bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered mechanical interaction between rat plantar flexors due to changes in intermuscular connectivity
Authors: Bernabei M. , van Dieën J. H. , Maas H. 
Published: January 2016

Connective tissue formation following muscle injury and remedial surgery may involve changes in the stiffness and configuration of the connective tissues linking adjacent muscles. We investigated changes in mechanical interaction of muscles by implanting either a tissue‐integrating mesh (n = 8) or an adhesion barrier (n = 8) to respectively increase or decrease the intermuscular connectivity between soleus muscle (SO) and the lateral gastrocnemius and plantaris complex (LG+PL) of the rat. As a measure of mechanical interaction, changes in SO tendon forces and proximal–distal LG+PL force differences in response to lengthening LG+PL proximally were assessed 1 and 2 weeks post‐surgery. The extent of mechanical interaction was doubled 1 week post‐implantation of the tissue‐integrating mesh compared to an unaffected compartment (n = 8), and was more than four times higher 2 weeks post‐surgery. This was found only for maximally activated muscles, but not when passive. Implanting the adhesion barrier did not result in a reduction of the mechanical interaction between these muscles. Our findings indicate that the ratio of force transmitted via myofascial, rather than myotendinous pathways, can increase substantially when the connectivity between muscles is enhanced. This improves our understanding of the consequences of connective tissue formation at the muscle boundary on skeletal muscle function.
Revisiting Political Islam: Explaining the Nexus Between Political Islam and Contentious Politics in the Arab World*
Authors: Achilov Dilshod 
Published: January 2016

ObjectiveThis study (1) introduces a new framework to conceptualize and measure political Islam, and (2) examines the empirical nexus among Islamic religiosity, ideological support for political Islam (ISPI), and collective protests in the Arab Middle East.MethodsAnalyzing cross‐national attitudes in five Arab states, I conduct a principal component analysis to construct a new index to account for a variation in ISPI, and examine the effects thereof on participation in collective protests.ResultsThe evidence shows that Islamic religiosity matters in challenging political elites via collective action. While politically moderate Muslims appear more likely to engage in nonviolent, collective political protests, political radicals seem less likely to do so.ConclusionThe findings suggest that political ideology plays a central role in moderating the intricate relationship between Islam and collective political activism. The evidence also supports the resource mobilization thesis, among other factors, to explain the dynamics of collective action in the Arab world.
Comprehensive analysis of RHD splicing transcripts reveals the molecular basis for the weak anti‐D reactivity of Del‐red blood cells
Authors: Chen D.‐P. , Sun C.‐F. , Ning H.‐C. , Wang W.‐T. , Tseng C.‐P. 
Published: January 2016

SUMMARYBackgroundOf the Rh blood type, Del is a rare variant that elicits the weakest anti‐D reactivity. In this study, we revisit the genetic changes of Del allele and characterise the RHD splicing transcripts to realise the molecular basis of Del formation in the Taiwanese population.Study design and methodsThe RHD exons from Del and D‐positive individuals were amplified by polymerase chain reaction (PCR) using different primer pairs followed by sequencing analyses. In addition, full‐length RHD transcripts were reversed transcribed and amplified by nested‐PCR. The type and frequency of the RHD splicing transcripts were analysed after sequencing the PCR products that were subcloned into a cloning vector.ResultsAll Del individuals had a characteristic 1227G>A mutation. No deletion of the exon sequences was found. At least nine types of RHD splicing transcripts including exons 7/8/9 deletion, 7/9 deletion, 8/9 deletion, 9 deletion, 2/3/7/9 deletion, 2/3/7/8/9 deletion, exons 7/8/9 deletion with replacement of exon 3 with RHCE exon 3, exon 9 deletion with cryptic insertion of 170 bp of intron 7 and exons 7/8/9 deletion with cryptic insertion of 117 bp of intron 3 were identified in the Del‐RBC. These aberrant splicing transcripts led to production of frame shift or truncated D antigen. Notably, no full‐length RHD transcript was identified in the Del‐RBC.ConclusionThe RHD 1227G>A mutation contributes to the molecular basis of Del phenotype in the Taiwanese population. The point mutation results in aberrant frame shift or exon deletion transcripts and generates D protein with weak antigen presenting function.
Comparison of corneal degeneration and calcific band keratopathy from 2000 to 2013 in 69 horses
Authors: Berryhill Emily H. , Thomasy Sara M. , Kass Philip H. , Reilly Christopher M. , Good Kathryn L. , Hollingsworth Steven R. , Maggs David J. , Magdesian K. Gary , Pusterla Nicola 
Published: January 2016

