bluuebunny/crossref_metadata_2025 huggingface dataset:
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
Authors: Tamborero David , Rubio-Perez Carlota , Deu-Pons Jordi , Schroeder Michael P , Vivancos Ana , Rovira Ana , Tusquets Ignasi , Albanell Joan , Rodon Jordi , Tabernero Josep , Torres Carmen de , Dienstmann Rodrigo , Gonzalez-Perez Abel , Lopez-Bigas Nuria
Published: May 2017

While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Most of the alterations observed in tumors, including those in well-known cancer genes, are of uncertain significance. Moreover, the information on tumor genomic alterations shaping the response to existing therapies is fragmented across the literature and several specialized resources. Here we present the Cancer Genome Interpreter (http://www.cancergenomeinterpreter.org), an open access tool that we have implemented to annotate genomic alterations and interpret their possible role in tumorigenesis and in the response to anti-cancer therapies.
Experimental and statistical re-evaluation provides no evidence forDrosophilacourtship song rhythms
Authors: Stern David L. , Clemens Jan , Coen Philip , Calhoun Adam J. , Hogenesch John B. , Arthur Ben , Murthy Mala
Published: May 2017

From 1980 to 1992, a series of influential papers reported on the discovery, genetics, and evolution of a periodic cycling of the interval betweenDrosophilamale courtship song pulses. The molecular mechanisms underlying this periodicity were never described. To reinitiate investigation of this phenomenon, we performed automated segmentation of songs, but failed to detect the proposed periodicity [Arthur BJ et al. (2013)BMC Biol11:11; Stern DL (2014)BMC Biol12:38]. Kyriacou CP et al. [(2017)PNAS114:1970-1975] report that we failed to detect song rhythms because i) our flies did not sing enough and ii) our segmenter did not identify many of the song pulses. Kyriacou et al. manually annotated a subset of our recordings and reported that two strains displayed rhythms with genotype-specific periodicity, in agreement with their original reports. We cannot replicate this finding and show that the manually-annotated data, the original automatically segmented data, and a new data set provide no evidence for either the existence of song rhythms or song periodicity differences between genotypes. Furthermore, we have re-examined our methods and analysis and find that our automated segmentation method was not biased to prevent detection of putative song periodicity. We conclude that there is currently no evidence for the existence ofDrosophilacourtship song rhythms.

Significance statement

Previous studies have reported that male vinegar flies sing courtship songs with a periodic rhythm of approximately 55 seconds. Several years ago, we showed that we could not replicate this observation. Recently, the original authors have claimed that we failed to find rhythms because 1) our flies did not sing enough and 2) our software for detecting song did not detect all song events. They claimed that they could detect rhythms in song annotated by hand. We report here that we cannot replicate their observation of rhythms in the hand-annotated data or in any dataset and that our original methods were not biased against detecting rhythms. We conclude that song rhythms cannot be detected.
Framework for quality assessment of whole genome, cancer sequences
Authors: Whalley Justin P. , Buchhalter Ivo , Rheinbay Esther , Raine Keiran M. , Kleinheinz Kortine , Stobbe Miranda D. , Werner Johannes , Beltran Sergi , Gut Marta , Huebschmann Daniel , Hutter Barbara , Livitz Dimitri , Perry Marc , Rosenberg Mara , Saksena Gordon , Trotta Jean-Rémi , Eils Roland , Korbel Jan , Gerhard Daniela S. , Campbell Peter , Getz Gad , Schlesner Matthias , Gut Ivo G.
Published: May 2017

Working with cancer whole genomes sequenced over a period of many years in different sequencing centres requires a validated framework to compare the quality of these sequences. The Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC), a project a cohort of over 2800 donors provided us with the challenge of assessing the quality of the genome sequences. A non-redundant set of five quality control (QC) measurements were assembled and used to establish a star rating system. These QC measures reflect known differences in sequencing protocol and provide a guide to downstream analyses of these whole genome sequences. The resulting QC measures also allowed for exclusion samples of poor quality, providing researchers within PCAWG, and when the data is released for other researchers, a good idea of the sequencing quality. For a researcher wishing to apply the QC measures for their data we provide a Docker Container of the software used to calculate them. We believe that this is an effective framework of quality measures for whole genome, cancer sequences, which will be a useful addition to analytical pipelines, as it has to the PCAWG project.
Inferring Functional Neural Connectivity with Deep Residual Convolutional Networks
Authors: Dunn Timothy W. , Koo Peter K.
Published: May 2017

Measuring synaptic connectivity in large neuronal populations remains a major goal of modern neuroscience. While this connectivity is traditionally revealed by anatomical methods such as electron microscopy, an efficient alternative is to computationally infer functional connectivity from recordings of neural activity. However, these statistical techniques still require further refinement before they can be reliably applied to real data. Here, we report significant improvements to a deep learning method for functional connectomics, as assayed on synthetic ChaLearn Connectomics data. The method, which integrates recent advances in convolutional neural network architecture and model-free partial correlation coefficients, outperforms published methods on competition data and can achieve over 90% precision at 1% recall on validation datasets. This suggests that future application of the model toin vivowhole-brain imaging data in larval zebrafish could reliably recover on the order of 106synaptic connections with a 10% false discovery rate. The model also generalizes to networks with different underlying connection probabilities and should scale well when parallelized across multiple GPUs. The method offers real potential as a statistical complement to existing experiments and circuit hypotheses in neuroscience.
Attitudinal factors, financial literacy, and stock market participation
Authors: Sivaramakrishnan Sreeram , Srivastava Mala , Rastogi Anupam
Published: May 2017

Purpose

The purpose of this paper is to study the influence of factors such as financial literacy on a consumer’s investment decisions, particularly in the stock market. Based on two empirical studies, the theory of planned behaviour (TPB) was used to understand stock market participation (SMP) in India while developing a model to represent the relationships between the various factors. Consumer financial literacy was conceptualised to be a part of perceived behavioural control and included in the TPB.

