bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau
Authors: Zhong Zhi-Ping , Liu Ying , Miao Li-Li , Wang Fang , Chu Li-Min , Wang Jia-Li , Liu Zhi-Pei 
Published: January 2016

ABSTRACT

The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by
Bacteria
in lakes with salinities of <100 g/liter and by
Archaea
in Lake Gasikule. The clades At12OctB3 and
Salinibacter
, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg
2+
, K
+
, Cl
−
, Na
+
, SO
4
2−
, and Ca
2+
) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO
4
3−
concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.
The Bacteriome of Bat Flies (Nycteribiidae) from the Malagasy Region: a Community Shaped by Host Ecology, Bacterial Transmission Mode, and Host-Vector Specificity
Authors: Wilkinson David A. , Duron Olivier , Cordonin Colette , Gomard Yann , Ramasindrazana Beza , Mavingui Patrick , Goodman Steven M. , Tortosa Pablo 
Published: January 2016

ABSTRACT

The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) flies that parasitize bats. Depending on species, these wingless flies exhibit either high specialism or generalism toward their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bat populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission through egg cytoplasm to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development, but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles that were obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes
Rickettsia
,
Wolbachia
, and several
Arsenophonus
-like organisms, as well as other members of the
Enterobacteriales
and a widespread association of
Bartonella
bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are important drivers of bacterial community structure.
A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2
Authors: Chow Virginia , Kim Young Sik , Rhee Mun Su , Sawhney Neha , St. John Franz J. , Nong Guang , Rice John D. , Preston James F. 
Published: January 2016

ABSTRACT

Paenibacillus
sp. strain JDR-2 (
Paenibacillus
JDR-2) secretes a multimodular cell-associated glycoside hydrolase family 10 (GH10) endoxylanase (XynA10A
1
) that catalyzes the depolymerization of methylglucuronoxylan (MeGX
n
) and rapidly assimilates the products of depolymerization. Efficient utilization of MeGX
n
has been postulated to result from the coupling of the processes of exocellular depolymerization and assimilation of oligosaccharide products, followed by intracellular metabolism. Growth and substrate utilization patterns with barley glucan and laminarin similar to those observed with MeGX
n
as a substrate suggest similar processes for 1,3-1,4-β-glucan and 1,3-β-glucan depolymerization and product assimilation. The
Paenibacillus
JDR-2 genome includes a cluster of genes encoding a secreted multimodular GH16 β-glucanase (Bgl16A
1
) containing surface layer homology (SLH) domains, a secreted GH16 β-glucanase with only a catalytic domain (Bgl16A
2
), transporter proteins, and transcriptional regulators. Recombinant Bgl16A
1
and Bgl16A
2
catalyze the formation of trisaccharides, tetrasaccharides, and larger oligosaccharides from barley glucan and of mono-, di-, tri-, and tetrasaccharides and larger oligosaccharides from laminarin. The lack of accumulation of depolymerization products during growth and a marked preference for polymeric glucan over depolymerization products support a process coupling extracellular depolymerization, assimilation, and intracellular metabolism for β-glucans similar to that ascribed to the GH10/GH67 xylan utilization system in
Paenibacillus
JDR-2. Coordinate expression of genes encoding GH16 β-glucanases, transporters, and transcriptional regulators supports their role as a regulon for the utilization of soluble β-glucans. As in the case of the xylan utilization regulons, this soluble β-glucan regulon provides advantages in the growth rate and yields on polymeric substrates and may be exploited for the efficient conversion of plant-derived polysaccharides to targeted products.
Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9
Authors: Kanitkar Yogendra H. , Stedtfeld Robert D. , Steffan Robert J. , Hashsham Syed A. , Cupples Alison M. 
Published: January 2016

ABSTRACT

Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes
vcrA
,
bvcA
, and
tceA
are commonly used to quantify
Dehalococcoides
spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (
vcrA
,
bvcA
, and
tceA
) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain
Dehalococcoides
species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only
vcrA
was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for
vcrA
and
tceA
genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used
Dehalococcoides
species-containing cultures.
Microbial Diversity in the Early
In Vivo
-Formed Dental Biofilm
Authors: Heller D. , Helmerhorst E. J. , Gower A. C. , Siqueira W. L. , Paster B. J. , Oppenheim F. G. 
Published: January 2016

