bluuebunny/crossref_metadata_2025 huggingface dataset:
QTL‐seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)
Authors: Pandey Manish K. , Khan Aamir W. , Singh Vikas K. , Vishwakarma Manish K. , Shasidhar Yaduru , Kumar Vinay , Garg Vanika , Bhat Ramesh S. , Chitikineni Annapurna , Janila Pasupuleti , Guo Baozhu , Varshney Rajeev K.
Published: December 2016

Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co‐occurrence leads to significant yield loss in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling resistance to rust and LLS, whole‐genome resequencing (WGRS)‐based approach referred as ‘QTL‐seq’ was deployed. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent and the resistant and susceptible bulks for rust and LLS. Sequence analysis of bulks for rust and LLS with reference‐guided resistant parent assembly identified 3136 single‐nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of ≥7 in the identified genomic region on pseudomolecule A03. Detailed analysis identified 30 nonsynonymous SNPs affecting 25 candidate genes for rust resistance, while 14 intronic and three synonymous SNPs affecting nine candidate genes for LLS resistance. Subsequently, allele‐specific diagnostic markers were identified for three SNPs for rust resistance and one SNP for LLS resistance. Genotyping of one RIL population (TAG 24 × GPBD 4) with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of QTL‐seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.
Increased rhizosphere populations of Trichoderma asperellum strain T34 caused by secretion pattern of root exudates in tomato plants inoculated with Botrytis cinerea
Authors: Fernández E. , Trillas M. I. , Segarra G.
Published: December 2016

Root exudates secreted from plants can modify rhizosphere microbiota by enhancing or inhibiting the growth of biological control agents (BCAs) and/or pathogens. Similarly, microorganisms can modify the secretion of plant root exudates. The aim of this study was to analyse the effect of a Botrytis cinerea leaf infection on the secretion of tomato root exudates and on the populations of the BCA Trichoderma asperellum strain T34 (T34). This study found that the secretion pattern of root exudates in tomato plants was influenced by B. cinerea infection in plant leaves. An increase in the levels of gluconic acid was observed, while levels of sucrose and inositol decreased. A decrease in the severity of B. cinerea by the induction of systemic resistance triggered by T34 was also observed. Tomato plants infected with B. cinerea maintained the populations of T34 in the roots, while populations of T34 decreased in plants not inoculated with the pathogen. Samples exposed to media containing gluconic acid (as the only carbon source or at the same concentration found in roots exudates) saw an increase in the in vitro growth of T34 compared to media without gluconic acid. In conclusion, a change in the secretion pattern of root exudates caused by B. cinerea, together with the enhanced growth of T34 in the presence of gluconic acid, indicates the existence of leaf to root communication. The result of this is enhanced populations of T34, and in turn induced disease resistance and a consequential reduction in disease severity.
Editors' Introduction
Authors: Balfour Danny L. , Newbold Stephanie P.
Published: December 2016

Related Content: Roberts (PAR January/February 2017)

Related Content: Eckerd (PAR January/February 2017)

Related Content: Vidal‐Aparicio (PAR January/February 2017)

Related Content: Gerrits and Verweij (PAR January/February 2017)

Related Content: Robbins (PAR January/February 2017)
What's Changed? A Comparison of Army Suicide Surveillance Data to Cases from 1975 to 1982
Authors: Reger Mark A. , Reger Greg M. , Krieg Christina , Pruitt Larry , Smolenski Derek J. , Skopp Nancy A. , Bush Nigel
Published: December 2016

US Army suicide rates increased significantly in the last decade and have remained high. To inform future research hypotheses, Army suicide surveillance data (2012–2014) were compared to similar Army data for suicides from 1975 to 1982. Preliminary data suggest that suicide rates increased across most demographic groups, but may have decreased among divorced soldiers. Mental health utilization increased over time. Legal problems and physical health problems were identified in a higher percentage of cases in the recent data relative to the 1975–1982 era. Potential implications for suicide prevention are discussed.
Risk Factors of a Suicide Reattempt by Seasonality and the Method of a Previous Suicide Attempt: A Cohort Study in a Japanese Primary Care Hospital
Authors: Sawa Minoru , Koishikawa Hiraki , Osaki Yoneatsu
Published: December 2016

Suicide has a great impact on the individual whose life is lost and the bereaved family members. The risk of a suicide reattempt is particularly high during the first 12 months after a suicide attempt. In this cohort study, risk factors for a suicide reattempt were explored among 291 patients at suicide risk. Clinical and demographic data were collected from a Japanese primary care hospital. Past psychiatric history and multiple diagnoses were associated with suicide reattempts in both genders. Drug overdose, past psychiatric history, and the summer season were linked to suicide reattempts among males. Past psychiatric history and multiple diagnoses were linked to suicide reattempts among females. Appropriate assessment of past psychiatric history, season and method of suicide attempt, gender, and diagnosis may play a role in preventing suicide.
Changes in soil aggregate‐associated enzyme activities and nutrients under long‐term chemical fertilizer applications in a phosphorus‐limited paddy soil
Authors: Li W. T. , Liu M. , Jiang C. Y. , Wu M. , Chen X. F. , Ma X. Y. , Li Z. P.
Published: December 2016

