bluuebunny/crossref_metadata_2025 huggingface dataset:
Archaeal grpE: transcription in two different morphologic stages of Methanosarcina mazei and comparison with dnaK and dnaJ
Authors: Conway De Macario E , Clarens M , Macario A J
Published: November 2016

Transcription of the heat shock gene grpE was studied in two different morphologic stages of the archaeon Methanosarcina mazei S-6 that differ in resistance to physical and chemical traumas: single cells and packets. While single cells are directly exposed to environmental changes, such as temperature elevations, cells in packets are surrounded by intercellular and peripheral material that keeps them together in a globular structure which can reach several millimeters in diameter. grpE transcript levels determined by Northern (RNA) blotting peaked after a 15-min heat shock in single cells. In contrast, the highest transcript levels in packets were observed after the longest heat shock tested, 60 min. The same response profiles were demonstrated by primer extension experiments and S1 nuclease analysis. A comparison of the grpE response to heat shock with those of dnaK and dnaJ showed that the grpE transcript level was the most increased, closely followed by that of the dnaK transcript, with that of the dnaJ gene being the least augmented. Transcription of grpE started at the same site under normal and heat shock temperatures, and the transcript was consistently approximately 700 bases long. Codon usage patterns revealed that the three archaeal genes use most codons and have the same codon preference for 61% of the amino acids.
Purification and characterization of the IM-2-binding protein from Streptomyces sp. strain FRI-5
Authors: Ruengjitchatchawalya M , Nihira T , Yamada Y
Published: November 2016

IM-2 [(2R,3R,1'R)-2-(1'-hydroxybutyl)-3-(hydroxymethyl)butanolide] of Streptomyces sp. strain FRI-5 is one of the butyrolactone autoregulators of Streptomyces species and triggers production of blue pigment as well as the nucleoside antibiotics showdomycin and minimycin. A tritium-labeled IM-2 analogue, 2,3-trans-2(1'-beta-hydroxy-[4',5'-3H]pentyl)-3-(hydroxymethyl)butano lide ([3H]IM-2-C5; 40 Ci/mmol), was synthesized for a competitive binding assay, and an IM-2-specific binding protein was found to be present in the crude cell extract of Streptomyces sp. strain FRI-5. During cultivation for 24 h, the specific IM-2-binding activity increased rapidly, reached a plateau at 10 to 14 h, and declined sharply thereafter, showing only 6% activity after 24 h of cultivation. A Scatchard plot of the binding data demonstrated that the dissociation constant (Kd) for [3H]IM-2-C5 was 1.3 nM, while the Kd for a 3H-labeled virginiae butanolide (VB) analogue, 2-(1'-alpha-hydroxy-[6',7'-3H]heptyl)-3-(hydroxymethyl)butanolide ([3H]VB-C7), another butyrolactone autoregulator possessing the opposite configuration at C-1' was 35 nM. Furthermore, at a 15-fold molar excess, the effectiveness of several autoregulators as nonlabeled competitive ligands against [3H]IM-2-C5 was IM-2 type > VB-C type > A-factor type, indicating that the binding protein in Streptomyces sp. strain FRI-5 is highly specific toward IM-2. Ultracentrifugation showed that the IM-2-binding protein is present almost exclusively in the 100,000 x g supernatant fraction, indicating that the binding protein is a cytoplasmic soluble protein. The binding protein was purified by ammonium sulfate precipitation, DEAE-Sephacel chromatography, Sephacryl S-100 HR gel filtration, DEAE-5PW high-performance liquid chromatography (HPLC), and phenyl-5PW HPLC. The apparent Mr of the native IM-2-binding protein as determined by molecular sieve HPLC was about 60,000 in the presence of 0.5, 0.3, or 0.1 M KCl, while by sodium dodecyl sulfate-polyacrylamide gel electrophoresis it was about 27,000, suggesting that the native binding protein is present in the form of a dimer.
Primary structure and functional analysis of the lysis genes of Lactobacillus gasseri bacteriophage phi adh
Authors: Henrich B , Binishofer B , Bläsi U
Published: November 2016

The lysis genes of the Lactobacillus gasseri bacteriophage phi adh were isolated by complementation of a lambda Sam mutation in Escherichia coli. Nucleotide sequencing of a 1,735-bp DNA fragment revealed two adjacent coding regions of 342 bp (hol) and 951 bp (lys) in the same reading frame which appear to belong to a common transcriptional unit. Proteins corresponding to the predicted gene products, holin (12.9 kDa) and lysin (34.7 kDa), were identified by in vitro and in vivo expression of the cloned genes. The phi adh holin is a membrane-bound protein with structural similarity to lysis proteins of other phage, known to be required for the transit of murein hydrolases through the cytoplasmic membrane. The phi adh lysin shows homology with mureinolytic enzymes encoded by the Lactobacillus bulgaricus phage mv4, the Streptococcus pneumoniae phage Cp-1, Cp-7, and Cp-9, and the Lactococcus lactis phage phi LC3. Significant homology with the N termini of known muramidases suggests that phi adh lysin acts by a similar catalytic mechanism. In E. coli, the phi adh lysin seems to be associated with the total membrane fraction, from which it can be extracted with lauryl sarcosinate. Either one of the phi adh lysis proteins provoked lysis of E. coli when expressed along with holins or lysins of phage lambda or Bacillus subtilis phage phi 29. Concomitant expression of the combined holin and lysin functions of phi adh in E. coli, however, did not result in efficient cell lysis.
Isolation and characterization of plasmid mutations that enable partitioning of pSC101 replicons lacking the partition (par) locus
Authors: Conley D L , Cohen S N
Published: November 2016

