bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding context in knowledge translation: a concept analysis study protocol
Authors: Squires Janet E. , Graham Ian D. , Hutchinson Alison M. , Linklater Stefanie , Brehaut Jamie C. , Curran Janet , Ivers Noah , Lavis John N. , Michie Susan , Sales Anne E. , Fiander Michelle , Fenton Shannon , Noseworthy Thomas , Vine Jocelyn , Grimshaw Jeremy M.
Published: November 2014

Aim

To conduct a concept analysis of clinical practice contexts (work environments) that facilitate or militate against the uptake of research evidence by healthcare professionals in clinical practice. This will involve developing a clear definition of context by describing its features, domains and defining characteristics.

Background

The context where clinical care is delivered influences that care. While research shows that context is important to knowledge translation (implementation), we lack conceptual clarity on what is context, which contextual factors probably modify the effect of knowledge translation interventions (and hence should be considered when designing interventions) and which contextual factors themselves could be targeted as part of a knowledge translation intervention (context modification).

Design

Concept analysis.

Methods

The Walker and Avant concept analysis method, comprised of eight systematic steps, will be used: (1) concept selection; (2) determination of aims; (3) identification of uses of context; (4) determination of defining attributes of context; (5) identification/construction of a model case of context; (6) identification/construction of additional cases of context; (7) identification/construction of antecedents and consequences of context; and (8) definition of empirical referents of context. This study is funded by the Canadian Institutes of Health Research (January 2014).

Discussion

This study will result in a much needed framework of context for knowledge translation, which identifies specific elements that, if assessed and used to tailor knowledge translation activities, will result in increased research use by nurses and other healthcare professionals in clinical practice, ultimately leading to better patient care.
Admixture of ancient mitochondrial lineages in three‐spined stickleback populations from the North Pacific
Authors: Lescak Emily A. , Marcotte Robert W. , Kenney Leah A. , von Hippel Frank A. , Cresko William A. , Sherbick Mary L. , Colgren Jeffrey J. , Andrés López J.
Published: November 2014

Aim

We test the hypothesis that the North Pacific coastline from British Columbia to the Kuril Islands forms a broad region of admixture between two divergent mitochondrial‐genome (mtDNA) lineages in three‐spined stickleback (Gasterosteus aculeatus): the Euro‐North American (ENA) and Trans‐North‐Pacific (TNPor Japanese) clades. We test whether distance is the primary determinant of geographical patterns of haplotype distributions and whether deep‐water trenches in the Aleutian and Kuril archipelagos impede gene flow.

Location

Coastal marine and freshwater sites from the Kuril Islands (north‐western Pacific Ocean) to Oregon (north‐eastern Pacific Ocean).

Methods

We determined the mtDNAclade for 1327 individuals from 67 locations across 8000 km of the North Pacific using restriction fragment length polymorphism assays of the cytochromebmitochondrial gene. We supplemented this with published clade designations from coastal Pacific populations and applied generalized linear modelling and Mantel tests. We used analysis of molecular variation (AMOVA) to test for significant partitioning of genetic variation by deep‐water trenches.

Results

The western boundary of theENAclade was Simushir (Kuril Islands) and the eastern boundary of theTNPclade was British Columbia. Coastline distance from Japan was a significant predictor ofTNPabundance. Clade composition variance was high at small geographical scales, in apparent discordance with the broader‐scale pattern of admixture. Deep‐water trenches were not found to significantly partition genetic variation in the Aleutian and Kuril island chains.

Main conclusions

The North Pacific coastline forms a broad region of secondary contact between divergent mitochondrial lineages, but with clear western and eastern boundaries. Patterns of clade abundance in the Kuril and Aleutian islands are similar to those observed in other taxa, suggesting shared biogeographical histories and common barriers shaping species distributions along the North Pacific coast. Overall patterns of clade distributions are likely to be driven by a combination of factors, including geomorphological impediments to migration, ecology, asymmetrical dispersal patterns and differences in timing of population expansions.
Packrat middens and the Holocene palaeohistory of Colorado piñon (Pinus edulis) in western Colorado
Authors: Emslie Steven D. , Coats Larry , Oleksy Eva
Published: November 2014

Aim

Our aim was to determine the age and dispersal history of Colorado piñon (Pinus edulis) in western Colorado during the early to late Holocene using radiocarbon‐dated needles and nutshells from packrat (Neotoma spp.) middens.

Location

The Uncompahgre Plateau (UP) comprises more than 600,000 ha of public and private lands in west‐central Colorado, USA. Elevations within UP range from 1400 to 3140 m and it is characterized by numerous deep canyons and flat‐topped mesas. The Upper Gunnison Basin (UGB) encompasses a 243,000‐ha area enclosed within the southern Rocky Mountains in south‐western Colorado, USA. It spans 2200–4300 m in elevation, with no outlet apart from the Black Canyon of the Gunnison lower than 2650 m.

Methods

Middens were sampled by breaking off small sections of solidified deposits located in caves and crevices that were then disaggregated in water with repeated rinsing to separate all the plant remains. Single conifer needles and nutshells from 28 middens were radiocarbon dated to determine the age and timing of dispersal into western Colorado.