Design/methodology/approach

A mixed methods research was followed where qualitative research preceded a quantitative survey-based study. In-depth interviews were conducted with investors and experts, results of which, when combined with the literature review, revealed seven variables including financial literacy which were pooled into three distinct groups based on the TPB. Responses obtained from 506 retail investors from four cities in India were analysed. Structural equation modelling was used to test the models and arrive at a final empirical model.

Findings

Results of the study indicated that investment intention predicts actual investments in the stock market (which represented behaviour). Financial literacy – both subjective and objective – were also found to be significant influencers on intention while only objective financial literacy seemed to affect behaviour. Three variables – perception of regulator, risk avoidance, and hassle factor – were combined to form a second-order construct which was named “Attitude to Investment Behaviour”. This had a negative impact on intention to invest in the equity markets. Financial well-being seemed to have a negative impact on intention while having a positive relationship with behaviour.

Practical implications

The results present significant investor behaviour and policy implications for financial services marketing. Some interventions, especially in the area of consumer financial literacy, are more likely than others to help consumers bridge the gap between non-participation and participation in the stock market.

Originality/value

The study makes a contribution to investor behaviour theory in the form of a comprehensive model to explain SMP in an emerging market. This can be further tested across geographies.
Impact of board structure on firm performance: evidence from an emerging economy
Authors: Yasser Qaiser Rafique , Mamun Abdullah Al , Rodrigs Marcus
Published: May 2017

Purpose

The aim of this paper is to examine the association between board demographics and firm financial performance of Karachi Stock Exchange companies and describe the attributes of these firms and their boards. The connection between board structure and firm performance has attracted much attention, especially in emerging economies, yet yielded many inconsistent empirical results.

Design/methodology/approach

This study examines the relationship between board structure and the performance of Pakistani public listed companies by using a sample of Karachi Stock Exchange 100 (KSE-100) indexed companies. This study exploits the corporate performance by accounting-based measures (return on assets), market-based measures (Tobin’s Q), and economic profit (economic value added).

Findings

The outcome of the study shows the positive relationship between the board size, minority representation in board, and family director’s in-board and firm performance. The authors also find that, instead of adding value, independent directors in Pakistan are negatively associated with firm value.

Research limitations/implications

The study is based on KSE-100 indexed companies from 2009 to 2013; however, a large sample and multiple years’ data are required.

Practical implications

The paper provides empirical evidence that board independence is not necessary for public-listed companies in Pakistan and would be of interest to regulatory bodies, business practitioners, and academic researchers.

Originality/value

The paper contributes to the literature on corporate governance and firm performance by introducing a framework for identifying and analyzing moderating variables that affect the relationship between board structure and firm performance.
Modeling the Scaling Up of Early Crime Prevention
Authors: Sullivan Christopher J. , Welsh Brandon C. , Ilchi Omeed S.
Published: May 2017

Research Summary

Although the amount of research evidence on the effectiveness of developmental crime prevention has grown considerably in recent decades, the translation of this scientific knowledge into policy and practice has lagged behind. In this article, we consider the challenges as well as the opportunities associated with scaling up evidence‐based programs and we offer an approach for considering the potential effects of deviations in implementation protocols during replications. We use results from the series of studies on the Nurse‐Family Partnership (NFP) to develop a computer simulation model. Based on a large number of simulations, we systematically adjusted key inputs (e.g., target population and fidelity) to mimic a range of possible implementation conditions and to observe the impacts on the estimated intervention effects. As the process progresses from the baseline condition, which reflects the initial implementation conditions specified in the NFP model, to alternative experimental scenarios reflecting problematic deviations in implementation, the number of arrests accumulated by treatment participants begins to increase. This indicates that these implementation challenges have a negative impact on program effects and that we can go some way toward predicting what might occur in implementation as they emerge and interact.

Policy Implications

The challenges facing program dissemination and their impact on program results have not been enumerated all that precisely in the literature, which has resulted in the assignment of arbitrary penalties when evaluating the prospects for taking programs to scale. Establishing efficacious interventions is only one part of the process of moving research to practice, and further consideration of the scaling‐up process is integral to translational criminology. Informed computer simulation may be one tool to help guide this program implementation process.
Low‐intensity endurance exercise plus nandrolone decanoate modulates cardiac adiponectin and its receptors
Authors: Karimi A. , Joukar S. , Najafipour H. , Masoumi‐Ardakani Y. , Shahouzehi B.
Published: May 2017

Vast adverse effects of anabolic‐androgenic steroids (AASs) on athletes’ cardiovascular systems have been reported. However, there is still a lack of adequate information regarding the pathways and mechanisms involved.

