bluuebunny/crossref_metadata_2025 huggingface dataset:
Housing type after the Great East Japan Earthquake and loss of motor function in elderly victims: a prospective observational study
Authors: Ito Kumiko , Tomata Yasutake , Kogure Mana , Sugawara Yumi , Watanabe Takashi , Asaka Tadayoshi , Tsuji Ichiro
Published: November 2016

Objective

Previous studies have reported that elderly victims of natural disasters might be prone to a subsequent decline in motor function. Victims of the Great East Japan Earthquake (GEJE) relocated to a wide range of different types of housing. As the evacuee lifestyle varies according to the type of housing available to them, their degree of motor function loss might also vary accordingly. However, the association between postdisaster housing type and loss of motor function has never been investigated. The present study was conducted to investigate the association between housing type after the GEJE and loss of motor function in elderly victims.

Methods

We conducted a prospective observational study of 478 Japanese individuals aged ≥65 years living in Miyagi Prefecture, one of the areas most significantly affected by the GEJE. Information on housing type after the GEJE, motor function as assessed by the Kihon checklist and other lifestyle factors was collected by interview and questionnaire in 2012. Information on motor function was then collected 1 year later. The multiple logistic regression model was used to estimate the multivariate adjusted ORs of motor function loss.

Results

We classified 53 (11.1%) of the respondents as having loss of motor function. The multivariate adjusted OR (with 95% CI) for loss of motor function among participants who were living in privately rented temporary housing/rental housing was 2.62 (1.10 to 6.24) compared to those who had remained in the same housing as that before the GEJE, and this increase was statistically significant.

Conclusions

The proportion of individuals with loss of motor function was higher among persons who had relocated to privately rented temporary housing/rental housing after the GEJE. This result may reflect the influence of a move to a living environment where few acquaintances are located (lack of social capital).
Pretzel scheme for CEPC
Authors: Geng Huiping
Published: November 2016

CEPC was proposed as an electron and positron collider ring with a circumference of 50–100 km to study the Higgs boson. Since the proposal was made, the lattice design for CEPC has been carried out and a preliminary conceptual design report has been written at the end of 2014. In this paper, we will describe the principles of pretzel scheme design, which is one of most important issues in CEPC lattice design. Then, we will show the modification of the lattice based on the lattice design shown in the Pre-CDR. The latest pretzel orbit design result will also be shown. The issues remained to be solved in the present design will be discussed and a brief summary will be given at the end.
Functionally Graded Piezoelectric Energy Harvester Using Thin Cylindrical Shell
Authors: Fan Tao , Shao Xiaohua
Published: November 2016

Presented herein is a functionally graded piezoelectric energy harvester using a thin cylindrical shell. The torsional mode for the thin cylindrical shell is studied and the effects of the functionally graded parameters on the power density are discussed. The analytical expressions for the power density are derived. From the results obtained, it can be observed that the functionally graded constant has obvious influences on the peak value of the power density. Moreover, larger values of the power density may be obtained by increasing the elastic parameter and the mass density. This work is expected to be useful in the analysis and design of energy harvester as well as new kinds of energy systems.
Theory of long-term interest rates
Authors: Rey Sebastián A.
Published: November 2016

This paper develops a general framework for deriving an arbitrage-free interest rates term structure related to long maturities that are not observed (traded) in the market. The original contribution is that the obtained long-term curve depends on variables that can be observed in the market or can be derived from it, avoiding the necessity of establishing arbitrary assumptions related to the ultimate long-term rate and how the convergence takes place.
Trading VIX futures under mean reversion with regime switching
Authors: Li Jiao
Published: November 2016

This paper studies the optimal VIX futures trading problems under a regime-switching model. We consider the VIX as mean reversion dynamics with dependence on the regime that switches among a finite number of states. For the trading strategies, we analyze the timings and sequences of the investor’s market participation, which leads to several corresponding coupled system of variational inequalities. The numerical approach is developed to solve these optimal double stopping problems by using projected-successive-over-relaxation (PSOR) method with Crank–Nicolson scheme. We illustrate the optimal boundaries via numerical examples of two-state Markov chain model. In particular, we examine the impacts of transaction costs and regime-switching timings on the VIX futures trading strategies.
Extending the Kernel of a Relational DBMS with Comprehensive Support for Sequenced Temporal Queries
Authors: Dignös Anton , Böhlen Michael H. , Gamper Johann , Jensen Christian S.
Published: November 2016

Many databases contain temporal, or time-referenced, data and use intervals to capture the temporal aspect. While SQL-based database management systems (DBMSs) are capable of supporting the management of interval data, the support they offer can be improved considerably. A range of proposed temporal data models and query languages offer ample evidence to this effect. Natural queries that are very difficult to formulate in SQL are easy to formulate in these temporal query languages. The increased focus on analytics over historical data where queries are generally more complex exacerbates the difficulties and thus the potential benefits of a temporal query language. Commercial DBMSs have recently started to offer limited temporal functionality in a step-by-step manner, focusing on the representation of intervals and neglecting the implementation of the query evaluation engine.

