bluuebunny/crossref_metadata_2025_split huggingface dataset:
Home-grown school feeding: assessment of a pilot program in Nepal
Authors: Shrestha Rachana Manandhar , Schreinemachers Pepijn , Nyangmi Mamta Gurung , Sah Manoj , Phuong Judy , Manandhar Shraddha , Yang Ray-Yu 
Published: January 2020

Abstract
Background
The Nepal School Meals Program reached 600,000 schoolchildren in basic education in 2017 and plays a key role in the government’s strategy to increase children’s academic and nutritional outcomes. A large part of the program is implemented through cash transfers with schools responsible for the school meal delivery. Home-grown school feeding, an approach in which local communities are given greater control over the school meals program and part of the food is sourced locally, may strengthen local ownership and improve meal quality, but there is a lack of evidence for impact.

Methods
This study piloted home-grown school feeding in 30 schools reaching nearly 4000 children in Sindhupalchok and Bardiya districts in Nepal with the aim to assess operations and outcomes in comparison to the regular cash-based school meals program. The study used a one-time post evaluation with a mixed methods approach. Qualitative data were collected through 12 focus group discussions and 28 key informant interviews with government and school staff, parents, cooks, cooperative members, World Food Programme representatives and other stakeholders involved in the pilot program. The quantitative part applied a quasi-experimental design and used cross-sectional data collected from 1512 children in 30 pilot and 30 control schools.

Results
The quantitative data indicated that children in the pilot schools had a significantly higher provision of midday school meals (+ 19%; p < 0.01) and a higher school meal quality in terms of dietary diversity (+ 44%; p < 0.01) and nutritional content (e.g. a 21%-points higher consumption of vitamin A-rich fruit and vegetables; p < 0.01). The qualitative data identified key drivers of these positive outcomes as the use of standard meal options, capacity building of local stakeholders, strengthened community ownership and accountability mechanisms, and local food supply chains. Maintaining the observed gains would require a 20–33% increase in the current budget per school meal in addition to the cost of capacity building.

Conclusions
This study for Nepal shows that home-grown school feeding strengthened operations of the school meals program and led to a significantly higher meal provision and quality of school meals.
A systematic review with meta-analysis of gastroesophageal reflux disease and exacerbations of chronic obstructive pulmonary disease
Authors: Huang Chunrong , Liu Yahui , Shi Guochao 
Published: January 2020

Abstract
Background
Gastroesophageal reflux disease (GERD) was suggested to be associated with exacerbations of chronic obstructive pulmonary disease (COPD) in recent years. The aim of this study was to examine the association between GERD and COPD exacerbation through a meta-analysis.

Methods
Databases including EMBASE, MEDLINE, and the Cochrane Central Register of Controlled Trials were searched with a systematic searching strategy for original articles, published until Jan 2019, without language restriction.

Results
A total of 13,245 patients from 10 observational articles were included in the meta-analysis. The meta-analysis indicated that GERD is associated with increased risk of COPD exacerbation (OR: 5.37; 95% CI 2.71–10.64). Patients with COPD and GERD had increased number of exacerbation (WMD: 0.48; 95% CI: 0.31 to 0.65).

Conclusions
The meta-analysis showed that there was a significant correlation between GERD and COPD exacerbation.
Co-infection with Streptococcus anginosus and Mycobacterium tuberculosis in an immunocompetent pediatric patient. A case report
Authors: Saldaña Napoleon González , Bejarano José Iván Castillo , Porras Marte Hernández , de la Garza Eduardo Arias , Gutiérrez Sofia Fortes , Gutiérrez Jose Luis Copado , Olguin Hugo Juarez 
Published: January 2020