Second-site mutations that allow stable inheritance of partition-defective pSC101 plasmids mapped to seven distinct sites in the 5' half of the plasmid repA gene. While the mutations also elevated pSC101 copy number, there was no correlation between copy number increase and plasmid stability. Combinations of mutations enabled pSC101 DNA replication in the absence of integration host factor and also stabilized par-deleted plasmids in cells deficient in DNA gyrase or defective in DnaA binding. Our findings suggest that repA mutations compensate for par deletion by enabling the origin region RepA-DNA-DnaA complex to form under suboptimal conditions. They also provide evidence that this complex has a role in partitioning that is separate from its known ability to promote plasmid DNA replication.
The octopine-type Ti plasmid pTiA6 of Agrobacterium tumefaciens contains a gene homologous to the chromosomal virulence gene acvB
Authors: Kalogeraki V S , Winans S C
Published: November 2016

Although the majority of genes required for the transfer of T-DNA from Agrobacterium tumefaciens to plant nuclei are located on the Ti plasmid, some chromosomal genes, including the recently described acvB gene, are also required. We show that AcvB shows 50% identity with the product of an open reading frame, designated virJ, that is found between the virA and virB genes in the octopine-type Ti plasmid pTiA6. This reading frame is not found in the nopaline-type Ti plasmid pTiC58. acvB is required for tumorigenesis by a strain carrying a nopaline-type Ti plasmid, and virJ complements this nontumorigenic phenotype, indicating that the products of these genes have similar functions. A virJ-phoA fusion expressed enzymatically active alkaline phosphatase, indicating that VirJ is at least partially exported. virJ is induced in a VirA/VirG-dependent fashion by the vir gene inducer acetosyringone. Primer extension analysis and subcloning of the virJ-phoA fusion indicate that the acetosyringone-inducible promoter lies directly upstream of the virJ structural gene. Although the roles of the two homologous genes in tumorigenesis remain to be elucidated, strains lacking acvB and virJ (i) are proficient for induction of the vir regulon, (ii) are able to transfer their Ti plasmids by conjugation, and (iii) are resistant to plant wound extracts. Finally, mutations in these genes cannot be complemented extracellularly.
Heat shock-dependent transcriptional activation of the metA gene of Escherichia coli
Authors: Biran D , Brot N , Weissbach H , Ron E Z
Published: November 2016

In Escherichia coli, the growth rate at elevated temperatures is controlled by the availability of endogenous methionine, which is limited because of the temperature sensitivity of the metA gene product, homoserine transsuccinylase (HTS). In order to determine the relationship between this control mechanism and the heat shock response, we estimated the cellular levels of HTS during heat shock by Western (immunoblot) analysis and found an increase following induction by temperature shift and by addition of ethanol or cadmium ions. The elevated level of HTS was a result of transcriptional activation of the metA gene. This activation was heat shock dependent, as it did not take place in rpoH mutants, and probably specific to the metA gene, as another gene of the methionine regulon (metE) was not activated. These results suggest a metabolic link between the two systems that control the response of E. coli to elevated temperatures: the metA gene, which codes for the enzyme responsible for regulating cell growth as a function of temperature elevation (HTS), is transcriptionally activated by the heat shock response.
Molecular and expression analysis of the Rhizobium meliloti phosphoenolpyruvate carboxykinase (pckA) gene
Authors: Osterås M , Driscoll B T , Finan T M
Published: November 2016

The pckA gene of Rhizobium meliloti, encoding phosphoenolpyruvate carboxykinase, was isolated from a genomic cosmid library by complementation of the succinate growth phenotype of a Pck- mutant. The gene region was mapped by subcloning and Tn5 insertion mutagenesis. The DNA sequence for a 2-kb region containing the structural gene and its promoter was determined. The pckA gene encodes as 536-amino-acid protein that shows homology with other ATP-dependent Pck enzymes. The promoter was identified following primer extension analysis and is similar to sigma 70-like promoters. Expression analysis with a pckA::lacZ gene fusion indicated that the pckA gene was strongly induced at the onset of stationary phase in complex medium. When defined carbon sources were tested, the expression level of the pckA gene was found to be high when cells were grown in minimal media with succinate or arabinose as the sole carbon source but almost absent when glucose, sucrose, or glycerol was the sole carbon source. Glucose and sucrose were not found to strongly repress pckA induction by succinate.
New beta-glucoside (bgl) genes in Bacillus subtilis: the bglP gene product has both transport and regulatory functions similar to those of BglF, its Escherichia coli homolog
Authors: Le Coq D , Lindner C , Krüger S , Steinmetz M , Stülke J
Published: November 2016