We tested the hypothesis that adiponectin and its receptors in the heart may be affected by long‐term use of AASs alongside exercising.

Male Wistar rats were randomized into the control (CTL), exercise (EX), nandrolone (Nan), arachis (Arach) group which treated with arachis as vehicle, trained vehicle (EX+Arach) and trained nandrolone (EX+Nan) groups that were treated for 8 weeks. One day after the end of the protocol, animals were sacrificed and their hearts were frozen. TNF‐α and adiponectin proteins of hearts were evaluated quantitatively by ELISA kits, and Western blot analysis was used for measuring adiponectin receptor protein expression.

TNF‐α protein increased significantly in the EX+Nan group (P<.05 vs CTL group). The AdipoR1 protein was significantly higher in the presence of nandrolone alongside exercise (P<.05 vs Nan and EX+Arach groups, P<.01 vs CTL and Arach groups). In addition, AdipoR2 protein enhanced in the EX+Nan group when compared with the other groups (P<.05 vs EX and EX+Arach groups, P<.01 vs CTL, Arach and Nan groups).

Chronic nandrolone plus mild endurance exercise may be associated with imbalance in pro‐/anti‐inflammatory cytokines and may induce a positive modulatory effect on cardiac adiporeceptors in rat. Further studies are required before these findings can be generalized to humans.
Evidence of Altered Mitochondrial Protein Expression After Chronic Ethanol Consumption in the Aged Estrogen‐Deficient Female Rat Heart
Authors: Garvin Alexandra M. , Miller‐Lee Jennifer L. , Sharda Daniel R. , Kanski Gregory M. , Hunter J. Craig , Korzick Donna H.
Published: May 2017

Background

Estrogen loss has been implicated to increase the risk of alcoholic cardiomyopathy in postmenopausal women. The purpose of this study was to identify novel mitochondrial protein targets for the treatment of alcoholic cardiomyopathy in aged women using a state‐of‐the‐art proteomic approach. We hypothesized that chronic ethanol (EtOH) ingestion exacerbates maladaptive mitochondrial protein expression in the aged female heart.

Methods

Adult (3 months) and aged (18 months) F344 ovary‐intact or ovariectomized (OVX) rats were randomly assigned an EtOH or control Lieber–DeCarli “all‐liquid” diet for 20 weeks. Proteomic analyses were conducted in mitochondria isolated from left ventricles using isobaric tags for relative and absolute quantification (iTRAQ) 8plex labeling and mass spectrometry (n = 3 to 5/group).

Results

After EtOH, significant differences (false discovery rate <5%) were observed in electron transport chain components (NADH dehydrogenase [ubiquinone] flavoprotein 2) as well as proteins involved in lipid metabolism (2,4 dienoyl‐CoA reductase) and cellular defense (catalase), suggesting a possible link to congestive heart failure. Directional changes in protein levels were confirmed by Western blotting. Additionally, EtOH significantly reduced state 3 mitochondrial respiration in all groups, yet only reduced respiratory control index in the aged OVX rat heart (p < 0.05).

Conclusions

Collectively, the data reveal that EtOH‐induced changes in the mitochondrial proteome exacerbate cardiac dysfunction in aged and estrogen‐deficient hearts, but not in adult. In conclusion, iTRAQ is a powerful tool for investigating new mitochondrial targets of alcoholic cardiomyopathy.
A cluster‐randomized controlled trial evaluating the effects of delaying onset of adolescent substance abuse on cognitive development and addiction following a selective, personality‐targeted intervention programme: the Co‐Venture trial
Authors: O'Leary‐Barrett Maeve , Mâsse Benoit , Pihl Robert O. , Stewart Sherry H. , Séguin Jean R. , Conrod Patricia J.
Published: May 2017

Aims

Substance use and binge drinking during early adolescence are associated with neurocognitive abnormalities, mental health problems and an increased risk for future addiction. The trial aims to evaluate the protective effects of an evidence‐based substance use prevention programme on the onset of alcohol and drug use in adolescence, as well as on cognitive, mental health and addiction outcomes over 5 years.

Design

Thirty‐eight high schools will be recruited, with a final sample of 31 schools assigned to intervention or control conditions (3826 youth). Brief personality‐targeted interventions will be delivered to high‐risk youth attending intervention schools during the first year of the trial. Control school participants will receive no intervention above what is offered to them in the regular curriculum by their respective schools.

Setting

Public/private French and English high schools in Montreal (Canada).

Participants

All grade 7 students (12–13 years old) will be invited to participate. High‐risk youth will be identified as those scoring one standard deviation or more above the school mean on one of the four personality subscales of the Substance Use Risk Profile Scale (40–45% youth).

Measurements

Self‐reported substance use and mental health symptoms and cognitive functioning measured annually throughout 5 years. Primary outcomes are the onset of substance use disorders at 4 years post‐intervention (year 5). Secondary intermediate outcomes are the onset of alcohol and substance use 2 years post‐intervention and neuropsychological functions; namely, the protective effects of substance use prevention on cognitive functions generally, and executive functions and reward sensitivity specifically.