This article demonstrates how it is possible to extend the relational database engine to achieve a full-fledged, industrial-strength implementation of sequenced temporal queries, which intuitively are queries that are evaluated at each time point. Our approach reduces temporal queries to nontemporal queries over data with adjusted intervals, and it leaves the processing of nontemporal queries unaffected. Specifically, the approach hinges on three concepts:
interval adjustment
,
timestamp propagation
, and
attribute scaling
. Interval adjustment is enabled by introducing two new relational operators, a temporal normalizer and a temporal aligner, and the latter two concepts are enabled by the replication of timestamp attributes and the use of so-called scaling functions. By providing a set of reduction rules, we can transform any temporal query, expressed in terms of temporal relational operators, to a query expressed in terms of relational operators and the two new operators. We prove that the size of a transformed query is linear in the number of temporal operators in the original query. An integration of the new operators and the transformation rules, along with query optimization rules, into the kernel of PostgreSQL is reported. Empirical studies with the resulting temporal DBMS are covered that offer insights into pertinent design properties of the article's proposal. The new system is available as open-source software.
Optimized Standard Cells for All-Spin Logic
Authors: Mankalale Meghna G. , Sapatnekar Sachin S.
Published: November 2016

All-Spin Logic (ASL) devices provide a promising spintronics-based alternative for Boolean logic implementations in the post-Complementary Metal-Oxide Semiconductor (CMOS) era. In principle, any logic functionality can be implemented in ASL. In practice, the performance of an ASL gate is significantly affected by layout choices, but such implications have not been adequately explored in the past. This article proposes a systematic approach for building standard cells in ASL, which are a basic building block in an overall design methodology for implementing large ASL-based circuits. We first propose a new technique to reduce the magnet count for an ASL majority gate but still ensure correct functioning through layout optimization methods. Building on physics-based analysis, we then build a standard cell library with diverse functionality and characterize the library for delay, energy, and area. We perform delay-optimized technology mapping on ISCAS85 benchmark circuits using our library. Our approach results in circuits that are 12.90% faster, consume 26.16% less energy, and are 33.56% more area efficient compared to a standard cell library that does not incorporate layout-based optimization techniques of our work.
Guarded-Based Disjunctive Tuple-Generating Dependencies
Authors: Bourhis Pierre , Manna Marco , Morak Michael , Pieris Andreas
Published: November 2016

We perform an in-depth complexity analysis of query answering under guarded-based classes of disjunctive tuple-generating dependencies (DTGDs), focusing on (unions of) conjunctive queries ((U)CQs). We show that the problem under investigation is very hard, namely 2E
xp
T
ime
-complete, even for fixed sets of dependencies of a very restricted form. This is a surprising lower bound that demonstrates the enormous impact of disjunction on query answering under guarded-based tuple-generating dependencies, and also reveals the source of complexity for expressive logics such as the guarded fragment of first-order logic. We then proceed to investigate whether prominent subclasses of (U)CQs (i.e., queries of bounded treewidth and hypertree-width, and acyclic queries) have a positive impact on the complexity of the problem under consideration. We show that queries of bounded treewidth and bounded hypertree-width do not reduce the complexity of our problem, even if we focus on predicates of bounded arity or on fixed sets of DTGDs. Regarding acyclic queries, although the problem remains 2E
xp
T
ime
-complete in general, in some relevant settings the complexity reduces to E
xp
T
ime
-complete. Finally, with the aim of identifying tractable cases, we focus our attention on atomic queries. We show that atomic queries do not make the query answering problem easier under classes of guarded-based DTGDs that allow more than one atom to occur in the body of the dependencies. However, the complexity significantly decreases in the case of dependencies that can have only one atom in the body. In particular, we obtain a P
time
-completeness if we focus on predicates of bounded arity, and

AC
0

-membership when the set of dependencies and the query are fixed. Interestingly, our results can be used as a generic tool for establishing complexity results for query answering under various description logics.
Learning from Collective Intelligence
Authors: Zhang Hanwang , Shang Xindi , Luan Huanbo , Wang Meng , Chua Tat-Seng
Published: November 2016