The Bacillus subtilis sacY and sacT genes encode antiterminator proteins, similar to the Escherichia coli bglG gene product and required for transcription of sucrose metabolism genes. A Tn10 insertion into bglP (formerly sytA) has been previously identified as restoring sucrose utilization to a strain with deletions of both sacY and sacT. The nucleotide sequence of bglP showed a high degree of homology with the E. coli bglF gene (BglF is a beta-glucoside permease of the phosphotransferase system and also acts as a negative regulator of the BglG antiterminator). Complementation studies of an E. coli strain with a deletion of the bgl operon showed that BglP was a functional beta-glucoside permease. In B. subtilis, bglP complemented in trans both the bglP::Tn10 original insertion and a phenotypically similar bglP deletion. Disruption of licT abolished the suppressor phenotype in a bglP mutant. LicT is a recently identified third B. subtilis antiterminator of the BglG/SacY family. These observations indicated that BglP was also a negative regulator of LicT. Both LicT and BglP seem to be involved in the induction by beta-glucosides of an operon containing at least two genes, bglP itself and bglH, encoding a phospho-beta-glucosidase. Other beta-glucoside genes homologous to bglP and bglH have been recently described in B. subtilis. Thus, B. subtilis possesses several sets of beta-glucoside genes, like E. coli, but these genes do not appear to be cryptic.
Imidazole acetol phosphate aminotransferase in Zymomonas mobilis: molecular genetic, biochemical, and evolutionary analyses
Authors: Gu W , Zhao G , Eddy C , Jensen R A
Published: November 2016

hisH encodes imidazole acetol phosphate (IAP) aminotransferase in Zymomonas mobilis and is located immediately upstream of tyrC, a gene which codes for cyclohexadienyl dehydrogenase. A plasmid containing hisH was able to complement an Escherichia coli histidine auxotroph which lacked the homologous aminotransferase. DNA sequencing of hisH revealed an open reading frame of 1,110 bp, encoding a protein of 40,631 Da. The cloned hisH product was purified from E. coli and estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to have a molecular mass of 40,000 Da. Since the native enzyme had a molecular mass of 85,000 Da as determined by gel filtration, the active enzyme species must be a homodimer. The purified enzyme was able to transaminate aromatic amino acids and histidine in addition to histidinol phosphate. The existence of a single protein having broad substrate specificity was consistent with the constant ratio of activities obtained with different substrates following a variety of physical treatments (such as freeze-thaw, temperature inactivation, and manipulation of pyridoxal 5'-phosphate content). The purified enzyme did not require addition of pyridoxal 5'-phosphate, but dependence upon this cofactor was demonstrated following resolution of the enzyme and cofactor by hydroxylamine treatment. Kinetic data showed the classic ping-pong mechanism expected for aminotransferases. Km values of 0.17, 3.39, and 43.48 mM for histidinol phosphate, tyrosine, and phenylalanine were obtained. The gene structure around hisH-tyrC suggested an operon organization. The hisH-tyrC cluster in Z. mobilis is reminiscent of the hisH-tyrA component of a complex operon in Bacillus subtilis, which includes the tryptophan operon and aroE. Multiple alignment of all aminotransferase sequences available in the database showed that within the class I superfamily of aminotransferases, IAP aminotransferases (family I beta) are closer to the I gamma family (e.g., rat tyrosine aminotransferase) than to the I alpha family (e.g., rat aspartate aminotransferase or E. coli AspC). Signature motifs which distinguish the IAP aminotransferase family were identified in the region of the active-site lysine and in the region of the interdomain interface.
A novel member of the cspA family of genes that is induced by cold shock in Escherichia coli
Authors: Nakashima K , Kanamaru K , Mizuno T , Horikoshi K
Published: November 2016

Escherichia coli contains a major cold shock protein, CspA (or CS7.4), whose production is predominantly induced at low temperatures. This bacterium is known to possess five additional genes, each encoding a protein highly similar to CspA (referred to as the CspA family). Here we identified a gene that encodes a cold-shock-inducible analog of CspA and CspB. This newly cloned cspG gene is located at 22 min on the E. coli genetic map, apart from the other cspA family genes. Its gene product (70 amino acids) is 73 and 77% identical to CspA (70 amino acids) and CspB (71 amino acids), respectively. Analyses of a cspG-lacZ transcriptional fusion and Northern (RNA) hybridization revealed that cspG is a low-temperature-responsive gene. Its low-temperature-inducible promoters were determined, and the results indicated that the cspG sequence is highly similar to both the cspA and cspB sequences not only in the coding regions but also in the 5'-upstream noncoding regions surrounding their own promoters.
Cloning of genes involved in carbazole degradation of Pseudomonas sp. strain CA10: nucleotide sequences of genes and characterization of meta-cleavage enzymes and hydrolase
Authors: Sato S I , Ouchiyama N , Kimura T , Nojiri H , Yamane H , Omori T
Published: November 2016

The DNA fragment encoding meta-cleavage enzymes and the meta-cleavage compound hydrolase, involved in carbazole degradation, was cloned from the carbazole-utilizing bacterium Pseudomonas sp. strain CA10. DNA sequence analysis of this 2.6-kb SmaI-SphI fragment revealed that there were three open reading frames (ORF1, ORF2, and ORF3, in this gene order). ORF1 and ORF2 were indispensable for meta-cleavage activity for 2'-aminobiphenyl-2,3-diol and its easily available analog, 2,3-dihydroxybiphenyl, and were designated carBa and carBb, respectively. The alignment of CarBb with other meta-cleavage enzymes indicated that CarBb may have a non-heme iron cofactor coordinating site. On the basis of the phylogenetic tree, CarBb was classified as a member of the protocatechuate 4,5-dioxygenase family. This unique extradiol dioxygenase, CarB, had significantly higher affinity and about 20-times-higher meta-cleavage activity for 2,3-dihydroxybiphenyl than for catechol derivatives. The putative polypeptide encoded by ORF3 was homologous with meta-cleavage compound hydrolases in other bacteria, and ORF3 was designated carC. The hydrolase activity of CarC for 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid, the meta-cleavage compound of 2,3-dihydroxybiphenyl, was 40 times higher than that for 2-hydroxy-6-oxohepta-2,4-dienoic acid, the meta-cleavage compound of 3-methylcatechol. Alignment analysis and the phylogenetic tree indicate that CarC has greatest homologies with hydrolases involved in the monoaromatic compound degradation pathway. These results suggest the possibility that CarC is a novel type of hydrolase.
The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase of Candida albicans is a surface antigen
Authors: Gil-Navarro I , Gil M L , Casanova M , O'Connor J E , Martínez J P , Gozalbo D
Published: November 2016