AbstractBackgroundSimultaneous infection in tuberculosis (TB) is rare. The mixed infection betweenStreptococcus anginosusgroup (SAG) andM. tuberculosis(MTB) has not been reported in children. The aim of this report was to describe a pediatric case with a pulmonary abscess caused by the duality SAG-MTB co-infection.Case presentationAn 11-year-old boy with an acute onset of throbbing pain of two-day evolution located in the anterior chest wall. The patient reported a history of fever, cough and rhinorrhea during the last seven days. An anterior chest radiography revealed a heterogenic opacity at the lower right lobe while the lateral projection showed an obliteration at the anterior diaphragmatic insertion. Parenteral Ceftriaxone (100 mg/kg/day) and Dicloxacillin (200 mg/kg/day) was started. The abscess was subsequently drained and analyzed. After a year of follow-up, the patient remained asymptomatic.ConclusionThis case represents the first reported case of pulmonary co-infection involving MTB and SAG in an immunocompetent pediatric patient.
Influence of extension stem length and diameter on clinical and radiographic outcomes of revision total knee arthroplasty
Authors: Lee Sheng-Hsun , Shih Hsin-Nung , Chang Chih-Hsiang , Lu Tung-Wu , Chang Yu-Han , Lin Yu-Chih 
Published: January 2020

AbstractBackgroundExtension stems provide stability to revision total knee arthroplasty (RTKA). Little is known regarding the relationship between stem characteristics and RTKA stability. We aimed to identify the relationship between canal filling ratio (CFR) and aseptic loosening following RTKA.MethodsWe retrospectively reviewed demographics, radiographic parameters, and outcomes associated with RTKA performed between 2008 and 2013 in a tertiary hospital. The inclusion criteria were: revision for aseptic loosening, hybrid fixation, minor bone defect, Zimmer® LCCK prosthesis, and follow-up > 24 months. Using the modified Knee Society radiographic scoring system, radiographic prosthesis loosening was defined as a radiolucent line (RLL) score ≥ 9 on the femoral side or ≥ 10 on the tibial side. We utilized receiver operating characteristic (ROC) curve analysis to evaluate the cutoff value for stem length and diameter in terms of prosthesis loosening or not. Furthermore, CFR-related parameters were analyzed with logistic regression to clarify their relationships with prosthesis loosening.ResultsProsthesis loosening was detected in 17 of 65 patients included. On logistic regression analysis, male sex and severity of the tibial bone defect were associated with loosening. On multivariate analysis, male sex and bone defect severity were associated with loosening on the femoral side, while malalignment was associated with loosening on the tibial side. Protective factors included femoral CFR > 0.85, CFR > 0.7 for > 2 cm, and CFR > 0.7 for > 4 cm, as well as tibial CFR > 0.85.ConclusionsTo minimize loosening post-RTKA, femoral CFR > 0.7 for > 2 cm and tibial CFR > 0.85 are recommended. Risk factors may include male sex, bone defect severity, and malalignment.
Pigmented villous nodular synovitis mimicking metastases on 18F-FDG PET/CT in a patient with rectal mucosal melanoma: a case report
Authors: Yen Yu-An , Wu Li-Chun , Lu Na-Mi , Lee Chiang Hsuan 
Published: January 2020

Abstract
Background
Mucosal melanomas are rare and have a high potential for metastasizing. Surgical resection is the treatment of choice for single distant metastases. Malignant melanoma usually shows the highest uptake of fluorine-18 fluorodeoxyglucose (18F-FDG). 18F- FDG positron emission tomography /computed tomography (PET/CT) is usually used for melanoma staging. An extensive literature review revealed only 4 published case reports and an original paper involving 8 cases (12 cases in total) of patients with skin melanomas in whom pigmented villous nodular synovitis (PVNS) mimicked metastatic melanoma, however, none of the melanomas reported were of rectal mucosal origin.

Case presentation
A 60-year-old woman presented with recent diagnosis of rectal mucosal melanoma, two additional 18F-FDG-avid lesions in the left ankle and left foot were detected on 18F-FDG PET/CT. Metastases were initially suspected; however, the final diagnosis was PVNS.