Feature representation for visual content is the key to the progress of many fundamental applications such as annotation and cross-modal retrieval. Although recent advances in deep feature learning offer a promising route towards these tasks, they are limited in application domains where high-quality and large-scale training data are expensive to obtain. In this article, we propose a novel deep feature learning paradigm based on social collective intelligence, which can be acquired from the inexhaustible social multimedia content on the Web, in particular, largely social images and tags. Differing from existing feature learning approaches that rely on high-quality image-label supervision, our weak supervision is acquired by mining the visual-semantic embeddings from noisy, sparse, and diverse social image collections. The resultant image-word embedding space can be used to (1) fine-tune deep visual models for low-level feature extractions and (2) seek sparse representations as high-level cross-modal features for both image and text. We offer an easy-to-use implementation for the proposed paradigm, which is fast and compatible with any state-of-the-art deep architectures. Extensive experiments on several benchmarks demonstrate that the cross-modal features learned by our paradigm significantly outperforms others in various applications such as content-based retrieval, classification, and image captioning.
The Equivalence of the Torus and the Product of Two Circles in Homotopy Type Theory
Authors: Sojakova Kristina
Published: November 2016

Homotopy type theory is a new branch of mathematics that merges insights from abstract homotopy theory and higher category theory with those of logic and type theory. It allows us to represent a variety of mathematical objects as basic type-theoretic construction, higher inductive types. We present a proof that in homotopy type theory, the torus is equivalent to the product of two circles. This result indicates that the synthetic definition of torus as a higher inductive type is indeed correct.
FTT-openFlow, on the way towards real-time SDN
Authors: Ternon Cédric , Goossens Joël , Dricot Jean-Michel
Published: November 2016

Software-defined networking proposes a new paradigm to operate computer networks. Where routers and switches execute predetermined distributed protocols, OpenFlow offers to replace them with devices where the logic that determines the flows of packets is freely programmable and centralized. Applied to the field of real-time networks, this freedom would allow design networks to overcome existing standards and to make experimentation easier. However, neither OpenFlow nor Ethernet were designed having real-time constraints in mind. FTT-Ethernet is a master-slave protocol allowing the meeting of real-time constraints using commodity Ethernet hardware. This paper's aim is to study: (i) how FTT (Flexible Time Triggered) principles could be applied to OpenFlow, allowing its usage in a hard real-time context; (ii) which benefits OpenFlow can bring to the FTT paradigm.
Development of automatic reasoning tools in GeoGebra
Authors: Abánades Miguel , Botana Francisco , Kovács Zoltán , Recio Tomás , Sólyom-Gecse Csilla
Published: November 2016

Much effort has been put into the implementation of automatic proving in interactive geometric environments (e.g. Java Geometry Expert, GeoGebra). The closely related concept of automatic discovery, remains however almost unexplored.

This software presentation will demonstrate our results towards the incorporation of automatic discovery capabilities into GeoGebra, an educational software with tens of millions of users worldwide. As main result, we report on a new command, currently available in the official version, that allows the automatic discovery of loci of points in diagrams defined by implicit conditions. This represents an extension of a previous command, similar in nature, but restricted to loci defined by the standard mover-tracer construction. Our proposal successfully automates the `dummy locus dragging' in dynamic geometry. This makes the cycle conjecturing-checking-proving accessible for general users in elementary geometry.
Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes
Authors: Schutze Mark K. , Virgilio Massimiliano , Norrbom Allen , Clarke Anthony R.
Published: November 2016

Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.
Anthropogenic Forcing of Carbonate and Organic Carbon Preservation in Marine Sediments
Authors: Keil Richard
Published: November 2016

Carbon preservation in marine sediments, supplemented by that in large lakes, is the primary mechanism that moves carbon from the active surficial carbon cycle to the slower geologic carbon cycle. Preservation rates are low relative to the rates at which carbon moves between surface pools, which has led to the preservation term largely being ignored when evaluating anthropogenic forcing of the global carbon cycle. However, a variety of anthropogenic drivers—including ocean warming, deoxygenation, and acidification, as well as human-induced changes in sediment delivery to the ocean and mixing and irrigation of continental margin sediments—all work to decrease the already small carbon preservation term. These drivers affect the cycling of both carbonate and organic carbon in the ocean. The overall effect of anthropogenic forcing in the modern ocean is to decrease delivery of carbon to sediments, increase sedimentary dissolution and remineralization, and subsequently decrease overall carbon preservation.
Biological roles of microRNAs in the control of insulin secretion and action
Authors: Calderari Sophie , Diawara Malika R. , Garaud Alois , Gauguier Dominique
Published: November 2016

