bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics
Authors: Wen Yalu , Chen Fushun , Zhang Qingzheng , Zhuang Yan , Li Zhiguang
Published: August 2016

Motivation: DNA methylation is an important epigenetic modification that has essential role in gene regulation, cell differentiation and cancer development. Bisulfite sequencing is a widely used technique to obtain genome-wide DNA methylation profiles, and one of the key tasks of analyzing bisulfite sequencing data is to detect differentially methylated regions (DMRs) among samples under different treatment conditions. Although numerous tools have been proposed to detect differentially methylated single CpG site (DMC) between samples, methods for direct DMR detection, especially for complex study designs, are largely limited.

Results: We present a new software, GetisDMR, for direct DMR detection. We use beta-binomial regression to model the whole-genome bisulfite sequencing data, where variations in methylation levels and confounding effects have been accounted for. We employ a region-wise test statistic, which is derived from local Getis-Ord statistics and considers the spatial correlation between nearby CpG sites, to detect DMRs. Unlike existing methods, that attempt to infer DMRs from DMCs based on empirical criteria, we provide statistical inference for direct DMR detection. Through extensive simulations and an application to two mouse datasets, we demonstrate that GetisDMR achieves better sensitivities, positive predictive values, more exact locations and better agreement of DMRs with current biological knowledge.

Availability and Implementation: It is available at https://github.com/DMU-lilab/GetisDMR.

Contacts:  y.wen@auckland.ac.nz or zhiguangli@dlmedu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of Erwinia rhapontici as the Causal Agent of Crown and Shoot Rot and Pink Seed of Pea in Nebraska
Authors: Adesemoye Anthony O. , Wei Hsin-Ho , Harveson Robert M.
Published: August 2016

Dry yellow pea production has been increasing in the central High Plains. One of the emerging pathogens of pea in the region is Erwinia rhapontici. In a Nebraska disease survey, a pea field exhibited a high incidence of bacterial-like symptoms. Four of the isolates recovered from samples were identified as E. rhapontici by sequencing the 16s rDNA. Similar symptoms to those seen on the field were also reestablished by these strains in pathogenicity tests through rolled towel and greenhouse assays.

Accepted for publication 2 June 2016. Published 6 July 2016.
Soybean Cyst Nematode HG Type Test Results Differ Among Multiple Samples from the Same Field but the Management Implications Are the Same
Authors: Beeman Augustine Q. , Harbach Chelsea J. , Marett Christopher C. , Tylka Gregory L.
Published: August 2016

The objective of this study was to determine how HG type test results might vary among SCN populations in independent samples collected from the same field or area of a field.

Accepted for publication 20 June 2016. Published 22 July 2016.
Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis
Authors: Malinverni Duccio , Lopez Alfredo Jost , Los Rios Paolo De , Hummer Gerhard , Barducci Alessandro
Published: August 2016

The interaction between the Heat Shock Proteins 70 and 40 is at the core of the ATPase regulation of the chaperone machinery that maintains protein homeostasis. However, the structural details of this fundamental interaction are still elusive and contrasting models have been proposed for the transient Hsp70/Hsp40 complexes. Here we combine molecular simulations based on both coarsegrained and atomistic models with co-evolutionary sequence analysis to shed light on this problem by focusing on the bacterial DnaK/DnaJ system. The integration of these complementary approaches resulted into a novel structural model that rationalizes previous experimental observations. We identify an evolutionary-conserved interaction surface formed by helix II of the DnaJ J-domain and a groove on lobe IIA of the DnaK nucleotide binding domain, involving the inter-domain linker.
Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks
Authors: Zagorski Marcin , Burda Zdzislaw , Waclaw Bartlomiej
Published: August 2016

Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 aminoacids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case ofK> 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases withKand can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higherK. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of sizeN~ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task.
Adverse Effects of Culture Media on Human Pluripotent Stem Cells
Authors: Bangalore Megha Prakash , Mukherjee Odity , Adhikarla Syama , Panicker Mitradas M.
Published: August 2016

Culture conditions play an important role in regulating the genomic integrity of HPSCs. We report that HPSCs cultured in Essential 8 (E8) and mTeSR, two widely used media for off-feeder culturing of HPSCs, had many fold higher levels of ROS and higher mitochondrial potential than cells cultured in KSR containing media. HPSCs also exhibited increased levels of 8-hydroxyguanosine, phospho-histone-H2A.X and p53, as well as increased sensitivity to γ-irradiation in these two media. HPSCs in E8 and mTeSR had increased incidence of alterations in their DNA sequence, reflecting genotoxic stress, in addition to changes in nucleolar morphology and number. Supplementing E8 and mTeSR with antioxidants provided only a partial rescue. Our results suggest that it is essential to determine cellular ROS levels in designing culture media as it affects the genomic integrity of HPSCs and will limit their use in studying development and in regenerative medicine.