Conclusions
This is the first report of PVNS mimicking metastases on 18F-FDG PET/CT in a patient with rectal mucosal melanoma. Although high 18F-FDG-avid lesions in patients with rectal mucosal melanoma are highly suspected to be metastasis and warrant an meticulous examination, the present case is a reminder that in such patients, not all lesions with high 18F-FDG uptake, especially those near a joint, are metastases and that more extensive resection is unnecessary.
Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge
Authors: Liao Chen , Xavier Joao B. , Zhu Zhenduo 
Published: January 2020

Abstract
Background
Accurate network models of species interaction could be used to predict population dynamics and be applied to manage real world ecosystems. Most relevant models are nonlinear, however, and data available from real world ecosystems are too noisy and sparsely sampled for common inference approaches. Here we improved the inference of generalized Lotka–Volterra (gLV) ecological networks by using a new optimization algorithm to constrain parameter signs with prior knowledge and a perturbation-based ensemble method.

Results
We applied the new inference to long-term species abundance data from the freshwater fish community in the Illinois River, United States. We constructed an ensemble of 668 gLV models that explained 79% of the data on average. The models indicated (at a 70% level of confidence) a strong positive interaction from emerald shiner (Notropis atherinoides) to channel catfish (Ictalurus punctatus), which we could validate using data from a nearby observation site, and predicted that the relative abundances of most fish species will continue to fluctuate temporally and concordantly in the near future. The network shows that the invasive silver carp (Hypophthalmichthys molitrix) has much stronger impacts on native predators than on prey, supporting the notion that the invader perturbs the native food chain by replacing the diets of predators.

Conclusions
Ensemble approaches constrained by prior knowledge can improve inference and produce networks from noisy and sparsely sampled time series data to fill knowledge gaps on real world ecosystems. Such network models could aid efforts to conserve ecosystems such as the Illinois River, which is threatened by the invasion of the silver carp.
Students’ perceptions towards self-directed learning in Ethiopian medical schools with new innovative curriculum: a mixed-method study
Authors: Kidane Haftom Hadush , Roebertsen Herma , van der Vleuten Cees P. M. 
Published: January 2020

AbstractBackgroundSelf-directed learning (SDL) is an appropriate and preferred learning process to prepare students for lifelong learning in their professions and make them stay up-to-date. The purpose of this study was to explore preclinical students following a hybrid curriculum in Ethiopia experiences to SDL and the support of several learning activities from the curriculum on their SDL. A mixed-method research design was employed.MethodsQuantitative data were collected by using a self-administered questionnaire of 80 items measuring students’ perceptions on their SDL capability as well as to explore students’ views about the influence of components of the curriculum on their SDL. Additional two focus group discussions, each containing eight participants from year-1 and year− 2students, were conducted. The quantitative data were analyzed using SPSS. The focus group discussions were reviewed, coded, and then thematically analyzed.ResultsOur study showed a significant increase in SDL score on comparing students at year-1 with students at year-2 (p = 0.002). Both year-1 and 2 students rated PBL tutorial discussion and tutors had high influence on their individual learning; whereas, other curricular components such as lectures and testes had low influence on their SDL ability. PBL tutorial discussion and module objectives showed strong correlation with students’ SDL scores, r = 0.718 & r = 0.648 (p < 0.01), respectively. Besides, PBL tutorial discussion was found strongly correlated with tutors (r = 0.599 (p < 0.01)) and module objectives (r = 0.574 (p < 0.01)). Assessment was highly correlated with lectures (r = 0.595 (p < 0.01)). Findings from qualitative data showed that certain curricular components played role in promoting students’ SDL. Tutorials analyzing problems played a major role on students’ self-directed learning abilities.ConclusionsAlthough the study implied that components of the hybrid curriculum, mainly PBL, could encourage preclinical students’ self-directed learning, the curriculum is still not free from teacher-centred culture as the majority of teachers still have high power in deciding the learning process. A further longitudinal study is needed to verify the actual level and ability of medical students’ SDL.
Digital pills: a scoping review of the empirical literature and analysis of the ethical aspects
Authors: Martani Andrea , Geneviève Lester Darryl , Poppe Christopher , Casonato Carlo , Wangmo Tenzin 
Published: January 2020