microRNAs (miRNAs) are intracellular and circulating molecular components contributing to genome expression control through binding mRNA targets, which generally results in downregulated mRNA expression. One miRNA can target several mRNAs, and one transcript can be targeted by several miRNAs, resulting in complex fine-tuning of regulation of gene networks and signaling pathways. miRNAs regulate metabolism, adipocyte differentiation, pancreatic development, β-cell mass, insulin biosynthesis, secretion, and signaling, and their role in diabetes and obesity is emerging. Their pathophysiological effects are essentially dependent on cellular coexpression with their mRNA targets, which can show tissue-specific transcriptional responses to disease conditions and environmental challenges. Current knowledge of miRNA biology and their impact on the pathogenesis of diabetes and obesity is based on experimental data documenting miRNA expression generally in single tissue types that can be correlated with expression of target mRNAs to integrate miRNA in functional pathways and gene networks. Here we present results from the most significant studies dealing with miRNA function in liver, fat, skeletal muscle, and endocrine pancreas and their implication in diabetes and obesity.
Autophagy Prevents Oxidative Stress-Induced Loss of Self-Renewal Capacity and Stemness in Human Tendon Stem Cells by Reducing ROS Accumulation
Authors: Chen Hua , Ge Heng-an , Wu Gen-bing , Cheng Biao , Lu Yong , Jiang Chaoyin
Published: November 2016

Background/Aims: Tendon stem cells (TSCs) exhibit a high self-renewal capacity, multi-differentiation potential, and low immunogenicity; thus, these cells might provide a new cell source for tendon repair and regeneration. TSCs are exposed to increased oxidative stress at tendon injury sites; however, how TSCs maintain their stemness under oxidative stress is not clear. Methods and Results: In this study, we found that H2O2 treatment increased ROS accumulation in human TSCs (hTSCs) and resulted in loss of self-renewal capacity and stemness, as reflected in reduced colony formation and proliferation, decreased expression of the stemness markers Nanog, Oct-4, NS, and SSEA-4, and impaired differentiation capability. These H2O2-induced damages were prevented by pretreatment with starvation or rapamycin. Pretreatment with starvation or rapamycin prior to H2O2 exposure also led to decreased intracellular and mitochondrial ROS accumulation along with increased autophagic activity, as manifested in increased LC3 cleavage, Beclin-1 expression, and GFP-LC3-labeled autophagosome formation. Autophagy inhibition by 3-MA or CQ, or by shRNA silencing of Agt-7 or Beclin-1 reduced the protective effects of starvation and rapamycin on H2O2-treated hTSCs. Conclusion: Thus, the findings of this study suggest that autophagy prevents oxidative stress-induced loss of self-renewal capacity and stemness in hTSCs through suppression of ROS accumulation.
Biofilm Formation Restrained by Subinhibitory Concentrations of Tigecyclin in Acinetobacter baumannii Is Associated with Downregulation of Efflux Pumps
Authors: Chen Huale , Cao Jianming , Zhou Cui , Liu Haiyang , Zhang Xiaoxiao , Zhou Tieli
Published: November 2016

Background: Tigecycline, one of the few therapeutic options against multidrug-resistant Acinetobacter baumannii, reaches subinhibitory serum concentrations only with cautious clinical dosing and pharmacokinetics. Subinhibitory concentrations of tigecycline might induce an A. baumannii biofilm. Methods: Biofilm formation was assessed via the crystal violet staining method. We further analyzed the main biofilm components with NaIO4, proteinase K, and DNase. Real-time RT-PCR was applied for quantitative detection of biofilm potential-associated genes. Results: In this study, A. baumannii proved to be a strong biofilm producer, and we found that proteins and extracellular DNA are crucial components of the A. baumannii biofilm. Quantitative real-time RT-PCR revealed positive correlations between biofilm formation restrained by subinhibitory concentrations of tigecycline and the expression of biofilm potential-associated genes, especially the AdeFGH efflux pump gene. Conclusion: Our results suggest that downregulation of efflux pumps, especially the AdeFGH efflux pump, is probably responsible for the decline in biofilm formation in A. baumannii treated with subinhibitory concentrations of tigecyclin.
Tachysystole Following Cervical Ripening and Induction of Labor Is Not Associated with Adverse Outcomes
Authors: Bofill James A. , Darby Marie M. , Castillo Javier , Sawardecker Sandip U. , Magann Everett F. , Morrison John C.
Published: November 2016

Purpose: This study was aimed at determining if significant uterine tachysystole was associated with adverse fetal or neonatal outcomes during cervical ripening and induction of labor. Methods: Women undergoing cervical ripening and subsequent labor induction (n = 905) were assessed for tachysystole, defined as ≥6 contractions in each of 2 consecutive 10-minute windows. Women with ≥3 episodes of tachysystole were compared to women with no tachysystole. Results: Over a 5-year period, 70% of the 905 participants (n = 631) had no tachysystole, 143 had 1 or 2 episodes whereas 131 or 15% had ≥3 episodes (p = 0.991). The cesarean delivery rate was lower among those with tachysystole (28.2 vs. 34.1%), but the difference was not significant (p = 0.197). Non-reassuring fetal tracings were more common in the tachysystole group (14.4 vs. 21.4%, p = 0.017), but the Apgar scores at 5 min and the umbilical cord pH and base excess were similar between the 2 groups (p = 0.502, p = 0.435, and p = 0.535, respectively). Conclusions: Tachysystole was not associated with adverse perinatal outcomes when compared to women with no tachysystole during cervical ripening and induction of labor.
Computed Tomographic Perfusion Improves Diagnostic Power of Coronary Computed Tomographic Angiography in Women
Authors: Penagaluri Ashritha , Higgins Angela Y. , Vavere Andrea L. , Miller Julie M. , Arbab-Zadeh Armin , Betoko Aisha , Steveson Chloe , Zimmermann Elke , Cox Christopher , Rochitte Carlos E. , Dewey Marc , Kofoed Klaus F. , Niinuma Hiroyuki , Di Carli Marcelo F. , Lima João A.C. , Chen Marcus Y.
Published: November 2016