A lambda gt11 cDNA library from Candida albicans ATCC 26555 was screened by using pooled sera from two patients with systemic candidiasis and five neutropenic patients with high levels of anti-C. albicans immunoglobulin M antibodies. Seven clones were isolated from 60,000 recombinant phages. The most reactive one contained a 0.9-kb cDNA encoding a polypeptide immunoreactive only with sera from patients with systemic candidiasis. The whole gene was isolated from a genomic library by using the cDNA as a probe. The nucleotide sequence of the coding region showed homology (78 to 79%) to the Saccharomyces cerevisiae TDH1 to TDH3 genes coding for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and their amino acid sequences showed 76% identity; thus, this gene has been named C. albicans TDH1. A rabbit polyclonal antiserum against the purified cytosolic C. albicans GAPDH (polyclonal antibody [PAb] anti-CA-GAPDH) was used to identify the GAPDH in the beta-mercaptoethanol extracts containing cell wall moieties. Indirect immunofluorescence demonstrated the presence of GAPDH at the C. albicans cell surface, particularly on the blastoconidia. Semiquantitative flow cytometry analysis showed the sensitivity of this GAPDH form to trypsin and its resistance to be removed with 2 M NaCl or 2% sodium dodecyl sulfate. The decrease in fluorescence in the presence of soluble GAPDH indicates the specificity of the labelling. In addition, a dose-dependent GAPDH enzymatic activity was detected in intact blastoconidia and germ tube cells. This activity was reduced by pretreatment of the cells with trypsin, formaldehyde, and PAb anti-CA-GAPDH. These observations indicate that an immunogenic, enzymatically active cell wall-associated form of the glycolytic enzyme GAPDH is found at the cell surface of C. albicans cells.
Characterization by electron paramagnetic resonance of the role of the Escherichia coli nitrate reductase (NarGHI) iron-sulfur clusters in electron transfer to nitrate and identification of a semiquinone radical intermediate
Authors: Magalon A , Rothery R A , Giordano G , Blasco F , Weiner J H
Published: November 2016

We have used Escherichia coli cytoplasmic membrane preparations enriched in wild-type and mutant (NarH-C16A and NarH-C263A) nitrate reductase (NarGHI) to study the role of the [Fe-S] clusters of this enzyme in electron transfer from quinol to nitrate. The spectrum of dithionite-reduced membrane bound NarGHI has major features comprising peaks at g = 2.04 and g = 1.98, a peak-trough at g = 1.95, and a trough at g = 1.87. The oxidized spectrum of NarGHI in membranes comprises an axial [3Fe-4S] cluster spectrum with a peak at g = 2.02 (g(z)) and a peak-trough at g = 1.99 (g(xy)). We have shown that in two site-directed mutants of NarGHI which lack the highest potential [4Fe-4S] cluster (B. Guigliarelli, A. Magalon, P. Asso, P. Bertrand, C. Frixon, G. Giordano, and F. Blasco, Biochemistry 35:4828-4836, 1996), NarH-C16A and NarH-C263A, oxidation of the NarH [Fe-S] clusters is inhibited compared to the wild type. During enzyme turnover in the mutant enzymes, a distinct 2-n-heptyl-4-hydroxyquinoline-N-oxide-sensitive semiquinone radical species which may be located between the hemes of NarI and the [Fe-S] clusters of NarH is observed. Overall, these studies indicate (i) the importance of the highest-potential [4Fe-4S] cluster in electron transfer from NarH to the molybdenum cofactor of NarG and (ii) that a semiquinone radical species is an important intermediate in electron transfer from quinol to nitrate.
Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli
Authors: Yamanaka K , Inouye M
Published: November 2016

The cspD gene of Escherichia coli encodes a protein of high sequence similarity with the cold shock protein CspA, but cspD expression is not induced by cold shock. In this study, we analyzed the regulation of cspD gene expression. By using a cspD-lacZ fusion and primer extension analysis, the expression of cspD was found to be dramatically induced by stationary-phase growth. However, this induction does not depend on the stationary-phase sigma factor sigmaS. Moreover, the expression of cspD is inversely dependent on growth rates and induced upon glucose starvation. Using a (p)ppGpp-depleted strain, we found that (p)ppGpp is one of the positive factors for the regulation of cspD expression.
Q fever hepatitis and endocarditis in the context of haemochromatosis
Authors: Elgouhari Hesham , Huntington Mark K
Published: November 2016

Hereditary haemochromatosis is associated with increased susceptibility to some infections. We report here a case of Q fever in a patient with coexistent haemochromatosis. The literature is reviewed in regard to the effect of haemochromatosis on susceptibility to infectious disease in general and Q fever in particular. Although there is documented increased risk in these patients for some infectious conditions, a specific association with Q fever has not been previously reported. The present report raises the possibility of such a clinically relevant connection.
Strategies and factors associated with preparing for competing in the heat: a cohort study at the 2015 IAAF World Athletics Championships
Authors: Périard Julien D , Racinais Sébastien , Timpka Toomas , Dahlström Örjan , Spreco Armin , Jacobsson Jenny , Bargoria Victor , Halje Karin , Alonso Juan-Manuel
Published: November 2016

Purpose

Assess exertional heat illness (EHI) history and preparedness in athletes competing in a World Athletics Championships under hot/humid conditions and identify the factors associated with preparedness strategies.

