bluuebunny/crossref_metadata_2025 huggingface dataset:
Trapping the Metasemantic Metaphilosophical Deflationist?
Authors: Warren Jared
Published: January 2016

Some philosophers are metaphilosophical deflationists for metasemantic reasons. These theorists take standard philosophical assertions to be defective in some manner. There are various versions ofmetasemantic metaphilosophical deflationism, but a trap awaits any global version of it: metasemantics itself is a part of philosophy, so in deflating philosophy these theorists have thereby deflated the foundation of their deflationism. The present article discusses this issue and the prospects for an adequate response to the trap. Contrary to most historical responses (some of which it discusses), the article argues that the best response to the trap is to adopt a local but still pervasive metasemantic deflationism. Such a response might seem ad hoc, but the article argues that the human activity of philosophy isn't a natural kind, and that a heterogeneous metaphilosophy of the appropriate kind is well motivated.
Non‐paraneoplastic limbic encephalitis and central nervous HHV‐6B reactivation: Causality or coincidence?
Authors: Niehusmann Pitt , Widman Guido , Eis‐Hübinger Anna M. , Greschus Susanne , Robens Barbara K. , Grote Alexander , Becker Albert J.
Published: January 2016

Autoantibody‐related encephalopathies represent an important differential diagnosis in adult onset epilepsy. Here, we report the case of a 25‐year‐old patient with new‐onset epilepsy and psychotic syndrome, who underwent biopsy resection for etiological classification. MRI analysis and neuropathological examination showed a T‐lymphocytic dominated encephalitis with involvement of the limbic system. An indirect immunohistochemistry approach identified autoantibodies against glutamic acid decarboxylase (GAD) in cerebral spinal fluid and serum, which were confirmed by affinity purification / mass spectrometry analysis. Further examinations revealed evidence of chromosomally integrated human herpes virus type 6B (HHV‐6B). However, astrocytic expression of HHV‐6 lytic protein was detected by double immunofluorescence analysis. The cerebral expression of HHV‐6 antigen, a clinical improvement under antiviral therapy as well as an initial finding of HHV‐6 IgM antibodies strongly argue for an additional active HHV‐6B infection. Review of the literature reveals singular reports of patients with GAD antibody‐positive limbic encephalitis and central nervous system infections with HHV‐6B. Since herpes simplex virus encephalitis has been recently reported as a trigger of N‐methyl‐D‐aspartate receptor antibody encephalitis, it is tempting to speculate that HHV‐6B infections may trigger a non‐paraneoplastic form of limbic encephalitis in a parallel cascade.
Electronic cigarettes: what are they and what do they do?
Authors: Breland Alison , Soule Eric , Lopez Alexa , Ramôa Carolina , El‐Hellani Ahmad , Eissenberg Thomas
Published: January 2016

Electronic cigarettes (ECIGs) use electricity to power a heating element that aerosolizes a liquid containing solvents, flavorants, and the dependence‐producing drug nicotine for user inhalation. ECIGs have evolved rapidly in the past 8 years, and the changes in product design and liquid constituents affect the resulting toxicant yield in the aerosol and delivery to the user. This rapid evolution has been accompanied by dramatic increases in ECIG use prevalence in many countries among adults and, especially, adolescents in the United States. The increased prevalence of ECIGs that deliver nicotine and other toxicants to users’ lungs drives a rapidly growing research effort. This review highlights the most recent information regarding the design of ECIGs and their liquid and aerosol constituents, the epidemiology of ECIG use among adolescents and adults (including correlates of ECIG use), and preclinical and clinical research regarding ECIG effects. The current literature suggests a strong rationale for an empirical regulatory approach toward ECIGs that balances any potential ECIG‐mediated decreases in health risks for smokers who use them as substitutes for tobacco cigarettes against any increased risks for nonsmokers who may be attracted to them.
The functional relationship between hematopoietic stem cells and developing T lymphocytes
Authors: Staal Frank J.T. , Wiekmeijer Anna‐Sophia , Brugman Martijn H. , Pike‐Overzet Karin
Published: January 2016