Paddy soils in subtropical China are usually deficient in phosphorus (P) and require regular application of chemical fertilizers. This study evaluated the effects of chemical fertilizers on the distribution of soil organic carbon (SOC), total nitrogen (N) and available P, and on the activity of the associated enzymes in bulk soil and aggregates. Surface soils (0–20 cm) were collected from a 24‐yr‐old field experiment with five treatments: unfertilized control (CK), N only (N), N and potassium (NK), N and P (NP), and N, P and K (NPK). Undisturbed bulk soils were separated into >2, 1–2, 0.25–1, 0.053–0.25 and <0.053 mm aggregate classes using wet sieving. Results showed that both NP‐ and NPK‐treated soils significantly increased mean weight diameter of aggregates, SOC, available P in bulk soil and aggregates, as compared to CK. Most SOC and total N adhered to macro‐aggregates (>0.25 mm), which accounted for 64–81% of SOC and 54–82% of total N in bulk soil. The activities of invertase and acid phosphatase in the 1–2 mm fraction were the highest under NPK treatment. The highest activity of urease was observed in the <0.053 mm fraction under NP treatment. Soil organic carbon and available P were major contributors to variation of enzyme activities at the aggregate scale. In conclusion, application of NP or NPK fertilizers promoted the formation of soil aggregates, nutrient contents and activities of associated enzymes in P‐limited paddy soils, and thus enhanced soil quality.
DRO1 influences root system architecture in Arabidopsis and Prunus species
Authors: Guseman Jessica M. , Webb Kevin , Srinivasan Chinnathambi , Dardick Chris
Published: December 2016

Roots provide essential uptake of water and nutrients from the soil, as well as anchorage and stability for the whole plant. Root orientation, or angle, is an important component of the overall architecture and depth of the root system; however, little is known about the genetic control of this trait. Recent reports in Oryza sativa (rice) identified a role for DEEPER ROOTING 1 (DRO1) in influencing the orientation of the root system, leading to positive changes in grain yields under water‐limited conditions. Here we found that DRO1 and DRO1‐related genes are present across diverse plant phyla, and fall within the IGT gene family. The IGT family also includes TAC1 and LAZY1, which are known to affect the orientation of lateral shoots. Consistent with a potential role in root development, DRO1 homologs in Arabidopsis and peach showed root‐specific expression. Promoter–reporter constructs revealed that AtDRO1 is predominantly expressed in both the root vasculature and root tips, in a distinct developmental pattern. Mutation of AtDRO1 led to more horizontal lateral root angles. Overexpression of AtDRO1 under a constitutive promoter resulted in steeper lateral root angles, as well as shoot phenotypes including upward leaf curling, shortened siliques and narrow lateral branch angles. A conserved C‐terminal EAR‐like motif found in IGT genes was required for these ectopic phenotypes. Overexpression of PpeDRO1 in Prunus domestica (plum) led to deeper‐rooting phenotypes. Collectively, these data indicate a potential application for DRO1‐related genes to alter root architecture for drought avoidance and improved resource use.
The ghosts of Islam and the unseen world in Bruneian horror stories
Authors: MOHD DAUD KATHRINA
Published: December 2016

One of the most dynamic and contemporary aspects of Bruneian literature today is the proliferation of bilingual short stories online. In a country in which fewer than a hundred local prose and poetry works are published annually, Mode Seram, a website in which readers are encouraged to send in stories, which updates itself daily and can boast over 40,000 readers since its inception in 2010, is one of the most‐read (albeit unofficial) disseminators of prose in the country. By performing a close reading of selected stories from the site, with particular attention to the ‘imam’ figure, this article suggests that the bi‐ and tri‐lingual stories of Mode Seram constitute an alternative reading of the national Islamic religious ideology, and challenge contemporary Anglophone Southeast Asian representations of the sacred and the supernatural, and represent an important step in the carving out of a unique national literature rooted firmly in the cultural and religious traditions of Southeast Asia.
A research bibliography for Brunei English
Authors: MCLELLAN JAMES , CHIN GRACE V. S.
Published: December 2016

This bibliography sets out to provide a guide to research publications dealing with the status, functions and features of English in Brunei. It includes publications related to the sociolinguistic background, the linguistic features of Brunei English, discourse studies, literary studies and creative writing, English language teaching, language policy and planning, and scholarly theses.
Butyrate stimulates adipose lipolysis and mitochondrial oxidative phosphorylation through histone hyperacetylation‐associated β3‐adrenergic receptor activation in high‐fat diet‐induced obese mice
Authors: Jia Yimin , Hong Jian , Li Huifang , Hu Yun , Jia Longfei , Cai Demin , Zhao Ruqian
Published: December 2016

New Findings

What is the central question of this study?

