bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Insights into
l
-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme
Authors: Wakamatsu Taisuke , Sakuraba Haruhiko , Kitamura Megumi , Hakumai Yuichi , Fukui Kenji , Ohnishi Kouhei , Ashiuchi Makoto , Ohshima Toshihisa 
Published: November 2016

ABSTRACT

l
-Tryptophan dehydrogenase from
Nostoc punctiforme
NIES-2108 (NpTrpDH), despite exhibiting high amino acid sequence identity (>30%)/homology (>50%) with NAD(P)
+
-dependent
l
-Glu/
l
-Leu/
l
-Phe/
l
-Val dehydrogenases, exclusively catalyzes reversible oxidative deamination of
l
-Trp to 3-indolepyruvate in the presence of NAD
+
. Here, we determined the crystal structure of the apo form of NpTrpDH. The structure of the NpTrpDH monomer, which exhibited high similarity to that of
l
-Glu/
l
-Leu/
l
-Phe dehydrogenases, consisted of a substrate-binding domain (domain I, residues 3 to 133 and 328 to 343) and an NAD
+
/NADH-binding domain (domain II, residues 142 to 327) separated by a deep cleft. The apo-NpTrpDH existed in an open conformation, where domains I and II were apart from each other. The subunits dimerized themselves mainly through interactions between amino acid residues around the β-1 strand of each subunit, as was observed in the case of
l
-Phe dehydrogenase. The binding site for the substrate
l
-Trp was predicted by a molecular docking simulation and validated by site-directed mutagenesis. Several hydrophobic residues, which were located in the active site of NpTrpDH and possibly interacted with the side chain of the substrate
l
-Trp, were arranged similarly to that found in
l
-Leu/
l
-Phe dehydrogenases but fairly different from that of an
l
-Glu dehydrogenase. Our crystal structure revealed that Met-40, Ala-69, Ile-74, Ile-110, Leu-288, Ile-289, and Tyr-292 formed a hydrophobic cluster around the active site. The results of the site-directed mutagenesis experiments suggested that the hydrophobic cluster plays critical roles in protein folding,
l
-Trp recognition, and catalysis. Our results provide critical information for further characterization and engineering of this enzyme.

IMPORTANCE
In this study, we determined the three-dimensional structure of
l
-Trp dehydrogenase, analyzed its various site-directed substitution mutants at residues located in the active site, and obtained the following informative results. Several residues in the active site form a hydrophobic cluster, which may be a part of the hydrophobic core essential for protein folding. To our knowledge, there is no previous report demonstrating that a hydrophobic cluster in the active site of any
l
-amino acid dehydrogenase may have a critical impact on protein folding. Furthermore, our results suggest that this hydrophobic cluster could strictly accommodate
l
-Trp. These studies show the structural characteristics of
l
-Trp dehydrogenase and hence would facilitate novel applications of
l
-Trp dehydrogenase.
White Syndrome-Affected Corals Have a Distinct Microbiome at Disease Lesion Fronts
Authors: Pollock F. Joseph , Wada Naohisa , Torda Gergely , Willis Bette L. , Bourne David G. 
Published: November 2016

ABSTRACT

Coral tissue loss diseases, collectively known as white syndromes (WSs), induce significant mortality on reefs throughout the Indo-Pacific, yet definitive confirmation of WS etiologies remains elusive. In this study, we integrated ecological disease monitoring, bacterial community profiling,
in situ
visualization of microbe-host interactions, and cellular responses of the host coral through an 18-month repeated-sampling regime. We assert that the observed pathogenesis of WS lesions on acroporid corals at Lizard Island (Great Barrier Reef) is not the result of apoptosis or infection by
Vibrio
bacteria, ciliates, fungi, cyanobacteria, or helminths. Histological analyses detected helminths, ciliates, fungi, and cyanobacteria in fewer than 25% of WS samples, and helminths and fungi were also observed in 12% of visually healthy samples. The abundances of
Vibrio
-affiliated sequences (assessed using 16S rRNA amplicon sequencing) did not differ significantly between health states and never exceeded 3.3% of reads in any individual sample.
In situ
visualization detected
Vibrio
bacteria only in summer WS lesion samples and revealed no signs of these bacteria in winter disease samples (or any healthy tissue samples), despite continued disease progression year round. However, a 4-fold increase in
Rhodobacteraceae
-affiliated bacterial sequences at WS lesion fronts suggests that this group of bacteria could play a role in WS pathogenesis and/or serve as a diagnostic criterion for disease differentiation. While the causative agent(s) underlying WSs remains elusive, the microbial and cellular processes identified in this study will help to identify and differentiate visually similar but potentially distinct WS etiologies.

