bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐resolution studies of hydride transfer in the ferredoxin:NADP+ reductase superfamily
Authors: Kean Kelsey M. , Carpenter Russell A. , Pandini Vittorio , Zanetti Giuliana , Hall Andrea R. , Faber Rick , Aliverti Alessandro , Karplus P. Andrew 
Published: August 2017

Ferredoxin: NADP+ reductase (FNR) is an FAD‐containing enzyme best known for catalysing the transfer of electrons from ferredoxin (Fd) to NADP+ to make NADPH during photosynthesis. It is also the prototype for a broad enzyme superfamily, including the NADPH oxidases (NOXs) that all catalyse similar FAD‐enabled electron transfers between NAD(P)H and one‐electron carriers. Here, we define further mechanistic details of the NAD(P)H ⇌ FAD hydride‐transfer step of the reaction based on spectroscopic studies and high‐resolution (~ 1.5 Å) crystallographic views of the nicotinamide–flavin interaction in crystals of corn root FNR Tyr316Ser and Tyr316Ala variants soaked with either nicotinamide, NADP+, or NADPH. The spectra obtained from FNR crystal complexes match those seen in solution and the complexes reveal active site packing interactions and patterns of covalent distortion of the FAD that imply significant active site compression that would favour catalysis. Furthermore, anisotropic B‐factors show that the mobility of the C4 atom of the nicotinamide in the FNR:NADP+ complex has a directionality matching that expected for boat‐like excursions of the nicotinamide ring thought to enhance hydride transfer. Arguments are made for the relevance of this binding mode to catalysis, and specific consideration is given to how the results extrapolate to provide insight to structure‐function relations for the membrane‐bound NOX enzymes for which little structural information has been available.DatabasesStructural data are available in the PDB database under the accession numbers 3LO8 (wild‐type), 5VW4 [Y316S:nicotinamide (P3221)], 5VW9 [Y316S:nicotinamide (P3121)], 5VW3 [Y316S:NADP+ (P3221)], 5VW8 [Y316S:NADP+ (P3121)], 5VW2 [Y316S:NADPH (P3221)], 5VW5 [Y316A:nicotinamide (P3221)], 5VW6 [Y316A:NADP+ (P3221)], 5VW7 [Y316A:NADPH (P3221)], 5VWA [Y316F (P3221)], and 5VWB [Y316F:NADP+ (P3121)]. Enzyme Commission number: ferredoxin:NADP+ reductase – E C1.18.1.2.
Patients’ views on the use of an Option Grid for knee osteoarthritis in physiotherapy clinical encounters: An interview study
Authors: Kinsey Katharine , Firth Jill , Elwyn Glyn , Edwards Adrian , Brain Katherine , Marrin Katy , Nye Alan , Wood Fiona 
Published: August 2017

AbstractBackgroundPatient decision support tools have been developed as a means of providing accurate and accessible information in order for patients to make informed decisions about their care. Option Grids™ are a type of decision support tool specifically designed to be used during clinical encounters.ObjectiveTo explore patients’ views of the Option Grid encounter tool used in clinical consultations with physiotherapists, in comparison with usual care, within a patient population who are likely to be disadvantaged by age and low health literacy.MethodsSemi‐structured interviews with 72 patients (36 who had been given an Option Grid in their consultation and 36 who had not). Thematic analysis explored patients’ understanding of treatment options, perceptions of involvement, and readability and utility of the Option Grid.ResultsInterviews suggested that the Option Grid facilitated more detailed discussion about the risks and benefits of a wider range of treatment options for osteoarthritis of the knee. Participants indicated that the Option Grid was clear and aided their understanding of a structured progression of the options as their condition advanced, although it was not clear whether the Option Grid facilitated greater engagement in shared decision making.Discussion and conclusionThe Option Grid for osteoarthritis of the knee was well received by patient participants who reported that it helped them to understand their options, and made the notion of choice explicit. Use of Option Grids should be considered within routine consultations.
Risk stratification in the investigation of pulmonary nodules in a high‐risk cohort: positron emission tomography/computed tomography outperforms clinical risk prediction algorithms
Authors: Gibson Glenna , Kumar Aravind Ravi , Steinke Karin , Bashirzadeh Farzad , Roach Rebecca , Windsor Morgan , Ware Robert , Fielding David 
Published: August 2017