In contrast to all other blood and immune cells, T lymphocytes do not develop in the bone marrow (BM), but in the specialized microenvironment provided by the thymus. Similar to the other lineages, however, all T cells arise from multipotent hematopoietic stem cells (HSCs) that reside in the BM. Not all HSCs give rise to T cells; but how many and what kind of developmental checkpoints are located along this intricate differentiation path is the subject of intense research. Traditionally, this process has been studied almost exclusively using mouse cells, but recent advances in immunodeficient mouse models, high‐speed cell sorting, lentiviral transduction protocols, and deep sequencing techniques have allowed these questions to be addressed using human cells. Here we review the process of thymic seeding by BM‐derived cells and T cell commitment in humans, discussing recent insights into the clonal composition of the thymus and the definition of developmental checkpoints, on the basis of insights from human severe combined immunodeficiency patients.
Cryptosporidium Infection Risk: Results of New Dose‐Response Modeling
Authors: Messner Michael J. , Berger Philip
Published: January 2016

Cryptosporidium human dose‐response data from seven species/isolates are used to investigate six models of varying complexity that estimate infection probability as a function of dose. Previous models attempt to explicitly account for virulence differences among C. parvum isolates, using three or six species/isolates. Four (two new) models assume species/isolate differences are insignificant and three of these (all but exponential) allow for variable human susceptibility. These three human‐focused models (fractional Poisson, exponential with immunity and beta‐Poisson) are relatively simple yet fit the data significantly better than the more complex isolate‐focused models. Among these three, the one‐parameter fractional Poisson model is the simplest but assumes that all Cryptosporidium oocysts used in the studies were capable of initiating infection. The exponential with immunity model does not require such an assumption and includes the fractional Poisson as a special case. The fractional Poisson model is an upper bound of the exponential with immunity model and applies when all oocysts are capable of initiating infection. The beta Poisson model does not allow an immune human subpopulation; thus infection probability approaches 100% as dose becomes huge. All three of these models predict significantly (>10x) greater risk at the low doses that consumers might receive if exposed through drinking water or other environmental exposure (e.g., 72% vs. 4% infection probability for a one oocyst dose) than previously predicted. This new insight into Cryptosporidium risk suggests additional inactivation and removal via treatment may be needed to meet any specified risk target, such as a suggested 10−4 annual risk of Cryptosporidium infection.
Being Met as marked – patients’ experiences of being infected with community‐acquired methicillin‐resistant Staphylococcus aureus (MRSA)
Authors: Skyman Eva , Lindahl Berit , Bergbom Ingegerd , Sjöström Harrieth Thunberg , Åhrén Christina
Published: January 2016

Background

It is known that patients who acquired methicillin‐resistant Staphylococcus aureus (MRSA) in hospitals suffer and feel as plague. Moreover, the patient interaction with nurses and physicians is described as frightening. Little is known about patient experiences after having acquired CA‐MRSA concerning care and everyday life.

Aim

To reveal and interpret otherwise healthy patients’ lived experiences of receiving care and their everyday life after having acquired community MRSA (CA‐MRSA).

Methods

A phenomenological hermeneutic approach guided by Ricouer was conducted. Interviews with twelve patients were transcribed verbatim into a text. The text was analysed in three phases: naive understanding, structural analysis and comprehensive understanding to reveal a possible being in the world. In this study, this referred to what it means to be infected with CA‐MRSA.

Results

The findings indicate that patients who acquired MRSA experience a changed body image. They suffer from ignorant and frightened behavior from healthcare workers, social contacts, and also of being bullied by colleagues. Despite this, patients assume great responsibility for protecting others. However, knowledgeable staff alleviate suffering and bring peace of mind to the patients.