Conclusion

This longitudinal, cluster‐randomized controlled trial will investigate the impact of a brief personality‐targeted intervention program on reducing the onset of addiction 4 years‐post intervention. Results will tease apart the developmental sequences of uptake and growth in substance use and cognitive development in adolescence using developmentally sensitive neuropsychological measures.
Utilisation possibility of Enterococcus faecalis isolates from neonate's faeces for production of fermented sausages as starter cultures
Authors: Ba Hoa Van , Seo Hyun‐Woo , Cho Soo‐Hyun , Kim Yoon‐Seok , Kim Jin‐Hyoung , Park Beom‐Young , Kim Hyun‐Wook , Ham Jun‐Sang , Seong Pil‐Nam
Published: May 2017

This study aimed at assessing the utilisation possibility of Enterococcus faecalis as starter cultures for production of fermented sausages. The E. faecalis isolates isolated from faeces samples of 5‐day‐old healthy newborn babies, identified by 16SrDNA sequencing and free from virulence determinants as proven by genomic sequencing, were used for fermented sausages production as starter culture. Six treatments (four inoculated with four different E. faecalis isolates, one with commercial starter culture and one control) were prepared. The inoculation with E. faecalis showed a stronger acidification compared with the control. The treatments with E. faecalis showed significantly higher flavour and acceptability scores in comparison with the control or commercial starter culture. Both of commercial starter culture and E. faecalis were positive with tyramine. Apart from the amine production, the inoculation with E. faecalis generally improved the acidifying activity and flavour of the products, suggesting their application potentials in fermented sausages production as starter cultures.
Optimisation of culture conditions and development of a novel fed‐batch strategy for high production of β‐galactosidase by Kluyveromyces lactis
Authors: You Sheng‐ping , Wang Xiao‐nan , Qi Wei , Su Rong‐xin , He Zhi‐min
Published: May 2017

The aim of this study was to enhance β‐galactosidase production by Kluyveromyces lactis CICC1773. Firstly, the optimum culture conditions were obtained by response surface methodology, and the maximum β‐galactosidase activity reached 20.6 U mL−1, about two‐fold increase than that of the initial conditions (initial fermentation medium and conditions). To further improve β‐galactosidase production, a new fed‐batch strategy based on pH feedback control was developed successfully in a 7‐L fermenter, using 400 g L−1 lactose as feeding medium. As a result, the β‐galactosidase activity and productivity reached up to 111.61 U mL−1 and 5.31 U/(mL·h), enhanced by 15.3‐fold and 17.6‐fold superior than the results of initial conditions, respectively. To our knowledge, β‐galactosidase activity obtained was the highest value among the results reported by nonrecombinant strains. These results demonstrated that the new fed‐batch strategy based on optimum culture conditions could be automatic control easily and be conductive to further scale up for industrial fermentation.
Back into the wild: establishing a migratory Northern bald ibis Geronticus eremita population in Europe
Authors: Fritz J. , Kramer R. , Hoffmann W. , Trobe D. , Unsöld M.
Published: May 2017

From the perspective of zoological institutions reintroduction projects offer many possibilities to link conservation and research programmes. An example of the multi‐layered and diverse contributions that zoological institutions in general and, specifically, Vienna Zoo, Austria, can make is the reintroduction of the Northern bald ibis Geronticus eremita in central Europe. The involvement of zoological institutions ranges from the provision of eggs or birds for release trials, to financial and advocacy support, including with government agencies and non‐governmental organizations. Through involvement at a steering level at the coordinative association ‘Förderverein Waldrappteam’ and as a partner in the EU LIFE+ reintroduction project, Vienna Zoo directly contributes to the shape of the reintroduction project for this Critically Endangered species, and provides much more than technical and infrastructural support. The reintroduction of the Northern bald ibis is broadly in line with the reintroduction guidelines of the International Union for Conservation of Nature. This project provides added benefits not only through its work to prevent the illegal hunting of migratory birds but also the production and dissemination of scientific research.
Comparison of nine different methods to assess fish communities in lentic flood‐plain habitats
Authors: Mueller M. , Pander J. , Knott J. , Geist J.
Published: May 2017

This study compares the effectiveness and representativeness of electrofishing, snorkelling, seining, baited lift netting, multi‐mesh gillnetting, baited fish traps, fyke netting, angling and longline fishing, considering three typical lentic flood‐plain habitats at different times of day. Electrofishing was by far the most effective method yielding highest species richness, species trait representation and catch per unit of effort (CPUE), followed by seining. For single species like dace Leuciscus leuciscus, European ruffe Gymnocephalus cernua, common bream Abramis brama and silver bream Blicca bjoerkna, seining was more effective than electrofishing. With both methods, some species were more consistently caught during night, dusk or dawn than during daylight. All other methods tested cannot be generally recommended for fish community assessments in shallow backwaters due to their low representativeness of species inventory and generally low CPUE. Based on these results, electrofishing of 30 m transect replicates at different times of day for monitoring the fish community in shallow backwaters, can be recommended, enabling the maximum possible comparability to adjacent river habitats. Seining should be considered as an alternative if accessibility of habitats is restricted or electrofishing is prohibited. The 25 species detected in the backwaters also suggest that these habitats contribute a large proportion of fish diversity and should be included in standard assessments of river ecological status.
New predictive model for acute gastrointestinal bleeding in patients taking oral anticoagulants: A cohort study
Authors: Shimomura Akira , Nagata Naoyoshi , Shimbo Takuro , Sakurai Toshiyuki , Moriyasu Shiori , Okubo Hidetaka , Watanabe Kazuhiro , Yokoi Chizu , Akiyama Junichi , Uemura Naomi
Published: May 2017

Background and Aim

The study developed a predictive model of long‐term gastrointestinal (GI) bleeding risk in patients receiving oral anticoagulants and compared it with the HAS‐BLED (Hypertension, Abnormal renal/liver function, Stroke, Bleeding history or predisposition, Labile international normalized ratios, Elderly, Drugs/alcohol concomitantly) score.