Highlights

Culture media can dramatically alter nuclear and nucleolar morphology

HPSCs in E8 and mTeSR media have increased ROS levels and mitochondrial potential

There is increased nuclei acid damage in HPSCs cultured in E8 and mTeSR media

Nucleolar morphology of HPSCs can act as a “stress reporter”
Single Cell Transcriptome Conservation in Cryopreserved Cells and Tissues
Authors: Guillaumet-Adkins Amy , Rodríguez-Esteban Gustavo , Mereu Elisabetta , Villanueva Alberto , Vidal August , Gut Marta , Gut Ivo , Heyn Holger
Published: August 2016

A variety of single cell RNA preparation procedures have been described. So far these protocols require fresh starting material, hindering complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells and so allows to disconnect time and place of sampling from subsequent processing steps. To demonstrate the potential, we sequenced single cell transcriptomes from >1,000 fresh and conserved cells. Our results confirmed that the conservation process did not alter transcriptional profiles. This substantially broadens the scope of applications in single cell transcriptomics and could lead to a paradigm shift in future study designs.
Low activity microstates during sleep
Authors: Miyawaki Hiroyuki , Billeh Yazan N. , Diba Kamran
Published: August 2016

A better understanding of sleep requires evaluating the distinct activity patterns of the brain during sleep. We performed extracellular recordings of large populations of hippocampal region CA1 neurons in freely moving rats across sleep and waking states. Throughout non-REM (non-rapid eye movement) sleep, we observed periods of diminished oscillatory and population spiking activity lasting on the order of seconds, which we refer to as “LOW” activity sleep states. LOW states featured enhanced firing in a subset of “LOW-active” cells, and greater firing in putative interneurons compared to DOWN/OFF states. LOW activity sleep was preceded and followed by increased sharp-wave ripple (SWR) activity. We also observed decreased slow-wave activity (SWA) and sleep spindles in the hippocampus local-field potential (LFP) and neocortical electroencephalogram (EEG) upon LOW onset, but only a partial rebound immediately after LOW. LOW states demonstrated LFP, EEG, and EMG patterns consistent with sleep, but frequently transitioned into microarousals (MAs) and showed EMG and LFP spectral differences from previously described small-amplitude irregular activity (SIA) during quiet waking. Their likelihood increased over the course of sleep, particularly following REM sleep. To confirm that LOW is a brain-wide phenomenon, we analyzed data from the entorhinal cortex of rats, medial prefrontal cortex, and anterior thalamus of mice, obtained from crcns.org and found that LOW states corresponded to markedly diminished activity simultaneously in all of these regions. We propose that LOW states are an important microstate within non-REM sleep that provide respite from high-activity sleep, and may serve a restorative function.
Direct correlation between motile behavior and protein abundance in single cells
Authors: Dufour Yann S , Gillet Sébastien , Frankel Nicholas W , Weibel Douglas B , Emonet Thierry
Published: August 2016

Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy within situhydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity inEscherichia colimotility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.
Insights into mortality patterns and causes of death through a process point of view model
Authors: Anderson James J. , Li Ting , Sharrow David J.
Published: August 2016

Process point of view models of mortality, such as the Strehler-Mildvan and stochastic vitality models, represent death in terms of the loss of survival capacity through challenges and dissipation. Drawing on hallmarks of aging, we link these concepts to candidate biological mechanisms through a framework that defines death as challenges to vitality where distal factors defined the age-evolution of vitality and proximal factors define the probability distribution of challenges. To illustrate the process point of view, we hypothesize that the immune system is a mortality nexus, characterized by two vitality streams: increasing vitality representing immune system development and immunosenescence representing vitality dissipation. Proximal challenges define three mortality partitions: juvenile and adult extrinsic mortalities and intrinsic adult mortality. Model parameters, generated from Swedish mortality data (1751-2010), exhibit biologically meaningful correspondences to economic, health and cause-of-death patterns. The model characterizes the 20thcentury epidemiological transition mainly as a reduction in extrinsic mortality resulting from a shift from high magnitude disease challenges on individuals at all vitality levels to low magnitude stress challenges on low vitality individuals. Of secondary importance, intrinsic mortality was described by a gradual reduction in the rate of loss of vitality presumably resulting from reduction in the rate of immunosenescence. Extensions and limitations of a distal/proximal framework for characterizing more explicit causes of death, e.g. the young adult mortality hump or cancer in old age are discussed.
The bridge between ontological concepts and empirical evidence: an interview with Rob Stones
Authors: Stones Rob , Jack Lisa
Published: August 2016

Purpose

The purpose of this paper is to share interdisciplinary ideas about the purpose of social theory in empirical research.

