bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Bacillus velezensis 3A-25B, a Strain with Biocontrol Activity against Fungal and Oomycete Root Plant Phytopathogens, Isolated from Grassland Soil
Authors: Martínez-Raudales Inés , De La Cruz-Rodríguez Yumiko , Vega-Arreguín Julio , Alvarado-Gutiérrez Alejandro , Fraire-Mayorga Atzin , Alvarado-Rodríguez Miguel , Balderas-Hernández Victor , Gómez-Soto José Manuel , Fraire-Velázquez Saúl 
Published: September 2017

ABSTRACT

Here, we present the draft genome of
Bacillus velezensis
3A-25B, which totaled 4.01 Mb with 36 contigs, 3,948 genes, and a GC content of 46.34%. This strain, which demonstrates biocontrol activity against root rot causal phytopathogens in horticultural crops and friendly interactions in roots of pepper plantlets, was obtained from grassland soil in Zacatecas Province, Mexico.
Draft Genome Sequence of the Type Strain Pseudomonas jessenii DSM 17150
Authors: Furmanczyk Ewa M. , Kaminski Michal A. , Dziembowski Andrzej , Lipinski Leszek , Sobczak Adam 
Published: September 2017

ABSTRACT

We present the draft genome sequence of
Pseudomonas jessenii
type strain DSM 17150. The assembly consists of 13 contigs, contains 6,537,206 bp, and has a GC content of 59.7%.
Draft Genome Sequence of Streptomyces olivochromogenes NBRC 3561, a Bioactive Peptide-Producing Actinobacterium
Authors: Dohra Hideo , Miyake Yuto , Kodani Shinya 
Published: September 2017

ABSTRACT

Recently, we found that
Streptomyces olivochromogenes
NBRC 3561 produced a bioactive peptide, so we sequenced its genome to clarify its biosynthesis. We report here the draft genome sequence of
S. olivochromogenes
NBRC 3561, in which 40 potential secondary metabolite gene clusters were predicted by antiSMASH.
Complete Genome Sequences of Human Immunodeficiency Type 1 Viruses Genetically Engineered To Be Tropic for Rhesus Macaques
Authors: Nomaguchi Masako , Doi Naoya , Koma Takaaki , Adachi Akio 
Published: September 2017

ABSTRACT
We have constructed two human immunodeficiency type 1 (HIV-1) derivatives, CXCR4 tropic and CCR5 tropic, that replicate in rhesus macaques. They are genetically engineered to be resistant to macaque restriction factors against HIV-1, including TRIM5α, APOBEC3, and tetherin proteins. The two HIV-1 variants described here are fundamental clones aiming for rhesus infection studies of HIV-1.
Draft Genome Sequence of
Xenophilus
sp., a Novel Bacterium Isolated from the Skin of a Southern Leopard Frog (
Rana sphenocephala
) in Florida, USA
Authors: Lebert Brittany M. , Sanford Samantha A. , Reisinger Levi M. , Forsman Anna M. , Savage Anna E. 
Published: September 2017

ABSTRACT

We report here the draft genome sequence of a novel
Xenophilus
species cultured from the skin of a southern leopard frog (
Rana sphenocephala
). Compared to previously sequenced bacterial genomes, our novel isolate showed the most significant homology with
Xenophilus azovorans
. The assembled genome is 3,978,285 bp, with 3,704 predicted genes and one predicted plasmid.
Draft Genome Sequence of
Pseudomonas
sp. Strain DrBHI1 (Phylum
Proteobacteria
)
Authors: Wilson Alexandria K. , Watral Virginia G. , Kent Michael L. , Sharpton Thomas J. , Gaulke Christopher A. 
Published: September 2017

ABSTRACT

Here, we report the draft genome sequence of
Pseudomonas
sp. strain DrBHI1. The total assembly length is 5,649,751 bp in 146 contigs. This strain was isolated from zebrafish (
Danio rerio
) feces.
Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
Authors: Yang Guanhua , Billings Gabriel , Hubbard Troy P. , Park Joseph S. , Yin Leung Ka , Liu Qin , Davis Brigid M. , Zhang Yuanxing , Wang Qiyao , Waldor Matthew K. 
Published: October 2017

ABSTRACTTransposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE). From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant’s fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples ofEdwardsiella piscicida(a fish pathogen) collected over a 2-week infection period from a natural host (the flatfish turbot). PACE uncovered more genes that affectE. piscicida’s fitnessin vivothan were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses.IMPORTANCETransposon insertion sequencing (TIS) enables genome-wide mapping of the genetic determinants of fitness, typically based on observations at a single sampling point. Here, we move beyond analysis of endpoint TIS data to create a framework for analysis of time series TIS data, termed pattern analysis of conditional essentiality (PACE). We applied PACE to identify genes that contribute to colonization of a natural host by the fish pathogenEdwardsiella piscicida.PACE uncovered more genes that affectE. piscicida’s fitnessin vivothan were detected using a terminal sampling point, and its clustering of mutants with related fitness profiles informed design of new live vaccine candidates. PACE yields insights into patterns of fitness dynamics and circumvents major limitations of existing methodologies. Finally, the PACE method should be applicable to additional “omic” time series data, including screens based on clustered regularly interspaced short palindromic repeats with Cas9 (CRISPR/Cas9).
U.S. Regulatory Considerations for Development of Live Biotherapeutic Products as Drugs
Authors: Dreher-Lesnick Sheila M. , Stibitz Scott , Carlson, Jr. Paul E. 
Published: October 2017

ABSTRACT
Interest in the use of bacteria-containing products for the treatment or prevention of disease has increased in recent years. Bacterial preparations for human consumption are commercially available in the form of dietary supplements and typically contain strains with a history of use in food fermentation. Advances in our understanding of the role of the microbiota in health and disease are likely to lead to development of products containing more novel bacterial species, along with genetic modification of strains to provide specific functions. By law, any substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease in humans meets the definition of a drug, and an Investigational New Drug (IND) application for clinical investigation must be filed with the FDA. This article is meant to provide information about the IND submission process and additional considerations with regard to chemistry, manufacturing, and controls information for live biotherapeutic products.
Glucose-lowering effects and safety of DS-8500a, a G protein-coupled receptor 119 agonist, in Japanese patients with type 2 diabetes: results of a randomized, double-blind, placebo-controlled, parallel-group, multicenter, phase II study
Authors: Inagaki Nobuya , Chou Hubert S , Tsukiyama Shuji , Washio Takuo , Shiosakai Kazuhito , Nakatsuka Yasuhiko , Taguchi Takashi 
Published: September 2017

ObjectiveDS-8500a is a novel G protein-coupled receptor 119 agonist being developed for the treatment of type 2 diabetes. The study objective was to assess the efficacy and safety of DS-8500a in Japanese patients with type 2 diabetes.Research design and methodsIn this double-blind, parallel-group, phase II study, 99 Japanese patients with type 2 diabetes were randomized to receive placebo, or DS-8500a 10 mg or 75 mg once daily for 28 days. The primary efficacy endpoint was change in the 24-hour weighted mean glucose (WMG) from baseline (day −1) to day 28. Other endpoints included changes in fasting plasma glucose, postprandial glucose, lipids, and safety.ResultsThe 24-hour WMG decreased significantly after 28 days of treatment in the 10 mg and 75 mg groups with placebo-subtracted least squares mean differences (95% CI) of −0.74 (−1.29 to –0.19) mmol/L and −1.05 (−1.59 to –0.50) mmol/L, respectively. Reductions in 24-hour WMG in both DS-8500a groups were observed on day 14 and were greater on day 28 than on day 14. The reductions in fasting plasma glucose and 2-hour postprandial glucose were significantly greater in the 75 mg DS-8500a group versus placebo. Total cholesterol, low-density lipoprotein cholesterol, and triglycerides decreased significantly; high-density lipoprotein cholesterol increased significantly in the 75 mg group versus placebo. Both doses of DS-8500a were well tolerated without significant treatment-related adverse events, hypoglycemia, or discontinuations due to adverse events.ConclusionsDS-8500a significantly improved glycemic control and lipids and was well tolerated over 28 days of administration in Japanese patients with type 2 diabetes.Trial registration numberNCT02222350; Post-results.
Is the sustainable development goal target for financial risk protection in health realistic?
Authors: Verguet Stéphane , Woldemariam Addis Tamire , Durrett Warren N , Norheim Ole F , Kruk Margaret E 
Published: September 2017