Butyrate can prevent diet‐induced obesity through increasing energy expenditure. However, it is unclear whether β3‐adrenergic receptors (ARβ3) mediate butyrate‐induced adipose lipolysis.

What is the main finding and its importance?

Short‐term oral administration of sodium butyrate is effective in alleviating diet‐induced obesity through activation of ARβ3‐mediated lipolysis in white adipose tissue.

Butyrate can prevent diet‐induced obesity through increasing energy expenditure. However, it is unclear whether ARβ3 mediates butyrate‐induced adipose lipolysis. In this study, weaned mice were were fed control (Con) or high‐fat (HF) diet for 8 weeks to establish obesity. High‐fat diet‐induced obese mice maintained on the HF diet were divided into two subgroups; the HFB group was gavaged with 80 mg sodium butyrate (SB) per mouse every other day for 10 days, whereas the HF group received vehicle. Chromatin immunoprecipitation assay was performed to determine the status of histone H3 lysine 9 acetylation (H3K9Ac) on the promoter of the β3‐adrenergic receptor (ARβ3) gene in epididymal white adipose tissue. It was shown that five gavage doses of SB significantly alleviated HF diet‐induced obesity and restored plasma leptin concentration to the control level. Protein contents of ARβ3 and PKA, as well as ATGL and p‐HSL (Ser563), were significantly upregulated in the HFB group compared with the HF group. Mitochondrial oxidative phosphorylation was enhanced by SB treatment. Sodium butyrate significantly increased the expression of four out of 13 mitochondrial DNA‐encoded genes and significantly upregulated the protein contents of peroxisome proliferator‐activated receptor‐γ coactivator 1α and COX4. Moreover, SB administration enhanced the expression of ARβ3 and its downstream signalling. The G protein‐coupled receptor 43 and p‐CREB (Ser133) were significantly stimulated by SB. In addition, an active transcription marker, H3K9Ac, was significantly enriched on the promoter of the ARβ3 gene. Our results indicate that short‐term oral administration of SB is effective in alleviating diet‐induced obesity through activation of the ARβ3‐mediated lipolysis in the epididymal white adipose tissue.
Metabolic systems biology: a brief primer
Authors: Edwards Lindsay M.
Published: December 2016

In the early to mid‐20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these – systems thinking, high‐dimensional data and computation – defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing‐based technologies, however, offer full coverage. Other ‘omics’ platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either ‘bottom‐up’ (mechanistic) or ‘top‐down’ (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, ‘middle‐out’. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large‐scale data integration.

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Residual force enhancement is regulated by titin in skeletal and cardiac myofibrils
Authors: Shalabi Nabil , Cornachione Anabelle , de Souza Leite Felipe , Vengallatore Srikar , Rassier Dilson E.
Published: December 2016

Key points

When a skeletal muscle is stretched while it contracts, the muscle produces a relatively higher force than the force from an isometric contraction at the same length: a phenomenon referred to as residual force enhancement.

Residual force enhancement is puzzling because it cannot be directly explained by the classical force–length relationship and the sliding filament theory of contraction, the main paradigms in the muscle field.

We used custom‐built instruments to measure residual force enhancement in skeletal myofibrils, and, for the first time, in cardiac myofibrils.

Our data report that residual force enhancement is present in skeletal muscles, but not cardiac muscles, and is regulated by the different isoforms of the titin protein filaments.

When a skeletal muscle contracts isometrically, the muscle produces a force that is relative to the final isometric sarcomere length (SL). However, when the same final SL is reached by stretching the muscle while it contracts, the muscle produces a relatively higher force: a phenomenon commonly referred to as residual force enhancement. In this study, we investigated residual force enhancement in rabbit skeletal psoas myofibrils and, for the first time, cardiac papillary myofibrils. A custom‐built atomic force microscope was used in experiments that stretched myofibrils before and after inhibiting myosin and actin interactions to determine whether the different cardiac and skeletal titin isoforms regulate residual force enhancement. At SLs ranging from 2.24 to 3.13 μm, the skeletal myofibrils enhanced the force by an average of 9.0%, and by 29.5% after hindering myosin and actin interactions. At SLs ranging from 1.80 to 2.29 μm, the cardiac myofibrils did not enhance the force before or after hindering myosin and actin interactions. We conclude that residual force enhancement is present only in skeletal muscles and is dependent on the titin isoforms.
Expansions for the radiation impedance of a rectangular piston in an infinite baffle
Authors: Mellow Tim , Kärkkäinen Leo
Published: December 2016