AbstractObjectiveTo compare signalment, presentation, treatment, and outcome in horses diagnosed with corneal degeneration (CD) or calcific band keratopathy (CBK) at a referral hospital.Animals studiedSixty‐nine horses (87 eyes) diagnosed with either CD or CBK.ProceduresMedical records of horses diagnosed with CD or CBK at the University of California‐Davis Veterinary Medical Teaching Hospital (UCD‐VMTH) between 2000 and 2013 were reviewed. Signalment, concurrent ophthalmic diagnoses, previous therapies, diagnostic tests, systemic diagnoses, treatment, follow‐up, and outcomes were compared between horses diagnosed with CD or CBK. Age, breed, and gender were compared between the CD/CBK and UCD‐VMTH populations.ResultsThirty‐three horses (42 eyes) and 36 horses (45 eyes) were diagnosed with CD and CBK, respectively. Horses with CD or CBK were significantly older (P < 0.001) than the UCD‐VMTH population with a median age of 16 or 18 years, respectively. Appaloosas were significantly overrepresented in the CD/CBK population (33%) in comparison with the UCD‐VMTH population (1.8%, P < 0.001). Equine recurrent uveitis was concurrently diagnosed in 67% and 84% of horses with CD or CBK, respectively. Pituitary pars intermedia dysfunction (PPID) was diagnosed significantly less often in horses with CD vs. CBK (P = 0.03). Chemical chelation with ethylenediaminetetraacetic acid was performed significantly less frequently in horses diagnosed with CD (7.1%) vs. CBK (31.1% of eyes) (P = 0.012).ConclusionsDespite some differences, equine CD and CBK are relatively similar conditions and may represent a continuum of disease severity. Horses with PPID should be monitored closely for corneal disease including CBK.
Comparison of Arthroscopic Lavage and Needle Lavage Techniques, and Lavage Volume on the Recovery of Colored Microspheres From the Tarsocrural Joints of Cadaver Horses
Authors: Loftin Patrick G. , Beard Warren L. , Guyan Megan E. , White Brad J. 
Published: January 2016

ObjectiveTo quantify recovery of colored microspheres from normal cadaver tarsocrural joints using arthroscopic or needle lavage with 1–5 L of fluid.Study DesignEx vivo experimental study.AnimalsAdult Quarter Horse cadavers (n = 8).MethodsAfter euthanasia, 1.5 × 106 colored microspheres were injected into each tarsocrural joint. Each joint was randomly assigned to receive lavage (5 L 0.9% NaCl) with an arthroscope (dorsomedial arthroscope and dorsolateral egress cannula) or three 14 g needles (dorsomedial ingress, dorsolateral, and plantarolateral egress). Egress fluid from each liter was collected separately over time and the number of microspheres present in each recovered liter determined by spectrophotometry.ResultsA significant interaction was present between treatment group and liter of fluid (P < .01). The number of microspheres recovered in the first liter of lavage fluid was significantly higher in the needle lavage group than in the arthroscopic lavage group (P < .01). For both groups, the number of microspheres recovered in the first liter of lavage fluid represented a majority of the total microspheres collected and was significantly different from each subsequent liter collected (P < .01). The number of microspheres recovered did not differ between liters 2, 3, 4, and 5 within or between treatment groups.ConclusionIn this model, tarsocrural lavage with three 14 g needles was more effective at removing colored microspheres from the joint than arthroscopic lavage, suggesting that the number or placement of portals present may be more important than portal size and flow rate. No difference in microsphere recovery was seen with lavage volumes >1 L.
The Effectiveness of Neck Stretching Exercises Following Total Thyroidectomy on Reducing Neck Pain and Disability: A Randomized Controlled Trial
Authors: Ayhan Hatice , Tastan Sevinc , Iyigün Emine , Oztürk Erkan , Yildiz Ramazan , Görgülü Semih 
Published: January 2016