Results

Thirty‐two midden samples were collected, of which 28 produced identifiable plant remains that were radiocarbon dated. Piñon needles and/or nutshells were identified and radiocarbon dated from 20 of these middens from seven localities in UP. The results indicated that piñon did not become established in UP until c. 6000 yr bp, which contrasts with the nearby UGB, where piñon charcoal has been identified from seven archaeological sites with dates ranging from 8000 to 3000 yr bp.

Main conclusions

Our data are consistent with a model of late Pleistocene/early Holocene piñon migration into the Colorado Plateau from Arizona and New Mexico before becoming established in western Colorado. The timing of the piñon migration into south‐central Colorado along the Rio Grande corridor from New Mexico remains uncertain. While piñon–juniper woodlands currently dominate the lower elevations of UP, piñon had disappeared from UGB by c. 3000 yr bp and remains absent there today except for a few isolated trees.
The effectiveness of a computer‐assisted math learning program
Authors: De Witte K. , Haelermans C. , Rogge N.
Published: November 2014

Computer‐assisted instruction (CAI) programs are considered as a way to improve learning outcomes of students. However, little is known on the schools who implement such programs as well as on the effectiveness of similar information and communication technology programs. We provide a literature review that pays special attention to the existing causal evidence of computer‐assisted programs on learning outcomes. The paper relies on a rich data set consisting of (i) pupil‐level information on the use of a Dutch computer‐assisted program and (ii) detailed school‐level information on, among others, outcomes on national exams. The results suggest that schools with lower educational attainments use more frequently CAI programs. This suggests that they use CAI programs to catch up on learning outcomes. Moreover, using an instrumental variable design, we argue that given the participation in the CAI program, making more exercises leads to higher test results. Working with a CAI program seems therefore effective.
Evidence‐informed person‐centered healthcare part I: Do ‘cognitive biases plus’ at organizational levels influence quality of evidence?
Authors: Seshia Shashi S. , Makhinson Michael , Phillips Dawn F. , Young G. Bryan
Published: November 2014

Introduction

There is increasing concern about the unreliability of much of health care evidence, especially in its application to individuals.

Hypothesis

Cognitive biases, financial and non‐financial conflicts of interest, and ethical violations (which, together with fallacies, we collectively refer to as ‘cognitive biases plus’) at the levels of individuals and organizations involved in health care undermine the evidence that informs person‐centred care.

Methods

This study used qualitative review of the pertinent literature from basic, medical and social sciences, ethics, philosophy, law etc.

Results

Financial conflicts of interest (primarily industry related) have become systemic in several organizations that influence health care evidence. There is also plausible evidence for non‐financial conflicts of interest, especially in academic organizations. Financial and non‐financial conflicts of interest frequently result in self‐serving bias. Self‐serving bias can lead to self‐deception and rationalization of actions that entrench self‐serving behaviour, both potentially resulting in unethical acts. Individuals and organizations are also susceptible to other cognitive biases. Qualitative evidence suggests that ‘cognitive biases plus’ can erode the quality of evidence.

Conclusions

‘Cognitive biases plus’ are hard wired, primarily at the unconscious level, and the resulting behaviours are not easily corrected. Social behavioural researchers advocate multi‐pronged measures in similar situations: (i) abolish incentives that spawn self‐serving bias; (ii) enforce severe deterrents for breaches of conduct; (iii) value integrity; (iv) strengthen self‐awareness; and (v) design curricula especially at the trainee level to promote awareness of consequences to society. Virtuous professionals and organizations are essential to fulfil the vision for high‐quality individualized health care globally.
The pollen tube clear zone: Clues to the mechanism of polarized growth
Authors: Hepler Peter K. , Winship Lawrence J.
Published: November 2014

Pollen tubes usually exhibit a prominent region at their apex called the “clear zone” because it lacks light refracting amyloplasts. A robust, long clear zone often associates with fast growing pollen tubes, and thus serves as an indicator of pollen tube health. Nevertheless we do not understand how it arises or how it is maintained. Here we review the structure of the clear zone, and attempt to explain the factors that contribute to its formation. While amyloplasts and vacuolar elements are excluded from the clear zone, virtually all other organelles are present including secretory vesicles, mitochondria, Golgi dictyosomes, and the endoplasmic reticulum (ER). Secretory vesicles aggregate into an inverted cone appressed against the apical plasma membrane. ER elements move nearly to the extreme apex, whereas mitochondria and Golgi dictyosomes move less far forward. The cortical actin fringe assumes a central position in the control of clear zone formation and maintenance, given its role in generating cytoplasmic streaming. Other likely factors include the tip‐focused calcium gradient, the apical pH gradient, the influx of water, and a host of signaling factors (small G‐proteins). We think that the clear zone is an emergent property that depends on the interaction of several factors crucial for polarized growth.