Methods

The study periodically followed a cohort of 508 patients taking oral anticoagulants (66 direct oral anticoagulants users and 442 warfarin users). Absence of GI bleeding at an initial examination and any subsequent GI bleeding were confirmed endoscopically. The bleeding model was developed by multivariate survival analysis and evaluated by Harrell's c‐index.

Results

During a median follow‐up of 31.4 months, 42 GI bleeds (8.3%) occurred: 42.8% in the upper GI tract, 50.0% in the lower GI tract, and 7.1% in the middle GI tract. The cumulative 5 and 10‐year probability of GI bleeding was 12.6% and 18.5%, respectively. Patients who bled had a significantly higher cumulative incidence of all‐cause mortality (hazard ratio 2.9, P < 0.001). Multivariate analysis revealed that absence of proton pump inhibitor therapy, chronic kidney disease, chronic obstructive pulmonary disease, history of peptic ulcer disease, and liver cirrhosis predicted GI bleeding. The c‐statistic for the new predictive model using these five factors was 0.65 (P < 0.001), higher than the HAS‐BLED score of 0.57 (P = 0.145).

Conclusions

Gastrointestinal bleeding increased the risk of subsequent mortality during follow‐up of anticoagulated patients, highlighting the importance of prevention. The study developed a new scoring model for acute GI bleeding risk based on five factors (no‐proton pump inhibitor use, chronic kidney disease, chronic obstructive pulmonary disease, history of peptic ulcer disease, and liver cirrhosis), which was superior to the HAS‐BLED score.
Trilobite ‘pelotons’: possible hydrodynamic drag effects between leading and following trilobites in trilobite queues
Authors: Trenchard Hugh , Brett Carlton E. , Perc Matjaž
Published: May 2017

Energy saving mechanisms in nature allow following organisms to expend less energy than leaders. Queues, or ordered rows of individuals, may form when organisms exploit the available energy saving mechanism while travelling at near‐maximal sustainable metabolic capacities; compact clusters form when group members travel well below maximal sustainable metabolic capacities. The group size range, given here as the ratio of the difference between the size of the largest and smallest group members, and the size of the largest member (as a percentage), has been hypothesized to correspond proportionately to the energy saving quantity because weaker, smaller, individuals sustain the speeds of stronger, larger, individuals by exploiting the energy saving mechanism (as a percentage). During migration, small individuals outside this range may perish, or form sub‐groups, or simply not participate in migratory behaviour. We approximate drag forces for leading and following individuals in queues of the late Devonian (c. 370 Ma) trilobite Trimerocephalus chopini. Applying data from literature on Rectisura herculea, a living crustacean, we approximate the hypothetical walking speed and maximal sustainable speeds for T. chopini. Our findings reasonably support the hypothesis that among the population of fossilized queues of T. chopini reported in the literature, trilobite size range was 75%, while the size range within queues was 63%; this corresponds reasonably with drag reductions in following positions that permit c. 61.5% energy saving for trilobites following others in optimal low‐drag positions. We model collective trilobite behaviour associated with hydrodynamic drafting.
The effect of repeated periods of speed endurance training on performance, running economy, and muscle adaptations
Authors: Skovgaard C. , Almquist N. W. , Bangsbo J.
Published: May 2017

The effect of repeated intense training interventions was investigated in eight trained male runners (maximum oxygen uptake [VO2‐max]: 59.3±3.2 mL/kg/min, mean±SD) who performed 10 speed endurance training (SET; repeated 30‐seconds “all‐out” bouts) and 10 aerobic moderate‐intensity training sessions during two 40‐day periods (P1 and P2) separated by ~80 days of habitual training. Before and after both P1 and P2, subjects completed an incremental test to exhaustion to determine VO2‐max and a repeated running test at 90% vVO2‐max to exhaustion (RRT) to determine short‐term endurance capacity. In addition, running economy (RE) was measured at 60% vVO2‐max (11.9±0.5 km/h) and v10‐km (14.3±0.9 km/h), a 10‐km track‐running test was performed, and a biopsy from m. vastus lateralis was collected. 10‐km performance and VO2‐max (mL/min) were the same prior to P1 and P2, whereas RE was better (P<.05) before P2 than before P1. During P1 and P2, 10‐km performance (2.9% and 2.3%), VO2‐max (2.1% and 2.6%), and RE (1.9% and 1.8% at 60% vVO2‐max; 1.6% and 2.0% at v10‐km) improved (P<.05) to the same extent, respectively. Performance in RRT was 20% better (P<.05) after compared to before P2, with no change in P1. No changes in muscle expression of Na+,K+‐ATPase α1, α2 and β1, NHE1, SERCA1 and SERCA2, actin, and CaMKII were found during neither P1 nor P2. Thus, the present study demonstrates that a second period of intense training leads to improved short‐term performance and further improved RE, whereas 10‐km performance and VO2‐max improve to the same extent as during the first period.
Are heart rate monitors valuable tools for diagnosing arrhythmias in endurance athletes?
Authors: Gajda R. , Biernacka E. K. , Drygas W.
Published: May 2017