Methods

Of the 207 registered national teams invited to participate in the study, 50 (24%) accepted. The 957 athletes (49% of all 1965 registered) in these teams were invited to complete a precompetition questionnaire evaluating EHI history, heat stress prevention (heat acclimatisation, precooling and hydration) and recovery. Responses from 307 (32%) athletes were separated in field events, sprints, middle-distance and long-distance running, and decathlon/heptathlon for analysis.

Results

48% of athletes had previously experienced EHI symptoms and 8.5% had been diagnosed with EHI. 15% heat acclimatised (∼20 days) before the championships. 52% had a precooling strategy, ice slurry ingestion (24%) being the most prevalent and women using it more frequently than men (p=0.005). 96% of athletes had a fluid consumption strategy, which differed between event categories (p<0.001). The most common volumes planned on being consumed were 0.5–1 L (27.2%) and ≥2 L (21.8%), water being the most frequent. 89% of athletes planned on using at least one recovery strategy. Female sex (p=0.024) and a previous EHI diagnosis increased the likelihood of using all 3 prevention strategies (p<0.001).

Conclusions

At a World Championships with expected hot/humid conditions, less than one-fifth of athletes heat acclimatised, half had a precooling strategy and almost all a hydration plan. Women, and especially athletes with an EHI history, were more predisposed to use a complete heat stress prevention strategy. More information regarding heat acclimatisation should be provided to protect athlete health and optimise performance at major athletics competitions in the heat.
Persistent effects of playing football and associated (subconcussive) head trauma on brain structure and function: a systematic review of the literature
Authors: Tarnutzer A A , Straumann D , Brugger P , Feddermann-Demont N
Published: November 2016

Aim/objective

There is ongoing controversy about persistent neurological deficits in active and former football (soccer) players. We reviewed the literature for associations between football activities (including heading/head injuries) and decline in brain structure/function.

Design

Systematic literature review.

Data sources

MEDLINE, Embase, PsycINFO, CINAHL, Cochrane-CRCT, SportDiscus, Cochrane-DSR=4 (accessed 2 August 2016).

Eligibility criteria for selecting studies

Original studies reporting on football-related persistent effects on brain structure/function. Results from neurocognitive testing, neuroimaging and EEG were compared with controls and/or correlated with heading frequency and/or head injuries. Methodological quality was rated for risk-of-bias, including appropriateness of controls, correction for multiple statistical testing and assessment of heading frequency and head injuries.

Results

30 studies with 1691 players were included. Those 57% (8/14) of case–control studies reporting persistent neurocognitive impairment had higher odds for inappropriate control of type 1 errors (OR=17.35 (95% CI (10.61 to 28.36)) and for inappropriate selection of controls (OR=1.72 (1.22 to 2.43)) than studies observing no impairment. Studies reporting a correlation between heading frequency and neurocognitive deficits (6/17) had lower quality of heading assessment (OR=14.20 (9.01 to 22.39)) than studies reporting no such correlation. In 7 of 13 studies (54%), the number of head injuries correlated with the degree of neurocognitive impairment. Abnormalities on neuroimaging (6/8 studies) were associated with subclinical neurocognitive deficits in 3 of 4 studies.

Summary/conclusions

Various methodological shortcomings limit the evidence for persistent effects of football play on brain structure/function. Sources of bias include low-quality assessment of heading frequency, inappropriate control for type 1 errors and inappropriate selection of controls. Combining neuroimaging techniques with neurocognitive testing in prospective studies seems most promising to further clarify on the impact of football on the brain.
Clustering patterns of obesity-related multiple lifestyle behaviours and their associations with overweight and family environments: a cross-sectional study in Japanese preschool children
Authors: Watanabe Etsuko , Lee Jung Su , Mori Katsumi , Kawakubo Kiyoshi
Published: November 2016

Objectives

The purpose of this study is (1) to identify obesity-related lifestyle behaviour patterns of diet, physical activity, sedentary and sleep behaviours in preschool children, (2) to examine the association between identified behaviour clusters and overweight/obesity and (3) to investigate differences in children's family environments according to clusters.

Design setting and participants

A cross-sectional study on 2114 preschool children aged 3–6 years who attended childcare facilities (24 nursery schools and 10 kindergartens) in Tsuruoka city, Japan in April 2003 was conducted.

Main outcome measures

Children's principal caregivers completed a questionnaire on children's lifestyle behaviours (dinner timing, outside playtime, screen time and night-time sleep duration), family environment (family members, maternal employment, mealtime regularity and parents' habitual exercise and screen time) and measurements of weight and height. Cluster analysis was performed using children's 4 lifestyle behaviours based on those non-missing values (n=1545). The χ2tests and analysis of variance (ANOVA) estimated cluster differences in overweight/obesity and family environments.