Relatively compact analytical expressions in the form of fast-convergin g expansions are derived for the radiation resistance and reactance of a rectangular rigid piston in an infinite rigid baffle, which are computationally efficient at high frequencies or large aspect ratios and yield simple approximations (asymptotic expressions) at low frequencies. Plots of the normalized radiation resistance and reactance are shown for various aspect ratios with constant width as well as constant area. Comparisons are also made with the impedance of an elliptic piston.
A mixture approach to the acoustic properties of a macroscopically inhomogeneous porous aluminum in the equivalent fluid approximation
Authors: Sacristan C. J. , Dupont T. , Sicot O. , Leclaire P. , Verdière K. , Panneton R. , Gong X. L.
Published: December 2016

The acoustic properties of an air-saturated macroscopically inhomogeneous aluminum foam in the equivalent fluid approximation are studied. A reference sample built by forcing a highly compressible melamine foam with conical shape inside a constant diameter rigid tube is studied first. In this process, a radial compression varying with depth is applied. With the help of an assumption on the compressed pore geometry, properties of the reference sample can be modelled everywhere in the thickness and it is possible to use the classical transfer matrix method as theoretical reference. In the mixture approach, the material is viewed as a mixture of two known materials placed in a patchwork configuration and with proportions of each varying with depth. The properties are derived from the use of a mixing law. For the reference sample, the classical transfer matrix method is used to validate the experimental results. These results are used to validate the mixture approach. The mixture approach is then used to characterize a porous aluminium for which only the properties of the external faces are known. A porosity profile is needed and is obtained from the simulated annealing optimization process.
Automatic measurement of vowel duration via structured prediction
Authors: Adi Yossi , Keshet Joseph , Cibelli Emily , Gustafson Erin , Clopper Cynthia , Goldrick Matthew
Published: December 2016

A key barrier to making phonetic studies scalable and replicable is the need to rely on subjective, manual annotation. To help meet this challenge, a machine learning algorithm was developed for automatic measurement of a widely used phonetic measure: vowel duration. Manually-annotated data were used to train a model that takes as input an arbitrary length segment of the acoustic signal containing a single vowel that is preceded and followed by consonants and outputs the duration of the vowel. The model is based on the structured prediction framework. The input signal and a hypothesized set of a vowel's onset and offset are mapped to an abstract vector space by a set of acoustic feature functions. The learning algorithm is trained in this space to minimize the difference in expectations between predicted and manually-measured vowel durations. The trained model can then automatically estimate vowel durations without phonetic or orthographic transcription. Results comparing the model to three sets of manually annotated data suggest it outperformed the current gold standard for duration measurement, an hidden Markov model-based forced aligner (which requires orthographic or phonetic transcription as an input).
Relationship Between Fundamental Motor Skill Ability and Body Mass Index in Young Adults
Authors: Jiménez Judith , Morera Maria , Salazar Walter , Gabbard Carl
Published: December 2016

Purpose:

Motor skill competence has been associated with physical activity level, fitness, and other relevant health-related characteristics. Recent research has focused on understanding these relationships in children and adolescents, but little is known about subsequent years. The aim of this study was to examine the relationship between fundamental motor skill (FMS) ability and body mass index (BMI) in young adults.

Method:

Participants, 40 men and 40 women (M age = 19.25 yr, SD = 2.48), were assessed for BMI and motor competence with 10 fundamental motor skills (FMSs) using the Test for Fundamental Motor Skills in Adults (TFMSA).

Results:

BMI was negatively associated with total motor ability (r = –.257; p = .02) and object control skills (r = –.251; p = .02); the relationship with locomotor skills was marginally insignificant (r = –.204; p = .07). In regard to individual skills, a significant negative association was found for running, jumping, striking, and kicking (ps < .05). Multiple regression analysis indicated that BMI and gender predicted 42% of the variance in total FMS score; gender was the only significant predictor.

Conclusion:

Overall, these preliminary findings suggest that young adults with higher FMS ability are more likely to have lower BMI scores.
The Role of Vision and Movement Automization on the Focus of Attention Effect
Authors: Porter Jared , Makaruk Hubert , Starzak Marcin
Published: December 2016

According to the constrained action hypothesis, an external focus of attention is beneficial for motor learning due to improvements in movement automization. In contrast, an internal focus of attention interferes with automaticity and decreases the effects of motor learning. This study was designed to test the automaticity assumption of the focus of attention effect within a highly skilled population. We examined the effects of attentional focus on kinematics in rope jumping and visual control. Participants practiced the rope-jumping task over five days of acquisition, which was followed by a retention and transfer test. The findings provided evidence that the learning of the task was improved and automaticity was increased by the external focus compared with the internal focus and no attentional (i.e., control condition) conditions. In addition, these findings indicate that visual attention as a function of attentional focus has a stronger relationship with practice performance rather than with motor learning effects.
Focus of Attention and Instructional Feedback From NCAA Division 1 Collegiate Coaches
Authors: Diekfuss Jed A. , Raisbeck Louisa D.
Published: December 2016