Millions of physically active individuals worldwide use heart rate monitors (HRMs) to control their exercise intensity. In many cases, the HRM indicates an unusually high heart rate (HR) or even arrhythmias during training. Unfortunately, studies assessing the reliability of these devices to help control HR disturbances during exercise do not exist. We examined 142 regularly training endurance runners and cyclists, aged 18‐51 years, with unexplained HR abnormalities indicated by various HRMs to assess the utility of HRMs in diagnosing exertion‐induced arrhythmias. Each athlete simultaneously wore a Holter electrocardiogram (ECG) recorder and an HRM during typical endurance training in which they had previously detected “arrhythmias” to verify the diagnosis. Average HRs during exercise were precisely recorded by all types of HRMs. No signs of arrhythmia were detected during exercise in approximately 39% of athletes, and concordant HRs were recorded by the HRMs and Holter ECG. HRMs indicated surprisingly high short‐term HRs in 45% of athletes that were not detected by the Holter ECG and were artifacts. In 15% of athletes, single ventricular/supraventricular beats were detected by the Holter ECG but not by the HRM. We detected a serious tachyarrhythmia in the HRM and Holter ECG data with concomitant clinical symptoms in only one athlete, who was forced to cease exercising. We conclude that the HRM is not a suitable tool for monitoring heart arrhythmias in athletes and propose an algorithm to exclude the suspicion of exercise‐induced arrhythmia detected by HRMs in asymptomatic, physically active individuals.
Creating Meaning through Multimodality: Multiliteracies Assessment and Photo Projects for Online Portfolios
Authors: Schmerbeck Nicola , Lucht Felecia
Published: May 2017

Actively engaged in online media, learners today are surrounded by texts overtly and covertly transmitted by visual images, sound effects, and voices as well as the written word. Language learning portfolios can engage students in the literacy‐oriented learning processes of interpretation, collaboration, and problem solving as outlined by Kern () to understand how meaning is created through a variety of different modes of communication. Based on the multiliteracies approach, this article demonstrates how photo projects can be incorporated in portfolios to assess learners' development as multimodal language users. To this end, the article first reviews the multiliteracies approach including Kern's () seven principles of literacies. It then proceeds to examine the advantages of using photo projects in foreign language classes, before it discusses assessment based on the multiliteracies framework as suggested by Paesani, Allen, and Dupuy (). A sample portfolio project featuring evaluation criteria and organizational procedures demonstrates how a pedagogy of multiliteracies can be used to assess the literacy and cultural understanding of intermediate learners of German. Finally, the article concludes with a summary of the benefits of portfolio assessment based on the multiliterarcies approach.
Prevalence of diabetes mellitus in Chinese children with thalassaemia major
Authors: Liang Yuzhen , Bajoria Rekha , Jiang Yan , Su Hongwei , Pan Hongfei , Xia Ning , Chatterjee Ratna , Lai Yongrong
Published: May 2017

Objective

Diabetes mellitus is a common endocrinopathy in patients with β‐thalassaemia major (β‐TM), which is high prevalent in southern China. This study aimed to determine the cause and prevalence of glycaemic disorders in Chinese children with β‐TM.

Methods

In this prospective study, fasting glucose and insulin (FINS) levels were assessed in 267 β‐TM and 80 non‐TM control children. Homeostatic model assessment (HOMA) and the quantitative insulin sensitivity check index (QUICKI) were evaluated. Iron overload was assessed by serum ferritin (SF), total units of blood transfused and cardiac T2*.

Results

β‐TM had higher FPG (P < 0.001), FINS (P < 0.001) and HOMA‐IR (P < 0.05), but lower QUICKI (P < 0.01) than those of controls. The impaired fasting glucose (IFG) was present in 30% of children, whereas 2% had diabetes. The prevalence of IFG in β‐TM group was higher in children aged >10 years (OR 6.5; 95% CI 3.7–11.4; P < 0.001), SF of >2500 μg/l (OR 4.8; 95% CI 2.1–11.1; P < 0.01), serum ALT levels of >50 IU/l (OR 2.1; 95% CI 1.2–3.7; P < 0.05) and cardiac T2* of <20 ms (OR 3.3; 95% CI 1.7–6.6; P < 0. 01). The children on deferiprone (DFP) had a reduced incidence of glycaemic aberrations than those on other chelating agents (OR 0.4; 95% CI 0.23–0.8; P < 0.05).

