bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using consensus methods to develop a Social Prescribing Learning Needs Framework for practitioners in Wales
Authors: Wallace C , Elliott M , Thomas S , Davies-McIntosh E , Beese S , Roberts G , Ruddle N , Groves K , Rees S , Pontin D 
Published: January 2020

Aims: Social prescribing is being widely implemented in Wales, but there is no consensus on the necessary learning, training and education needs for people delivering social prescribing. The purpose of the study was to develop an education and training needs conceptual framework for social prescribers in Wales, which could be used by commissioners and providers for the development of social prescribing curricula. Methods: This study used two consensus methods. First, Group Concept Mapping using Concept Systems Global MaxTM software which identified the important and available learning needs of 18 ( n = 18) geographically spread social prescribing practitioners. Second, a world café style workshop asked 85 ( n = 85) social prescribers to identify when training and support would be most appropriate and valuable in developing their role and skills. Results: A Social Prescribing Learning Needs Framework was developed identifying important learning needs and their availability across a timeline from induction onwards. This was conceptualised from a group concept mapping cluster map and go-zone report. The map comprises five clusters of statements (compassion, interpersonal relationships, socioeconomic disadvantage, networking and monitoring data) from the original 120 statements of learning needs identified by participants. The Go-Zone report displayed how each learning need was rated by participants on scales of importance and availability. A large number of training needs (45%) that were identified as important, are not currently available to social prescribers. All training needs were placed within the first year of the social prescriber working timeline, with 39% placed in an induction period. Conclusion: The use of two different consensus methods enabled social prescribers geographically spread across Wales to engage with the study. The Social Prescribing Learning Needs Framework will be used to inform the commissioning and decommissioning of training for people delivering social prescribing in Wales.
QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data
Authors: Anyansi Christine , Keo Arlin , Walker Bruce J. , Straub Timothy J. , Manson Abigail L. , Earl Ashlee M. , Abeel Thomas 
Published: January 2020

Abstract
Background
Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains of M. tuberculosis within a sample. Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such as M. tuberculosis.
Here we present QuantTB, a method to identify and quantify individual M. tuberculosis strains in whole genome sequencing data. QuantTB uses SNP markers to determine the combination of strains that best explain the allelic variation observed in a sample. QuantTB outputs a list of identified strains, their corresponding relative abundances, and a list of drugs for which resistance-conferring mutations (or heteroresistance) have been predicted within the sample.

Results
We show that QuantTB has a high degree of resolution and is capable of differentiating communities differing by less than 25 SNPs and identifying strains down to 1× coverage. Using simulated data, we found QuantTB outperformed other metagenomic strain identification tools at detecting strains and quantifying strain multiplicity. In a real-world scenario, using a dataset of 50 paired clinical isolates from a study of patients with either reinfections or relapses, we found that QuantTB could detect mixed infections and reinfections at rates concordant with a manually curated approach.

Conclusion
QuantTB can determine infection multiplicity, identify hetero-resistance patterns, enable differentiation between relapse and re-infection, and clarify transmission events across seemingly unrelated patients – even in low-coverage (1×) samples. QuantTB outperforms existing tools and promises to serve as a valuable resource for both clinicians and researchers working with clinical TB samples.
The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation
Authors: Zhang Yating , An Dong , Li Changsheng , Zhao Zhixuan , Wang Wenqin 
Published: January 2020

Abstract
Background
Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles.

Results
Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli.

Conclusions
The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.
Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Authors: Li Xiaohong , Cooper Nigel G. F. , O’Toole Timothy E. , Rouchka Eric C. 
Published: January 2020