Background—

Coronary computed tomographic angiography (CTA) and myocardial perfusion imaging (CTP) is a validated approach for detection and exclusion of flow-limiting coronary artery disease (CAD), but little data are available on gender-specific performance of these modalities. In this study, we aimed to evaluate the diagnostic accuracy of combined coronary CTA and CTP in detecting flow-limiting CAD in women compared with men.

Methods and Results—

Three hundred and eighty-one patients who underwent both CTA-CTP and single-photon emission computed tomography myocardial perfusion imaging preceding invasive coronary angiography as part of the CORE320 multicenter study (Coronary Artery Evaluation Using 320-row Multidetector Computed Tomography Angiography and Myocardial Perfusion) were included in this ancillary study. All 4 image modalities were analyzed in blinded, independent core laboratories. Prevalence of flow-limiting CAD defined by invasive coronary angiography equal to 50% or greater with an associated single-photon emission computed tomography myocardial perfusion imaging defect was 45% (114/252) and 23% (30/129) in males and females, respectively. Patient-based diagnostic accuracy defined by the area under the receiver operating curve for detecting flow-limiting CAD by CTA alone in females was 0.83 (0.75–0.89) and for CTA-CTP was 0.92 (0.86–0.97;
P
=0.003) compared with men where the area under the receiver operating curve for detecting flow-limiting CAD by CTA alone was 0.82 (0.77–0.87) and for CTA-CTP was 0.84 (0.80–0.89;
P
=0.29).

Conclusions—

The combination of CTA-CTP was performed similarly in men and women for identifying flow-limiting coronary stenosis; however, in women, CTP had incremental value over CTA alone, which was not the case in men.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00934037.
Effect of Exhaust- and Nonexhaust-Related Components of Particulate Matter on Long-Term Survival After Stroke
Authors: Desikan Anita , Crichton Siobhan , Hoang Uy , Barratt Benjamin , Beevers Sean D. , Kelly Frank J. , Wolfe Charles D.A.
Published: November 2016

Background and Purpose—

Outdoor air pollution represents a potentially modifiable risk factor for stroke. We examined the link between ambient pollution and mortality up to 5 years poststroke, especially for pollutants associated with vehicle exhaust.

Methods—

Data from the South London Stroke Register, a population-based register covering an urban, multiethnic population, were used. Hazard ratios (HR) for a 1 interquartile range increase in particulate matter <2.5 µm diameter (PM
2.5
) and PM <10 µm (PM
10
) were estimated poststroke using Cox regression, overall and broken down into exhaust and nonexhaust components. Analysis was stratified for ischemic and hemorrhagic strokes and was further broken down by Oxford Community Stroke Project classification.

Results—

The hazard of death associated with PM
2.5
up to 5 years after stroke was significantly elevated (
P
=0.006) for all strokes (HR=1.28; 95% confidence interval [CI], 1.08–1.53) and ischemic strokes (HR, 1.32; 95% CI, 1.08–1.62). Within ischemic subtypes, PM
2.5
pollution increased mortality risk for total anterior circulation infarcts by 2-fold (HR, 2.01; 95% CI, 1.17–3.48;
P
=0.012) and by 78% for lacunar infarcts (HR, 1.78; 95% CI, 1.18–2.66;
P
=0.006). PM
10
pollution was associated with 45% increased mortality risk for lacunar infarct strokes (HR, 1.45; 95% CI, 1.06–2.00;
P
=0.022). Separating PM
2.5
and PM
10
into exhaust and nonexhaust components did not show increased mortality.