Conclusions

Preventing patient's feelings of being a pest, an outsider living with fear, requires urgent education and understanding about resistant bacteria and how to meet an infected patient. The results describing patients, affected with MRSA, may contribute and touch the readers to better understanding of patient's changed body image and suffering and how to mitigate these feelings.
European Monetary Unification: A Few Lessons for East Asia
Authors: De Grauwe Paul
Published: January 2016

In this paper, I analyze the experience of European monetary and financial integration to shed some light on the question of the desirability and feasibility of monetary unification in East Asia. The experience of Europe shows that trying to fix the exchange rates when capital is freely moving is unsustainable and leads to frequent speculative crises. This leads to only two options: Either a monetary union or floating exchange rates. Monetary union requires very intrusive political unification. Given the complete absence of political unification in Asia, the only possible conclusion is that Asia will have to live with increasing exchange rate volatility.
It takes two to tango: A regime‐switching analysis of the correlation dynamics between the mainland Chinese and Hong Kong stock markets
Authors: Ho Kin‐Yip , Shi Yanlin , Zhang Zhaoyong
Published: January 2016

This paper proposes a regime‐switching model to examine the correlation dynamics of the mainland Chinese and Hong Kong stock markets with high‐frequency A‐, B‐, H‐shares and Red Chip indexes. We find significant evidence of volatility persistence and asymmetries in these markets. Our model further suggests all correlations are significantly time‐varying with various patterns and co‐persistence in both low‐ and high‐correlation states. Our findings have important implications for both policymakers and investors, such as understanding the extent and nature of integration between the mainland Chinese and Hong Kong stock markets over time and developing dynamic strategies for optimal hedging and portfolio management.
The Effect of China's Rise on FDI Competition in East Asia: Crowding‐out or Crowding‐in?
Authors: Sohn Chan‐Hyun
Published: January 2016

This paper investigates the China Effect on FDI competition in East Asia: Does China's FDI crowd out or crowd in FDIs in ASEAN countries? Previous research utilized a gravity equation that has no theoretical foundation for FDI flows. This study applies a theory‐based Knowledge‐Capital Model modified to incorporate preferential market‐openings by FTAs and BITs that directly affect investment and trade costs. Using country‐pair data for China and ASEAN with 34 OECD home countries during 1985–2010, panel analyses are performed. The results suggest that China's rise does not threaten ASEAN countries but induces a strong synergetic effect on FDIs into them. In attracting FDI inflows, China and ASEAN countries are friends, not foes.
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

Objective

This 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.

Methods

Analyzing 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.

Results

The 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.

Conclusion

The 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

Background

Of 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 methods

The 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.

Results

All 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.

Conclusion

The 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

Objective

To compare signalment, presentation, treatment, and outcome in horses diagnosed with corneal degeneration (CD) or calcific band keratopathy (CBK) at a referral hospital.

Animals studied

Sixty‐nine horses (87 eyes) diagnosed with either CD or CBK.

Procedures

Medical 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.

Results

Thirty‐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).

Conclusions

Despite 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.
COMPUTED TOMOGRAPHIC APPEARANCE OF THE TEMPOROMANDIBULAR JOINT IN 1018 ASYMPTOMATIC HORSES: A MULTI‐INSTITUTION STUDY
Authors: Carmalt James L. , Kneissl Sibylle , Rawlinson Jennifer E. , Zwick Timo , Zekas Lisa , Ohlerth Stefanie , Bienert‐Zeit Astrid
Published: January 2016