An external focus of attention, as opposed to an internal focus of attention, has been shown to increase performance and enhance learning. However, little research has examined whether these findings have been integrated into collegiate coaching and adopted by student-athlete performers. The purpose of this study was to examine the verbal instructions and instructional feedback provided by NCAA division 1 collegiate coaches during practice and how it influenced student-athletes’ focus of attention during competition. Thirty-one student-athletes completed a questionnaire that inquired about coaches’ verbal instructions and instructional feedback during practice and student-athletes’ focus of attention during competition. Fifty percent of participants reported that their coaches instructed them to focus their attention internally and only four participants reported that their coaches instructed them to focus externally. Our results also showed that coaches provided an equal amount of internal and external instructional feedback. During competition, however, the majority of participants reported statements that fell under the category of “winning and strategy.” These results suggest that the beneficial effects of an external focus of attention have not been integrated into NCAA division 1 collegiate coaching and the focus of attention adopted by student-athletes may be more complex than what is studied in laboratory research.
Indifference to Chaotic Motion May Be Related to Social Disinterest in Children With Autism
Authors: Haworth Joshua , Kyvelidou Anastasia , Fisher Wayne , Stergiou Nicholas
Published: December 2016

Children with autism spectrum disorder tend to have little interest in the presence, actions, and motives of other persons. In addition, these children tend to present with a limited and overly redundant movement repertoire, often expressing hyperfixation and aversion to novelty. We explore whether this is related to a more fundamental lack of appreciation for various temporal dynamics, including periodic, chaotic, and aperiodic motion structures. Seven children with ASD (age, gender, and height matched with children without ASD) were asked to stand and watch the motion of a visual stimulus displayed on a large (55") video monitor. Gaze and posture movements were recorded and assessed using cross recurrence quantification analysis for qualities of coordination, including rate and duration of bouts of coordination. Results showed that children with ASD do not express an affinity to chaotic motion of the stimulus in the same way as children without ASD. We contend that this indifference to chaotic motion is foundational to their general disinterest in biological motion.
TECHNOLOGY DEPLOYMENT BY LATE MOVERS
Authors: WANG KIM
Published: December 2016

It is widely accepted that the first firm to deploy the latest technology will enjoy monopoly profits. However, research shows that the first mover advantage is quickly eroded by late movers. Technology deployments by late movers remain largely under-explored. This study explores the impact of the technological and market capabilities of late movers on their deployment timing, and how this impact is moderated by the pace of frontier advancement. We find a positive association between a firm’s capabilities and the earliness of its deployment timing. A faster pace of frontier advancement exacerbates the impact of a firm’s capabilities on technology deployment timing. We draw empirical evidence from the thin film transistor-liquid crystal display (TFT-LCD) industry between 1995 and 2010. This paper contributes to the technology management literature by developing a deeper understanding of the trade-offs involved in the timing of technology deployments.
Valuing a Statistical Life Year in Relation to Clean Air
Authors: Hein Lars , Roberts Pete , Gonzalez Lucia
Published: December 2016

Environmental cost–benefit analysis is increasingly used to support the formulation of European air quality policies. In these analyses, typically around three-quarters of the societal benefits of cleaner air are related to monetised increases in statistical life expectancy. However, the literature presents widely diverging estimates for the value of a statistical life year (a ‘VOLY’). This paper presents a review of studies aimed at establishing a VOLY as used in European air quality policies and it examines the factors that cause the variations in VOLY estimates. We discuss the implications of our findings for European air quality policies and also present a novel approach to analyse the VOLY. We have labelled our approach the ‘maximum societal revenue VOLY’ (MSR-VOLY), and postulate that this approach may be particularly useful in the context of natural capital accounting.
A Comparison of SLAM Prediction Densities Using the Kolmogorov Smirnov Statistic
Authors: Rao Akshay , Han Wang , Senarathne P. G. C. N.
Published: December 2016

Accurate pose and trajectory estimates, are necessary components of autonomous robot navigation system. A wide variety of Simultaneous Localization and Mapping (SLAM) and localization algorithms have been developed by the robotics community to cater to this requirement. Some of the sensor fusion algorithms employed by SLAM and localization algorithms include the particle filter, Gaussian Particle Filter, the Extended Kalman Filter, the Unscented Kalman Filter, and the Central Difference Kalman Filter. To guarantee a rapid convergence of the state estimate to the ground truth, the prediction density of the sensor fusion algorithm must be as close to the true vehicle prediction density as possible. This paper presents a Kolmogorov–Smirnov statistic-based method to compare the prediction densities of the algorithms listed above. The algorithms are compared using simulations of noisy inputs provided to an autonomous robotic vehicle, and the obtained results are analyzed. The results are then validated using data obtained from a robot moving in controlled trajectories similar to the simulations.
Optimized Implementation of Multirate Mixed-Criticality Synchronous Reactive Models
Authors: Zhao Qingling , Al-Bayati Zaid , Gu Zonghua , Zeng Haibo
Published: December 2016