AbstractBackgroundClinical prediction models and 18‐fluorine‐fluorodeoxyglucose positron emission tomography/computed tomography (18F‐FDG‐PET/CT) are used for the assessment of solitary pulmonary nodules (SPN); however, a biopsy is still required before treatment, which carries risk.AimTo determine the combined predictive benefit of one such model combined with modern PET/CT data to improve decision‐making about biopsy prior to treatment and possibly reduce costs.MethodsPatients with a SPN undergoing 18F‐FDG‐PET/CT from January 2011 to December 2012 were retrospectively identified; 143 patients met inclusion criteria. PET/CT studies were rated (5‐point visual scale), and CT characteristics were determined. Tissue was obtained by endobronchial ultrasonography with guide sheath (EBUS‐GS), CT‐guided biopsy and/or surgery. EBUS‐transbronchial needle aspiration (TBNA) was used instead of nodule biopsy if there were PET‐positive sub‐centimetre lymph nodes.ResultsThe prediction model yielded an area under the receiver operating characteristic curve (AUC‐ROC) of 64% (95% confidence interval (CI) 0.55–0.75). PET/CT increased this to 75% (95% CI 0.65–0.84). The 11% improvement is statistically significant. PET/CT score was the best single predictor for malignancy. A PET score of 1–2 had a specificity of 100% (CI 0.73–1.0), whereas a score of 4–5 had a sensitivity of only 76% (CI 0.68–0.84). No significant difference in clinical prediction scores between groups was noted. PET/CT showed the greatest benefit in true negatives and in detecting small mediastinal lymph nodes to allow EBUS‐TBNA with a higher diagnostic rate. Cost analysis did not support a policy of resection‐without‐tissue diagnosis.ConclusionPET/CT improves the clinical prediction of SPN, but its greatest use is in proving benignity. High PET scores had high false positive rates and did not add to clinical prediction. PET should be incorporated early in decision‐making to allow for more effective biopsy strategies.
Prokineticin 1 is up‐regulated by insulin in decidualizing human endometrial stromal cells
Authors: Ujvari Dorina , Jakson Ivika , Oldmark Cecilia , Attarha Sanaz , Alkasalias Twana , Salamon Daniel , Gidlöf Sebastian , Hirschberg Angelica Lindén 
Published: August 2017

AbstractProkineticin 1 (PROK1), a hypoxia‐regulated angiogenic factor, has emerged as a crucial regulator of embryo implantation and placentation. Dysregulation of PROK1 has been linked to recurrent pregnancy loss, pre‐eclampsia, foetal growth restriction and preterm birth. These pregnancy complications are common in women with obesity and polycystic ovary syndrome, i.e. conditions associated with insulin resistance and compensatory hyperinsulinaemia. We investigated the effect of insulin on PROK1 expression during in vitro decidualization. Endometrial stromal cells were isolated from six healthy, regularly menstruating women and decidualized in vitro. Insulin induced a significant dose‐dependent up‐regulation of PROK1 on both mRNA and protein level in decidualizing endometrial stromal cells. This up‐regulation was mediated by hypoxia‐inducible factor 1‐alpha (HIF1α) via the phosphatidylinositol 3‐kinase (PI3K) pathway. Furthermore, we demonstrated that PROK1 did not affect the viability, but significantly inhibited the migration of endometrial stromal cells and the migratory and invasive capacity of trophoblast cell lines. This in vitro study provides new insights into the regulation of PROK1 by insulin in human decidualizing endometrial stromal cells, the action of PROK1 on migration of endometrial stromal cells, as well as migration and invasion of trophoblasts. We speculate that hyperinsulinaemia may be involved in the mechanisms by which PROK1 is linked to placenta‐related pregnancy complications.
Alcohol Use Among Concerned Partners of Heavy Drinking Service Members and Veterans
Authors: Rodriguez Lindsey M. , Osilla Karen Chan , Trail Thomas E. , Gore Kristie L. , Pedersen Eric R. 
Published: August 2017

Heavy drinking in relationships is complex and we focus on an understudied sample of concerned partners (CPs) worried about their U.S. service member/veteran partner's drinking. We evaluated the link between CP drinking and their own mental health, and how CP drinking moderated the efficacy of a web‐based intervention designed to address CPs' mental health and communication. CPs (N = 234) were randomly assigned to intervention or control and completed assessments at baseline and 5 months later. CP drinking was associated with greater CP depression, anxiety, and anger independent of partner drinking. Moreover, the intervention was more efficacious in reducing depression for heavy drinking CPs. CPs are often an overlooked population and resources to help support them are needed.
Prognostic value of the immunohistochemical detection of cancer‐associated fibroblasts in oral cancer: A systematic review and meta‐analysis
Authors: Dourado Mauricio Rocha , Guerra Eliete N. S. , Salo Tuula , Lambert Daniel W. , Coletta Ricardo D. 
Published: August 2017