Results

6 clusters were identified. Children's overweight/obesity varied across clusters (p=0.007). The cluster with the most screen time, shorter night-time sleep duration, average dinner timing and outside playtime had the highest overweight/obesity prevalence (15.1%), while the cluster with the least screen time, the longest sleep duration, the earliest dinner timing and average outside playtime had the lowest prevalence (4.0%). Family environments regarding mealtime regularity and both parents' screen time also significantly varied across clusters. The cluster having the highest overweight/obesity prevalence had the highest proportion of irregular mealtimes and the most screen time for both parents.

Conclusions

This study suggests that public health approaches to prevent children's overweight/obesity should focus on decreasing screen time and increasing night-time sleep duration. To shape those behaviours, regular mealtimes and decreasing parents' screen time within family environments need to be targeted among family members.
Novel coaching cricket bat: can it be used to enhance the backlift and performance of junior cricket batsmen?
Authors: Noorbhai M Habib , Woolmer Russell C , Noakes Timothy D
Published: November 2016

Background

In the current literature, it is questionable whether cricket bats in their current form and dimensions allow a young cricketer to hit the ball effectively. The aim of this study was to test the effectiveness of a novel coaching cricket bat among junior cricket batsmen with regard to enhancing performance and the direction of the backlift.

Methods

A cross-sectional research study with analytical research methods was employed, in which 2 groups (coached: n=12 and uncoached: n=35) of participants (ages 9–13) took part in a pilot and intervention study. Participants were required to use a novel coaching cricket bat in a coaching game format. Biomechanical and video analysis was conducted in the frontal and lateral planes. Effect sizes (ES) were calculated to determine the effectiveness and the level of significance was set at p<0.05.

Results

Pilot study results demonstrated that participants scored an additional 100 runs when using the coaching cricket bat compared with a conventional cricket bat (p=0.003). 6 weeks postintervention (training with the coaching cricket bat), the experimental group displayed improved performance (ES=5.41). Players' backlifts had subsequently become more lateral, which may have promoted more effective ball striking as a result of this training effect.

Conclusions

The recommendation from this study is that coaches should encourage young cricketers to use the coaching cricket bat as it is perceived to be a potentially significant training aid for enhancing their performance and the direction of their backlift when they use conventional cricket bats in match play.
Poison prevention practices and medically attended poisoning in young children: multicentre case–control study
Authors: Kendrick Denise , Majsak-Newman Gosia , Benford Penny , Coupland Carol , Timblin Clare , Hayes Mike , Goodenough Trudy , Hawkins Adrian , Reading Richard
Published: November 2016

Introduction

Childhood poisonings are common, placing a substantial burden on health services. Case–control studies have found inconsistent evidence about modifiable risk factors for poisonings among children aged 0–4 years. This study quantifies associations between poison prevention practices and medically attended poisonings in children aged 0–4 years.

Methods

Multicentre case–control study conducted at hospitals, minor injury units and family practices from four study centres in England between 2010 and 2013. Participants comprised 567 children presenting with unintentional poisoning occurring at home and 2320 community control participants matched on age, sex, date of event and study centre. Parents/caregivers provided data on safety practices, safety equipment use, home hazards and potential confounders by means of self-completion questionnaires. Data were analysed using conditional logistic regression.

Results

Compared with community controls, parents of poisoned children were significantly more likely not to store medicines out of reach (adjusted OR (AOR) 1.59; 95% CI 1.21 to 2.09; population attributable fraction (PAF) 15%), not to store medicines safely (locked or out of reach (AOR 1.83; 95% CI 1.38 to 2.42; PAF 16%) and not to have put all medicines (AOR 2.11; 95% CI 1.54 to 2.90; PAF 20%) or household products (AOR 1.79, 95% CI 1.29 to 2.48; PAF 11%) away immediately after use.

Conclusions

Not storing medicines out of reach or locked away and not putting medicines and household products away immediately after use increased the odds of secondary care attended poisonings in children aged 0–4 years. If associations are causal, implementing these poison prevention practices could each prevent between 11% and 20% of poisonings.
Effect of lingual gauze swab placement on pulse oximeter readings in anaesthetised dogs and cats
Authors: Mair A. , Martinez‐Taboada F. , Nitzan M.
Published: November 2016

This study aimed to evaluate the effect of lingual gauze swab placement on pulse oximeter readings in anaesthetised dogs and cats. Following anaesthetic induction, the following pulse oximeter probe configurations were performed: no gauze swab (control), placement of a gauze swab between the tongue and the probe, placement of different thicknesses of gauze swab, placement of red cotton fabric, placement of a sheet of white paper and placement of the probe and gauze swab on different locations on the tongue. Oxygen saturation (SpO2) and peripheral perfusion index (PI) were recorded. Placement of a gauze swab between the pulse oximeter probe and the tongue in anaesthetised dogs and cats resulted in significantly higher SpO2 values compared with the control group. In dogs, PI values were significantly higher than the control in all groups except the quarter thickness swab group. In cats, PI was significantly higher in the double thickness swab and white paper groups compared with the control. Cats had significantly higher SpO2 and lower PI values than dogs. The authors propose that increased contact pressure is responsible for significantly higher SpO2 and PI readings with the use of a lingual gauze swab resulting from changes in transmural pressure and arterial compliance.
Mitochondrial ROS, uncoupled from ATP synthesis, determine endothelial activation for both physiological recruitment of patrolling cells and pathological recruitment of inflammatory cells
Authors: Li Xinyuan , Fang Pu , Yang William Y. , Chan Kylie , Lavallee Muriel , Xu Keman , Gao Tracy , Wang Hong , Yang Xiaofeng
Published: November 2016