Model-based design using Synchronous Reactive (SR) models enables early design and verification of application functionality in a platform-independent manner, and the implementation on the target platform should guarantee the preservation of application semantic properties. Mixed-Criticality Scheduling (MCS) is an effective approach to addressing diverse certification requirements of safety-critical systems that integrate multiple subsystems with different levels of criticality. This article considers fixed-priority scheduling of mixed-criticality SR models, and considers two scheduling approaches: Adaptive MCS and Elastic MCS. We formulate the optimization problem of minimizing the total system cost of added functional delays in the implementation while guaranteeing schedulability, and present an optimal algorithm based on branch-and-bound search, and an efficient heuristic algorithm.
Static and Dynamic Frequency Scaling on Multicore CPUs
Authors: Bao Wenlei , Hong Changwan , Chunduri Sudheer , Krishnamoorthy Sriram , Pouchet Louis-Noël , Rastello Fabrice , Sadayappan P.
Published: December 2016

Dynamic Voltage and Frequency Scaling (DVFS) typically adapts CPU power consumption by modifying a processor’s operating frequency (and the associated voltage). Typical DVFS approaches include using default strategies such as running at the lowest or the highest frequency or reacting to the CPU’s runtime load to reduce or increase frequency based on the CPU usage. In this article, we argue that a compile-time approach to CPU frequency selection is achievable for affine program regions and can significantly outperform runtime-based approaches. We first propose a lightweight runtime approach that can exploit the properties of the power profile specific to a processor, outperforming classical Linux governors such as powersave or on-demand for computational kernels. We then demonstrate that, for affine kernels in the application, a purely compile-time approach to CPU frequency and core count selection is achievable, providing significant additional benefits over the runtime approach. Our framework relies on a one-time profiling of the target CPU, along with a compile-time categorization of loop-based code segments in the application. These are combined to determine at compile-time the frequency and the number of cores to use to execute each affine region to optimize energy or energy-delay product. Extensive evaluation on 60 benchmarks and 5 multi-core CPUs show that our approach systematically outperforms the powersave Linux governor while also improving overall performance.
Energy-Proportional Photonic Interconnects
Authors: Demir Yigit , Hardavellas Nikos
Published: December 2016

Photonic interconnects have emerged as the prime candidate technology for efficient networks on chip at future process nodes. However, the high optical loss of many nanophotonic components coupled with the low efficiency of current laser sources results in exceedingly high total power requirements for the laser. As optical interconnects stay on even during periods of system inactivity, most of this power is wasted, which has prompted research on laser gating. Unfortunately, prior work has been complicated by the long laser turn-on delays and has failed to deliver the full savings. In this article, we propose ProLaser, a laser control mechanism that monitors the requests sent on the interconnect, the cache, and the coherence directory to detect highly correlated events and turn on proactively the lasers of a photonic interconnect. While ProLaser requires fast lasers with a turn-on delay of a few nanoseconds, a technology that is still experimental, several types of such lasers that are suitable for power gating have already been manufactured over the last decade. Overall, ProLaser saves 42% to 85% of the laser power, outperforms the current state of the art by 2× on average, and closely tracks (within 2%--6%) a perfect prediction scheme with full knowledge of future interconnect requests. Moreover, the power savings of ProLaser allow the cores to exploit a higher-power budget and run faster, achieving speedups of 1.5 to 1.7× (1.6× on average).
Cardiometabolic risk improvement in response to a 3-yr lifestyle modification program in men: contribution of improved cardiorespiratory fitness vs. weight loss
Authors: Borel Anne-Laure , Nazare Julie-Anne , Baillot Aurélie , Alméras Natalie , Tremblay Angelo , Bergeron Jean , Poirier Paul , Després Jean-Pierre
Published: December 2016

Our objective was to examine the respective contributions of changes in visceral adiposity, subcutaneous adiposity, liver fat, and cardiorespiratory fitness (CRF) to the improvements in cardiometabolic risk markers in response to a 3-yr healthy eating/physical activity lifestyle intervention. Ninety-four out of 144 viscerally obese healthy men completed a 3-yr lifestyle intervention. Body weight, body composition, and fat distribution were assessed by anthropometry and DEXA/computed tomography. CRF, adipokines, lipoprotein/lipid profile, and 75 g of oral glucose tolerance were assessed. CRF and visceral and subcutaneous adiposity significantly improved over the 3-yr intervention, with a nadir in year 1 and a partial regain in year 3. Liver fat (estimated by insulin hepatic extraction) stabilized from year 1 to year 3, whereas HOMA-IR, ISI-Matsuda index, and adiponectin continued to improve. Multivariate analysis revealed that both visceral adiposity and estimated liver fat reductions contributed to the improved ISI-Matsuda index observed over 3 yr ( r2= 0.28, P < 0.001). Three-year changes in fat mass and CRF were independently associated with changes in visceral fat (adjusted r2= 0.40, P < 0.001), whereas only changes in CRF were associated with changes in estimated liver fat (adjusted r2= 0.18, P < 0.001). A long-term (3 yr) healthy eating/physical activity intervention in men improves several cardiometabolic risk markers over the long term (3 yr) despite a partial body weight regain observed between year 1 and year 3. The improvement in CRF contributes to visceral and estimated liver fat losses over the long term, which in turn explain the benefits of the lifestyle intervention on cardiometabolic risk profile.
The hypoxanthine-xanthine oxidase axis is not involved in the initial phase of clinical transplantation-related ischemia-reperfusion injury
Authors: Wijermars Leonie G. M. , Bakker Jaap A. , de Vries Dorottya K. , van Noorden Cornelis J. F. , Bierau Jörgen , Kostidis Sarantos , Mayboroda Oleg A. , Tsikas Dimitrios , Schaapherder Alexander F. , Lindeman Jan H. N.
Published: December 2016

