bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils
Authors: Heinsch Stephen C. , Hsu Szu-Yi , Otto-Hanson Lindsey , Kinkel Linda , Smanski Michael J. 
Published: December 2019

Abstract
Background
Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays.

Results
Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93–23, Streptomyces sp. 3211–3, and Streptomyces sp. S3–4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution.

Conclusions
Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93–23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.
Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L
Authors: Zhang Shulin , Tian Zailong , Li Haipeng , Guo Yutao , Zhang Yanqi , Roberts Jeremy A. , Zhang Xuebin , Miao Yuchen 
Published: December 2019

Abstract
Background
F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects.

Results
In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction.

Conclusion
The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.
Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce
Authors: Nakamura Miyuki , Köhler Claudia , Hennig Lars 
Published: December 2019

AbstractBackgroundSmall RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms.ResultsHere, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture.ConclusionOur data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.
The Safe Start trial to assess the effect of an infant hygiene intervention on enteric infections and diarrhoea in low-income informal neighbourhoods of Kisumu, Kenya: a study protocol for a cluster randomized controlled trial
Authors: Mumma Jane , Simiyu Sheillah , Aseyo Evalyne , Anderson John , Czerniewska Alexandra , Allen Elizabeth , Dreibelbis Robert , Baker Kelly K. , Cumming Oliver 
Published: December 2019

Abstract
Background
Symptomatic and asymptomatic enteric infections in early childhood are associated with negative effects on childhood growth and development, especially in low and middle-income countries, and food may be an important transmission route. Although basic food hygiene practices might reduce exposure to faecal pathogens and resulting infections, there have been few rigorous interventions studies to assess this, and no studies in low income urban settings where risks are plausibly very high. The aim of this study is to evaluate the impact of a novel infant food hygiene intervention on infant enteric infections and diarrhoea in peri-urban settlements of Kisumu, Kenya.

Methods
This is a cluster randomized control trial with 50 clusters, representing the catchment areas of Community Health Volunteers (CHVs), randomly assigned to intervention or control, and a total of 750 infants recruited on a rolling basis at 22 weeks of age and then followed for 15 weeks. The intervention targeted four key caregiver behaviours related to food hygiene: 1) hand washing with soap before infant food preparation and feeding; 2) bringing all infant food to the boil before feeding, including when reheating or reserving; 3) storing all infant food in sealed containers; and, 4) using only specific utensils for infant feeding which are kept separate and clean.

Results
The primary outcome of interest is the prevalence of one or more of 23 pre-specified enteric infections, determined using quantitative real-time polymerase chain reaction for enteric pathogen gene targets. In addition, infant food samples were collected at 33 weeks, and faecal indicator bacteria (Enterococcus) isolated and enumerated to assess the impact of the intervention on infant food contamination.

Conclusion
To our knowledge this is the first randomized controlled trial to assess the effect of an infant food hygiene intervention on enteric infections in a high burden, low income urban setting. Our trial responds to growing evidence that food may be a key pathway for early childhood enteric infection and disease and that basic food hygiene behaviours may be able to mitigate these risks. The Safe Start trial seeks to provide new evidence as to whether a locally appropriate infant food hygiene intervention delivered through the local health extension system can improve the health of young children.

Trial registration
The trial was registered at clinicaltrial.gov on March 16th 2018 before enrolment of any participants (https://clinicaltrials.gov/ct2/show/NCT03468114).
Identification of two novel COL10A1 heterozygous mutations in two Chinese pedigrees with Schmid-type metaphyseal chondrodysplasia
Authors: Kong Lingchi , Shi Li , Wang Wenbo , Zuo Rongtai , Wang Mengwei , Kang Qinglin 
Published: December 2019

Abstract
Background
Schmid-type metaphyseal chondrodysplasia (MCDS) is an autosomal dominant disorder caused by COL10A1 mutations, which is characterized by short stature, waddling gait, coxa vara and bowing of the long bones. However, descriptions of the expressivity of MCDS are rare.

Methods
Two probands and available family members affected with MCDS were subjected to clinical and radiological examination. Genomic DNA of all affected individuals was subjected to whole-exome sequencing, and candidate mutations were verified by Sanger sequencing in all available family members and in 250 healthy donors. A spatial model of the type X collagen (α1) C-terminal noncollagenous (NC1) domain was further constructed.

Results
We found that the phenotype of affected family members exhibited incomplete dominance. Mutation analysis indicated that there were two novel heterozygous missense mutations, [c.1765 T > A (p.Phe589Ile)] and [c.1846A > G (p.Lys616Glu)] in the COL10A1 gene in family 1 and 2, respectively. The two novel substitution sites were highly conserved and the mutations were predicted to be deleterious by in silico analysis. Furthermore, protein modeling revealed that the two substitutions were located in the NC1 domain of collagen X (α1), which potentially impacted the trimerization of collagen X (α1) and combination with molecules in the pericellular matrix.