Abstract
Background
Digital Pills (DP) are an innovative drug-device technology that permits to combine traditional medications with a monitoring system that automatically records data about medication adherence as well as patients’ physiological data. Although DP are a promising innovation in the field of digital medicine, their use has also raised a number of ethical concerns. These ethical concerns, however, have been expressed principally from a theoretical perspective, whereas an ethical analysis with a more empirically oriented approach is lacking. There is also a lack of clarity about the empirical evidence available concerning the application of this innovative digital medicine.

Methods
To map the studies where DP have been tested on patients and discuss the ethically relevant issues evident therein, we performed a scoping review of the empirical literature concerning DP.

Results
Our search allowed us to identify 18 papers reporting on studies where DP were tested on patients. These included studies with different designs and involving patients with a variety of conditions. In the empirical literature, a number of issues with ethical relevance were evident. At the patient level, the ethical issues include users’ interaction with DP, personal sphere, health-related risks and patients’ benefits. At the provider level, ethically relevant issues touch upon the doctor-patient relationship and the question of data access. At the societal level, they concern the benefits to society, the quality of evidence and the dichotomy device-medicine.

Conclusions
We conclude that evidence concerning DP is not robust and that more research should be performed and study results made available to evaluate this digital medicine. Moreover, our analysis of the ethically relevant aspects within empirical literature underscores that there are concrete and specific open questions that should be tackled in the ethical discussion about this new technological solution.
Predicting diabetes clinical outcomes using longitudinal risk factor trajectories
Authors: Simon Gyorgy J. , Peterson Kevin A. , Castro M. Regina , Steinbach Michael S. , Kumar Vipin , Caraballo Pedro J. 
Published: January 2020

Abstract
Background
The ubiquity of electronic health records (EHR) offers an opportunity to observe trajectories of laboratory results and vital signs over long periods of time. This study assessed the value of risk factor trajectories available in the electronic health record to predict incident type 2 diabetes.

Study design and methods
Analysis was based on a large 13-year retrospective cohort of 71,545 adult, non-diabetic patients with baseline in 2005 and median follow-up time of 8 years. The trajectories of fasting plasma glucose, lipids, BMI and blood pressure were computed over three time frames (2000–2001, 2002–2003, 2004) before baseline. A novel method, Cumulative Exposure (CE), was developed and evaluated using Cox proportional hazards regression to assess risk of incident type 2 diabetes. We used the Framingham Diabetes Risk Scoring (FDRS) Model as control.

Results
The new model outperformed the FDRS Model (.802 vs .660; p-values <2e-16). Cumulative exposure measured over different periods showed that even short episodes of hyperglycemia increase the risk of developing diabetes. Returning to normoglycemia moderates the risk, but does not fully eliminate it. The longer an individual maintains glycemic control after a hyperglycemic episode, the lower the subsequent risk of diabetes.

Conclusion
Incorporating risk factor trajectories substantially increases the ability of clinical decision support risk models to predict onset of type 2 diabetes and provides information about how risk changes over time.
Assessing stroke severity using electronic health record data: a machine learning approach
Authors: Kogan Emily , Twyman Kathryn , Heap Jesse , Milentijevic Dejan , Lin Jennifer H. , Alberts Mark 
Published: January 2020

Abstract
Background
Stroke severity is an important predictor of patient outcomes and is commonly measured with the National Institutes of Health Stroke Scale (NIHSS) scores. Because these scores are often recorded as free text in physician reports, structured real-world evidence databases seldom include the severity. The aim of this study was to use machine learning models to impute NIHSS scores for all patients with newly diagnosed stroke from multi-institution electronic health record (EHR) data.