AbstractBackgroundHigh-throughput RNA sequencing (RNA-seq) has evolved as an important analytical tool in molecular biology. Although the utility and importance of this technique have grown, uncertainties regarding the proper analysis of RNA-seq data remain. Of primary concern, there is no consensus regarding which normalization and statistical methods are the most appropriate for analyzing this data. The lack of standardized analytical methods leads to uncertainties in data interpretation and study reproducibility, especially with studies reporting high false discovery rates. In this study, we compared a recently developed normalization method, UQ-pgQ2, with three of the most frequently used alternatives including RLE (relative log estimate), TMM (Trimmed-mean M values) and UQ (upper quartile normalization) in the analysis of RNA-seq data. We evaluated the performance of these methods for gene-level differential expression analysis by considering the factors, including: 1) normalization combined with the choice of a Wald test fromDESeq2and an exact test/QL (Quasi-likelihood) F-Test fromedgeR; 2) sample sizes in two balanced two-group comparisons; and 3) sequencing read depths.ResultsUsing the MAQC RNA-seq datasets with small sample replicates, we found that UQ-pgQ2 normalization combined with an exact test can achieve better performance in term of power and specificity in differential gene expression analysis. However, using an intra-group analysis of false positives from real and simulated data, we found that a Wald test performs better than an exact test when the number of sample replicates is large and that a QL F-test performs the best given sample sizes of 5, 10 and 15 for any normalization. The RLE, TMM and UQ methods performed similarly given a desired sample size.ConclusionWe found the UQ-pgQ2 method combined with an exact test/QL F-test is the best choice in order to control false positives when the sample size is small. When the sample size is large, UQ-pgQ2 with a QL F-test is a better choice for the type I error control in an intra-group analysis. We observed read depths have a minimal impact for differential gene expression analysis based on the simulated data.
Discussing overweight in children during a regular consultation in general practice: a qualitative study
Authors: van der Maas Joline C. , Corbee Ronald J. , Kroese Floor M. , de Ridder Denise T. D. , Vos Rimke C. , Nielen Mirjam , Monninkhof Evelyn 
Published: January 2020

Abstract
Background
Overweight in children is a rising problem leading to serious consequences later in life. The Dutch guideline ‘Obesity’ for general practitioners recommends discussing obesity in children regardless of the reason of consultation and provides diagnostic and therapeutic tools. However, limited literature indicates that general practitioners experience barriers to discuss this topic. The aim of this study was to determine current perceived barriers of general practitioners in discussing overweight during a regular consultation in children aged 4 to 12 years and to what extent they discuss the topic. Furthermore, we attempt to get more insight in the specific needs and ideas for improvement among GPs.

Methods
A semi-structured in-depth interview study was conducted. Dutch general practitioners with a broad range of demographic characteristics were invited to participate. The transcripts were analysed using a modified version of the constant comparative method. Using this method, we identified perceived barriers of general practitioners.

Results
Ten general practitioners were included in the study. Four major themes were identified in the interviews: absence of physical or mental complaints related to overweight, internal barriers of the general practitioners, the child’s family background and logistics. Major barriers appeared to be a low consultation rate of these children, the sensitivity of the topic (e.g. fear for children’s or parents’ reactions and/or disturbance of the relation, influence on the self-esteem of the child, resistance in the parents), the absence of a long-standing relation between general practitioner and child or parent, the background of the child and lack of time or prioritizing.

Conclusion
Dutch general practitioners indicate to experience barriers and need tools for how to discuss children’s overweight during regular consultations within the limited time available. The low consultation rate among children aged 4 to 12 years due to lack of physical complaints is mentioned as a new and important barrier. Therefore, the prior focus might be raising awareness among parents concerning overweight in children aged 4 to 12 years and, thereby, stressing the potential supporting role of primary care professionals in tackling the overweight of their child.
Intensive psychotherapy and case management for Karen refugees with major depression in primary care: a pragmatic randomized control trial
Authors: Northwood Andrea K. , Vukovich Maria M. , Beckman Alison , Walter Jeffrey P. , Josiah Novia , Hudak Leora , O’Donnell Burrows Kathleen , Letts James P. , Danner Christine C. 
Published: January 2020