ABSTRACT

Although the mature dental biofilm composition is well studied, there is very little information on the earliest phase of
in vivo
tooth colonization. Progress in dental biofilm collection methodologies and techniques of large-scale microbial identification have made new studies in this field of oral biology feasible. The aim of this study was to characterize the temporal changes and diversity of the cultivable and noncultivable microbes in the early dental biofilm. Samples of early dental biofilm were collected from 11 healthy subjects at 0, 2, 4, and 6 h after removal of plaque and pellicle from tooth surfaces. With the semiquantitative Human Oral Microbiome Identification Microarray (HOMIM) technique, which is based on 16S rRNA sequence hybridizations, plaque samples were analyzed with the currently available 407 HOMIM microbial probes. This led to the identification of at least 92 species, with streptococci being the most abundant bacteria across all time points in all subjects. High-frequency detection was also made with
Haemophilus parainfluenzae
,
Gemella haemolysans
,
Slackia exigua
, and
Rothia
species. Abundance changes over time were noted for
Streptococcus anginosus
and
Streptococcus intermedius
(
P
= 0.02),
Streptococcus mitis
bv. 2 (
P
= 0.0002),
Streptococcus oralis
(
P
= 0.0002),
Streptococcus
cluster I (
P
= 0.003),
G. haemolysans
(
P
= 0.0005), and
Stenotrophomonas maltophilia
(
P
= 0.02). Among the currently uncultivable microbiota, eight phylotypes were detected in the early stages of biofilm formation, one belonging to the candidate bacterial division TM7, which has attracted attention due to its potential association with periodontal disease.
Trigger Point Dry Needling versus Strain–counterstrain Technique for Upper Trapezius Myofascial Trigger Points: A Randomised Controlled Trial
Authors: Segura-Ortí E , Prades-Vergara S , Manzaneda-Piña L , Valero-Martínez R , Polo-Traverso JA 
Published: January 2016

Background Treatment of active myofascial trigger points includes both invasive and non-invasive techniques. Objectives To compare the effects of upper trapezius trigger point dry needling (DN) and strain–counterstrain (SCS) techniques versus sham SCS. Study Design Randomised controlled trial. Method 34 study subjects with active trigger points were randomly assigned to one of three treatment groups, and received either three sessions of DN (n=12), six sessions of SCS (n=10), or sham SCS (n=12) over a 3-week period. Subjective pain response and subjects’ own ratings of perceived disability were measured. Results The analysis of variance mixed model showed a significant time effect for pain (p<0.001), elicited pain (p<0.001), pain pressure threshold (p<0.01), and neck disability index (p=0.016). Pain at rest decreased in all groups, as follows: DN 18.5 mm (95% CI 4.3 to 32.7 mm); SCS 28.3 mm (95% CI 12.4 to 44.1 mm); sham SCS 21.9 mm (95% CI 3.5 to 40.1 mm). Reductions in disability score (points) were significant in the SCS group (5.5, 95% CI 1.6 to 9.4) but not in the DN (1.4, 95% CI −4.9 to 2.1) or sham SCS (1.8, 95% CI −6.4 to 2.7) groups. There was no significant group×time interaction effect for any variables studied. Conclusions There were no differences between the sham SCS, SCS, and DN groups in any of the outcome measures. DN relieved pain after fewer sessions than SCS and sham SCS, and thus may be a more efficient technique. Future studies should include a larger sample size. Trial Registration Number NCT01290653.
Contributions of Adp and Atp to the Increase in Skeletal Muscle Blood Flow after Manual Acupuncture Stimulation in Rats
Authors: Nagaoka S , Shinbara H , Okubo M , Kawakita T , Hino K , Sumiya E 
Published: January 2016

Objective To investigate the contributions of adenosine triphosphate (ATP) and adenosine diphosphate (ADP) to the increase in skeletal muscle blood flow (MBF) observed following manual acupuncture (MA) stimulation in rats. Methods Male Sprague-Dawley rats were used as experimental animals (300–370 g, n=40). MA was applied to the right tibialis anterior muscle (TA) for 1 min using a stainless steel acupuncture needle. In eight rats, high-performance liquid chromatography with the microdialysis technique was used to measure local extracellular concentrations of ATP, ADP, adenosine monophosphate (AMP), and adenosine in the TA. In the remaining 32 rats, fluorescent microspheres (15 µm in diameter) were used to measure MBF in the TA following pre-treatment with either the P2 receptor antagonist suramin (100 mg/kg intra-arterially) or saline (control) (n=16 each). Rats receiving MA (Suramin+MA and Saline+MA groups, n=8 each) were compared with untreated rats (Suramin and Saline groups, n=8). Results MA significantly increased the local extracellular concentration of ATP, ADP, and adenosine (p<0.05, before MA vs 30 min after MA). In addition, MA significantly increased MBF in rats pre-treated with saline or suramin (p<0.01, Saline vs Saline+MA; p<0.05, Suramin vs Suramin+MA, respectively). However, suramin significantly suppressed this MA-induced increase in MBF (p<0.05, Saline+MA vs Suramin+MA). Conclusions These results suggest that both ATP and ADP partially contribute to the MA-induced increase in MBF via P2 receptors. However, further studies are needed to clarify the contributions of other vasodilators.
Physical performance tests predict injury in National Collegiate Athletic Association athletes: a three-season prospective cohort study
Authors: Hegedus Eric J , McDonough Suzanne , Bleakley Chris , Baxter G David , DePew J Tyler , Bradbury Ian , Cook Chad 
Published: January 2016