BackgroundSetting Millennium Development Goals and Sustainable Development Goals for health has largely focused on defining specific targets of mortality and morbidity reduction over given time periods. Yet, less attention has been devoted to setting targets for the systemic determinants of health delivery, such as access and financial risk protection (FRP)—prevention of medical impoverishment. We examined candidate targets for FRP among low and middle-income countries by 2040.MethodsWe used a data set on estimates of incidence of catastrophic health expenditure (CHE)—medical expenditure exceeding 40% of household capacity to pay—among 110 countries over 1995–2007, augmented by estimates of the percentage of out-of-pocket expenditure out of total health expenditure (OOPEXP), the share of health expenditure as a percentage of gross domestic product (HEXGDP) and the gross domestic product per capita (GDPC). Using a simple model and 2040 estimates for OOPEXP, HEXGDPand GDPCfrom the World Bank, the International Monetary Fund and the Institute for Health Metrics and Evaluation, we projected CHE incidence by 2040 for four country income groups.ResultsWe predicted that the 2040 incidence of CHE among households would be: 2.13% (Uncertainty interval: 0.60-6.87) among low-income countries, 1.15% (0.32–3.81) among lower-middle-income countries and 0.65% (0.18–2.21) among upper-middle-income countries. By 2040, the probability of achieving CHE <1.00% would be: 0.1 for low-income countries, 0.4 for lower-middle-income countries and 0.7 for upper-middle-income countries; for CHE <0.50% , it would be 0 for low-income countries, 0.1 for lower-middle-income countries and 0.3 for upper-middle-income countries.ConclusionsHistorical trends of CHE rates can help define post-2015 targets for FRP. The projected achievements suggest that elimination of medical impoverishment will not be achieved by 2040 and that countries must urgently enact dramatic changes in policy to ensure FRP to their populations.
Introducing visual participatory methods to develop local knowledge on HIV in rural South Africa
Authors: Brooks Chloe , D’Ambruoso Lucia , Kazimierczak Karolina , Ngobeni Sizzy , Twine Rhian , Tollman Stephen , Kahn Kathleen , Byass Peter 
Published: September 2017

IntroductionSouth Africa is a country faced with complex health and social inequalities, in which HIV/AIDS has had devastating impacts. The study aimed to gain insights into the perspectives of rural communities on HIV-related mortality.MethodsA participatory action research (PAR) process, inclusive of a visual participatory method (Photovoice), was initiated to elicit and organise local knowledge and to identify priorities for action in a rural subdistrict underpinned by the Agincourt Health and Socio-Demographic Surveillance System (HDSS). We convened three village-based discussion groups, presented HDSS data on HIV-related mortality, elicited subjective perspectives on HIV/AIDS, systematised these into collective accounts and identified priorities for action. Framework analysis was performed on narrative and visual data, and practice theory was used to interpret the findings.FindingsA range of social and health systems factors were identified as causes and contributors of HIV mortality. These included alcohol use/abuse, gender inequalities, stigma around disclosure of HIV status, problems with informal care, poor sanitation, harmful traditional practices, delays in treatment, problems with medications and problematic staff–patient relationships. To address these issues, developing youth facilities in communities, improving employment opportunities, timely treatment and extending community outreach for health education and health promotion were identified.DiscussionAddressing social practices of blame, stigma and mistrust around HIV-related mortality may be a useful focus for policy and planning. Research that engages communities and authorities to coproduce evidence can capture these practices, improve communication and build trust.ConclusionActions to reduce HIV should go beyond individual agency and structural forces to focus on how social practices embody these elements. Initiating PAR inclusive of visual methods can build shared understandings of disease burdens in social and health systems contexts. This can develop shared accountability and improve staff–patient relationships, which, over time, may address the issues identified, here related to stigma and blame.
Use of IMMPACT domains in clinical trials of acupuncture for chronic pain: a protocol for a methodological survey
Authors: Mazzei Lauren Giustti , Bergamaschi Cristiane de Cássia , Silva Marcus Tolentino , Lopes Luciane Cruz 
Published: September 2017