Conclusions—

Exposure to certain outdoor PM pollution, particularly PM
2.5
, increased mortality risk poststroke up to 5 years after the initial stroke.
Occurrence of the rare lobster Palinustus unicornutus Berry, 1979 (Decapoda, Palinuridae) in Taiwan
Authors: Chan Tin-Yam , Lin Chih-Chun , Jeng Ming-Shou
Published: November 2016

The deep-sea lobster Palinustus unicornutus Berry, 1979 is reported for the first time from Taiwan, with the largest male and female ever recorded for the species. Additional material of this rare species showed that many distinguishing characters previously suggested for this species are actually variable and its characteristics are re-diagnosed.
Participatory Ethnographic Evaluation and Research: Reflections on the Research Approach Used to Understand the Complexity of Maternal Health Issues in South Sudan
Authors: Elmusharaf Khalifa , Byrne Elaine , Manandhar Mary , Hemmings Joanne , O’Donovan Diarmuid
Published: November 2016

Many methodological approaches have been used to understand cultural dimensions to maternal health issues. Although a well-designed quantitative survey with a representative sample can provide essential information on trends in behavior, it does not necessarily establish a contextualized understanding of the complexity in which different behaviors occur. This article addresses how contextualized data can be collected in a short time and under conditions in which participants in conflict-affected zones might not have established, or time to establish, trust with the researchers. The solution, the Participatory Ethnographic Evaluation and Research (PEER) approach, is illustrated through a study whereby South Sudanese marginalized women were trained to design research instruments, and collect and analyze qualitative data. PEER overcomes the problem that many ethnographic or participatory approaches face—the extensive time and resources required to develop trusting relationships with the community to understand the local context and the social networks they form.
The psychophysiological mechanisms of alexithymia in autism spectrum disorder
Authors: Gaigg Sebastian B , Cornell Anna SF , Bird Geoffrey
Published: November 2016

Accumulating evidence indicates that co-occurring alexithymia underlies several facets of the social-emotional difficulties common in individuals with autism spectrum disorder. The mechanisms involved, however, remain poorly understood because measuring alexithymia relies heavily on self-report. To address this issue, carefully matched groups of individuals with autism spectrum disorder and comparison participants rated 70 emotion-inducing pictures on subjectively experienced arousal while skin conductance responses were monitored objectively. The results demonstrated reliable correlations between these subjective and objective measures, and in both groups, around 25% of individual differences in this correlation (i.e. in emotion-relevant interoception) were accounted for by self-reported alexithymia. In the context of the wider literature, this suggests that alexithymia involves a disruption in how physiological arousal modulates the subjective experience of feelings in those with and without a diagnosis of autism spectrum disorder. Since mindfulness-based therapies foster greater awareness of thoughts, feelings and bodily sensations, the findings also have implications for how the symptoms and consequences of alexithymia (e.g. anxiety) might be ameliorated.
Wind tunnel test and numerical simulation of wind characteristics at a bridge site in mountainous terrain
Authors: Li Yongle , Xu Xinyu , Zhang Mingjin , Xu Youlin
Published: November 2016

Wind tunnel test and computational fluid dynamics simulation were conducted to study the wind characteristics at a bridge site in mountainous terrain. The upstream terrains were classified into three types: open terrain, open terrain with a steep slope close to the bridge, and open terrain with a ridge close to the bridge. Results obtained from the two methods were compared, including mean speed profiles in the vertical direction and variations of wind speed and angle of attack along the bridge deck. In addition, turbulence intensities at the bridge site obtained from wind tunnel test were discussed. For mean speed profiles in the vertical direction, two methods are reasonably close for open terrain, while mountain shielding effects are evident for open terrain with a steep slope for both the methods, but the extents of effects appear different. Wind speed and angle of attack along the bridge deck are mainly influenced by the local terrain. Strong downslope wind is generated at the lee slope for the case of wind normal to top of the ridge. The comparative results are expected to provide useful references for the study of wind characteristics in mountainous terrain in the future.
muBLASTP: database-indexed protein sequence search on multicore CPUs
Authors: Zhang Jing , Misra Sanchit , Wang Hao , Feng Wu-chun
Published: November 2016

Background

The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search.

Results

muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST.

Conclusions

With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.
Telomere length and depression: Prospective cohort study and Mendelian randomisation study in 67 306 individuals
Authors: Wium-Andersen Marie Kim , Ørsted David Dynnes , Rode Line , Bojesen Stig Egil , Nordestgaard Børge Grønne
Published: November 2016

Background

Depression has been cross-sectionally associated with short telomeres as a measure of biological age. However, the direction and nature of the association is currently unclear.

Aims

We examined whether short telomere length is associated with depression cross-sectionally as well as prospectively and genetically.

Method

Telomere length and three polymorphisms, TERT, TERC and OBFC1, were measured in 67306 individuals aged 20–100 years from the Danish general population and associated with register-based attendance at hospital for depression and purchase of antidepressant medication.

Results

Attendance at hospital for depression was associated with short telomere length cross-sectionally, but not prospectively. Further, purchase of antidepressant medication was not associated with short telomere length cross-sectionally or prospectively. Mean follow-up was 7.6 years (range 0.0–21.5). The genetic analyses suggested that telomere length was not causally associated with attendance at hospital for depression or with purchase of antidepressant medication.