Mitochondrial reactive oxygen species (mtROS) are signaling molecules, which drive inflammatory cytokine production and T cell activation. In addition, cardiovascular diseases, cancers, and autoimmune diseases all share a common feature of increased mtROS level. Both mtROS and ATP are produced as a result of electron transport chain activity, but it remains enigmatic whether mtROS could be generated independently from ATP synthesis. A recent study shed light on this important question and found that, during endothelial cell (EC) activation, mtROS could be upregulated in a proton leak-coupled, but ATP synthesis-uncoupled manner. As a result, EC could upregulate mtROS production for physiological EC activation without compromising mitochondrial membrane potential and ATP generation, and consequently without causing mitochondrial damage and EC death. Thus, a novel pathophysiological role of proton leak in driving mtROS production was uncovered for low grade EC activation, patrolling immunosurveillance cell trans-endothelial migration and other signaling events without compromising cellular survival. This new working model explains how mtROS could be increasingly generated independently from ATP synthesis and endothelial damage or death. Mapping the connections among mitochondrial metabolism, physiological EC activation, patrolling cell migration, and pathological inflammation is significant towards the development of novel therapies for inflammatory diseases and cancers.
Novel 4,4′-{(diphenylmethylene) bis(4,1-phenylene)bis(oxy)}-bridged ball-type phthalocyanines: Electrochemical, electrocatalytic oxygen reducing and heavy metals ions sensing properties
Authors: Doğan Elvan , Özer Metin , Altındal Ahmet , Özkaya Ali Rıza , Salih Bekir , Bekaroğlu Özer
Published: November 2016

Novel 4,4′-{(diphenylmethylene)bis(4,1-phenylene)bis(oxy)} bridged ball-type metal-free, zinc(II), cobalt(II) and iron(II) ball-type metallophthalocyanines were achieved by the reaction of the bisphthalonitrile derivative in 2-dimetylaminoethanol. The isolation of the metal-free and metallophthalocyanines were carried out by both planar and column chromatography and also by hot soxhalet extraction. Their structures have been characterized by infrared, ultraviolet-visible,1H nuclear magnetic resonance and matrix assisted laser desorption/ionization mass spectroscopies. The redox characters of the ball-type metallophthalocyanines have been investigated by cyclic voltammetry, square wave voltammetry, controlled potential coulometry and spectroelectrochemistry in nonaqueous media. The investigation suggested that the ball-type complexes form ring-based and/or metal-based mixed-valence species as a result of the remarkable interaction between the two Pc rings and/or metal centers. Furthermore, these species were found to be stable as evidenced by the splitting of the relevant redox processes. The electrocatalytic oxygen reducing performances of the dinuclear ball-type complexes were also studied. The compound involving Fe(II) centers at the phthalocyanine cores displayed higher catalytic performance towards oxygen reduction than those of other ones. By using these compounds as sensing materials, a flow type quartz crystal microbalance sensor was developed for the detection of small concentrations of heavy metal ions. A cadmium ion sensitivity of 2.85 × 104Hz/mg.L[Formula: see text] was observed with ball-type iron(II) phthalocyanine coated quartz crystal microbalance sensor. Detection of other metal ions including Fe[Formula: see text], Zn[Formula: see text], Ag[Formula: see text] and Sn[Formula: see text] were also performed. The results indicated that 1– 4 functionalized quartz crystal microbalance sensors can be used for the detection of heavy metal ions in aqueous solution. Partition coefficients obtained from the linear response regimes of the calibration curves are in the 8.6 × 104–5.4 × 105range. Results show that the minor structural difference between metal free and metallophthalocyanine poses significant impact on metal ion partitioning.
And then there were none
Authors: Bacon David F. , Cheng Perry , Shukla Sunil
Published: November 2016

Programmers are turning to radical architectures such as reconfigurable hardware (FPGAs) to achieve performance. But such systems, programmed at a very low level in languages with impoverished abstractions, are orders of magnitude more complex to use than conventional CPUs. The continued exponential increase in transistors, combined with the desire to implement ever more sophisticated algorithms, makes it imperative that such systems be programmed at much higher levels of abstraction. One of the fundamental high-level language features is automatic memory management in the form of garbage collection.

We present the first implementation of a complete garbage collector in hardware (as opposed to previous "hardware-assist" techniques), using an FPGA and its on-chip memory. Using a completely concurrent snapshot algorithm, it provides single-cycle access to the heap, and never stalls the mutator for even a single cycle, achieving a deterministic mutator utilization (MMU) of 100%.