Conclusions

Our data suggest that IFG occurred in 30% of β TM children, perhaps due to insulin resistance secondary to iron overload. Deferiprone‐containing chelating agent may have a protective effect.
First Detection of a Fosfomycin Resistance Gene,
fosA7
, in Salmonella enterica Serovar Heidelberg Isolated from Broiler Chickens
Authors: Rehman Muhammad A. , Yin Xianhua , Persaud-Lachhman Marissa G. , Diarra Moussa S.
Published: May 2017

We previously described
Salmonella enterica
serovar Heidelberg isolates harboring a chromosomal gene cluster similar to the glutathione
S
-transferase gene, a putative
fosA
gene conferring resistance to fosfomycin. Here, we show that this new gene, named
fosA7
, confers resistance to fosfomycin. The introduction of
fosA7
into the fosfomycin-susceptible
Salmonella enterica
serovar Enteritidis resulted in a substantial increase in the fosfomycin MIC. This finding increases the awareness of antibiotic resistance in
Salmonella
Heidelberg from broilers as related to the food safety and public health.
Complete Genome Sequence of Photobacterium damselae subsp.
piscicida
Strain OT-51443 Isolated from Yellowtail (Seriola quinqueradiata) in Japan
Authors: Aoki Takashi , Teru Yuki , Morimoto Natsuki , Kono Tomoya , Sakai Masahiro , Takano Tomokazu , Hawke John P. , Fukuda Yutaka , Takeyama Haruko , Hikima Jun-ichi
Published: May 2017

Pseudotuberculosis caused by infection of
Photobacterium damselae
subsp.
piscicida
has caused serious economic damages to aquaculture farms worldwide. Here, the whole-genome sequence of
P. damselae
subsp.
piscicida
strain OT-51443, isolated in Japan, was determined and suggests that this genome consists of two chromosomes and five plasmids.
Worst Case Branching and Other Measures of Nondeterminism
Authors: Palioudakis Alexandros , Salomaa Kai , Akl Selim G.
Published: May 2017

Many nondeterminism measures for finite automata have been studied in the literature. The tree width of an NFA (nondeterministic finite automaton) counts the number of leaves of computation trees as a function of input length. The trace of an NFA is defined in terms of the largest product of the degrees of nondeterministic choices in computations on inputs of given length. Branching is the corresponding best case measure based on the product of nondeterministic choices in the computation that minimizes this value. We establish upper and lower bounds for the trace of an NFA in terms of its tree width. We give a tight bound for the size blow-up of determinizing an NFA with finite trace. Also we show that the trace of any NFA either is bounded by a constant or grows exponentially.
More on Minimizing Finite Automata with Errors — Nondeterministic Machines
Authors: Holzer Markus , Jakobi Sebastian
Published: May 2017

We continue our research on minimization problems and related problems for automata w.r.t. to different error profiles, now considering nondeterministic finite automata (NFAs) as inputs. Here the error profiles are almost-equivalence and E-equivalence. We show that the minimization problems and their underlying equivalence problems become PSPACE-complete in most cases. The obtained results nicely fit to the known ones on ordinary NFA minimization, and show a significant difference to the previously obtained results on deterministic finite state machines.
Minimal Reaction Systems Revisited and Reaction System Rank
Authors: Teh Wen Chean , Atanasiu Adrian
Published: May 2017

Some mathematical aspects of reaction systems introduced by Ehrenfeucht and Rozenberg are considered. Ehrenfeucht et al. have previously obtained a complete classification of functions specified by minimal reaction systems in terms of certain closure properties of the specified functions. In this work, a refined proof of this classification with slight extension is obtained. Furthemore, the recently introduced notion of reaction system rank is studied for functions belonging to this class, as well as for focus functions, the latter which play a significant role in the proof of the classification theorem.
Uniform Sampling of Subshifts of Finite Type on Grids and Trees
Authors: Mairesse Jean , Marcovici Irène
Published: May 2017

Let us color the vertices of the grid ℤd or the infinite regular tree 𝕋d, using a finite number of colors, with the constraint that some predefined pairs of colors are not allowed for adjacent vertices. The set of admissible colorings is called a nearest-neighbor subshift of finite type (SFT). We study “uniform” probability measures on SFT, with the motivation of having an insight into “typical” admissible configurations. We recall the known results on uniform measures on SFT on grids and we complete the picture by presenting some contributions to the description of uniform measures on SFT on 𝕋d. Then we focus on the problem of uniform random sampling of configurations of SFT. We propose a first method based on probabilistic cellular automata, which is valid under some restrictive conditions. Then we concentrate on the case of SFT on ℤ for which we propose several alternative sampling methods.
Fast Convolutions of Packed Strings and Pattern Matching with Wildcards
Authors: Zhang Meng
Published: May 2017

We give faster methods to compute discrete convolutions. We assume that all the inputs are packed, that is, strings are packed into words such that each word is packed with [Formula: see text] characters, where w is the length of a machine word and ∑ is the alphabet. The output of our methods is also packed, that is, each word of the output contains more than one element of the result. The approach is based on the word-level parallelism and the FFT. Given two strings with m and n ( n ≥ m ) characters that are packed into [Formula: see text] and [Formula: see text] words respectively, the convolution of them can be computed in [Formula: see text] time, where [Formula: see text] by the FFT. Experiments show that our method is three times faster than the convolution using the standard trick.