The hypoxanthine-xanthine oxidase (XO) axis is considered to be a key driver of transplantation-related ischemia-reperfusion (I/R) injury. Whereas interference with this axis effectively quenches I/R injury in preclinical models, there is limited efficacy of XO inhibitors in clinical trials. In this context, we considered clinical evaluation of a role for the hypoxanthine-XO axis in human I/R to be relevant. Patients undergoing renal allograft transplantation were included ( n = 40) and classified based on duration of ischemia (short, intermediate, and prolonged). Purine metabolites excreted by the reperfused kidney (arteriovenous differences) were analyzed by the ultra performance liquid chromatography-tandem mass spectrometer (UPLCMS/MS) method and tissue XO activity was assessed by in situ enzymography. We confirmed progressive hypoxanthine accumulation ( P < 0.006) during ischemia, using kidney transplantation as a clinical model of I/R. Yet, arteriovenous concentration differences of uric acid and in situ enzymography of XO did not indicate significant XO activity in ischemic and reperfused kidney grafts. Furthermore, we tested a putative association between hypoxanthine accumulation and renal oxidative stress by assessing renal malondialdehyde and isoprostane levels and allantoin formation during the reperfusion period. Absent release of these markers is not consistent with an association between ischemic hypoxanthine accumulation and postreperfusion oxidative stress. On basis of these data for the human kidney we hypothesize that the role for the hypoxanthine-XO axis in clinical I/R injury is less than commonly thought, and as such the data provide an explanation for the apparent limited clinical efficacy of XO inhibitors.
Principles of auditory processing differ between sensory and premotor structures of the songbird forebrain
Authors: Soyman Efe , Vicario David S.
Published: December 2016

Sensory and motor brain structures work in collaboration during perception. To evaluate their respective contributions, the present study recorded neural responses to auditory stimulation at multiple sites simultaneously in both the higher-order auditory area NCM and the premotor area HVC of the songbird brain in awake zebra finches ( Taeniopygia guttata). Bird’s own song (BOS) and various conspecific songs (CON) were presented in both blocked and shuffled sequences. Neural responses showed plasticity in the form of stimulus-specific adaptation, with markedly different dynamics between the two structures. In NCM, the response decrease with repetition of each stimulus was gradual and long-lasting and did not differ between the stimuli or the stimulus presentation sequences. In contrast, HVC responses to CON stimuli decreased much more rapidly in the blocked than in the shuffled sequence. Furthermore, this decrease was more transient in HVC than in NCM, as shown by differential dynamics in the shuffled sequence. Responses to BOS in HVC decreased more gradually than to CON stimuli. The quality of neural representations, computed as the mutual information between stimuli and neural activity, was higher in NCM than in HVC. Conversely, internal functional correlations, estimated as the coherence between recording sites, were greater in HVC than in NCM. The cross-coherence between the two structures was weak and limited to low frequencies. These findings suggest that auditory communication signals are processed according to very different but complementary principles in NCM and HVC, a contrast that may inform study of the auditory and motor pathways for human speech processing.

NEW & NOTEWORTHY Neural responses to auditory stimulation in sensory area NCM and premotor area HVC of the songbird forebrain show plasticity in the form of stimulus-specific adaptation with markedly different dynamics. These two structures also differ in stimulus representations and internal functional correlations. Accordingly, NCM seems to process the individually specific complex vocalizations of others based on prior familiarity, while HVC responses appear to be modulated by transitions and/or timing in the ongoing sequence of sounds.
Spinal cord direct current stimulation differentially modulates neuronal activity in the dorsal and ventral spinal cord
Authors: Song Weiguo , Martin John H.
Published: December 2016