We have synthesized the collector to hardware and show that it never consumes more than 1% of the logic resources of a high-end FPGA. For comparison we also implemented explicit (malloc/free) memory management, and show that real-time collection is about 4% to 17% slower than malloc, with comparable energy consumption. Surprisingly, in hardware real-time collection is superior to stop-the-world collection on every performance axis, and even for stressful micro-benchmarks can achieve 100% MMU with heaps as small as 1.01 to 1.4 times the absolute minimum.
Automated error diagnosis using abductive inference
Authors: Dillig Isil , Dillig Thomas , Aiken Alex
Published: November 2016

When program verification tools fail to verify a program, either the program is buggy or the report is a false alarm. In this situation, the burden is on the user to manually classify the report, but this task is time-consuming, error-prone, and does not utilize facts already proven by the analysis. We present a new technique for assisting users in classifying error reports. Our technique computes small, relevant queries presented to a user that capture exactly the information the analysis is missing to either discharge or validate the error. Our insight is that identifying these missing facts is an instance of the
abductive inference problem
in logic, and we present a new algorithm for computing the smallest and most general abductions in this setting. We perform the first user study to rigorously evaluate the accuracy and effort involved in manual classification of error reports. Our study demonstrates that our new technique is very useful for improving both the speed and accuracy of error report classification. Specifically, our approach improves classification accuracy from 33% to 90% and reduces the time programmers take to classify error reports from approximately 5 minutes to under 1 minute.
Parallelizing top-down interprocedural analyses
Authors: Albarghouthi Aws , Kumar Rahul , Nori Aditya V. , Rajamani Sriram K.
Published: November 2016

Modularity is a central theme in any scalable program analysis. The core idea in a modular analysis is to build summaries at procedure boundaries, and use the summary of a procedure to analyze the effect of calling it at its calling context. There are two ways to perform a modular program analysis: (1) top-down and (2) bottomup. A bottom-up analysis proceeds upwards from the leaves of the call graph, and analyzes each procedure in the most general calling context and builds its summary. In contrast, a top-down analysis starts from the root of the call graph, and proceeds downward, analyzing each procedure in its calling context. Top-down analyses have several applications in verification and software model checking. However, traditionally, bottom-up analyses have been easier to scale and parallelize than top-down analyses.

In this paper, we propose a generic framework, BOLT, which uses MapReduce style parallelism to scale top-down analyses. In particular, we consider top-down analyses that are demand driven, such as the ones used for software model checking. In such analyses, each intraprocedural analysis happens in the context of a reachability query. A query
Q
over a procedure
P
results in query tree that consists of sub-queries over the procedures called by
P
. The key insight in BOLT is that the query tree can be explored in parallel using MapReduce style parallelism -- the map stage can be used to run a set of enabled queries in parallel, and the reduce stage can be used to manage inter-dependencies between queries. Iterating the map and reduce stages alternately, we can exploit the parallelism inherent in top-down analyses. Another unique feature of BOLT is that it is parameterized by the algorithm used for intraprocedural analysis. Several kinds of analyses, including may analyses, mustanalyses, and may-must-analyses can be parallelized using BOLT.

We have implemented the BOLT framework and instantiated the intraprocedural parameter with a may-must-analysis. We have run BOLT on a test suite consisting of 45 Microsoft Windows device drivers and 150 safety properties. Our results demonstrate an average speedup of 3.71x and a maximum speedup of 7.4x (with 8 cores) over a sequential analysis. Moreover, in several checks where a sequential analysis fails, BOLT is able to successfully complete its analysis.
Race detection for web applications
Authors: Petrov Boris , Vechev Martin , Sridharan Manu , Dolby Julian
Published: November 2016

Modern web pages are becoming increasingly full-featured, and this additional functionality often requires greater use of asynchrony. Unfortunately, this asynchrony can trigger unexpected concurrency errors, even though web page scripts are executed sequentially.

We present the first formulation of a
happens-before relation
for common web platform features. Developing this relation was a non-trivial task, due to complex feature interactions and browser differences. We also present a logical memory access model for web applications that abstracts away browser implementation details.

Based on the above, we implemented WebRacer, the first dynamic race detector for web applications. WebRacer is implemented atop the production-quality WebKit engine, enabling testing of full-featured web sites. WebRacer can also simulate certain user actions, exposing more races.

We evaluated WebRacer by testing a large set of Fortune 100 company web sites. We discovered many harmful races, and also gained insights into how developers handle asynchrony in practice.
Self-stabilizing Java
Authors: Eom Yong hun , Demsky Brian
Published: November 2016

Self-stabilizing programs automatically recover from state corruption caused by software bugs and other sources to reach the correct state. A number of applications are inherently self-stabilizing---such programs typically overwrite all non-constant data with new input data. We present a type system and static analyses that together check whether a program is self-stabilizing. We combine this with a code generation strategy that ensures that a program continues executing long enough to self-stabilize. Our experience using SJava indicates that (1) SJava annotations are easy to write once one understands a program and (2) SJava successfully checked that several benchmarks were self-stabilizing.
Test-case reduction for C compiler bugs
Authors: Regehr John , Chen Yang , Cuoq Pascal , Eide Eric , Ellison Chucky , Yang Xuejun
Published: November 2016

To report a compiler bug, one must often find a small test case that triggers the bug. The existing approach to automated test-case reduction, delta debugging, works by removing substrings of the original input; the result is a concatenation of substrings that delta cannot remove. We have found this approach less than ideal for reducing C programs because it typically yields test cases that are too large or even invalid (relying on undefined behavior). To obtain small and valid test cases consistently, we designed and implemented three new, domain-specific test-case reducers. The best of these is based on a novel framework in which a generic fixpoint computation invokes modular transformations that perform reduction operations. This reducer produces outputs that are, on average, more than 25 times smaller than those produced by our other reducers or by the existing reducer that is most commonly used by compiler developers. We conclude that effective program reduction requires more than straightforward delta debugging.