ABSTRACTBackgroundAlthough there are a limited number of studies showing effects of neck stretching exercises following a thyroidectomy in reducing neck discomfort symptoms, no study has specifically dealt with and examined the effect of neck stretching exercises on neck pain and disability.ObjectiveTo analyze the effect of neck stretching exercises, following a total thyroidectomy, on reducing neck pain and disability.MethodsA randomized controlled trial was conducted. The participants were randomly assigned either to the stretching exercise group (n = 40) or to the control group (n = 40). The stretching exercise group learned the neck stretching exercises immediately after total thyroidectomy. The effects of the stretching exercises on the participants’ neck pain and disability, neck sensitivity, pain with neck movements as well as on wound healing, were evaluated at the end of the first week and at 1 month following surgery.ResultsWhen comparing neck pain and disability scale (NPDS) scores, neck sensitivity and pain with neck movement before thyroidectomy, after 1 week and after 1‐month time‐points, it was found that patients experienced significantly less pain and disability in the stretching exercise group than the control group (p < .001). At the end of the first week, the NPDS scores (mean [SD] = 8.82 [12.23] vs. 30.28 [12.09]), neck sensitivity scores (median [IR] = 0 [.75] vs. 2.00 [4.0]) and pain levels with neck movements (median [IR] = 0 [2.0] vs. 3.5 [5.75]) of the stretching exercise group were significantly lower than those of the control group. However, there was no significant difference between the groups with regard to the scores at the 1‐month evaluation (p > .05).Linking Evidence to ActionNeck stretching exercises done immediately after a total thyroidectomy reduce short‐term neck pain and disability symptoms.
DepR1, a TetR Family Transcriptional Regulator, Positively Regulates Daptomycin Production in an Industrial Producer, Streptomyces roseosporus SW0702
Authors: Yuan Peng-Hui , Zhou Ri-Cheng , Chen Xuepeng , Luo Shuai , Wang Feng , Mao Xu-Ming , Li Yong-Quan 
Published: January 2016

ABSTRACT

Daptomycin is a potent cyclic lipopeptide antibiotic. It is widely used against various Gram-positive bacterial pathogens. Historically, a poor understanding of the transcriptional regulation of daptomycin biosynthesis has limited the options for targeted genetic engineering toward titer improvement. Here, we isolated a TetR family transcriptional regulator, DepR1, from the industrial producer
Streptomyces roseosporus
SW0702 using a biotinylated
dptE
promoter (
dptEp
) as a probe. The direct interaction between DepR1 and
dptEp
then was confirmed by electrophoretic mobility shift assays and DNase I footprinting assays. The deletion of
depR1
led to a reduction in
dptEp
activity and the cessation of daptomycin production. The
ΔdepR1
mutant produced less red pigment and failed to sporulate on R5 medium. This suggests that DepR1 plays a positive role in the control of morphological differentiation. Moreover, DepR1 was positively autoregulated by directly binding to its own promoter. This might account for the positive feedback regulation of daptomycin production. Based on these positive effects, genetic engineering by overexpression of
depR1
raised daptomycin production and shortened the fermentation period both in flask and in fermentor.
Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis
Authors: Zaburannyi Nestor , Bunk Boyke , Maier Josef , Overmann Jörg , Müller Rolf 
Published: January 2016