AbstractBackgroundDespite an unparalleled global refugee crisis, there are almost no studies in primary care addressing real-world conditions and longer courses of treatment that are typical when resettled refugees present to their physician with critical psychosocial needs and complex symptoms. We studied the effects of a year of psychotherapy and case management in a primary care setting on common symptoms and functioning for Karen refugees (a newly arrived population in St Paul, Minnesota) with depression.MethodsA pragmatic parallel-group randomized control trial was conducted at two primary care clinics with large resettled Karen refugee patient populations, with simple random allocation to 1 year of either: (1) intensive psychotherapy and case management (IPCM), or (2) care-as-usual (CAU). Eligibility criteria included Major Depression diagnosis determined by structured diagnostic clinical interview, Karen refugee, ages 18–65. IPCM (n = 112) received a year of psychotherapy and case management coordinated onsite between the case manager, psychotherapist, and primary care providers; CAU (n = 102) received care-as-usual from their primary care clinic, including behavioral health referrals and/or brief onsite interventions. Blinded assessors collected outcomes of mean changes in depression and anxiety symptoms (measured by Hopkins Symptom Checklist-25), PTSD symptoms (Posttraumatic Diagnostic Scale), pain (internally developed 5-item Pain Scale), and social functioning (internally developed 37-item instrument standardized on refugees) at baseline, 3, 6 and 12 months. After propensity score matching, data were analyzed with the intention-to-treat principle using repeated measures ANOVA with partial eta-squared estimates of effect size.ResultsOf 214 participants, 193 completed a baseline and follow up assessment (90.2%). IPCM patients showed significant improvements in depression, PTSD, anxiety, and pain symptoms and in social functioning at all time points, with magnitude of improvement increasing over time. CAU patients did not show significant improvements. The largest mean differences observed between groups were in depression (difference, 5.5, 95% CI, 3.9 to 7.1,P < .001) and basic needs/safety (difference, 5.4, 95% CI, 3.8 to 7.0,P < .001).ConclusionsAdult Karen refugees with depression benefited from intensive psychotherapy and case management coordinated and delivered under usual conditions in primary care. Intervention effects strengthened at each interval, suggesting robust recovery is possible.Trial registrationclinicaltrials.gov Identifier:NCT03788408. Registered 20 Dec 2018. Retrospectively registered.
Effects of a smartphone-based videoconferencing program for older nursing home residents on depression, loneliness, and quality of life: a quasi-experimental study
Authors: Tsai Hsiu-Hsin , Cheng Ching-Yu , Shieh Wann-Yun , Chang Yue-Cune 
Published: January 2020

Abstract
Background
Smartphones can optimize the opportunities for interactions between nursing home residents and their families. However, the effectiveness of smartphone-based videoconferencing programs in enhancing emotional status and quality of life has not been explored. The purpose of this study was to evaluate of the effect of a smartphone-based videoconferencing program on nursing home residents’ feelings of loneliness, depressive symptoms and quality of life.

Methods
This study used a quasi-experimental research design. Older residents from seven nursing homes in Taiwan participated in this study. Nursing homes (NH) were randomly selected as sites for either the intervention group (5 NH) or the control group (2 NH); NH residents who met the inclusion criteria were invited to participate. The intervention group was comprised of 32 participants; the control group was comprised of 30 participants. The intervention group interacted with their family members once a week for 6 months using a smartphone and a “LINE” application (app). Data were collected with self-report instruments: subjective feelings of loneliness, using the University of California Los Angeles Loneliness Scale; depressive symptoms, using the Geriatric Depression Scale; and quality of life using the SF-36. Data were collected at four time points (baseline, and at 1-month, 3-months and 6-months from baseline). Data were analysed using the generalized estimating equation approach.

Results
After the intervention, as compared to those in the control group, participants in interventional group had significant decreases in baseline loneliness scores at 1 months (β = − 3.41, p < 0.001), 3 months (β = − 5.96, p < 0.001), and 6 months (β = − 7.50, p < 0.001), and improvements in physical role (β = 36.49, p = 0.01), vitality (β = 13.11, p < 0.001) and pain scores (β = 16.71, p = 0.01) at 6 months. However, changes in mean depression scores did not significantly differ between groups.