Design/methodology/approach

The formal interview took place in front of an audience at the Strong Structuration Theory and Management Research workshop at IAE de Paris, Université Paris I Panthéon-Sorbonne, on 10 May 2016. A recording was made, transcribed, and then edited. Elements from a recorded lecture on the same day are also included. A conversational format is retained to enhance the sense of interdisciplinary dialogue that characterises the research project.

Findings

The use of SST as a conceptual methodology is explained, and the use of agent’s conduct and agent’s context analyses is elucidated providing pointers regarding how accounting research can be developed further by basing the analysis in an understanding of the status and adequacy of knowledge on which people act to produce and reproduce structure.

Originality/value

The value of the interview is to provide insights into the process of empirical research and conceptualisation, which are likely to be particularly helpful for early career researchers.
Understanding management accounting change using strong structuration frameworks
Authors: Makrygiannakis Georgios , Jack Lisa
Published: August 2016

Purpose

The purpose of this paper is to suggest a strong structuration-based framework for the study of management accounting change.

Design/methodology/approach

A retrospective field study was designed to investigate the impact of the 2008 financial crisis on budgeting and control practices of Greek hospitality organisations. Conduct analysis addresses agents’ perceptions of the changes upon themselves. Context analysis explores the changing context, and how the agents modified their in-situ control structures accordingly. The framework is demonstrated through one case study.

Findings

The agents in the case, triggered by the crisis, gradually come to criticise the way they practice budgeting. The first response is to practice budgeting more normatively, but later they criticise and modify these norms. As their formal mentalities co-mediated action, variance management became proactive rather than reactive. Variations in the ways agents draw upon structures – unreflectively or critically – and on how they act to reproduce structures – routinely or strategically – characterise change in management accounting practice. Agents’ reasoning and conduct leading to action is local, and these local changes in conduct and context are significant in understanding management accounting change.

Originality/value

This framework for studying management accounting change balances structural conditions of action, with action and interaction. It can be used to study how, why, and by whom institutionalised management accounting practices may change.
Store brand evaluative process in an international context
Authors: Gómez-Suárez Mónica , Quinones Myriam , Yagúe Maria Jesús
Published: August 2016

Purpose

– The purpose of this paper is to analyse the relationships between the different phases of the store brand (SB) evaluative process (i.e. attitude, preference and purchase intention) in an international context and to investigate how each of them is influenced by selected perceptual characteristics of consumers, psychographic consumer traits and product evaluative criteria.

Design/methodology/approach

– The data were obtained from a survey of 1,118 shoppers from six different countries. Consecutive chained multiple and logistic regression models that incorporated the main antecedents into each stage were applied.

Findings

– The main results are as follows: first, quality inferences based on brand image and reputation have a significant positive effect on SB attitude; second, shoppers’ propensity to explore and their risk perceptions are antecedents of SB preference rather than SB attitude; and finally, impulsiveness has a significant positive impact on SB purchase intention.

Practical implications

– The results can assist retailers in developing strategies according to the specific phase of their customers’ evaluative process: promoting expert recommendations and opinion-leader testimonials in the attitude formation stage, investing in innovation in the preference formation stage and improving the overall shopping experience in the purchase intention stage.

Originality/value

– This paper extends research on the consumer decision-making process by empirically demonstrating that SB preference is a mediating variable between SB attitude and SB purchase intention. From a practical perspective, this work involves an extensive empirical study that aggregates data from shoppers across six Western countries. This multinational sample offers a high degree of external validity and generalisation of the results obtained.
Human capital and the decision to exploit innovative opportunity
Authors: Bayon Manoj Chandra , Lafuente Esteban , Vaillant Yancy
Published: August 2016

Purpose

– The purpose of this paper is to examine the direct and interaction effect of individuals’ human capital input and human capital output in the form of entrepreneurial self-confidence on the decision to exploit innovative opportunities.

Design/methodology/approach

– Using a strategic entrepreneurship perspective, the authors suggest that when individuals with high human capital decide to exploit opportunities they do so by thinking and acting strategically. Strategic action(s) involves pursuing competitive advantages that enable a new venture to get a foothold in the market. The authors argue that such competitive advantages arise from the exploitation of innovative opportunities and individuals with high human capital are more likely to exploit innovative opportunities when they develop entrepreneurial self-confidence. The empirical analysis is based on a random sample of individuals from the adult population who are in the process of creating a new venture.