We consider the problem of pattern matching with wildcards on packed strings. It finds all the occurrences of a pattern in a text, both of which may contain wildcards. By the convolution of packed strings, we present algorithms that are faster than the previous [Formula: see text]-time algorithm, where m is the length of the pattern and n the length of the text. The algorithm runs in [Formula: see text] time, where occ is the number of occurrences of the pattern in the input. Experiments show that the method is faster than the bit-parallel wildcard matching algorithm for long patterns.
Tropicana translated: a foreland thrust system imbricate fan setting for
c.
2520 Ma orogenic gold mineralization at the northern margin of the Albany–Fraser Orogen, Western Australia
Authors: Occhipinti S. A. , Tyler I. M. , Spaggiari C. V. , Korsch R. J. , Kirkland C. L. , Smithies R. H. , Martin K. , Wingate M. T. D.
Published: May 2017

Neoarchean rocks of the Tropicana Zone, including granites with subduction-zone affinities, formed in a terrane adjacent to, or on the margin of, the Yilgarn Craton at the commencement of a long-lived, amphibolite to granulite facies event – the 2722–2554 Ma Atlantis Event. Early stages of this event overlap with extensive komatiite emplacement within the Eastern Goldfields Superterrane (Yilgarn Craton), suggestive of a plume-related rift environment, which was followed by 2660–2630 Ma greenschist facies, orogenic gold mineralization. This indicates differences in the tectonic evolution of the Tropicana Zone compared with within the craton, although isotopic data show similarities in crustal sources. At
c.
2520 Ma, the Tropicana Zone was retrogressed to greenschist facies as it was thrust onto the Yamarna Terrane (Yilgarn Craton), forming a northwesterly directed fold-and-thrust belt above the flat-lying Plumridge Detachment. This fold-and-thrust belt is host to the
c.
2520 Ma, Tropicana gold deposit. The Plumridge Detachment may extend north to the Yamarna greenstone belt, linking to the Yamarna Shear Zone – the boundary between the Burtville and Yamarna Terranes. The fertility of the Tropicana Zone is related to its Neoarchean geodynamic setting within a continental arc environment, implying that deformed margins of Archean cratons may be prospective for Neoarchean Au deposits.
Detailed Distribution of Corneal Epithelial Thickness and Correlated Characteristics Measured with SD-OCT in Myopic Eyes
Authors: Wu Yanan , Wang Yan
Published: May 2017

Purpose.To investigate the detailed distribution of corneal epithelial thickness in single sectors and its correlated characteristics in myopic eyes.Methods.SD-OCT was used to measure the corneal epithelial thickness distribution profile. Differences of corneal epithelial thickness between different parameters and some correlations of characteristics were calculated.Results.The thickest and thinnest part of epithelium were found at the nasal-inferior sector (P<0.05) and at the superior side (P<0.05), respectively. Subjects in the low and moderate myopia groups have thicker epithelial thickness than those in the high myopia group (P<0.05). Epithelial thickness was 1.39 μm thicker in male subjects than in female subjects (P<0.001). There was a slight negative correlation between corneal epithelial thickness and age (r=−0.13,P=0.042). Weak positive correlations were found between corneal epithelial thickness and corneal thickness (r=0.148,P=0.031). No correlations were found between corneal epithelial thickness, astigmatism axis, corneal front curvature, and IOP.Conclusions.The epithelial thickness is not evenly distributed across the cornea. The thickest location of the corneal epithelium is at the nasal-inferior sector. People with high myopia tend to have thinner corneal epithelium than low–moderate myopic patients. The corneal epithelial thickness is likely to be affected by some parameters, such as age, gender, and corneal thickness.
HIPK2 Overexpression and Its Prognostic Role in Human Papillomavirus-Positive Tonsillar Squamous Cell Carcinoma
Authors: Kwon Mi Jung , Kang So Young , Nam Eun Sook , Cho Seong Jin , Rho Young-Soo
Published: May 2017

Tonsillar squamous cell carcinomas (TSCCs) are the most common human papillomavirus- (HPV-) associated oropharyngeal cancers with poor prognosis. Homeodomain-interacting protein kinase 2 (HIPK2) is a central regulator of p53, which participates in apoptosis during the DNA damage response. HIPK2 is involved in HPV-associated uterine cervical and cutaneous carcinogenesis through its binding of HPV E6, thereby preventing apoptosis and contributing to tumor progression. However, its clinical and prognostic significance in TSCC remains unclear. HIPK2 mRNA levels were analyzed in 20 normal tonsils and 20 TSCC specimens using real-time reverse transcription polymerase chain reaction. Immunohistochemistry of HIPK2 was performed in 79 resected specimens. HIPK2 was expressed in 57% of the TSCCs, and HIPK2 protein expression and HIPK2 mRNA levels were higher in TSCCs than in normal tonsils. HIPK2 overexpression was associated with poorly differentiated carcinoma and low alcohol consumption and was an independent prognostic factor for overall survival and disease-free survival (DFS) in TSCC and a negative independent prognostic factor for DFS in patients receiving postoperative radiotherapy. HIPK2 overexpression had a significant association with poorer DFS in HPV-positive TSCCs, but not in HPV-negative tumors. HIPK2 overexpression may be a potential prognostic marker for predicting prognoses and a high risk of recurrence, particularly in patients with HPV-positive TSCC.