Methods
NIHSS scores available in the Optum© de-identified Integrated Claims-Clinical dataset were extracted from physician notes by applying natural language processing (NLP) methods. The cohort analyzed in the study consists of the 7149 patients with an inpatient or emergency room diagnosis of ischemic stroke, hemorrhagic stroke, or transient ischemic attack and a corresponding NLP-extracted NIHSS score. A subset of these patients (n = 1033, 14%) were held out for independent validation of model performance and the remaining patients (n = 6116, 86%) were used for training the model. Several machine learning models were evaluated, and parameters optimized using cross-validation on the training set. The model with optimal performance, a random forest model, was ultimately evaluated on the holdout set.

Results
Leveraging machine learning we identified the main factors in electronic health record data for assessing stroke severity, including death within the same month as stroke occurrence, length of hospital stay following stroke occurrence, aphagia/dysphagia diagnosis, hemiplegia diagnosis, and whether a patient was discharged to home or self-care. Comparing the imputed NIHSS scores to the NLP-extracted NIHSS scores on the holdout data set yielded an R2 (coefficient of determination) of 0.57, an R (Pearson correlation coefficient) of 0.76, and a root-mean-squared error of 4.5.

Conclusions
Machine learning models built on EHR data can be used to determine proxies for stroke severity. This enables severity to be incorporated in studies of stroke patient outcomes using administrative and EHR databases.
Qualitative evaluation of a community health representative program on patient experiences in Navajo Nation
Authors: Lalla Amber , Salt Shine , Schrier Elizabeth , Brown Christian , Curley Cameron , Muskett Olivia , Begay Mae-Gilene , Shirley Lenora , Clark Clarina , Singer Judy , Shin Sonya , Nelson Adrianne Katrina 
Published: January 2020

Abstract
Background
Community Health Representatives (CHRs) overcome health disparities in Native communities by delivering home care, health education, and community health promotion. The Navajo CHR Program partners with the non-profit Community Outreach and Patient Empowerment (COPE), to provide home-based outreach to Navajo clients living with diabetes. COPE has created an intervention (COPE intervention) focusing on multiple levels of improved care including trainings for CHRs on Motivational Interviewing and providing CHRs with culturally-appropriate education materials. The objective of this research is to understand the participant perspective of the CHR-COPE collaborative outreach through exploring patient-reported outcomes (PROs) of clients who consent to receiving the COPE intervention (COPE clients) using a qualitative methods evaluation.

Methods
Seven COPE clients were selected to participate in semi-structured interviews one year after finishing COPE to explore their perspective and experiences. Qualitative interviews were recorded, transcribed, and coded to identify themes.

Results
Clients revealed that health education delivered by CHRs facilitated lifestyle changes by helping them understand key health indicators and setting achievable goals through the use of accessible material and encouragement. Clients felt comfortable with CHRs who respected traditional practices and made regular visits. Clients also appreciated when CHRs educated their family members, who in turn were better able to support the client in their health management. Finally, CHRs who implemented the COPE intervention helped patients who were unable to regularly see a primary care doctor for critical care and support in their disease management.

Conclusion
The COPE-CHR collaboration facilitated trusting client-CHR relationships and allowed clients to better understand their diagnoses. Further investment in materials that respect traditional practices and aim to educate clients’ families may foster these relationships and improve health outcomes.

Trial registration
clinicaltrials.gov: NCT03326206. Registered 9/26/2017 (retrospectively registered).
Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data
Authors: Armstrong Ellie E. , Taylor Ryan W. , Miller Danny E. , Kaelin Christopher B. , Barsh Gregory S. , Hadly Elizabeth A. , Petrov Dmitri 
Published: January 2020

Abstract
Background
The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade.

Results
Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity.

Conclusions
We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.