Findings

– The results suggest that although human capital inputs and human capital output in the form of entrepreneurial self-confidence are significant factors in influencing the decision to exploit innovative opportunities, human capital inputs interact in different ways with human capital output in influencing this decision.

Research limitations/implications

– The main limitation of the authors’ study is the use of single item measures as indicators of innovative opportunity and human capital output (entrepreneurial self-confidence).

Practical implications

– From a macro-perspective, the main implication of the study is that it is possible to assess the quality of entrepreneurship in an economy through individuals’ human capital and the proportion of innovative opportunities in the economy. Moreover, because not all types of human capital inputs influences the exploitation of innovative opportunities, policy makers can be selective in their policy interventions in spawning quality entrepreneurship in their economy.

Originality/value

– Based on population-level data the authors’ study provides empirical evidence of the nature of entrepreneurial decisions being at the earliest phases of the entrepreneurial process. The study shows the importance of founders’ human capital inputs and outputs in influencing the quality of entrepreneurship in an economy. Moreover, the study extends the understanding the individual-opportunity nexus in promoting innovative entrepreneurship in an economy.
Unfolding critical events and strategic decisions: the role of spatial and temporal cognition
Authors: Haider Sajjad , Mariotti Francesca
Published: August 2016

Purpose

– The purpose of this paper is to examine strategic decisions surrounding critical events to show how the decision-making processes evolve and how the dominant logic changesvis-à-visthose decisions. Further, this study explores the processes of managerial decision making focusing on spatial and temporal cognition dimensions.

Design/methodology/approach

– The methodology adopted in this study is a case study using the retrospective processual analysis approach. Data were collected using both primary and secondary sources. In all, 40 years of secondary data on key critical events and decision making were collected using a range of secondary sources. Those events were further examined using 49 in-depth semi structured interviews.

Findings

– The findings of this study explain the relationship between operant conditions, strategic actions and outcomes of strategic decisions by highlighting the significance of knowledge strategy, strategic agility and intentionality in shaping and reshaping managers’ dominant logic. Further, the authors show that the dominant coalition, among other factors, plays an important role in building decision-making capacity and in the formation and transformation of an existing dominant logic.

Research limitations/implications

– The study identified a number of limitations. First, the issue of generalization as the data were collected from only two case study companies. Second, in some cases respondents were asked to respond to research questions using “memory of the events” which took place a long time ago, hence the issue of credibility. Further, sometimes respondents reported information collected through hearsay. To overcome the limitations of this research, the authors made all efforts to ensure that the data collected were reliable and credible such as by using diverse data sources, confirmation of events at multiple level and personal observations.

Practical implications

– The study identifies and explains a number of factors which influence decision making. The authors also present the revised dominant logic model which can act as a tool in managerial decision making.

Originality/value

– The paper shows how managerial decision making changes knowledge strategy, which in turn leads to changes in existing dominant logic or the creation of a new dominant logic, hence looking at the issues of decision making using an evolutionary perspective. Second, the paper empirically tests and explains the relationship between intentionality, actions and organizational outcomes using spatial and temporal learning. Finally, the use of the longitudinal retrospective processual analysis and events analysis, is a novel way of understanding a particular phenomenon.
The Impact of Nursing Home Pay‐for‐Performance on Quality and Medicare Spending: Results from the Nursing Home Value‐Based Purchasing Demonstration
Authors: Grabowski David C. , Stevenson David G. , Caudry Daryl J. , O'Malley A. James , Green Lisa H. , Doherty Julia A. , Frank Richard G.
Published: August 2016

Objective

To evaluate the impact of the Nursing Home Value‐Based Purchasing demonstration on quality of care and Medicare spending.

Data Sources/Study Setting

Administrative and qualitative data from Arizona, New York, and Wisconsin nursing homes over the base‐year (2008–2009) and 3‐year (2009–2012) demonstration period.

Study Design

Nursing homes were randomized to the intervention in New York, while the comparison facilities were constructed via propensity score matching in Arizona and Wisconsin. We used a difference‐in‐difference analysis to compare outcomes across the base‐year relative to outcomes in each of the three demonstration years. To provide context and assist with interpretation of results, we also interviewed staff members at participating facilities.

Principal Findings

Medicare savings were observed in Arizona in the first year only and Wisconsin for the first 2 years; no savings were observed in New York. The demonstration did not systematically impact any of the quality measures. Discussions with nursing home administrators suggested that facilities made few, if any, changes in response to the demonstration, leading us to conclude that the observed savings likely reflected regression to the mean rather than true savings.