IntroductionPain is one of the most common and most debilitating complaints among patients. It affects the individual, their relationship with friends and family, their ability to function at work, and their sociability. Acupuncture is one of the therapeutic resources for managing chronic pain. Given the variability of outcome measures in controlled randomised clinical trials on non-oncologicchronic pain (CRCT-NOCP), the Initiative in Methods, Measurements and Pain Assessment in Clinical Trials (IMMPACT) recommends six domains to be covered in evaluating the effectiveness of treatments for chronic pain.ObjectiveTo check whether the methodological quality of outcome reporting in published trials has used IMMPACT recommendations in measuring CRCT-NOCP outcomes when acupuncture was used as a treatment.MethodThis is a methodological study. We will systematically search for eligible studies in specific databases with a defined strategy. We will use the MeSHterms of ‘acupuncture’, ‘chronic pain’ and similar terms, without restrictions on idiom. Eligible studies will include those which are randomised and chose NOCP patients to be treated with acupuncture or control (sham acupuncture or no acupuncture), recruited after September 2004, with ≥100 patients. The measured outcomes are to be the presence of outcome domains recommended by IMMPACT, domains reported by the patient or clinician, tools used to measure such domains, as well as other features of the studies. We shall conduct a regression analysis to explore factors which can be associated with the presence of outcome domains according to IMMPACT recommendations.Ethics and disseminationThis survey will be submitted for presentation at congresses and for publication in a scientific journal. The findings obtained in this study will allow us to measure the quality of the evidence and provide greater transparency in decisions regarding the use of acupuncture as a viable alternative to managing chronic pain.
The potential clinical benefits of medicines optimisation through comprehensive geriatric assessment, carried out by secondary care geriatricians, in a general practice care setting in North Staffordshire, UK: a feasibility study
Authors: Lea Simon Christian , Watts Keira Louise , Davis Nathan Ashley , Panayiotou Barnabas , Bankart Michael John , Arora Amit , Chambers Ruth 
Published: September 2017

ObjectivesTo evaluate the feasibility and potential clinical benefits of medicines optimisation through comprehensive geriatric assessment (CGA) of frail patients with multiple conditions, by secondary care geriatricians in a general practice care setting.MethodsSeven general practitioner (GP) practices in one region of Stoke-on-Trent volunteered to take part. GPs selected patients (n=186) who were local permanent residents, at least 65 years old and on eight or more medications per day. Patients were sent a written invitation outlining the assessment purpose/format. Prior to patient assessments, primary care staff prepared packs detailing patient medical history, recent consultations, current medications, recent laboratory tests and social circumstances. One hour was allocated for the CGA per patient, with one of three geriatricians, to enable sufficient time to explore all relevant aspects. Assessment comprised a full history, thorough clinical examination, assessment of balance and mobility, mental function and information on home environment and support arrangements. After consultation, geriatricians made recommendations regarding further assessments, investigations or medication changes. Geriatricians entered their main findings and recommendations onto a standard template.ResultsIn total, 687 recommendations for changes in patients’ medication regimens were made for 169 (91%) patients. In 17 (9%) patients there was no recommendation to alter medications. This resulted in an average of four alterations in medication per patient. The predominant changes to medications were to stop medications (34%) or to reduce the dosage (24%). Starting a new medication represented 18% of all the medication changes. Adherence rates to geriatrician medication recommendations were 72% at 6 months and 65% at 12 months.ConclusionsCGA of older patients with complex needs, by geriatricians in a general practice care setting, is feasible. Our study demonstrated constructive collaboration between GPs and geriatricians from secondary care, suggesting further studies and clinical trials are feasible and have scope to yield beneficial outcomes.
Non-adherence to immunosuppressants following renal transplantation: a protocol for a systematic review
Authors: Hucker Abigail , Bunn Frances , Carpenter Lewis , Lawrence Christopher , Farrington Ken , Sharma Shivani 
Published: September 2017