Peter K. Hepler
MultipleCa2+Channel‐Dependent Components in Growth Hormone Secretion from Rat Anterior Pituitary Somatotrophs
Authors: Sosial E. , Nussinovitch I.
Published: November 2014

The involvement of L‐typeCa2+channels in both ‘basal’ and ‘stimulated’ growth hormone (GH) secretion is well established; however, knowledge regarding the involvement of non‐L‐typeCa2+channels is lacking. We investigated whether non‐L‐typeCa2+channels regulateGHsecretion from anterior pituitary (AP) cells. To this end,GHsecretion was monitored from dissociatedAPcells, which were incubated for 15 min with 2 mmK+(‘basal’ secretion) or 60 mmK+(‘stimulated’ secretion). The role of non‐L‐type Ca2+influx was investigated using specific channel blockers, including ω‐agatoxin‐IVA, ω‐conotoxinGVIAorSNX‐482, to block P/Q‐, N‐ or R‐type Ca2+channels, respectively. Our results demonstrate that P/Q‐, N‐ and R‐type Ca2+channels contributed 21.2 ± 1.9%, 20.2 ± 7.6% and 11.4 ± 1.8%, respectively, to ‘basal’GHsecretion and 18.3 ± 1.0%, 24.4 ± 5.4% and 14.2 ± 4.8%, respectively, to ‘stimulated’GHsecretion. After treatment with a ‘cocktail’ that comprised the previously described non‐L‐type blockers, non‐L‐type Ca2+channels contributed 50.9 ± 0.4% and 45.5 ± 2.0% to ‘basal’ and ‘stimulated’GHsecretion, respectively. Similarly, based on the effects of nifedipine (10 μM), L‐type Ca2+channels contributed 34.2 ± 3.7% and 54.7 ± 4.1% to ‘basal’ and ‘stimulated’GHsecretion, respectively. Interestingly, the relative contributions of L‐type/non‐L‐type Ca2+channels to ‘stimulated’GHsecretion were well correlated with the relative contributions of L‐type/non‐L‐type Ca2+channels to voltage‐gated Ca2+influx inAPcells. Finally, we demonstrated that compartmentalisation of Ca2+channels is important forGHsecretion. Lipid raft disruption (methyl‐β‐cyclodextrin, 10 mm) abrogated the compartmentalisation of Ca2+channels and substantially reduced ‘basal’ and ‘stimulated’GHsecretion by 43.2 ± 3.4% and 58.4 ± 4.0%, respectively. In summary, we have demonstrated that multiple Ca2+channel‐dependent pathways regulateGHsecretion. The proper function of these pathways depends on their compartmentalisation withinAPcell membranes.
Photoperiodic Effects on Seasonal Physiology, Reproductive Status and Hypothalamic Gene Expression in Young Male F344 Rats
Authors: Tavolaro F. M. , Thomson L. M. , Ross A. W. , Morgan P. J. , Helfer G.
Published: November 2014

Seasonal or photoperiodically sensitive animals respond to altered day length with changes in physiology (growth, food intake and reproductive status) and behaviour to adapt to predictable yearly changes in the climate. Typically, different species of hamsters, voles and sheep are the most studied animal models of photoperiodism. Although laboratory rats are generally considered nonphotoperiodic, one rat strain, the inbred Fischer 344 (F344) rat, has been shown to be sensitive to the length of daylight exposure by changing its physiological phenotype and reproductive status according to the season. The present study aimed to better understand the nature of the photoperiodic response in the F344 rat. We examined the effects of five different photoperiods on the physiological and neuroendocrine responses. Young male F344 rats were held under light schedules ranging from 8 h of light/day to 16 h of light/day, and then body weight, including fat and lean mass, food intake, testes weights and hypothalamic gene expression were compared. We found that rats held under photoperiods of ≥ 12 h of light/day showed increased growth and food intake relative to rats held under photoperiods of ≤ 10 h of light/day. Magnetic resonance imaging analysis confirmed that these changes were mainly the result of a change in lean body mass. The same pattern was evident for reproductive status, with higher paired testes weight in photoperiods of ≥ 12 h of light/day. Accompanying the changes in physiological status were major changes in hypothalamic thyroid hormone (Dio2 and Dio3), retinoic acid (Crabp1 and Stra6) and Wnt/β‐Catenin signalling genes (sFrp2 and Mfrp). Our data demonstrate that a photoperiod schedule of 12 h of light/day is interpreted as a stimulatory photoperiod by the neuroendocrine system of young male F344 rats.
Construct validity and reliability of the Chinese version of the Disaster Preparedness Evaluation Tool in Taiwan
Authors: Chen Tzu‐Fei , Chou Kuei‐Ru , Liao Yuan‐Mei , Ho Cheng‐Hsun , Chung Min‐Huey
Published: November 2014

Aims and objectives

To develop a Chinese version of the Disaster Preparedness Evaluation Tool and validate its psychometric properties.

Background

An adequate disaster preparation programme for nurses has not been developed in Taiwan. To develop an exhaustive and effective educational programme on disaster preparation for nurses, a multidimensional instrument is required for assessing the disaster preparation level of nurses.

Design

A cross‐sectional study was conducted.

Methods

In total, 1550 of 2226 public health nurses in 15 counties completed the self‐administrated questionnaire. We randomly selected 805 samples to examine the factor structure and factor model by using exploratory factor analysis and confirmatory factor analysis. The convergent validity was measured using the average variance extracted and composite reliability.

Results

Five factors, namely postdisaster management, skills, knowledge of self‐preparation in a disaster, knowledge to respond in the community, and knowledge to respond in the workplace, were extracted, and explained 65·13% of the total variance. An acceptable model fit was identified using confirmatory factor analysis. The Cronbach's α coefficient of the Chinese version of the Disaster Preparedness Evaluation Tool was 0·97. Significant values of the average variance extracted greater than 0·5 indicated convergent validity.