Conclusion

The Federal nursing home pay‐for‐performance demonstration had little impact on quality or Medicare spending.
Validity and reliability of the Bristol Stool Form Scale in healthy adults and patients with diarrhoea‐predominant irritable bowel syndrome
Authors: Blake M. R. , Raker J. M. , Whelan K.
Published: August 2016

Background

The Bristol Stool Form Scale (BSFS) is a 7‐point scale used extensively in clinical practice and research for stool form measurement, which has undergone limited validity and reliability testing.

Aim

To determine the validity and reliability of the BSFS in measuring stool form in healthy adults and patients with diarrhoea‐predominant irritable bowel syndrome (IBS‐D).

Methods

One hundred and sixty‐nine healthy volunteers provided a stool sample and used the BSFS to classify stool form, which was compared with measured stool water content and with values from 19 patients with IBS‐D. Eighty‐six volunteers used the BSFS to classify 26 stool models to determine accuracy and reliability.

Results

Volunteers’ classifications of stool type correlated with stool water (Spearman's rho = 0.491, P < 0.001), which increased in hard (Types 1–2), normal (Types 3–5) and loose stools (Types 6–7) (P < 0.001). The BSFS detected differences in stool form between healthy volunteers (mean 3.7, s.d. 1.5) and IBS‐D patients (mean 5.0, s.d. 1.2) (P < 0.001). Overall, 977/1204 (81%) stool models were correctly classified (substantial accuracy, κ = 0.78), although <80% of Types 2, 3, 5 and 6 were classified correctly. On 852/1118 (76%) occasions, volunteers classified covert duplicate models to the same stool type (substantial reliability, κ = 0.72), but with only moderate reliability for Types 2 (63%, κ = 0.57) and 3 (62%, κ = 0.55).

Conclusions

The BSFS demonstrated substantial validity and reliability, although difficulties arose around clinical decision points (Types 2, 3, 5, 6) that warrant investigation in larger clinical populations. Potential for improving validity and reliability through modifications to the BSFS or training in its use should be explored.
Normal fault evolution and coupled landscape response: examples from the Southern Apennines, Italy
Authors: Roda‐Boluda Duna C. , Whittaker Alexander C.
Published: August 2016

We present new data addressing the evolution, activity and geomorphic impact of three normal faults in the Southern Apennines: the Vallo di Diano, East Agri and Monti della Maddalena faults. We show that these faults have minimum total throws of ca. 1000–2000 m, and throw rates of ca. 0.7–1 mm year−1 for at least the last ca. 18 ka. We demonstrate that for the Vallo di Diano and East Agri faults, the landscape is effectively recording tectonics, with relief, channel and catchment slopes varying along fault strike in the same manner as normal fault activity does, with little apparent influence of lithology. We therefore use these data to reconstruct the time‐integrated history of fault interaction and growth. From the distribution of knickpoints on the footwall channels, we infer two episodes of base level change, which we attribute to fault interaction episodes. We reconstruct the amount of throw accumulated after each of these events, and the segments involved in each, from the fault throw profiles, and use fault interaction theory to estimate the magnitude of the perturbations and past throw rates. We estimate that fault linkage events took place 0.7 ± 0.2 Ma and 1.4 ± 0.3 Ma in the Vallo di Diano fault, and 1 ± 0.1 in the East Agri Fault, and that both faults likely started their activity between 3 and 3.5 Ma. These fault linkage scenarios are consistent with the observed knickpoint heights. This method for reconstructing fault evolution could potentially be applied for any normal faults for which there is information about throw and throw rates, and in which channels are transiently responding to tectonics.
Acute effects of walking and combined exercise on oxidative stress and vascular function in peripheral artery disease
Authors: Lima Aluísio H. R. A. , Correia Marilia A. , Soares Antônio H. G. , Farah Breno Q. , Forjaz Cláudia L. M. , Silva Alexandre S. , Brasileiro‐Santos Maria S. , Santos Amilton C. , Ritti‐Dias Raphael M.
Published: August 2016

The aim of this study was to compare the effects of a single session of walking and combined exercise on oxidative stress and vascular function in peripheral arterial disease patients. Thirteen patients with peripheral arterial disease underwent two experimental sessions in random order: walking (ten sets of 2‐min walking at the speed corresponding to the onset of claudication pain with 2‐min interval between sets) and combined exercise (1 × 10 reps in eight resistance exercises plus five‐two‐minute sets of walking). Before and after the exercise, vascular function (blood flow, leg vascular resistance and blood‐flow postreactive hyperaemia) and oxidative stress (malondialdehyde and plasma nitrite levels) were obtained. Blood flow increased similarly after both sessions, whilst leg vascular resistance decreased similarly after both sessions. Plasma nitrite increased only after the combined exercise. Malondialdehyde decreased after both sessions, and the decrease was greater after combined exercise. As a conclusion, a single session of combined exercise improves blood flow and leg vascular resistance similarly to walking session; however, combined exercise promoted better effects on oxidative stress.
Eliciting and structuring business indicators in data warehouse requirements engineering
Authors: Bhardwaj Hanu , Prakash Naveen
Published: August 2016