ABSTRACT

Here, we report the complete genome sequence of the type strain of the myxobacterial genus
Chondromyces
,
Chondromyces crocatus
Cm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr−) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family,
Sorangium cellulosum
, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.
Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species
Authors: Lacroix Christelle , Renner Kurra , Cole Ellen , Seabloom Eric W. , Borer Elizabeth T. , Malmstrom Carolyn M. 
Published: January 2016

ABSTRACT

Ecological understanding of disease risk, emergence, and dynamics and of the efficacy of control strategies relies heavily on efficient tools for microorganism identification and characterization. Misdetection, such as the misclassification of infected hosts as healthy, can strongly bias estimates of disease prevalence and lead to inaccurate conclusions. In natural plant ecosystems, interest in assessing microbial dynamics is increasing exponentially, but guidelines for detection of microorganisms in wild plants remain limited, particularly so for plant viruses. To address this gap, we explored issues and solutions associated with virus detection by serological and molecular methods in noncrop plant species as applied to the globally important
Barley yellow dwarf virus
PAV (
Luteoviridae
), which infects wild native plants as well as crops. With enzyme-linked immunosorbent assays (ELISA), we demonstrate how virus detection in a perennial wild plant species may be much greater in stems than in leaves, although leaves are most commonly sampled, and may also vary among tillers within an individual, thereby highlighting the importance of designing effective sampling strategies. With reverse transcription-PCR (RT-PCR), we demonstrate how inhibitors in tissues of perennial wild hosts can suppress virus detection but can be overcome with methods and products that improve isolation and amplification of nucleic acids. These examples demonstrate the paramount importance of testing and validating survey designs and virus detection methods for noncrop plant communities to ensure accurate ecological surveys and reliable assumptions about virus dynamics in wild hosts.
A TonB-Dependent Transporter Is Responsible for Methanobactin Uptake by Methylosinus trichosporium OB3b
Authors: Gu Wenyu , Farhan Ul Haque Muhammad , Baral Bipin S. , Turpin Erick A. , Bandow Nathan L. , Kremmer Elisabeth , Flatley Andrew , Zischka Hans , DiSpirito Alan A. , Semrau Jeremy D. 
Published: January 2016

ABSTRACTMethanobactin, a small modified polypeptide synthesized by methanotrophs for copper uptake, has been found to be chromosomally encoded. The gene encoding the polypeptide precursor of methanobactin,mbnA, is part of a gene cluster that also includes several genes encoding proteins of unknown function (but speculated to be involved in methanobactin formation) as well asmbnT, which encodes a TonB-dependent transporter hypothesized to be responsible for methanobactin uptake. To determine ifmbnTis truly responsible for methanobactin uptake, a knockout was constructed inMethylosinus trichosporiumOB3b using marker exchange mutagenesis. The resultingM. trichosporiummbnT::Gmrmutant was found to be able to produce methanobactin but was unable to internalize it. Further, if this mutant was grown in the presence of copper and exogenous methanobactin, copper uptake was significantly reduced. Expression ofmmoXandpmoA, encoding polypeptides of the soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO), respectively, also changed significantly when methanobactin was added, which indicates that the mutant was unable to collect copper under these conditions. Copper uptake and gene expression, however, were not affected in wild-typeM. trichosporiumOB3b, indicating that the TonB-dependent transporter encoded bymbnTis responsible for methanobactin uptake and that methanobactin is a key mechanism used by methanotrophs for copper uptake. When thembnT::Gmrmutant was grown under a range of copper concentrations in the absence of methanobactin, however, the phenotype of the mutant was indistinguishable from that of wild-typeM. trichosporiumOB3b, indicating that this methanotroph has multiple mechanisms for copper uptake.
Temperature Sensitivity Conferred by
ligA
Alleles from Psychrophilic Bacteria upon Substitution in Mesophilic Bacteria and a Yeast Species
Authors: Pankowski Jarosław A. , Puckett Stephanie M. , Nano Francis E. 
Published: January 2016