Conclusion

The Chinese version of the Disaster Preparedness Evaluation Tool is a reliable and valid instrument for measuring disaster preparation.

Relevance to clinical practice

The Chinese version of the Disaster Preparedness Evaluation Tool provides reliable and valid measures that can be used to evaluate the disaster preparedness of nurses. The items in the instrument can be used to identify the dimension of disaster management in all stages, and can form the essential foundation of an education and training programme for public health nurses to reduce the harm of disasters and promote community resilience.
Efficient Inoculation of Rice black‐streaked dwarf virus to Maize Using Laodelphax striatellus Fallen
Authors: Miao Hong‐Qin , Di Dian‐Ping , Zhang Ai‐Hong , Lu Yin‐Gui , Tian Lan‐Zhi , Stewart Lucy R. , Redinbaugh Margaret G.
Published: November 2014

Maize rough dwarf disease caused by Rice black‐streaked dwarf virus (RBSDV) is the most important disease of maize in China. Although deploying disease resistant hybrids would be the most effective way to control the disease, development of resistant hybrids has been limited by virus transmission rates that are too low for effective screening. An efficient inoculation technique for RBSDV was developed using Laodelphax striatellus Fallen, in which a virus‐free planthopper colony was developed and viruliferous planthoppers were obtained by allowing a 3‐ to 4‐day acquisition access period on RBSDV‐infected wheat plants. Planthoppers were then allowed a 25‐ to 28‐day latent period on wheat seedlings followed by a 3‐day inoculation access period on two‐to‐three‐leaf stage maize seedlings. By 35 days postinoculation, susceptible hybrid ‘Zhengdan 958’, inbred lines of ‘Ye 107’ and ‘Ye 478’ plants showed 100% RBSDV infection with symptoms of stunting plants, darkening leaves and white waxy swellings on underside of leaves. At tasseling stage, average disease indices were from 96.4 to 100.0%. Enzyme‐linked immunosorbent assays were correlated with the presence of symptoms. The high efficiency of RBSDV transmission obtained using this technique provides a reliable procedure to screen for RBSDV resistance in maize.
Sleep characteristics, chronotype and winter depression in 10–20‐year‐olds in northern European Russia
Authors: Borisenkov Mikhail F. , Petrova Natalia B. , Timonin Vladimir D. , Fradkova Lyudmila I. , Kolomeichuk Sergey N. , Kosova Anna L. , Kasyanova Olga N.
Published: November 2014

The purpose of this work was to examine the relationships between geographical coordinates and the prevalence of winter depression (SADW), and to compare the sleep characteristics and chronotype of youths with and without SADW. We conducted a cross‐sectional study of self‐reported sleep characteristics, chronotype and winter depression in northern European Russia. Two questionnaires, the Munich Chronotype Questionnaire (MCTQ) and the Seasonal Pattern Assessment Questionnaire (SPAQ), were administered to a total of 3435 adolescents aged 10–20 years (1517 males and 1918 females). The prevalence of SADW in the study population was 8.4% and sub‐SADW 11.8%. Four variables predicted the likelihood of SADW in youths: sex [higher in females: odds ratio (OR): 1.87, P < 0.0001], age (increases with age: OR: 1.09, P < 0.001), latitude (higher in the North: OR: 1.49, P < 0.029) and position in the time zone (higher in the West: OR: 1.61, P < 0.001). Later sleeping and waking, longer sleep latencies, more severe sleep inertia, shorter total sleep times and lower sleep efficiencies were observed in both males and females with SADW. The influence of SADW on sleep characteristics was more pronounced on school days. Significant phase delays of the sleep–wake rhythm and severe social jetlag (the difference between the mid‐point of sleep phase at weekends and on workdays) were observed in females with SADW, but not in males. There are significant differences in sleep characteristics and chronotype between people with SADW and no‐SAD. We demonstrate that both latitude of residence and location within the time zone are significant predictors of SADW in young inhabitants of the North.
Vine Copula Specifications for Stationary Multivariate Markov Chains
Authors: Beare Brendan K. , Seo Juwon
Published: November 2014

Vine copulae provide a graphical framework in which multiple bivariate copulae may be combined in a consistent fashion to yield a more complex multivariate copula. In this article, we discuss the use of vine copulae to build flexible semiparametric models for stationary multivariate higher‐order Markov chains. We propose a new vine structure, the M‐vine, that is particularly well suited to this purpose. Stationarity may be imposed by requiring the equality of certain copulae in the M‐vine, while the Markov property may be imposed by requiring certain copulae to be independence copulae.
Contemplative Methods Meet Social Sciences: Back to Human Experience as It Is
Authors: Giorgino Vincenzo Mario Bruno
Published: November 2014

The aim of this paper is to trace a pathway connecting contemplative knowledge and practices with the social sciences. Contemplative knowledge and practices offer material for reflection in social science even concerning their very foundation. I'll found an opportunity for meshing our disciplinary tools with this knowledge as I introduced it in a health promotion program. The result will be a transdisciplinary confluence of different lines of inquiry contributing to a new perspective of self and social action.