Traditionally, data warehouse requirements engineering is oriented towards determining the information contents of the warehouse to be. This has resulted in a de‐emphasis of the functional perspective of data warehouses. Consequently, it is difficult to specify functions needed for computing business indicators. Our approach aims to elicit needed business indicators from organizational decision makers. Thereafter, indicator hierarchies are built. Then we associate functions with business indicators of the hierarchy. These functions are visualized as use case diagrams. To do this, we extend these diagrams to allow for actor aggregation in addition to actor specialization. Further, we introduce the ‘estimated from’ relationship between use cases, in addition to the ‘extend’ and ‘include’ relationships of UML. We illustrate our proposals with an example.
The Distinctiveness of Polyamory
Authors: Brunning Luke
Published: August 2016

Polyamory is a form of consensual non‐monogamy. To render it palatable to critics, activists and theorists often accentuate its similarity to monogamy. I argue that this strategy conceals the distinctive character of polyamorous intimacy. A more discriminating account of polyamory helps me answer objections to the lifestyle whilst noting some of its unique pitfalls. I define polyamory, and explain why people pursue this lifestyle. Many think polyamory is an inferior form of intimacy; I describe four of their main objections. I explain how commitment to ‘the polyamorous possibility’ prompts one to viscerally experience personal, practical, and social constraints. Unlike monogamous dynamics, these confrontations are mediated by third parties who destabilise the familiar dynamics of coupled life. Polyamory can be emotionally challenging but, as I outline in the article, it is sustained by interpersonal emotional work that helps people feel and understand their emotions, communicate without confrontation, and contain the difficult emotions of others. This work is qualitatively and quantitatively intensified in polyamory. Finally, I rebut objections to polyamory whilst also acknowledging the ways polyamory has its own pitfalls.
Using robot animation to promote gestural skills in children with autism spectrum disorders
Authors: So W.‐C. , Wong M.K.‐Y. , Cabibihan J.‐J. , Lam C.K.‐Y. , Chan R.Y.‐Y. , Qian H.‐H.
Published: August 2016

School‐aged children with autism spectrum disorders (ASDs) have delayed gestural development, in comparison with age‐matched typically developing children. In this study, an intervention program taught children with low‐functioning ASD gestural comprehension and production using video modelling (VM) by a computer‐generated robot animation. Six to 12‐year‐old children with ASD (N = 20; IQ < 70) were taught to recognize 20 gestures produced by the robot animation (phase I), to imitate these gestures (phase II) and to produce them in appropriate social contexts (phase III). Across the three phases, significant differences were found between the results of the pretest and the immediate and follow‐up posttests; the results of both posttests were comparable, after controlling for the children's motor and visual memory skills. The children generalized their acquired gestural skills to a novel setting with a human researcher. These results suggest that VM by a robot animation is effective in teaching children with low‐functioning ASD to recognize and produce gestures.

Lay Description

What is already known about this topic:

Children with autism spectrum disorders (ASDs) have difficulties with nonverbal communication.

Children with ASD have difficulties in recognizing and producing gestures.

What this paper adds:

A multiphase therapeutic intervention program using video modelling (VM) of robot animation is effective to promoting the gestural communication skills, both recognition and production, in children with low‐functioning ASD.

Children with ASD have improved their skills to recognize the taught gestures (phase I), imitate them (phase II) and produce them in appropriate social contexts (phase III).

Children with ASD are able to generalize the acquired skills to human‐to‐human interactions after the intervention program.

Implications for practice and/or policy:

VM of a robot animation is effective in teaching children with low‐functioning ASD both gesture recognition and gesture production.

The multiphase therapeutic intervention protocol can be recommended for clinicians or teachers in special schools to teach children with low‐functioning ASD gestural communication skills.
Evaluation of a novel strategy of triage in the haematology ambulatory care setting
Authors: Slusar Joanna , Couban Stephen , Shivakumar Sudeep Pappur
Published: August 2016

Background

In 2010, wait‐times for new patients referred to see a haematologist at our outpatient tertiary care centre clinic exceeded 6 months. The provision of written recommendations for a subset of referred patients was undertaken to reduce patient wait‐times. These recommendation letters outlined possible causes of the abnormality for which the patient was being referred and suggested a course of action for follow‐up, and patients were then managed by their referring practitioner. We sought to characterize the cohort of patients for whom written recommendations were written and assess whether written recommendations were a satisfactory alternative for the referring practitioner.