Conclusion
Two novel mutations were identified in the present study, which will facilitate diagnosis of MCDS and further expand the spectrum of the COL10A1 mutations associated with MCDS patients. In addition, our research revealed the phenomenon of incomplete dominance in MCDS.
Psychological well-being as part of the public health debate? Insight into dimensions, interventions, and policy
Authors: Trudel-Fitzgerald Claudia , Millstein Rachel A. , von Hippel Christiana , Howe Chanelle J. , Tomasso Linda Powers , Wagner Gregory R. , VanderWeele Tyler J. 
Published: December 2019

Abstract
Background
Increasing evidence suggests that psychological well-being (PWB) is associated with lower disease and mortality risk, and may be enhanced with relatively low-cost interventions. Yet, dissemination of these interventions remains limited, in part because insufficient attention has been paid to distinct PWB dimensions, which may impact physical health outcomes differently.

Methods
This essay first reviews the empirical evidence regarding differential relationships between all-cause mortality and multiple dimensions of PWB (e.g., life purpose, mastery, positive affect, life satisfaction, optimism). Then, individual-level positive psychology interventions aimed at increasing PWB and tested in randomized-controlled trials are reviewed as these allow for easy implementation and potentially broad outreach to improve population well-being, in concert with efforts targeting other established social determinants of health.

Results
Several PWB dimensions relate to mortality, with varying strength of evidence. Many of positive psychology trials indicate small-to-moderate improvements in PWB; rigorous institution-level interventions are comparatively few, but preliminary results suggest benefits as well. Examples of existing health policies geared towards the improvement of population well-being are also presented. Future avenues of well-being epidemiological and intervention research, as well as policy implications, are discussed.

Conclusions
Although research in the fields of behavioral and psychosomatic medicine, as well as health psychology have substantially contributed to the science of PWB, this body of work has been somewhat overlooked by the public health community. Yet, the growing interest in documenting well-being, in addition to examining its determinants and consequences at a population level may provoke a shift in perspective. To cultivate optimal well-being—mental, physical, social, and spiritual—consideration of a broader set of well-being measures, rigorous studies, and interventions that can be disseminated is critically needed.
MultiSourcDSim: an integrated approach for exploring disease similarity
Authors: Deng Lei , Ye Danyi , Zhao Junmin , Zhang Jingpu 
Published: December 2019

Abstract
Background
A collection of disease-associated data contributes to study the association between diseases. Discovering closely related diseases plays a crucial role in revealing their common pathogenic mechanisms. This might further imply treatment that can be appropriated from one disease to another. During the past decades, a number of approaches for calculating disease similarity have been developed. However, most of them are designed to take advantage of single or few data sources, which results in their low accuracy.

Methods
In this paper, we propose a novel method, called MultiSourcDSim, to calculate disease similarity by integrating multiple data sources, namely, gene-disease associations, GO biological process-disease associations and symptom-disease associations. Firstly, we establish three disease similarity networks according to the three disease-related data sources respectively. Secondly, the representation of each node is obtained by integrating the three small disease similarity networks. In the end, the learned representations are applied to calculate the similarity between diseases.

Results
Our approach shows the best performance compared to the other three popular methods. Besides, the similarity network built by MultiSourcDSim suggests that our method can also uncover the latent relationships between diseases.

Conclusions
MultiSourcDSim is an efficient approach to predict similarity between diseases.
Selection process for botulinum toxin injections in patients with chronic-stage hemiplegic stroke: a qualitative study
Authors: Arai Sawako , Fukase Yuko , Okii Akira , Suzukamo Yoshimi , Suga Toshimitsu 
Published: December 2019

Abstract
Background
Botulinum toxin (BT) injection is a new treatment for spasticity with hemiplegia after stroke. How a patient decides to receive BT injections after becoming aware of the treatment remains unclear. In this exploratory qualitative study, we aimed to investigate patients’ decision-making about treatment strategies in collaboration with family and health professionals and to identify conflicts in patients’ feelings about BT treatment.

Methods
The study included six patients with stroke sequelae. Data were collected using comprehensive interviews and were analyzed using the grounded theory approach and trajectory equifinality modeling.

Results
After patients learned about BT treatment, they clearly exhibited the following two concurrent perceptions: “the restriction of one’s life due to disabilities” and “the ability to do certain things despite one’s disabilities.” Some patients reported a “fear of not being able to maintain the status quo owing to the side effects of BT.” To alleviate this fear, timely support from family members was offered, and patients overcame anxiety through creative thinking. However, there were also expressions that revealed patients’ difficulties dealing with negative events. These factors influenced the patients’ development of “expectations of BT” or “hesitations about BT.”