AimTo perform a meta‐analysis to assess whether the presence of cancer‐associated fibroblasts (CAF) is a prognostic marker of oral squamous cell carcinomas (OSCC).MethodsImmunohistochemical studies assessing the prognostic relevance of CAF (alpha smooth muscle actin (α‐SMA)‐positive fibroblasts) in patients with OSCC were systematically reviewed using Cochrane, Lilacs, PubMed, Scopus, and Web of Science databases. The outcomes assessed were overall survival (OS) and disease‐free survival (DFS). The meta‐analysis was performed using the random‐ and fixed‐effects model with adjusted hazard ratio (HR) and 95% confidence intervals (95% CI) as effect measures. The methodological quality of the included studies was assessed using the Meta‐Analysis of Statistics Assessment and Review Instrument (MAStARI) tool, and the evidence quality was assessed by the Grading of Recommendation, Assessment, Development, and Evaluation (GRADE) system.ResultsThe presence of high levels of CAF in the stroma of OSCC predicted shortened time to DFS (HR = 3.32, 95% CI: 2.09‐5.26, P < .00001) and an overall decrease in survival (HR: 2.16, 95% CI: 1.60‐2.92, P < .00001). Moreover, high presence of CAF was frequently reported in association with parameters that worsen the prognosis in OSCC, including advanced disease stage (TNM classification), recurrence, tumor grade, depth of invasion, vascular, lymphatic and neural invasion, and extranodal metastatic spread.ConclusionThe presence of CAF, as assessed by α‐SMA‐positive fibroblasts in the stroma, indicates poor prognosis in patients with OSCC.
Nutrition behaviour change communication causes sustained effects on IYCN knowledge in two cluster‐randomised trials in Bangladesh
Authors: Hoddinott John , Ahmed Akhter , Karachiwalla Naureen I. , Roy Shalini 
Published: August 2017

AbstractBehaviour change communication (BCC) can improve infant and young child nutrition (IYCN) knowledge, practices, and health outcomes. However, few studies have examined whether the improved knowledge persists after BCC activities end. This paper assesses the effect of nutrition sensitive social protection interventions on IYCN knowledge in rural Bangladesh, both during and after intervention activities. We use data from two, 2‐year, cluster randomised control trials that included nutrition BCC in some treatment arms. These data were collected at intervention baseline, midline, and endline, and 6–10 months after the intervention ended. We analyse data on IYCN knowledge from the same 2,341 women over these 4 survey rounds. We construct a number correct score on 18 IYCN knowledge questions and assess whether the impact of the BCC changes over time for the different treatment groups. Effects are estimated using ordinary least squares accounting for the clustered design of the study. There are 3 main findings: First, the BCC improves IYCN knowledge substantially in the 1st year of the intervention; participants correctly answer 3.0–3.2 more questions (36% more) compared to the non‐BCC groups. Second, the increase in knowledge between the 1st and 2nd year was smaller, an additional 0.7–0.9 correct answers. Third, knowledge persists; there are no significant decreases in IYCN knowledge 6–10 months after nutrition BCC activities ended.
The TNL gene Rdr1 confers broad‐spectrum resistance to Diplocarpon rosae
Authors: Menz Ina , Straube Jannis , Linde Marcus , Debener Thomas 
Published: August 2017

SummaryBlack spot disease, which is caused by the ascomycete Diplocarpon rosae, is the most severe disease in field‐grown roses in temperate regions and has been distributed worldwide, probably together with commercial cultivars. Here, we present data indicating that muRdr1A is the active Rdr1 gene, a single‐dominant TIR‐NBS‐LRR (Toll/interleukin‐1 receptor‐nucleotide binding site‐leucine rich repeat) (TNL)‐type resistance gene against black spot disease, which acts against a broad range of pathogenic isolates independent of the genetic background of the host genotype. Molecular analyses revealed that, compared with the original donor genotype, the multiple integrations that are found in the primary transgenic clone segregate into different integration patterns in its sexual progeny and do not show any sign of overexpression. Rdr1 provides resistance to 13 different single‐spore isolates belonging to six different races and broad field mixtures of conidia; thus far, Rdr1 is only overcome by two races. The expression of muRdr1A, the active Rdr1 gene, leads to interaction patterns that are identical in the transgenic clones and the non‐transgenic original donor genotype. This finding indicates that the interacting avirulence (Avr) factor on the pathogen side must be widespread among the pathogen populations and may have a central function in the rose–black spot interaction. Therefore, the Rdr1 gene, pyramided with only a few other R genes by sexual crosses, might be useful for breeding roses that are resistant to black spot because the spread of new pathogenic races of the fungus appears to be slow.
Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae)
Authors: Trucchi Emiliano , Frajman Božo , Haverkamp Thomas H. A. , Schönswetter Peter , Paun Ovidiu 
Published: August 2017