Methods

All haematology patient referrals managed with written recommendations in 2010 were included in the study and were assessed one year later. Referring practitioners who received written recommendations were sent a short survey to evaluate their satisfaction with this process.

Results

A total of 444 of 2400 referrals were managed with a letter. At 1‐year follow‐up, 58 (13%, 95% CI) of the abnormalities which prompted the referral had resolved and 201 (45%, 95%CI) had remained stable. There was a single haematology‐related death during the 1‐year follow‐up and the haematological abnormality worsened in 4 (1%) patients. Of 203 (71%) referring practitioners who responded to the satisfaction survey, 90% (95% CI) indicated that they would be satisfied with written recommendations in the future.

Interpretation

The provision of written recommendations appears to be a safe and satisfactory alternative to an inperson outpatient assessment in certain well‐defined subsets of stable outpatients with haematologic abnormalities.
Respect, Coercion, and Religious Reasons
Authors: Friberg‐Fernros Henrik
Published: August 2016

It is often assumed that people of faith should not endorse a law for religious reasons, since such an endorsement is considered to be disrespectful. Such a position is increasingly opposed by scholars who argue that such demands unjustifiably force people of faith to compromise their religious ideals. In order to defend their opposition to such demands, some scholars have invoked thought experiments as reductio arguments against the claim that endorsing laws dependent on religious reasons is necessarily disrespectful. I argue that these attempts have failed, and present an alternative thought experiment that demonstrates that such a law is not necessarily disrespectful. Because I conclude that previously proposed principles cannot defend this conclusion, I defend an alternative way of accommodating this intuition; a post‐secular deliberative approach based on the principle of double effect.
Rapid and accurate identification of Xanthomonas citri subspecies citri by fluorescence in situ hybridization
Authors: Waite D.W. , Griffin R. , Taylor R. , George S.
Published: August 2016

Citrus canker is an economically important disease caused by the bacterial pathogen Xanthomonas citri subsp. citri (Xcc). This organism targets a wide range of citrus plants, including sweet orange, grapefruit, lemon and lime. As Xcc is spread by environmental factors such as wind and rain, it is difficult to control its movement once the disease has established. In order to facilitate monitoring of citrus canker we sought to design a novel diagnostic protocol based on fluorescence in situ hybridization (FISH) for identification of bacterial cells directly from canker pustules without cultivation or DNA extraction. This method was validated for specificity against a range of Xanthomonas species and strains. We show that our assay is extremely rapid (typically requiring between 2 and 3 h), and possesses a similar specificity to existing PCR diagnostic tools. The sensitivity of the assay is comparable to that of an existing PCR-based technique and sufficient for identifying Xcc in symptomatic plant material. The method is easily transferable to diagnosticians without prior experience using FISH.

Significance and Impact of the Study

Xanthomonas citri subsp. citri (Xcc) is an aggressive and hardy pathogen of citrus plants worldwide. Outbreaks are difficult and costly to contain and the establishment of citrus canker results in restricted trade. In order to extend the existing toolkit for identification of Xcc we developed a novel diagnostic approach based on fluorescence in situ hybridization. Our approach is of comparable specificity and sensitivity to existing methods but can be performed directly on infected tissue making it significantly faster than existing PCRs, and requiring fewer laboratory resources.
Host Th1/Th2 immune response to Taenia solium cyst antigens in relation to cyst burden of neurocysticercosis
Authors: Tharmalingam J. , Prabhakar A. T. , Gangadaran P. , Dorny P. , Vercruysse J. , Geldhof P. , Rajshekhar V. , Alexander M. , Oommen A.
Published: August 2016

Neurocysticercosis (NCC), Taenia solium larval infection of the brain, is an important cause of acquired seizures in endemic countries, which relate to number, location and degenerating cysts in the brain. Multicyst infections are common in endemic countries although single‐cyst infection prevails in India. Single‐cyst infections in an endemic country suggest a role for host immunity limiting the infection. This study examined ex vivo CD4+ T cells and in vitro Th1 and Th2 cytokine responses to T. solium cyst antigens of peripheral blood mononuclear cells of healthy subjects from endemic and nonendemic regions and of single‐ and multicyst‐infected patients for association with cyst burden of NCC. T. solium cyst antigens elicited a Th1 cytokine response in healthy subjects of T. solium‐endemic and T. solium‐non‐endemic regions and those with single‐cyst infections and a Th2 cytokine response from subjects with multicyst neurocysticercosis. Multicyst neurocysticercosis subjects also exhibited low levels of effector memory CD4+ T cells. Th1 cytokine response of T. solium exposure and low infectious loads may aid in limiting cyst number. Th2 cytokines and low effector T cells may enable multiple‐cyst infections to establish and persist.
HLA‐A*23:01:19, a novel variant of HLA‐A*23:01, discovered in a West African stem cell transplantation patient
Authors: Sidahmed A. M. Elhassan , Anderson J. , Stamm L. , Khan F. , Berka N.
Published: August 2016