Conclusions
Smartphone-based videoconferencing effectively improved residents’ feelings of loneliness, and physiological health, vitality and pain, but not depressive symptoms. Future investigations might evaluate the effectiveness of other media-based technologies in nursing homes as well as their effectiveness within and between different age cohorts.
Estimating nationwide cases of sexually transmitted diseases in 2015 from sentinel surveillance data in Japan
Authors: Kawado Miyuki , Hashimoto Shuji , Ohta Akiko , Oba Mari S. , Uehara Ritei , Taniguchi Kiyosu , Sunagawa Tomimasa , Nagai Masaki , Murakami Yoshitaka 
Published: January 2020

Abstract
Background
The rates of newly diagnosed cases of sexually transmitted diseases, including genital chlamydial infection and gonorrhea, are important for prevention and control of these diseases. However, nationwide rates are not reported in Japan.

Methods
We used the number of cases of sexually transmitted diseases reported by nationwide sentinel surveillance in 2015, together with the number of all disease outpatients in September 2014 at all medical institutions, drawn from the Survey of Medical Institutions of Japan. The number of cases of sexually transmitted diseases in the total population was estimated using the ratio estimation method with the number of all disease outpatients as auxiliary information. This method is currently used for estimating influenza cases from sentinel surveillance data in Japan.

Results
The estimated number of newly diagnosed cases per 100,000 population in 2015 in Japan was 244 (95% confidence interval 211–277) for genital chlamydial infection, 87 (95% confidence interval 74–100) for genital herpes, 61 (95% confidence interval 29–93) for condyloma acuminatum, and 89 (95% confidence interval 64–113) for gonorrhea.

Conclusion
We estimated the nationwide number of newly diagnosed cases of sexually transmitted diseases in Japan from sentinel surveillance data. This provides useful information for public health policy-making.
Prevalence of chronic kidney disease in the Lazio region, Italy: a classification algorithm based on health information systems
Authors: Marino Claudia , Ferraro Pietro Manuel , Bargagli Matteo , Cascini Silvia , Agabiti Nera , Gambaro Giovanni , Davoli Marina 
Published: January 2020

Abstract
Background
Estimating CKD prevalence is difficult. Information on CKD prevalence is rather scanty in Italy and available figures come from surveys in selected geographical areas. Administrative data have been already demonstrated to be an effective tool in estimating the epidemiological burden of diseases, however there is limited experience in literature as far as CKD is concerned.

Methods
The aim of this study is to develop an algorithm based on regional Health Administrative Databases to identify individuals with CKD and provide estimates of disease prevalence in Lazio Region (Italy); about 5.500.000 inhabitants in 2017. A population-level analysis based on a record-linkage strategy using data from Health Administrative Databases has been applied in Lazio Region. CKD cases were identified between January 1, 2012 and December 31, 2017 using Outpatient Specialist Service Information System, Hospital Discharge Registry, Ticket Exemption Registry and Drug Dispensing Registry. Age-specific and standardized prevalence rates were calculated by gender. CKD cases were classified as higher and lower severity.

Results
The algorithm identified 99,457 individuals with CKD (mean age 71 years, 55.8% males). The exclusive contributions of each regional source used were: 35,047 (35.2%) from Outpatient Specialist Service Information System, 27,778 (27.9%) from Hospital Discharge Registry, 4143 (4.2%) from Ticket Exemption Registry and 463 (0.5%) from Drug Dispensing Registry; 5.1% of cases were found in all databases. The standardized prevalence rate at December 31, 2017 was 1.76, 2.06% for males and 1.50% for females. The prevalence increased with age, rising from 0.33% (age 0–18) up to 14.18% (age 85+) among males and from 0.25% up to 8.18% among females. The proportion of CKD individuals with lower severity disease was 78.7% in both genders.

Conclusions
The proposed algorithm represents a novel tool to monitor the burden of CKD disease, that can be used by the regional government to guide the development and implementation of evidence-based pathways of care for CKD patients. The high prevalence of people with CKD of lower severity should be carefully considered in order to promote diagnosis and optimal management at early stages.