-stage renal disease on dialysis, hyperlipidemia and history of prior stroke, were accounted for.

Results
A total of 1871 patients (mean (SD) age, 64.11 (16) years; 965(51.6%) males; 1494 (79.9%) African Americans; 809 (43.2%) with ≥ 3 comorbidities) were included in the study. During their stay at the hospital, 613 patients (32.8%) died, 489 (26.1%) needed mechanical ventilation, and 592 (31.6%) required ICU admission. In fully adjusted models, patients with preexisting respiratory diseases had significantly higher mortality (adjusted Odds ratio (aOR), 1.36; 95% CI, 1.08–1.72; p = 0.01), higher rate of ICU admission (aOR, 1.34; 95% CI, 1.07–1.68; p = 0.009) and increased need for mechanical ventilation (aOR, 1.36; 95% CI, 1.07–1.72; p = 0.01). Additionally, patients with a history of smoking had significantly higher need for ICU admission (aOR, 1.25; 95% CI, 1.01–1.55; p = 0.03) in fully adjusted models.

Conclusion
Preexisting respiratory diseases are an important predictor for mortality and severe disease outcomes, in COVID-19 patients. These results can help facilitate efficient resource allocation for critical care services.
In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework
Authors: Gunnarsson Sophie , Prabakaran Sudhakaran 
Published: February 2021

Abstract
Background
Plasmodium falciparum causes the deadliest form of malaria, which remains one of the most prevalent infectious diseases. Unfortunately, the only licensed vaccine showed limited protection and resistance to anti-malarial drug is increasing, which can be largely attributed to the biological complexity of the parasite’s life cycle. The progression from one developmental stage to another in P. falciparum involves drastic changes in gene expressions, where its infectivity to human hosts varies greatly depending on the stage. Approaches to identify candidate genes that are responsible for the development of infectivity to human hosts typically involve differential gene expression analysis between stages. However, the detection may be limited to annotated proteins and open reading frames (ORFs) predicted using restrictive criteria.

Methods
The above problem is particularly relevant for P. falciparum; whose genome annotation is relatively incomplete given its clinical significance. In this work, systems proteogenomics approach was used to address this challenge, as it allows computational detection of unannotated, novel Open Reading Frames (nORFs), which are neglected by conventional analyses. Two pairs of transcriptome/proteome were obtained from a previous study where one was collected in the mosquito-infectious oocyst sporozoite stage, and the other in the salivary gland sporozoite stage with human infectivity. They were then re-analysed using the proteogenomics framework to identify nORFs in each stage.

Results
Translational products of nORFs that map to antisense, intergenic, intronic, 3′ UTR and 5′ UTR regions, as well as alternative reading frames of canonical proteins were detected. Some of these nORFs also showed differential expression between the two life cycle stages studied. Their regulatory roles were explored through further bioinformatics analyses including the expression regulation on the parent reference genes, in silico structure prediction, and gene ontology term enrichment analysis.

Conclusion
The identification of nORFs in P. falciparum sporozoites highlights the biological complexity of the parasite. Although the analyses are solely computational, these results provide a starting point for further experimental validation of the existence and functional roles of these nORFs,
Recruitment, training and supervision of nurses and nurse assistants for a task-shifting depression intervention in two RCTs in Brazil and Peru
Authors: Rocha Thais Izabel Ugeda , Aschar Suzana Crismanis de Almeida Lopes , Hidalgo-Padilla Liliana , Daley Kate , Claro Heloísa Garcia , Martins Castro Hellen Carolina , dos Santos Daniela Vera Cruz , Miranda J. Jaime , Araya Ricardo , Menezes Paulo Rossi 
Published: February 2021

Abstract
Background
Task-shifting and technology in psychological interventions are two solutions to increasing access to mental health intervention and overcoming the treatment gap in low and middle-income countries. The CONEMO intervention combines a smartphone app with support from non-specialized professionals, aiming to treat depression in patients with diabetes and/or hypertension. The aim of this paper is to describe the process of recruitment, training and supervision of the non-specialized professionals who participated in the CONEMO task-shifting intervention in Brazil and Peru.

Methods
We described and analyzed data related to the recruitment, training and supervision of 62 nurse assistants from the health system in Sao Paulo, Brazil, and three hired nurses in Lima, Peru. The data were collected from information provided by nurses and nurse assistants, supervisor records from supervision meetings and the CONEMO platform database.

Results
We found that task-shifting was feasible using existing resources in Sao Paulo and additional human resources in Lima. Training and supervision were found to be crucial and well received by the staff; however, time was a limitation when using existing human resources. Ensuring technological competence prior to the start of the intervention was essential. Group supervision meetings allowed non-specialized professionals to learn from each other’s experiences.

Conclusion
Carefully considering recruitment, training and supervision of non-specialized professionals is important for effective task-shifting when delivering an mHealth intervention for depression. Opportunities and challenges of working in different health systems are described, which should be considered in future implementation, either for research or real settings.
Trial registration NCT028406662 (Sao Paulo), NCT03026426 (Peru).