Spinal cord direct current stimulation (sDCS) has the potential for promoting motor function after injury through its modulatory actions on sensory processing, reflex functions, the motor cortex (M1) motor map, and motor output. Here we addressed systems-level mechanisms underlying sDCS neuromodulation of spinal circuits activated by M1 and peripheral forelimb electrical stimulation in anesthetized healthy rats. We determined the effects of cathodal and anodal sDCS (c- and a-sDCS) on local field potentials (LFP) and single-unit activity recorded at 32 sites simultaneously within the sixth cervical segment using a silicon multielectrode array. M1 stimulation produced distinctive dorsomedial and ventral LFP responses that showed polarity-dependent sDCS modulation. c-sDCS enhanced and a-sDCS depressed significantly ventral M1 responses; neither modulated dorsal responses significantly. Using evoked changes in β- and γ-oscillations to assay network function, c-sDCS enhanced and a-sDCS reduced oscillation power ventrally. c-sDCS increased and a-sDCS decreased background firing and firing synchrony of recorded pairs of single units. Peripheral stimulation produced a region-dependent response that showed polarity-dependent sDCS modulation. The dorsomedial LFP was unaffected by c-sDCS and weakly suppressed with a-sDCS. Peripheral-evoked unit responses showed limited polarity dependence. Our findings stress that ventral motor network behavior is enhanced by the neuromodulatory actions of c-sDCS. The combined actions of c-sDCS on M1-evoked neural responses and network behavior in the cervical spinal cord help explain the reported enhanced motor effects of this neuromodulation approach and inform the mechanisms of sDCS for promoting motor rehabilitation after spinal cord or brain injury.

NEW & NOTEWORTHY Spinal cord direct current stimulation (sDCS) modulates spinal functions and shows potential for neural rehabilitation after motor systems injury. Using a multichannel electrode array, we found that cathodal DCS enhanced, and anodal depressed, M1-evoked local field potentials, network oscillations, neuronal activity, and neuronal synchrony, especially in the ventral horn. With this new understanding, it is hoped that sDCS can be developed into a tunable spinal neuromodulatory tool for promoting function after brain or spinal injury.
The Structure and Clinical Roles of MicroRNA in Colorectal Cancer
Authors: Zhu Linwensi , Fang Jingyuan
Published: December 2016

Colorectal cancer (CRC) is one of the most prevalent types of malignancies, particularly among individuals aged between 50 and 75. The global incidence of CRC has been steadily on the rise due in no small part to an aging population and a shift in lifestyle as well as eating habits. MicroRNAs are a group of small, noncoding, and endogenous RNA molecules that have recently emerged as key players in a broad range of pathological pathways. Moreover, dysregulation of microRNAs has been implicated in cancer development and metastasis. This review is intended to provide a brief overview of the structure, functions, and clinical roles of microRNAs. In particular, the review will focus on the discovery, the underlying mechanistic roles, and the diagnostic as well as therapeutic potentials of CRC-specific miRNAs.
Potential Distribution of Chagas Disease Vectors (Hemiptera, Reduviidae, Triatominae) in Colombia, Based on Ecological Niche Modeling
Authors: Parra-Henao Gabriel , Suárez-Escudero Laura C. , González-Caro Sebastián
Published: December 2016

Ecological niche modeling of Triatominae bugs allow us to establish the local risk of transmission of the parasiteTrypanosoma cruzi,which causes Chagas disease.This information could help to guide health authority recommendations on infection monitoring, prevention, and control. In this study, we estimated the geographic distribution of triatomine species in Colombia and identified the relationship between landscape structure and climatic factors influencing their occurrence. A total of 2451 records of 4 triatomine species (Panstrongylus geniculatus,Rhodnius pallescens,R. prolixus, andTriatoma maculata) were analyzed.The variables that provided more information to explain the ecologic niche of these vectors were related to precipitation, altitude, and temperature. We found that the species with the broadest potential geographic distribution wereP. geniculatus,R. pallescens, andR. prolixus. In general, the models predicted the highest occurrence probability of these vectors in the eastern slope of the Eastern Cordillera, the southern region of the Magdalena valley, and the Sierra Nevada of Santa Marta.
A Novel Bearing Fault Diagnosis Method Based on Gaussian Restricted Boltzmann Machine
Authors: He Xiao-hui , Wang Dong , Li Yan-feng , Zhou Chun-hua
Published: December 2016

To realize the fault diagnosis of bearing effectively, this paper presents a novel bearing fault diagnosis method based on Gaussian restricted Boltzmann machine (Gaussian RBM). Vibration signals are firstly resampled to the same equivalent speed. Subsequently, the envelope spectrums of the resampled data are used directly as the feature vectors to represent the fault types of bearing. Finally, in order to deal with the high-dimensional feature vectors based on envelope spectrum, a classifier model based on Gaussian RBM is applied. Gaussian RBM has the ability to provide a closed-form representation of the distribution underlying the training data, and it is very convenient for modeling high-dimensional real-valued data. Experiments on 10 different data sets verify the performance of the proposed method. The superiority of Gaussian RBM classifier is also confirmed by comparing with other classifiers, such as extreme learning machine, support vector machine, and deep belief network. The robustness of the proposed method is also studied in this paper. It can be concluded that the proposed method can realize the bearing fault diagnosis accurately and effectively.