First of all I will give a definition of contemplative knowledge and practices. Then, I will make a bridge between the contemplative approach and the social sciences, showing the contribution that symbolic interactionism can play. I will illustrate the perspective drawing on an action research program calledAurigaaimed at smoking cessation and reduction among health professionals. The aim of this paper is focused on the specification of the conceptual background in which such kind of program has been developed. Finally, I outline some implications it could represent for what might be called transformative sociology.

I believe that contemplative knowledge could contribute to disentangle some of the unanswered questions and concerns in the social sciences, once they dismiss for a while their scientistic perspective. The secular redefinition of tools mainly belonging to the wisdom traditions represents an innovation that can reshape what we intend by the self and experience, contributing to what is called the “social transformation from within,” a pragmatic and wise approach to change at any level.
What animals can live in cryoconite holes? A faunal review
Authors: Zawierucha K. , Kolicka M. , Takeuchi N. , Kaczmarek Ł.
Published: November 2014

Despite the large number of studies on glaciers, knowledge regarding biota in cryoconite holes is limited. Cryophilic animals are often neglected in ecological studies on glacial habitats, but are important for the functioning of these environments. Owing to climate change and the melting of polar ice, cryophilic fauna could be threatened in the near future. We provide the first comprehensive survey of invertebrates inhabiting the cryoconite holes of Alpine, Antarctic, Arctic, Himalayan and Patagonian glaciers. At present, the list of taxa is rather short and includes five phyla (Rotifera, Annelida, Tardigrada, Nematoda and Arthropoda). Owing to generally poor knowledge of the fauna of cryoconite holes, there could be more than the 25 currently known species. In addition, we present the geographical distributions of the taxa and discuss the diversity of invertebrates living in cryoconite holes and make predictions regarding the faunal diversity of these habitats.
Scottish, English, British?: Innovations in Attitude Measurement
Authors: Llamas Carmen , Watt Dominic
Published: November 2014

This paper reviews techniques used in the direct, quantitative measurement of attitudes, before discussing the advantages of employing Visual Analog Scales. Innovative uses of these methods were developed for utilization in the large‐scale sociophonetic studyAccent and Identity on the Scottish/English Border. The paper presents the ‘Attitude Analog Scale’ and the ‘Relational Analog Scale’, which were devised as a way of examining attitudes towards national identities among the inhabitants of this border region.
Challenges and Opportunities in Sociolinguistic Data and Metadata Sharing
Authors: Cieri Christopher
Published: November 2014

Advances in computing technology coupled with recent focus on big data in the social sciences have provided the motivation and some of the infrastructure necessary for sociolinguists to share data among themselves and with researchers in related fields such as human language technologies (HLT). Collaboration among sociolinguists offers the promise to extend current knowledge beyond the community studies that have dominated the field for the past 50 years and focus more on regional and national patterns of variation and change and what they indicate about linguistic theory. Collaboration with HLT developers while relatively new and still uncommon has led to advances both in sociolinguistic methodology and in technologies suited to sociolinguistic research. Before the field can make full use of these advances, however, sociolinguists must confront a number of challenges. Studies that were developed with the intent of describing a single speech community presumably need not ensure, and in many cases have not ensured, consistency with prior work. Given this practice, attempts to compare phenomena across studies must address mismatches at the levels of data elicitation and selection, coding practice, and the definition of underlying concepts. Adding to the confusion wrought by methodological differences, speech communities differ in ways that the field worker cannot always predict so that different and sometimes unique linguistic and non‐linguistic features are found to vary with linguistic structure. This paper underscores the motivation for data sharing by identifying some limitations of comparisons based only on published papers and reviewing advances fueled by data sharing among linguists and between linguists and technology developers. It also documents some of the challenges that hinder data sharing by reviewing work that has build upon available corpora. Finally, it summarizes efforts outside of sociolinguistics that have proposed frameworks for sharing and comparing metadata and categories setting the stage for the papers that follow in these special issues.
Coding for Demographic Categories in the Creation of Legacy Corpora: Asian American Ethnic Identities
Authors: Hall‐Lew Lauren , Wong Amy Wing‐mei
Published: November 2014

A set of shared coding conventions for speaker ethnicity is necessary for open‐source data sharing and cross‐study compatibility between linguistic corpora. However, ethnicity, like many other aspects of speaker identity, is continually negotiated and reproduced in discourse, and therefore a challenge to code representatively. This paper discusses some of the challenges facing researchers who want to use, create, or contribute to existing corpora that are annotated for the ethnic identity of a speaker. We specifically problematize the macro‐social label ‘Asian American’ and propose that researchers should consider different levels and types of specificity of ‘Asianness’ in order to ensure that the corpora best represent the reality of ethnic identity in the community sampled. This is particularly important given the limited incorporation of different Asian groups in most existing linguistic research). We argue that more rigorous coding for Asian American ethnicities in corpora will improve the utility of archived corpora and enhance sociolinguistic research on language variation and ethnic identity.
Introduction to the Special Issue on Archiving Sociolinguistic Data
Authors: Yaeger‐Dror Malcah , Cieri Christopher
Published: November 2014