Published descriptions of nonseptic arthritis of the equine temporomandibular joint (TMJ) are rare and large studies investigating variations in the TMJ for asymptomatic horses are lacking. The objectives of this cross‐sectional, retrospective, multi‐institutional study were to describe anatomical variations in the TMJ detected using computed tomography (CT) in an equid population asymptomatic for TMJ disease and determine whether these variations were associated with patient signalment, reason for CT examination, or CT slice width. Medical records at eight hospitals were searched for horses that had head/neck CT scans and no clinical signs of TMJ disease. Age, breed, sex, clinical presentation, and CT slice width data were recorded. Alterations in CT contour and density of the mandibular condyles, mandibular fossae, and TMJ intra‐articular discs were described for each horse. Generalized logistic regression was used to test associations between anatomical variations and horse age. A total of 1018 horses were sampled. Anatomical variations were found in TMJ CT images for 40% of horses and 29% of joints. These were dichotomous with regard to age. Horses <1 year old commonly had alterations in the shape and density of the mandibular condyle. Older horses commonly had spherical hypodensities within the mandibular condyles consistent with bone cysts; and hyperdense regions of the intra‐articular disc consistent with dystrophic mineralization. Findings indicated that TMJ anatomic variations were common in CT images of younger and older horses asymptomatic for TMJ disease. Future studies are needed to more definitively characterize these CT variations using gross pathology and histopathology.
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

Objective

To quantify recovery of colored microspheres from normal cadaver tarsocrural joints using arthroscopic or needle lavage with 1–5 L of fluid.

Study Design

Ex vivo experimental study.

Animals

Adult Quarter Horse cadavers (n = 8).

Methods

After 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.

Results

A 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.

Conclusion

In 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

Background

Although 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.

Objective

To analyze the effect of neck stretching exercises, following a total thyroidectomy, on reducing neck pain and disability.

Methods

A 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.

Results

When 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 Action

Neck stretching exercises done immediately after a total thyroidectomy reduce short‐term neck pain and disability symptoms.
Reading ability influences native and non-native voice recognition, even for unimpaired readers
Authors: Kadam Minal A. , Orena Adriel John , Theodore Rachel M. , Polka Linda
Published: January 2016

Research suggests that phonological ability exerts a gradient influence on talker identification, including evidence that adults and children with reading disability show impaired talker recognition for native and non-native languages. The present study examined whether this relationship is also observed among unimpaired readers. Learning rate and generalization of learning in a talker identification task were examined in average and advanced readers who were tested in both native and non-native language conditions. The results indicate that even among unimpaired readers, phonological competence as captured by reading ability exerts a gradient influence on perceptual learning for talkers' voices.
The aero-acoustic Galbrun equation in the time domain with perfectly matched layer boundary conditions
Authors: Feng Xue , Ben Tahar Mabrouk , Baccouche Ryan
Published: January 2016

This paper presents a solution for aero-acoustic problems using the Galbrun equation in the time domain with a non-uniform steady mean flow in a two-dimensional coordinate system and the perfectly matched layer technique as the boundary conditions corresponding to an unbounded domain. This approach is based on an Eulerian–Lagrangian description corresponding to a wave equation written only in terms of the Lagrangian perturbation of the displacement. It is an alternative to the Linearized Euler Equations for solving aero-acoustic problems. The Galbrun equation is solved using a mixed pressure-displacement Finite Element Method. A complex Laplace transform scheme is used to study the time dependent variables. Several numerical examples are presented to validate and illustrate the efficiency of the proposed approach.
Large-scale diversification without genetic isolation in nematode symbionts of figs
Authors: Susoy Vladislav , Herrmann Matthias , Kanzaki Natsumi , Kruger Meike , Nguyen Chau N. , Rödelsperger Christian , Röseler Waltraud , Weiler Christian , Giblin-Davis Robin M. , Ragsdale Erik J. , Sommer Ralf J.
Published: January 2016

A polyphenism discovered to consist of five discrete morphotypes shows that extreme diversification is possible within single species.
Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway
Authors: Keller Markus A. , Zylstra Andre , Castro Cecilia , Turchyn Alexandra V. , Griffin Julian L. , Ralser Markus
Published: January 2016

Iron and pH dependency enable metabolism-like attributes in a network of primordially plausible chemical reactions.
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