IMPORTANCE
Over the past decade, a virulent group of coral diseases known as white syndromes have impacted coral reefs throughout the Indian and Pacific Oceans. This article provides a detailed case study of white syndromes to combine disease ecology, high-throughput microbial community profiling, and cellular-scale host-microbe visualization over seasonal time scales. We provide novel insights into the etiology of this devastating disease and reveal new diagnostic criteria that could be used to differentiate visually similar but etiologically distinct forms of white syndrome.
Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats
Authors: Hokynar K. , Vesterinen E. J. , Lilley T. M. , Pulliainen A. T. , Korhonen S. J. , Paavonen J. , Puolakkainen M. 
Published: November 2016

ABSTRACT

Chlamydia
-like organisms (CLOs) are recently identified members of the
Chlamydiales
order. CLOs share intracellular lifestyles and biphasic developmental cycles, and they have been detected in environmental samples as well as in various hosts such as amoebae and arthropods. In this study, we screened bat feces for the presence of CLOs by molecular analysis. Using pan-
Chlamydiales
PCR targeting the 16S rRNA gene,
Chlamydiales
DNA was detected in 54% of the specimens. PCR amplification, sequencing, and phylogenetic analysis of the 16S rRNA and 23S rRNA genes were used to classify positive specimens and infer their phylogenetic relationships. Most sequences matched best with
Rhabdochlamydia
species or uncultured
Chlamydia
sequences identified in ticks. Another set of sequences matched best with sequences of the
Chlamydia
genus or uncultured
Chlamydiales
from snakes. To gain evidence of whether CLOs in bat feces are merely diet borne, we analyzed insects trapped from the same location where the bats foraged. Interestingly, the CLO sequences resembling
Rhabdochlamydia
spp. were detected in insect material as well, but the other set of CLO sequences was not, suggesting that this set might not originate from prey. Thus, bats represent another potential host for
Chlamydiales
and could harbor novel, previously unidentified members of this order.

IMPORTANCE
Several pathogenic viruses are known to colonize bats, and recent analyses indicate that bats are also reservoir hosts for bacterial genera.
Chlamydia
-like organisms (CLOs) have been detected in several animal species. CLOs have high 16S rRNA sequence similarity to
Chlamydiaceae
and exhibit similar intracellular lifestyles and biphasic developmental cycles. Our study describes the frequent occurrence of CLO DNA in bat feces, suggesting an expanding host species spectrum for the
Chlamydiales
. As bats can acquire various infectious agents through their diet, prey insects were also studied. We identified CLO sequences in bats that matched best with sequences in prey insects but also CLO sequences not detected in prey insects. This suggests that a portion of CLO DNA present in bat feces is not prey borne. Furthermore, some sequences from bat droppings not originating from their diet might well represent novel, previously unidentified members of the
Chlamydiales
order.
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

PurposeAssess 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.MethodsOf 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.Results48% 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).ConclusionsAt 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/objectiveThere 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.DesignSystematic literature review.Data sourcesMEDLINE, Embase, PsycINFO, CINAHL, Cochrane-CRCT, SportDiscus, Cochrane-DSR=4 (accessed 2 August 2016).Eligibility criteria for selecting studiesOriginal 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.Results30 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/conclusionsVarious 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

ObjectivesThe 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 participantsA 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 measuresChildren'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.Results6 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.ConclusionsThis 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

BackgroundIn 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.MethodsA 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.ResultsPilot 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.ConclusionsThe 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

IntroductionChildhood 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.MethodsMulticentre 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.ResultsCompared 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.ConclusionsNot 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.
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.
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.
The Lambda Lambda-Bar calculus
Authors: Goyet Alexis 
Published: November 2016

We present a calculus which combines a simple, CCS-like representation of finite behaviors, with two dual binders λ and λ¯. Infinite behaviors are obtained through a syntactical fixed-point operator, which is used to give a translation of λ-terms. The duality of the calculus makes the roles of a function and its environment symmetrical. As usual, the environment is allowed to call a function at any given point, each time with a different argument. Dually, the function is allowed to answer any given call, each time with a different behavior. This grants terms in our language the power of functional references.
The inspiration for this language comes from game semantics. Indeed, its normal forms give a simple concrete syntax for finite strategies, which are inherently non-innocent. This very direct correspondence allows us to describe, in syntactical terms, a number of features from game semantics. The fixed-point expansion of translated λ-terms corresponds to the generation of infinite plays from the finite views of an innocent strategy. The syntactical duality between terms and co-terms corresponds to the duality between Player and Opponent. This duality also gives rise to a Böhm-out lemma.
The paper is divided into two parts. The first one is purely syntactical, and requires no background in game semantics. The second describes the fully abstract game model.