Conclusions
To establish treatment strategies in collaboration with patients, healthcare professionals should show supportive attitudes and have discussions with patients and their family members to help patients resolve their conflicts and should establish treatment strategies that maintain the positive aspects of patients’ lives.
Implementation of a billable transitional care model for stroke patients: the COMPASS study
Authors: Gesell Sabina B. , Bushnell Cheryl D. , Jones Sara B. , Coleman Sylvia W. , Levy Samantha M. , Xenakis James G. , Lutz Barbara J. , Bettger Janet Prvu , Freburger Janet , Halladay Jacqueline R. , Johnson Anna M. , Kucharska-Newton Anna M. , Mettam Laurie H. , Pastva Amy M. , Psioda Matthew A. , Radman Meghan D. , Rosamond Wayne D. , Sissine Mysha E. , Halls Joanne , Duncan Pamela W. 
Published: December 2019

Abstract
Background
The COMprehensive Post-Acute Stroke Services (COMPASS) pragmatic trial compared the effectiveness of comprehensive transitional care (COMPASS-TC) versus usual care among stroke and transient ischemic attack (TIA) patients discharged home from North Carolina hospitals. We evaluated implementation of COMPASS-TC in 20 hospitals randomized to the intervention using the RE-AIM framework.

Methods
We evaluated hospital-level Adoption of COMPASS-TC; patient Reach (meeting transitional care management requirements of timely telephone and face-to-face follow-up); Implementation using hospital quality measures (concurrent enrollment, two-day telephone follow-up, 14-day clinic visit scheduling); and hospital-level sustainability (Maintenance). Effectiveness compared 90-day physical function (Stroke Impact Scale-16), between patients receiving COMPASS-TC versus not. Associations between hospital and patient characteristics with Implementation and Reach measures were estimated with mixed logistic regression models.

Results
Adoption: Of 95 eligible hospitals, 41 (43%) participated in the trial. Of the 20 hospitals randomized to the intervention, 19 (95%) initiated COMPASS-TC.
Reach: A total of 24% (656/2751) of patients enrolled received a billable TC intervention, ranging from 6 to 66% across hospitals.
Implementation: Of eligible patients enrolled, 75.9% received two-day calls (or two attempts) and 77.5% were scheduled/offered clinic visits. Most completed visits (78% of 975) occurred within 14 days.
Effectiveness: Physical function was better among patients who attended a 14-day visit versus those who did not (adjusted mean difference: 3.84, 95% CI 1.42–6.27, p = 0.002).
Maintenance: Of the 19 adopting hospitals, 14 (74%) sustained COMPASS-TC.

Conclusions
COMPASS-TC implementation varied widely. The greatest challenge was reaching patients because of system difficulties maintaining consistent delivery of follow-up visits and patient preferences to pursue alternate post-acute care. Receiving COMPASS-TC was associated with better functional status.

Trial registration
ClinicalTrials.gov number: NCT02588664. Registered 28 October 2015.
Implementing coordinated ambulatory cardiology care in southern Germany: a mixed-methods study
Authors: Hennrich Patrick , Bölter Regine , Wensing Michel 
Published: December 2019

AbstractBackgroundIn 2009 health insurers AOK and Bosch BKK introduced the “FacharztProgramm Kardiologie” - a program for coordinated ambulatory cardiology care in the German state of Baden-Württemberg. It aims for efficient, medical guideline-oriented cardiology care to reduce avoidable hospitalizations as well as costs of care. A high number of cardiologists participate and the program has served as blueprint for programs in other medical fields. With many prerequisites and conditions involved, its implementation cannot be expected to be self-directed. Still, only little data on the actual implementation exists. We aimed to determine to what extent medical specialists and cooperating general practitioners implemented the program, which components they adapted, and which contextual factors they deemed relevant.MethodsWe collected data from primary care practices of medical specialists and general practitioners within Baden-Württemberg.Qualitative data was obtained through structured telephone interviews with participating and non-participating medical specialists as well as general practitioners cooperating with the program and general practitioners not cooperating. Interviews were analyzed through content-structuring qualitative content analyses via MAXQDA.Quantitative data was obtained using anonymous written questionnaires completed by participating and non-participating medical specialists as well as general practitioners cooperating with the program. Analyses were performed using SPSS Statistics, mainly with regard to differences within and between groups of physicians.ResultsMost components of the program regarding medical care were well implemented. However, access to medical care was not completely as intended due to high numbers of patients participating in the program and prioritization by physicians. Procedures for communication and cooperation between medical specialists and general practitioners were only partially adhered to and standardized communication was not implemented. A range of regional and practice-related contextual factors influenced implementation and outcomes.ConclusionsImplementation of this program was mixed. Contextual factors posed individual challenges to participating physicians which can’t be captured by an encompassing program. Both control mechanisms and tailoring of the program to medical care seem needed.Trial registrationThough not a clinical study, we deemed registration appropriate to ensure transparency. The study has been registered as a non-interventional observation study at the German Clinical Trials Register under ID:DRKS00013070.