Advances in online networking have permitted an increasing interest in big data by the community of linguists. This special issue will address the needs of researchers hoping to take advantage of this expansion of our horizons, both by adapting their research design to permit their own corpus to conform to the expanded need for accurate metadata and to permit them to take full advantage of their own corpora that researcher can collect and analyze directly. In linguistics, this naturally leads to increased emphasis on data sharing, which is one way to amass data of sufficient size and variety to permit new kinds of insight. At the same time, there is a growing consensus among sociolinguists that researchers must refine their views on demographic, situational, and attitudinal factors that correlate with linguistic differences in order to permit not only more effective data sharing and comparison but also more accurate conclusions.
Age: Methods and Metadata
Authors: Bowie David
Published: November 2014

Age has proven to be an extremely useful variable in many social science fields, and linguistics is no exception: it is widely used in applied linguistics, psycholinguistics, and (especially) sociolinguistics. This makes sense – given that even casual observation tells us that humans behave differently at different points in the life cycle, it is quite reasonable to take age into account when investigating human behavior. In turn, the use of age as a variable has led to a wide range of methods and analytical tools that rely on the use of age (e.g., the apparent time construct in sociolinguistics). However, it turns out that even though age is often treated in a rather simple way, it is actually a complicated concept that can be difficult to pin down precisely and that the usual linguistic view of age as a simple reflection of the linear passage of time is lacking. That fact has repercussions for how linguists should deal with age, including not just issues like how to record metadata relating to it, but even methodological concerns such as how to do the initial elicitation in the first place.
The impacts of inbreeding, drift and selection on genetic diversity in captive breeding populations
Authors: Willoughby Janna R. , Fernandez Nadia B. , Lamb Maureen C. , Ivy Jamie A. , Lacy Robert C. , DeWoody J. Andrew
Published: November 2014

The goal of captive breeding programmes is often to maintain genetic diversity until re‐introductions can occur. However, due in part to changes that occur in captive populations, approximately one‐third of re‐introductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analysed six populations of white‐footed mice that were propagated for 20 generations using two replicates of three protocols: random mating (RAN), minimizing mean kinship (MK) and selection for docility (DOC). We found that MK resulted in the slowest loss of microsatellite genetic diversity compared to RAN and DOC. However, the loss of mtDNA haplotypes was not consistent among replicate lines. We compared our empirical data to simulated data and found no evidence of selection. Our results suggest that although the effects of drift may not be fully mitigated, MK reduces the loss of alleles due to inbreeding more effectively than random mating or docility selection. Therefore, MK should be preferred for captive breeding. Furthermore, our simulations show that incorporating microsatellite data into the MK framework reduced the magnitude of drift, which may have applications in long‐term or extremely genetically depauperate captive populations.
Rapid acclimation of juvenile corals to CO2‐mediated acidification by upregulation of heat shock protein and Bcl‐2 genes
Authors: Moya A. , Huisman L. , Forêt S. , Gattuso J.‐P. , Hayward D. C. , Ball E. E. , Miller D. J.
Published: November 2014

Corals play a key role in ocean ecosystems and carbonate balance, but their molecular response to ocean acidification remains unclear. The only previous whole‐transcriptome study (Moya et al. Molecular Ecology, 2012; 21, 2440) documented extensive disruption of gene expression, particularly of genes encoding skeletal organic matrix proteins, in juvenile corals (Acropora millepora) after short‐term (3 d) exposure to elevated pCO2. In this study, whole‐transcriptome analysis was used to compare the effects of such ‘acute’ (3 d) exposure to elevated pCO2 with a longer (‘prolonged’; 9 d) period of exposure beginning immediately post‐fertilization. Far fewer genes were differentially expressed under the 9‐d treatment, and although the transcriptome data implied wholesale disruption of metabolism and calcification genes in the acute treatment experiment, expression of most genes was at control levels after prolonged treatment. There was little overlap between the genes responding to the acute and prolonged treatments, but heat shock proteins (HSPs) and heat shock factors (HSFs) were over‐represented amongst the genes responding to both treatments. Amongst these was an HSP70 gene previously shown to be involved in acclimation to thermal stress in a field population of another acroporid coral. The most obvious feature of the molecular response in the 9‐d treatment experiment was the upregulation of five distinct Bcl‐2 family members, the majority predicted to be anti‐apoptotic. This suggests that an important component of the longer term response to elevated CO2 is suppression of apoptosis. It therefore appears that juvenile A. millepora have the capacity to rapidly acclimate to elevated pCO2, a process mediated by upregulation of specific HSPs and a suite of Bcl‐2 family members.
Structural basis for targeting the ribosomal protein S1 of Mycobacterium tuberculosis by pyrazinamide
Authors: Yang Juanjuan , Liu Yindi , Bi Jing , Cai Qixu , Liao Xinli , Li Wenqian , Guo Chenyun , Zhang Qian , Lin Tianwei , Zhao Yufen , Wang Honghai , Liu Jun , Zhang Xuelian , Lin Donghai
Published: November 2014