BackgroundThe ability to predict injury is difficult. Prior injury is the only risk factor that has been reported consistently in multiple research studies. Convenient and easy to perform, physical performance tests (PPTs) have great allure as prognostic factors.Methods11 PPTs were issued to 359 participants over the course of three seasons of National Collegiate Athletic Association Division I athletic competition. Injuries were monitored and reported in a centralised university tracking system. Exploratory factor analysis was performed in order to group the PPTs into constructs. The relationship between injury and these PPT-based constructs and other known predictors of injury was explored using univariate and multivariate regression.ResultsPPTs clustered into five constructs: (1) active motion, (2) power, (3) hip stability, (4) flexibility and (5) motor control. When these five were placed into a multiple regression equation along with known risk factors (age, body mass index (BMI), gender, excessive flexibility and past injury), hip stability and active motion were predicted injury. In addition, motor control predicted non-traumatic injury. Past injury did not predict injury in the multivariate model.SummaryIn college athletes, hip stability, active motion and motor control as assessed through PPTs can be useful as part of preseason screening. These PPT-related constructs seem to have a mediating effect on the relationship between past injury and future injury. This study provides the rationale to test targeted interventions to address these limitations.Clinical trial registration numberNCT01804894.
Hamstring injuries have increased by 4% annually in men's professional football, since 2001: a 13-year longitudinal analysis of the UEFA Elite Club injury study
Authors: Ekstrand Jan , Waldén Markus , Hägglund Martin 
Published: January 2016

BackgroundThere are limited data on hamstring injury rates over time in football.AimTo analyse time trends in hamstring injury rates in male professional footballers over 13 consecutive seasons and to distinguish the relative contribution of training and match injuries.Methods36 clubs from 12 European countries were followed between 2001 and 2014. Team medical staff recorded individual player exposure and time-loss injuries. Injuries per 1000 h were compared as a rate ratio (RR) with 95% CI. Injury burden was the number of lay off days per 1000 h. Seasonal trend for injury was analysed using linear regression.ResultsA total of 1614 hamstring injuries were recorded; 22% of players sustained at least one hamstring injury during a season. The overall hamstring injury rate over the 13-year period was 1.20 injuries per 1000 h; the match injury rate (4.77) being 9 times higher than the training injury rate (0.51; RR 9.4; 95% CI 8.5 to 10.4). The time-trend analysis showed an annual average 2.3% year on year increase in the total hamstring injury rate over the 13-year period (R2=0.431, b=0.023, 95% CI 0.006 to 0.041, p=0.015). This increase over time was most pronounced for training injuries—these increased by 4.0% per year (R2=0.450, b=0.040, 95% CI 0.011 to 0.070, p=0.012). The average hamstring injury burden was 19.7 days per 1000 h (annual average increase 4.1%) (R2=0.437, b=0.041, 95% CI 0.010 to 0.072, p=0.014).ConclusionsTraining-related hamstring injury rates have increased substantially since 2001 but match-related injury rates have remained stable. The challenge is for clubs to reduce training-related hamstring injury rates without impairing match performance.
Four biomechanical and anthropometric measures predict tibial stress fracture: a prospective study of 1065 Royal Marines
Authors: Nunns Michael , House Carol , Rice Hannah , Mostazir Mohammod , Davey Trish , Stiles Victoria , Fallowfield Joanne , Allsopp Adrian , Dixon Sharon 
Published: January 2016