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

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

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

Methanobactin, 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

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

Haloalkane 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.
The effects of compression garments on performance of prolonged manual-labour exercise and recovery
Authors: Chan Val , Duffield Rob , Watsford Mark
Published: January 2016

This study investigated the effects of wearing compression garments during and 24 h following a 4-h exercise protocol simulating manual-labour tasks. Ten physically trained male participants, familiar with labouring activities, undertook 4 h of work tasks characteristic of industrial workplaces. Participants completed 2 testing sessions, separated by at least 1 week. In the experimental condition, participants wore a full-length compression top and compression shorts during the exercise protocol and overnight recovery, with normal work clothes worn in the control condition. Testing for serum creatine kinase and C-reactive protein, handgrip strength, knee flexion and extension torque, muscle stiffness, perceived muscle soreness and fatigue as well as heart rate and rating of perceived exertion (RPE) responses to 4-min cycling were performed before, following, and 24 h after exercise. Creatine kinase, muscle soreness, and rating of perceived fatigue increased following the exercise protocol (p < 0.05) as did RPE to a standardised cycling warm-up bout. Conversely, no postexercise changes were observed in C-reactive protein, handgrip strength, peak knee flexion torque, or stiffness measures (p > 0.05). Knee extension torque was significantly higher in the control condition at 24 h postexercise (3.1% ± 5.4% change; compression: 2.2% ± 11.1% change), although no other variables were different between conditions at any time. However, compression demonstrated a moderate–large effect (d > 0.60) to reduce perceived muscle soreness, fatigue, and RPE from standardised warm-up at 24 h postexercise. The current findings suggest that compression may assist in perceptual recovery from manual-labour exercise with implications for the ability to perform subsequent work bouts.
Peroxisome proliferator-activated receptors (PPAR) downregulate the expression of pro-inflammatory molecules in an experimental model of myocardial infarction
Authors: Ibarra-Lara María de la Luz , Sánchez-Aguilar María , Soria Elizabeth , Torres-Narváez Juan Carlos , Del Valle-Mondragón Leonardo , Cervantes-Pérez Luz Graciela , Pérez-Severiano Francisca , Ramírez-Ortega Margarita del Carmen , Pastelín-Hernández Gustavo , Oidor-Chan Víctor Hugo , Sánchez-Mendoza Alicia
Published: January 2016

Myocardial infarction (MI) has been associated with an inflammatory response and a rise in TNF-α, interleukin (IL)-1β, and IL-6. Peroxisome proliferator-activated receptors (PPARs) promote a decreased expression of inflammatory molecules. We aimed to study whether PPAR stimulation by clofibrate decreases inflammation and reduces infarct size in rats with MI. Male Wistar rats were randomized into 3 groups: control, MI + vehicle, and MI + clofibrate (100 mg/kg). Treatment was administered for 3 consecutive days, previous to 2 h of MI. MI induced an increase in protein expression, mRNA content, and enzymatic activity of inducible nitric oxide synthase (iNOS). Additionally, MI incited an increased expression of matrix metalloproteinase (MMP)-2 and MMP-9, intercellular adhesion molecule (ICAM)-1, and IL-6. MI also elevated the nuclear content of nuclear factor-κB (NF-κB) and decreased IκB, both in myocyte nuclei and cytosol. Clofibrate treatment prevented MI-induced changes in iNOS, MMP-2 and MMP-9, ICAM-1, IL-6, NF-κB, and IκB. Infarct size was smaller in clofibrate-treated rats compared to MI-vehicle animals. In silico analysis exhibited 3 motifs shared by genes from renin–angiotensin system, PPARα, iNOS, MMP-2 and MMP-9, ICAM-1, and VCAM-1, suggesting a cross regulation. In conclusion, PPARα-stimulation prevents overexpression of pro-inflammatory molecules and preserves viability in an experimental model of acute MI.
Ursolic acid plays a protective role in obesity-induced cardiovascular diseases
Authors: Lin Yu-Ting , Yu Ya-Mei , Chang Weng-Cheng , Chiang Su-Yin , Chan Hsu-Chin , Lee Ming-Fen
Published: January 2016