IntroductionAdherence to immunosuppressant medication is essential for renal transplant recipients. This review aims to summarise what is known about non-adherence, with a view to providing comprehensive evidence to inform strategies aimed at advancing adherent behaviour.Methods and analysisA systematic review of quantitative studies that report adherence to immunosuppressants in adult (over 18 years) renal transplant recipients. The review will follow the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines; study quality will be assessed using the Downs and Black checklist. Systematic searches will be completed across relevant databases. Two reviewers will independently extract data using a predefined data extraction form. We will summarise the operationalisation of adherence across studies and use narrative synthesis to identify factors associated with non-adherence. A meta-analysis will be conducted if there is sufficient homogeneity, and available data, across studies to estimate the prevalence of non-adherence in renal transplant recipients. Heterogeneity will be assessed using the I2test. Survival analysis will be conducted to estimate hazard ratios to explore the impact of non-adherence on graft survival, graft failure and patient survival.Ethics and disseminationFindings will be published in a peer-reviewed journal and disseminated at conferences for professionals and researchers. Review outcomes will help support clinical practice by highlighting the extent of non-adherence among adults, and in doing so, signpost the need for suitable intervention.Trial registration numberPROSPERO registration number (CRD42016038751).
Protocol for the Northern babies longitudinal study: predicting postpartum depression and improving parent–infant interaction with The Newborn Behavioral Observation
Authors: Høifødt Ragnhild Sørensen , Nordahl Dag , Pfuhl Gerit , Landsem Inger Pauline , Thimm Jens C , Ilstad Linn Kathrin K , Wang Catharina Elisabeth Arfwedson 
Published: September 2017

IntroductionPostpartum depression (PPD) is a prevalent disorder. Studying the factors related to PPD will help to identify families at risk and provide preventive interventions. This can in turn improve the developmental trajectories for the children. Several previous studies have investigated risk factors for PPD. However, few studies have focused on cognitive vulnerability factors. The first aim of the present study is to explore a range of protective and risk factors, including cognitive factors, for PPD, parent–infant interactions and child development. The second aim of the study is to evaluate the effectiveness of The Newborn Behavioral Observation (NBO) as a universal preventive intervention delivered in routine practice. The NBO is a brief relationship-enhancing intervention that may reduce depressive symptomatology in mothers.MethodsThe study is a longitudinal observational study with an intervention. The observational study uses a prospective cohort design, whereas the intervention study has a non-randomised cluster-controlled design comparing a group receiving NBO with a group receiving standard care. The intervention group will receive three NBO sessions within the first 4 weeks postdelivery. Between 2015 and 2018, approximately 200 families will be recruited in the municipality of Tromsø, Norway. Parents are recruited during pregnancy, and assessments will be performed during gestational weeks 16–22, 24–30 and 31, and at 6 weeks, 4 months and 6 months postdelivery. Predictor variables include several cognitive vulnerability factors including early maladaptive schemas, implicit attitudes and cognitive processing of emotionally valenced infant facial information.Ethics and disseminationThe Regional Committee for Medical and Health Research Ethics in Northern Norway has approved the project. The research team has collaboration with local health services and can assist participants who need more extensive follow-up. Results from the project will be disseminated in international and national peer-reviewed journals, and at courses and conferences.Trials registration numberNCT02538497; Pre-results.