HLA‐A*23:01:19 differs from HLA‐A*23:01:01 by a single substitution in exon 4.
Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies
Authors: Stanfield Robyn L. , Wilson Ian A. , Smider Vaughn V.
Published: August 2016

The distinct architecture of bovine antibodies defines a unique immune diversity system.
Complete Genome Sequence of Zika Virus Isolated in Mexico, 2016
Authors: Díaz-Quiñonez José Alberto , Peña-Alonso Rocío , Mendieta-Condado Edgar , Garcés-Ayala Fabiola , González-Durán Elizabeth , Escobar-Escamilla Noé , Vázquez-Pichardo Mauricio , Torres-Rodríguez María de la Luz , Núñez-León Alma , Torres-Longoria Belem , López-Martínez Irma , Ruíz-Matus Cuitláhuac , Kuri-Morales Pablo , Ramírez-González José Ernesto
Published: August 2016

Zika virus belongs to the genus
Flavivirus
, and its spread remains an international public health emergency. In this report, we describe the obtainment and molecular characterization of a complete viral genome through the direct metagenomic analysis from saliva from an autochthonous transmission case in Mexico.
Draft Genome Sequence of
Streptomyces
sp. F-3
Authors: Sun Xiaomeng , Meng Jing , Liu Shijia , Zhang Huaiqiang , Wang Lushan
Published: August 2016

Streptomyces
sp. F-3 is a kind of thermophilic
Streptomyces
strain that can produce cellulolytic enzymes and diverse secondary metabolites. Here, we report the complete genome of this organism, whose genome length is 5,303,958 bp, containing 6,041 protein-coding genes, 69 tRNA operons, and three rRNA operons.
Acupuncture for Amnestic Mild Cognitive Impairment: A Meta-Analysis of Randomised Controlled Trials
Authors: Deng Min , Wang Xu-Feng
Published: August 2016

Objective

Mild cognitive impairment (MCI) is a pre-dementia state; 5–10% of cases per year will evolve into dementia. MCI can be amnestic (AMCI) or non-amnestic. AMCI is associated with a higher risk of progression. In recent years, interest in acupuncture as a potential treatment for AMCI has grown. The aim of this meta-analysis was to estimate the clinical effectiveness and safety of acupuncture for AMCI.

Methods

Randomised controlled trials (RCTs) of acupuncture versus medical treatment for AMCI were identified using the following databases from inception to July 2015: PubMed; Medline; CENTRAL; Chinese Scientific Journal Database; The Chinese Acupuncture Trials Register; China National Knowledge Infrastructure (CNKI); and Wanfang database. Data were extracted from RCTs meeting the inclusive criteria according to Cochrane methods. Meta-analyses were conducted using Rev Man V.5.3 software.

Results

Five trials involving 568 subjects were included. Meta-analysis showed that participants receiving acupuncture had better outcomes than those receiving nimodipine with greater clinical efficacy rates (odds ratio (OR) 1.78, 95% CI 1.19 to 2.65; p<0.01), mini-mental state examination (MMSE) scores (mean difference (MD) 0.99, 95% CI 0.71 to 1.28; p<0.01), and picture recognition score (MD 2.12, 95% CI 1.48 to 2.75; p<0.01). Meta-analysis also showed acupuncture in conjunction with nimodipine significantly improved MMSE scores (MD 1.09, 95% CI 0.29 to 1.89; p<0.01) compared to nimodipine alone. Three trials reported adverse events. Methodological quality of the included studies was judged to be generally poor.

Conclusions

Acupuncture appears effective for AMCI when used as an alternative or adjunctive treatment; however, caution must be exercised given the low methodological quality of included trials. Further, more rigorously designed studies are needed.
Cor triatriatum sinister with severe obstruction: a rare presentation in an adult
Authors: Narayanapillai Jayaprasad
Published: August 2016

Cor triatriatum sinister is a rare congenital anomaly usually presenting in infancy or childhood. Most cases reported in adulthood have minimal obstruction. A case of critically obstructed cor triatriatum sinister presenting for the first time in adulthood is described here. The characteristic ECG, radiological and echocardiographic findings of this rare anomaly are demonstrated in this case report. The clinical features closely mimic mitral stenosis. The clues to differentiate cor triatriatum from other causes of left ventricular inflow obstruction are described.