Conclusions

Short telomeres were not associated with depression in prospective or in causal, genetic analyses.
A general relationship links gait mechanics and running ground reaction forces
Authors: Clark Kenneth P. , Ryan Laurence J. , Weyand Peter G.
Published: November 2016

The relationship between gait mechanics and running ground reaction forces is widely regarded as complex. This viewpoint has evolved primarily via efforts to explain the rising-edge of vertical force-time waveforms observed during slow human running. Existing theoretical models do provide good rising-edge fits, but require more than a dozen input variables to sum the force contributions of four or more vague components of the body's total mass (mb). Here, we hypothesized that the force contributions of two discrete body mass components are sufficient to account for vertical ground reaction force-time waveforms patterns in full [stance foot and shank, m1=0.08•mb; remaining mass, m2=0.92•mb]. We tested this hypothesis directly by acquiring simultaneous limb motion and ground reaction force data across a broad range of running speeds (3.0-11.1 m•s−1) from 42 subjects who differed in body mass (range: 43-105 kg) and foot-strike mechanics. Predicted waveforms were generated from our two-mass model using body mass and three stride-specific measures: contact time, aerial time, and lower-limb vertical acceleration during impact. Measured waveforms (n=500) differed in shape and varied by more than two-fold in amplitude and duration. Nonetheless, the overall agreement between the 500 measured waveforms and those generated independently by the model approached unity (R2=0.95±0.04; mean±sd), with minimal variation across the slow, medium and fast running speeds tested (ΔR2≤0.04), and between rear-foot (R2=0.94±0.04, n=177) vs. fore-foot (R2=0.95±0.04, n=323) strike mechanics. We conclude that two, anatomically-discrete components of the body's mass are sufficient to fully explain running vertical ground reaction forces.
Comparative locomotor costs of domestic dogs reveal energetic economy of wolf-like breeds
Authors: Bryce C. M. , Williams T. M.
Published: November 2016

The broad diversity in morphology and geographic distribution of the 35 free-ranging members of the family Canidae is only rivaled by that of the domesticated dog, Canis lupus familiaris. Considered to be among nature's most elite endurance athletes, both domestic and wild canids provide a unique opportunity to examine the variability in mammalian aerobic exercise performance and energy expenditure. To determine the potential effects of domestication and selective breeding on locomotor gait and economy in canids, we measured the kinematics and mass-specific metabolism of three large (>20 kg) dog breed groups (northern breeds, retrievers, and hounds) of varying morphological and genomic relatedness to their shared progenitor, the gray wolf. By measuring all individuals moving in preferred steady-state gaits along a level transect and on a treadmill, we found distinct biomechanical, kinematic, and energetic patterns for each breed group. While all groups exhibited reduced total cost of transport (COT) at faster speeds, the total COT and net COT during trotting and galloping were significantly lower for northern breed dogs (3.0 and 2.1 J∙kg−1∙m−1, respectively) relative to hound (4.2 and 3.4 J∙kg−1∙m−1, respectively) and retriever dogs (3.8 and 3.0 J∙kg−1∙m−1, respectively) of comparable mass. Similarly, northern breeds expended less energy per stride (3.47 J∙kg−1∙stride−1) than hounds or retrievers (4.97 and 4.02 J∙kg−1∙stride−1, respectively). These results suggest that, in addition to their close genetic and morphological ties to gray wolves, northern breed dogs have retained highly cursorial kinematic and physiological traits that promote economical movement across the landscape.
A second visual rhodopsin gene,rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes
Authors: Morrow James M. , Lazic Savo , Fox Monica Dixon , Kuo Claire , Schott Ryan K. , Gutierrez Eduardo de A. , Santini Francesco , Tropepe Vincent , Chang Belinda S. W.
Published: November 2016

Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene, however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localize expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1. We also express, purify, and characterize Rh1-2, including investigations of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we find the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressures to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1. These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.
Developmental changes in head movement kinematics during swimming inXenopus laevistadpoles
Authors: Hänzi Sara , Straka Hans
Published: November 2016

During the post-embryonic developmental growth of animals, a number of physiological parameters such as locomotor performance, dynamics and behavioural repertoire are adjusted to match the requirements determined by changes in body size, proportions and shape. Moreover, changes in movement parameters also cause changes in the dynamics of self-generated sensory stimuli, to which motion-detecting sensory systems have to adapt. Here, we examined head movements and swimming kinematics of Xenopus laevis tadpoles with a body length of 10 to 45 mm (developmental stage 46 to 54) and compared these parameters to fictive swimming, recorded as ventral root activity in semi-intact in-vitro preparations. Head movement kinematics was extracted from high-speed video recordings of freely swimming tadpoles. Analysis of these locomotor episodes indicated that the swimming frequency decreased with development, along with the angular velocities and accelerations of the head, which represent self-generated vestibular stimuli. In contrast, neither head oscillation amplitudes nor forward velocities changed with development despite the ∼3-fold increase in body size. The comparison between free and fictive locomotor dynamics revealed very similar swimming frequencies for similarly sized animals, including a comparable developmental decrease of the swimming frequency. Body morphology and the motor output rhythm of the spinal central pattern generator therefore develop concurrently. This study thus describes development-specific naturalistic head motion profiles, which form the basis for more natural stimuli in future studies probing the vestibular system.
Spontaneous alternation behavior in larval zebrafish
Authors: Bögli Stefan Yu , Huang Melody Ying-Yu
Published: November 2016