Summary

The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south‐eastern Alps.

From six pairs of geographically close populations of the two ecotypes (120 individuals) we obtained a high‐coverage restriction site associated DNA sequencing (RADseq) dataset that was used for demographic inference to test the hypothesis of parallel evolution of the two ecotypes.

The data are consistent with repeated ecological divergence in H. pusillum, uncovering up to five polytopic origins of one ecotype from the other. A complex evolutionary history is evidenced, with local isolation‐with‐migration in two population pairs and intra‐ecotype migration in two others. In all cases, the time of divergence or secondary contact was inferred as postglacial. A metagenomic analysis on exogenous contaminant RAD sequences suggests divergent microbial communities between the ecotypes.

The lack of shared genomic regions of high divergence across population pairs illustrates the action of drift and/or local selection in shaping genetic divergence across repeated cases of ecological divergence.
Reviewing the relationship between OSA and cognition: Where do we go from here?
Authors: Bucks Romola S. , Olaithe Michelle , Rosenzweig Ivana , Morrell Mary J. 
Published: August 2017

ABSTRACTObstructive sleep apnoea (OSA) is a disorder of breathing during sleep resulting in temporary reduction in cerebral oxygenation and sleep disruption. A growing body of research reveals a relatively consistent pattern of deficits in cognition, particularly in attention, episodic memory, and executive function, which are partially remediated by treatment.This is where the consensus ends. Despite a number of competing explanations regarding how OSA affects cognition, reliable evidence is hard to find, which may relate to the many, common conditions co‐morbid with OSA or to the methodological challenges in this field. This paper reviews the evidence for cognitive impairment in OSA, the proposed models of cognitive harm, the impact of co‐morbidities and the many methodological and theoretical challenges of exploring the effect of OSA on cognition.To overcome some of these challenges, we end by proposing a number of future directions for the field, including suggesting some core design elements for future studies.
Independent Effects of Mental Disorders on Suicidal Behavior in the Community
Authors: Batterham Philip J. , Calear Alison L. , Christensen Helen , Carragher Natacha , Sunderland Matthew 
Published: August 2017

This study assessed the independent contributions of nine common mental disorders on suicide ideation and suicide attempt. A community‐based survey of Australian adults (N = 3,175) was conducted to identify common mental disorders associated with recent suicide attempt. Nine disorders were assessed using DSM‐5 clinical criteria. Logistic regression models indicated that all disorders were significantly and independently associated with suicide ideation. However, only obsessive‐compulsive disorder and posttraumatic stress disorder were significantly associated with suicide attempt among participants with ideation, independently of other disorders (OR = 2.0 for both). Increasing comorbidity had a significant monotonic association with suicide ideation but not attempts.
Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill
Authors: Engel Annette Summers , Liu Chang , Paterson Audrey T. , Anderson Laurie C. , Turner R. Eugene , Overton Edward B. 
Published: August 2017

ABSTRACT

Coastal salt marshes along the northern Gulf of Mexico shoreline received varied types and amounts of weathered oil residues after the 2010
Deepwater Horizon
oil spill. At the time, predicting how marsh bacterial communities would respond and/or recover to oiling and other environmental stressors was difficult because baseline information on community composition and dynamics was generally unavailable. Here, we evaluated marsh vegetation, physicochemistry, flooding frequency, hydrocarbon chemistry, and subtidal sediment bacterial communities from 16S rRNA gene surveys at 11 sites in southern Louisiana before the oil spill and resampled the same marshes three to four times over 38 months after the spill. Calculated hydrocarbon biomarker indices indicated that oil replaced native natural organic matter (NOM) originating from
Spartina alterniflora
and marine phytoplankton in the marshes between May 2010 and September 2010. At all the studied marshes, the major class- and order-level shifts among the phyla
Proteobacteria
,
Firmicutes
,
Bacteroidetes
, and
Actinobacteria
occurred within these first 4 months, but another community shift occurred at the time of peak oiling in 2011. Two years later, hydrocarbon levels decreased and bacterial communities became more diverse, being dominated by
Alphaproteobacteria
(
Rhizobiales
),
Chloroflexi
(
Dehalococcoidia
), and
Planctomycetes
. Compositional changes through time could be explained by NOM source differences, perhaps due to vegetation changes, as well as marsh flooding and salinity excursions linked to freshwater diversions. These findings indicate that persistent hydrocarbon exposure alone did not explain long-term community shifts.