ABSTRACT

We have assembled a collection of 13 psychrophilic
ligA
alleles that can serve as genetic elements for engineering mesophiles to a temperature-sensitive (TS) phenotype. When these
ligA
alleles were substituted into
Francisella novicida
, they conferred a TS phenotype with restrictive temperatures between 33 and 39°C. When the
F. novicida
ligA
hybrid strains were plated above their restrictive temperatures, eight of them generated temperature-resistant variants. For two alleles, the mutations that led to temperature resistance clustered near the 5′ end of the gene, and the mutations increased the predicted strength of the ribosome binding site at least 3-fold. Four
F. novicida ligA
hybrid strains generated no temperature-resistant variants at a detectable level. These results suggest that multiple mutations are needed to create temperature-resistant variants of these
ligA
gene products. One
ligA
allele was isolated from a
Colwellia
species that has a maximal growth temperature of 12°C, and this allele supported growth of
F. novicida
only as a hybrid between the psychrophilic and the
F. novicida
ligA
genes. However, the full psychrophilic gene alone supported the growth of
Salmonella enterica
, imparting a restrictive temperature of 27°C. We also tested two
ligA
alleles from two
Pseudoalteromonas
strains for their ability to support the viability of a
Saccharomyces cerevisiae
strain that lacked its essential gene,
CDC9
, encoding an ATP-dependent DNA ligase. In both cases, the psychrophilic bacterial alleles supported yeast viability and their expression generated TS phenotypes. This collection of
ligA
alleles should be useful in engineering bacteria, and possibly eukaryotic microbes, to predictable TS phenotypes.
Discovery of Novel Haloalkane Dehalogenase Inhibitors
Authors: Buryska Tomas , Daniel Lukas , Kunka Antonin , Brezovsky Jan , Damborsky Jiri , Prokop Zbynek 
Published: January 2016

ABSTRACTHaloalkane dehalogenases (HLDs) have recently been discovered in a number of bacteria, including symbionts and pathogens of both plants and humans. However, the biological roles of HLDs in these organisms are unclear. The development of efficient HLD inhibitors serving as molecular probes to explore their function would represent an important step toward a better understanding of these interesting enzymes. Here we report the identification of inhibitors for this enzyme family using two different approaches. The first builds on the structures of the enzymes' known substrates and led to the discovery of less potent nonspecific HLD inhibitors. The second approach involved the virtual screening of 150,000 potential inhibitors against the crystal structure of an HLD from the human pathogenMycobacterium tuberculosisH37Rv. The best inhibitor exhibited high specificity for the target structure, with an inhibition constant of 3 μM and a molecular architecture that clearly differs from those of all known HLD substrates. The new inhibitors will be used to study the natural functions of HLDs in bacteria, to probe their mechanisms, and to achieve their stabilization.
Error Detector Placement for Soft Computing Applications
Authors: Thomas Anna , Pattabiraman Karthik 
Published: January 2016

The scaling of Silicon devices has exacerbated the unreliability of modern computer systems, and power constraints have necessitated the involvement of software in hardware error detection. At the same time, emerging workloads in the form of soft computing applications (e.g., multimedia applications) can tolerate most hardware errors as long as the erroneous outputs do not deviate significantly from error-free outcomes. We term outcomes that deviate significantly from the error-free outcomes as Egregious Data Corruptions (EDCs).
In this study, we propose a technique to place detectors for selectively detecting EDC-causing errors in an application. We performed an initial study to formulate heuristics that identify EDC-causing data. Based on these heuristics, we developed an algorithm that identifies program locations for placing high coverage detectors for EDCs using static analysis. Our technique achieves an average EDC coverage of 82%, under performance overheads of 10%, while detecting 10% of the Non-EDC and benign faults. We also evaluate the error resilience of these applications under the 14 compiler optimizations.