Pyrazinamide (PZA) is a first‐line drug for tuberculosis (TB) treatment and is responsible for shortening the duration of TB therapy. The mode of action of PZA remains elusive. RpsA, the ribosomal protein S1 of Mycobacterium tuberculosis (Mtb), was recently identified as a target of PZA based on its binding activity to pyrazinoic acid (POA), the active form of PZA. POA binding to RpsA led to the inhibition of trans‐translation. However, the nature of the RpsA–POA interaction remains unknown. Key questions include why POA exhibits an exquisite specificity to RpsA of Mtb and how RpsA mutations confer PZA resistance. Here, we report the crystal structures of the C‐terminal domain of RpsA of Mtb and its complex with POA, as well as the corresponding domains of two RpsA variants that are associated with PZA resistance. Structural analysis reveals that POA binds to RpsA through hydrogen bonds and hydrophobic interactions, mediated mainly by residues (Lys303, Phe307, Phe310 and Arg357) that are essential for tmRNA binding. Conformational changes induced by mutation or sequence variation at the C‐terminus of RpsA abolish the POA binding activity. Our findings provide insights into the mode of action of PZA and molecular basis of PZA resistance associated with RpsA mutations.
Three explanations for biodiversity hotspots: small range size, geographical overlap and time for species accumulation. An Australian case study
Authors: Cook Lyn G. , Hardy Nate B. , Crisp Michael D.
Published: November 2014

To understand the generation and maintenance of biodiversity hotspots, we tested three major hypotheses: rates of diversification, ecological limits to diversity, and time for species accumulation.

Using dated molecular phylogenies, measures of species' range size and geographical clade overlap, niche modelling, and lineages‐through‐time plots of Australian Fabaceae, we compared the southwest Australia Floristic Region (SWAFR; a global biodiversity hotspot) with a latitudinally equivalent non‐hotspot, southeast Australia (SEA).

Ranges of species (real and simulated) were smaller in the SWAFR than in SEA. Geographical overlap of clades was significantly greater for Daviesia in the SWAFR than in SEA, but the inverse for Bossiaea. Lineage diversification rates over the past 10 Myr did not differ between the SWAFR and SEA in either genus.

Interaction of multiple factors probably explains the differences in measured diversity between the two regions. Steeper climatic gradients in the SWAFR probably explain the smaller geographical ranges of both genera there. Greater geographical overlap of clades in the SWAFR, combined with a longer time in the region, can explain why Daviesia is far more species‐rich there than in SEA. Our results indicate that the time for speciation and ecological limits hypotheses, in concert, can explain the differences in biodiversity.
Effects of Cartilage Oligomeric Matrix Protein on Bone Morphogenetic Protein‐2‐induced Differentiation of Mesenchymal Stem Cells
Authors: Guo Peng , Shi Zhong‐li , Liu An , Lin Tiao , Bi Fanggang , Shi Mingmin , Yan Shi‐gui
Published: November 2014

Objective

To investigate the effect of overexpression of cartilage oligomeric matrix protein (COMP) on bone morphogenetic protein‐2 (BMP‐2) induced osteogenic and chondrogenic differentiation of mesenchymal stem cells (MSCs). In this study, we used liposomes to transfect MSCs with plasmid encoding COMP and then induced the transfected MSCs to differentiate in osteogenic and chondrogenic differentiation media containing BMP‐2.

Methods

MSCs transfected with plasmid DNA encoding recombinant human COMP were induced to differentiate into osteocytes and chondrocytes by BMP‐2. Real‐time polymerase chain reaction (PCR) assays of osteogenesis‐related markers (collagen type I alpha 1, runt‐related transcription factor 2, osteopontin, bone gla protein) and chondrogenesis‐related markers (collagen type II alpha 1, sry‐related high‐mobility group box 9, Aggrecan) was performed to evaluate the process of cell differentiation. Cell differentiation was evaluated by alkaline phosphatase (ALP) and Alizarin red S stains for osteogenic differentiation and alcian blue staining for chondrogenic differentiation.

Results

Real‐time PCR assay showed significantly greater COMP expression by MSCs when COMP gene had been transfected into the cells (P < 0.01). Overexpression of COMP down‐regulated expression of osteogenesis‐related markers and up‐regulated expression of chondrogenesis‐related markers. ALP staining and Alizarin red S staining were weakened, whereas alcian blue staining was enhanced.

Conclusion

Overexpression of COMP inhibits BMP‐2‐induced osteogenic differentiation and promotes BMP‐2‐induced chondrogenic differentiation. These findings may provide new insights for cartilage tissue engineering. The experiments in the present study were all in vitro, which has potential limitations. Further in vivo studies to investigate the effects of COMP in animal models are necessary, which will be the next step in our research.
Arthroscopic Single‐row versus Double‐row Technique for Repairing Rotator Cuff Tears: a Systematic Review and Meta‐analysis
Authors: Ying Zhi‐min , Lin Tiao , Yan Shi‐gui
Published: November 2014

Objective

The purpose of this study was to systematically review published reports that compare the outcomes of single‐row and double‐row suture anchor fixation in arthroscopic rotator cuff repair.

Methods

Combined data regarding relevant patient characteristics, rotator cuff pathology, surgical techniques, postoperative rehabilitation regimens, University of California at Los Angeles (UCLA) Scores, Constant scores, American Shoulder and Elbow Society (ASES) scores, tendon healing, incidence of recurrent rotator cuff defects, shoulder muscle strength, range of motion, surgical time and patient satisfaction were assessed.