IMPORTANCE
Significant deterioration of coastal salt marshes in Louisiana has been linked to natural and anthropogenic stressors that can adversely affect how ecosystems function. Although microorganisms carry out and regulate most biogeochemical reactions, the diversity of bacterial communities in coastal marshes is poorly known, with limited investigation of potential changes in bacterial communities in response to various environmental stressors. The
Deepwater Horizon
oil spill provided an unprecedented opportunity to study the long-term effects of an oil spill on microbial systems in marshes. Compared to previous studies, the significance of our research stems from (i) a broader geographic range of studied marshes, (ii) an extended time frame of data collection that includes prespill conditions, (iii) a more accurate procedure using biomarker indices to understand oiling, and (iv) an examination of other potential stressors linked to
in situ
environmental changes, aside from oil exposure.
Transcriptome Response to Heavy Metals in Sinorhizobium meliloti CCNWSX0020 Reveals New Metal Resistance Determinants That Also Promote Bioremediation by Medicago lupulina in Metal-Contaminated Soil
Authors: Lu Mingmei , Jiao Shuo , Gao Enting , Song Xiuyong , Li Zhefei , Hao Xiuli , Rensing Christopher , Wei Gehong 
Published: August 2017

ABSTRACTThe symbiosis of the highly metal-resistantSinorhizobium melilotiCCNWSX0020 andMedicago lupulinahas been considered an efficient tool for bioremediation of heavy metal-polluted soils. However, the metal resistance mechanisms ofS. melilotiCCNWSX00200 have not been elucidated in detail. Here we employed a comparative transcriptome approach to analyze the defense mechanisms ofS. melilotiCCNWSX00200 against Cu or Zn exposure. Six highly upregulated transcripts involved in Cu and Zn resistance were identified through deletion mutagenesis, including genes encoding a multicopper oxidase (CueO), an outer membrane protein (Omp), sulfite oxidoreductases (YedYZ), and three hypothetical proteins (a CusA-like protein, a FixH-like protein, and an unknown protein), and the corresponding mutant strains showed various degrees of sensitivity to multiple metals. The Cu-sensitive mutant (ΔcueO) and three mutants that were both Cu and Zn sensitive (ΔyedYZ, ΔcusA-like, and ΔfixH-like) were selected for further study of the effects of these metal resistance determinants on bioremediation. The results showed that inoculation with the ΔcueOmutant severely inhibited infection establishment and nodulation ofM. lupulinaunder Cu stress, while inoculation with the ΔyedYZand ΔfixH-like mutants decreased just the early infection frequency and nodulation under Cu and Zn stresses. In contrast, inoculation with the ΔcusA-like mutant almost led to loss of the symbiotic capacity ofM. lupulinato even grow in uncontaminated soil. Moreover, the antioxidant enzyme activity and metal accumulation in roots ofM. lupulinainoculated with all mutants were lower than those with the wild-type strain. These results suggest that heavy metal resistance determinants may promote bioremediation by directly or indirectly influencing formation of the rhizobium-legume symbiosis.IMPORTANCERhizobium-legume symbiosis has been promoted as an appropriate tool for bioremediation of heavy metal-contaminated soils. Considering the plant-growth-promoting traits and survival advantage of metal-resistant rhizobia in contaminated environments, more heavy metal-resistant rhizobia and genetically manipulated strains were investigated. In view of the genetic diversity of metal resistance determinants in rhizobia, their effects on phytoremediation by the rhizobium-legume symbiosis must be different and depend on their specific assigned functions. Our work provides a better understanding of the mechanism of heavy metal resistance determinants involved in the rhizobium-legume symbiosis, and in further studies, genetically modified rhizobia harboring effective heavy metal resistance determinants may be engineered for the practical application of rhizobium-legume symbiosis for bioremediation in metal-contaminated soils.