BackgroundTibial stress fractures (TSFs) cause a significant burden to Royal Marines recruits. No prospective running gait analyses have previously been performed in military settings.AimWe aimed to identify biomechanical gait factors and anthropometric variables associated with increased risk of TSF.Methods1065 Royal Marines recruits were assessed in week 2 of training. Bilateral plantar pressure and three-dimensional lower limb kinematics were obtained for barefoot running at 3.6 m/s, providing dynamic arch index, peak heel pressure and lower limb joint angles. Age, bimalleolar breadth, calf girth, passive hip internal/external range of motion and body mass index (BMI) were also recorded. 10 recruits who sustained a TSF during training were compared with 120 recruits who completed training injury-free using a binary logistic regression model to identify injury risk factors.Results4 variables significantly (p<0.05) predicted increased risk of TSF (ORs and 95% CI): smaller bimalleolar width (0.73, 0.58 to 0.93), lower BMI (0.56, 0.33 to 0.95), greater peak heel pressure (1.25, 1.07 to 1.46) and lower range of tibial rotation (0.78, 0.63 to 0.96).SummaryReduced impact attenuation and ability to withstand load were implicated in tibial stress fracture risk.
Step training improves reaction time, gait and balance and reduces falls in older people: a systematic review and meta-analysis
Authors: Okubo Yoshiro , Schoene Daniel , Lord Stephen R 
Published: January 2016

ObjectiveTo examine the effects of stepping interventions on fall risk factors and fall incidence in older people.Data sourceElectronic databases (PubMed, EMBASE, CINAHL, Cochrane, CENTRAL) and reference lists of included articles from inception to March 2015.Study selectionRandomised (RCT) or clinical controlled trials (CCT) of volitional and reactive stepping interventions that included older (minimum age 60) people providing data on falls or fall risk factors.ResultsMeta-analyses of seven RCTs (n=660) showed that the stepping interventions significantly reduced the rate of falls (rate ratio=0.48, 95% CI 0.36 to 0.65, p<0.0001, I2=0%) and the proportion of fallers (risk ratio=0.51, 95% CI 0.38 to 0.68, p<0.0001, I2=0%). Subgroup analyses stratified by reactive and volitional stepping interventions revealed a similar efficacy for rate of falls and proportion of fallers. A meta-analysis of two RCTs (n=62) showed that stepping interventions significantly reduced laboratory-induced falls, and meta-analysis findings of up to five RCTs and CCTs (n=36–416) revealed that stepping interventions significantly improved simple and choice stepping reaction time, single leg stance, timed up and go performance (p<0.05), but not measures of strength.ConclusionsThe findings indicate that both reactive and volitional stepping interventions reduce falls among older adults by approximately 50%. This clinically significant reduction may be due to improvements in reaction time, gait, balance and balance recovery but not in strength. Further high-quality studies aimed at maximising the effectiveness and feasibility of stepping interventions are required.Systematic reviews registration numberCRD42015017357.
Factors associated with declining under-five mortality rates from 2000 to 2013: an ecological analysis of 46 African countries
Authors: Kipp Aaron M , Blevins Meridith , Haley Connie A , Mwinga Kasonde , Habimana Phanuel , Shepherd Bryan E , Aliyu Muktar H , Ketsela Tigest , Vermund Sten H 
Published: January 2016

ObjectiveInadequate overall progress has been made towards the 4th Millennium Development Goal of reducing under-five mortality rates by two-thirds between 1990 and 2015. Progress has been variable across African countries. We examined health, economic and social factors potentially associated with reductions in under-five mortality (U5M) from 2000 to 2013.SettingEcological analysis using publicly available data from the 46 nations within the WHO African Region.Outcome measuresWe assessed the annual rate of change (ARC) of 70 different factors and their association with the annual rate of reduction (ARR) of U5M rates using robust linear regression models.ResultsMost factors improved over the study period for most countries, with the largest increases seen for economic or technological development and external financing factors. The median (IQR) U5M ARR was 3.6% (2.8 to 5.1%). Only 4 of 70 factors demonstrated a strong and significant association with U5M ARRs, adjusting for potential confounders. Higher ARRs were associated with more rapidly increasing coverage of seeking treatment for acute respiratory infection (β=0.22 (ie, a 1% increase in the ARC was associated with a 0.22% increase in ARR); 90% CI 0.09 to 0.35; p=0.01), increasing health expenditure relative to gross domestic product (β=0.26; 95% CI 0.11 to 0.41; p=0.02), increasing fertility rate (β=0.54; 95% CI 0.07 to 1.02; p=0.07) and decreasing maternal mortality ratio (β=−0.47; 95% CI −0.69 to −0.24; p<0.01). The majority of factors showed no association or raised validity concerns due to missing data from a large number of countries.ConclusionsImprovements in sociodemographic, maternal health and governance and financing factors were more likely associated with U5M ARR. These underscore the essential role of contextual factors facilitating child health interventions and services. Surveillance of these factors could help monitor which countries need additional support in reducing U5M.