The metabolic disturbance of obesity is one of the most common risk factors of atherosclerosis. Resistin, an obesity-induced adipokine, can induce the expression of cell adhesion molecules and the attachment of monocytes to endothelial cells, which play an important role in the development of atherosclerosis. Ursolic acid, a pentacyclic triterpenoid found in fruits and many herbs, exhibits an array of biological effects such as anti-inflammatory and antioxidative properties. The aim of this study was to investigate the potential underlying mechanisms of the effect of ursolic acid on resistin-induced adhesion of U937 cells to human umbilical vein endothelial cells (HUVECs). Our data indicated that ursolic acid suppressed the adhesion of U937 to HUVECs and downregulated the expression of adhesion molecules, vascular cell adhesion molecule-1 (VCAM-1), intracellular cell adhesion molecule-1 (ICAM-1), and E-selectin, in resistin-induced HUVECs by decreasing the production of intracellular reaction oxygen species (ROS) and attenuating the nuclear translocation of NFκB. Ursolic acid appeared to inhibit resistin-induced atherosclerosis, suggesting that ursolic acid may play a protective role in obesity-induced cardiovascular diseases.
Genome size variation in the genus Avena
Authors: Yan Honghai , Martin Sara L. , Bekele Wubishet A. , Latta Robert G. , Diederichsen Axel , Peng Yuanying , Tinker Nicholas A.
Published: January 2016

Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.
CUDA Leaks
Authors: Pietro Roberto Di , Lombardi Flavio , Villani Antonio
Published: January 2016

Graphics processing units (GPUs) are increasingly common on desktops, servers, and embedded platforms. In this article, we report on new security issues related to CUDA, which is the most widespread platform for GPU computing. In particular, details and proofs-of-concept are provided about novel vulnerabilities to which CUDA architectures are subject. We show how such vulnerabilities can be exploited to cause severe information leakage. As a case study, we experimentally show how to exploit one of these vulnerabilities on a GPU implementation of the AES encryption algorithm. Finally, we also suggest software patches and alternative approaches to tackle the presented vulnerabilities.
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.
Dynamic Logging with Dylog in Networked Embedded Systems
Authors: Dong Wei , Luo Luyao , Huang Chao
Published: January 2016

Event logging is an important technique for networked embedded systems like wireless sensor networks. It can greatly help developers to understand complex system behaviors and diagnose program bugs. Existing logging facilities do not well satisfy three practical requirements:
flexibility
,
efficiency
, and
high synchronization accuracy
. To simultaneously satisfy these requirements, we present Dylog, a dynamic logging facility for networked embedded systems. Dylog employs several techniques. First, Dylog uses binary instrumentation for dynamically inserting or removing logging statements, enabling
flexible
and interactive debugging at runtime. Second, Dylog incorporates an
efficient
storage system and log collection protocol for recording and transferring the logging messages. Third, Dylog employs a lightweight data-driven approach for reconstructing the synchronized time of the logging messages. Dylog uses MAC-layer timestamping and drift compensation to achieve
high synchronization accuracy
. We implement Dylog on the TinyOS 2.1.1/TelosB platform. Results show the following: (1) Dylog incurs a small overhead. Indirections in Dylog incur an additional execution overhead of less than 1%. Dylog reduces the logging storage size by approximately 50% compared with the standard TinyOS radio printf library. Dylog reduces the patch size by more than 90%, compared with incremental reprogramming. (2) Dylog reduces the synchronization overhead by 78% in terms of transmission cost, compared with a traditional time synchronization protocol, FTSP, and it can achieve a high time synchronization accuracy of 5.4μs. (3) Dylog can help diagnose system problems effectively at the source-code level for three real-world scenarios.