Spontaneous alternation behavior (SAB) describes the tendency of animals to alternate their turn direction in consecutive turns. SAB, dissimilar from other mnestic tasks, does not require any prior training or reinforcement. Due to its close correlation to the development and function of hippocampus in mice, it is thought to reflect a type of memory. Adult zebrafish possess a hippocampus-like structure utilizing the same neurotransmitters as in human brains, and have thus been used to study memory. In the current study we established SAB in zebrafish larvae at 6 days post fertilization using a custom made forced-turn maze with a rate of 57%. Our demonstration of SAB's presence in larval zebrafish at a very early developmental stage not only provides evidence for early cognition in this species but suggests its future use as a high-throughput model for mnestic studies.
Reeleição para a Câmara dos Deputados em 2006: é possível vencer as incertezas do sistema eleitoral?
Authors: Augusto Álvaro
Published: November 2016

A pesquisa relaciona o sucesso ou o fracasso na tentativa de reeleição dos deputados federais no pleito de 2006 com o desempenho individual (votação maior ou menor) e o posicionamento de cada um na lista (não pior ou melhor), comparados a 2002, na tentativa de verificar se algum elemento intrínseco ao sistema eleitoral pode ser a garantia para a manutenção do mandato parlamentar. São encontradas situações correspondentes a cada uma das oito combinações possíveis, as quais, ao serem analisadas, demonstram que não há fórmula de sucesso na atual configuração do sistema eleitoral: fazer mais votos e/ou melhorar o posicionamento na lista não são suficientes para a manutenção do mandato, bem como desempenho pior em comparação ao pleito anterior não elimina esta possibilidade.
Recent advances in the management of pediatric acute lymphoblastic leukemia
Authors: Starý Jan , Hrušák Ondřej
Published: November 2016

Acute lymphoblastic leukemia (ALL) is the most common malignancy in childhood. Despite enormous improvement of prognosis during the last half century, ALL remains a major cause of childhood cancer-related mortality. During the past decade, whole genomic methods have enhanced our knowledge of disease biology. Stratification of therapy according to early treatment response measured by minimal residual disease allows risk group assignment into different treatment arms, ranging from reduction to intensification of treatment. Progress has been achieved in academic clinical trials by optimization of combined chemotherapy, which continues to be the mainstay of contemporary treatment. The availability of suitable volunteer main histocompatibility antigen-matched unrelated donors has increased the rates of hematopoietic stem cell transplantation (HSCT) over the past two decades. Allogeneic HSCT has become an alternative treatment for selected, very-high-risk patients. However, intensive treatment burdens children with severe acute toxic effects that can cause permanent organ damage and even toxic death. Immunotherapeutic approaches have recently come to the forefront in ALL therapy. Monoclonal antibodies blinatumomab and inotuzumab ozogamicin as well as gene-modified T cells directed to specific target antigens have shown efficacy against resistant/relapsed leukemia in phase I/II studies. Integration of these newer modalities into combined regimens with chemotherapy may rescue a subset of children not curable by contemporary therapy. Another major challenge will be to incorporate less toxic regimens into the therapy of patients with low-risk disease who have a nearly 100% chance of being cured, and the ultimate goal is to improve their quality of life while maintaining a high cure rate.
Report of the General Committee: 15
Authors: Wilson Karen L.
Published: November 2016

Decisions are reported on proposals in Reports 65 and 66 from the Nomenclature Committee for Vascular Plants (NCVP): (1) three proposals in Report 65; (2) 33 proposals to conserve or reject names recommended for acceptance in NCVP Report 66; (3) 17 such proposals recommended for rejection in that Committee Report; (4) five conservation proposals for which the NCVP could not reach a firm recommendation; (5) one request to suppress a work under Art. 34; (6) three requests for binding decisions under Art. 53.5 (confusingly similar names). Proposal (1933) on the name of the cultivated apple was referred back to the NCVP. Decisions are also reported on proposals in Report 9 of the Nomenclature Committee for Fossils: (1) 17 proposals to conserve or reject names recommended for acceptance; (2) seven such proposals recommended for rejection. Action is deferred on various proposals pending further discussion.