Results

Seven eligible randomized controlled studies and four prospective cohort studies were identified. There were no significant differences between the single‐row and double‐row groups in terms of Constant or ASES scores. However, UCLA scores, tendon healing, abduction shoulder strength index (SSI), external rotation SSI and internal rotation SSI were significantly better for double‐row technique than for single‐row technique. A statistically significant advantage for double‐row repair according to UCLA score and external rotation SSI was found in the subgroup with tears greater than 3 cm.

Conclusion

No definite conclusion could be drawn about differences in overall outcomes of double‐ and single‐row techniques for repairing for small to medium (<3 cm) or large to massive (>3 cm) rotator cuff tears, even though some measures of clinical outcome showed significant differences between these two techniques.
Primary Issues in the Selection of Surgical Procedures for Thoracic and Lumbar Spinal Tuberculosis
Authors: Shi Jian‐dang , Wang Qian , Wang Zi‐li
Published: November 2014

Debridement, spinal canal decompression, deformity correction, bone graft fusion and internal fixation are commonly used in the surgical treatment of spinal tuberculosis. A complete surgical plan for patients with spinal tuberculosis may include all or some of these five surgical procedures that involve both removing tuberculous lesions and re‐establishing spinal stability and function. All five procedures can be carried out via an anterior or posterior approach or a combination of these two approaches. A combined posterior–anterior approach is becoming a preferred choice for treating spinal tuberculosis. However, this procedure requires two incisions and two rounds of surgeries, which the associated extensive surgical trauma. Thus, a simple anterior or posterior approach may be preferable. Each of these approaches has its own advantages and disadvantages that must be considered during the clinician's evaluation. Selection of the most appropriate of these three approaches is vital to achieving cure of spinal tuberculosis. Spinal surgeons should comprehensively consider each patient's characteristics, the manifestations of their lesions and how familiar the surgeon is with the required surgical procedure(s). The primary consideration should be the potential outcome: the effectiveness of debridement is the key determinant of the surgical outcome.
Transpedicle Osteotomy Positioning in Pedicle‐lengthening Laminoplasty
Authors: Zhang Zhi‐gang , Mei Xin , Zhang Wen , Liu Peng , Gao Mao‐feng , Yang Hui‐lin , Luo Zong‐ping
Published: November 2014

Pedicle‐lengthening laminoplasty is a new minimally invasive technique for surgical treatment of lumbar spinal stenosis. The procedure is performed with the assistance of fluoroscopy and involves creating a pedicle passage, transpedicle osteotomy from inside the pedicle passage and lengthening it by using an implant bilaterally to enlarge the spinal canal and neural foramen. A critical component of the procedure is the precise determination of the osteotomy site on the pedicle. The objective of this study was to examine in vitro whether fluoroscopic positioning could be used to guide the osteotomy and to define the cutting site in the pedicle‐lengthening laminoplasty in relation to the posterior vertebral line. It was found that the osteotomy site was from 2.0 to 3.5 mm posterior to the posterior vertebral line. The maximum difference between the measured value and that theoretically simulated on 3‐dimensional (3D) computed tomography reconstruction was 0.3 mm. The spinal canal cross‐sectional area was significantly enlarged after pedicle‐lengthening. Accurate placement of the osteotomy is critical in pedicle‐lengthening laminoplasty. Guiding the positioning of the osteotomy based on the posterior vertebral line images provides satisfactory accuracy, suggesting a possible clinical application for our technique; however, further verification in vivo is needed.
A Pilot Study to Assess Benefit of Atrial Rhythm Control after Cardiac Resynchronization Therapy and Atrioventricular Node Ablation
Authors: SCHWARTZMAN DAVID , HOUSEL DEBRA , BAZAZ RAVEEN , JAIN SANDEEP , SABA SAMIR , GORCSAN JOHN , ADELSTEIN EVAN
Published: November 2014

Background

Atrial fibrillation (AF) is frequently comorbid in patients receiving cardiac resynchronization therapy (CRT), and suppression is typically difficult. Herein, we sought to understand the benefit of atrial rhythm control in the setting of ventricular rate and regularity control induced by atrioventricular node (AVN) ablation.

Methods

Fifty‐two patients with heart failure, persistent AF, left ventricular (LV) ejection fraction <35%, and left bundle branch block underwent cardiac resynchronization therapy (CRT) + AVN ablation, and were randomized to one of the following groups: (1) Atrial Rhythm Control (ARC); (2) AF. Patients were subsequently followed for up to 1 year.

Results

Similar numbers of patients in each group were lost to follow‐up or have withdrawn (ARC two; AF three). Rhythm control in four patients in the ARC group was inadequate. Among the remaining patients, the incidence of death (ARC=1, AF=2) or left ventricular assist device +/− transplantation (ARC=2, AF=1) were similar. Among the remaining patients (ARC 16, AF 19), at 1 year, there were no significant differences in CRT response rate, Minnesota Living with Heart Failure survey score, 6‐minute hall walk distance, ventricular tachyarrhythmia occurrence, or LV dimensions. A significantly higher hospital encounter rate among ARC patients was attributable to efforts to maintain uniform atrial rhythm.

Conclusions

In this pilot study, no incremental benefit for ARC was apparent. A larger study will be necessary to adequately examine these issues.