bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference Services Review: content analysis, 2012-2014
Authors: Clark Katherine W. 
Published: February 2016

Purpose
– The purpose of this paper is to present a retrospective analysis of content published in Reference Services Review between 2012 and 2014.

Design/methodology/approach
– This analysis utilizes the methods and format outlined by Katy Mahraj, author of Reference Services Review: content analysis, 2006-2011 (2012). The author manually reviewed the content of all journal issues from 2012 through 2014 using both print and online copies of the journal, accessed through the Emerald Group Publishing web site. Information reviewed included total number of articles per issue, author affiliations, article format and article content focus. The type, size and location of author institutions were confirmed using institutions’ official web sites as necessary. The results of this analysis are compared to Mahraj’s results to identify changing trends.

Findings
– Reference Services Review has published an average of 38 articles per year between 2012 and 2014. Articles have focused most commonly on information literacy and instruction and emerging technologies. Reference services, outreach and library management have also received regular coverage. All authors during this time period have been affiliated with academic institutions, primarily large academic institutions with 5,000 or more students.

Originality value
– This analysis continues the work of Katy Mahraj to consolidate data on the volume, focus and authorship of Reference Services Review. These data continue to provide an overview of trends in the field’s professional and scholarly literature, with implications for broader trends in academic librarianship.
HIV RNA and proviral HIV DNA can be detected in semen after 6 months of antiretroviral therapy although HIV RNA is undetectable in blood
Authors: Du Peiwei , Liu An , Jiao Yanmei , Liu Cuie , Jiang Taiyi , Zhu Weijun , Zhu Yunxia , Wu Hao , Sun Lijun 
Published: February 2016

ABSTRACTThe risk of sexual transmission of HIV is strongly correlated with amounts of genital HIV RNA. Few studies have reported amounts of HIV RNA and HIV DNA in semen in HIV‐infected Chinese patients undergoing antiviral treatment (ART). In this observational study, the amounts of HIV RNA and HIV DNA in semen were assessed after six months of ART in HIV‐infected Chinese individuals, when HIV RNA was undetectable in blood . This study included 19 HIV‐infected Chinese men undergoing ART for six months. Amounts of HIV in paired semen and blood samples were assessed using real‐time PCR. The C2‐V5 region of the HIV envelope (env) genes was cloned and sequenced and genotype and co‐receptor usage predicted based on the sequence. It was found that HIV RNA was undetectable in the plasma of most patients (17/19), whereas HIV RNA could be detected in the semen of most patients (16/19). HIV DNA could be detected in both semen and blood. Genetic diversity of HIV between the seminal and blood compartments was identified. Thus, amounts of HIV RNA and HIV DNA remain high in semen of HIV‐infected Chinese patients after six months of ART treatment, even when HIV RNA was undetectable in blood.
The rules for symbiont community assembly change along a mutualism–parasitism continuum
Authors: Skelton James , Doak Sam , Leonard Meredith , Creed Robert P. , Brown Bryan L. 
Published: February 2016

Summary

Symbiont community assembly is driven by host–symbiont and symbiont–symbiont interactions. The effects that symbionts exert on their hosts are often context‐dependent, and existing theoretical frameworks of symbiont community assembly do not consider the implications of variable outcomes to assembly processes.

We hypothesized that symbiont–symbiont interactions become increasingly important along a parasitism/mutualism continuum because; (i) negative outcomes favour host resistance which in turn reduces symbiont colonization and subsequently reduce symbiont–symbiont interactions, whereas (ii) positive host outcomes favour tolerance and consequently higher symbiont colonization rates, leading to stronger interactions among symbionts. We found support for this hypothesis in the cleaning symbiosis between crayfish and ectosymbiotic branchiobdellidan worms.

The symbiosis between crayfish and their worms can shift from parasitism/commensalism to mutualism as crayfish age. Here, field surveys identified changes in worm density, diversity and composition that were concomitant to changing symbiosis outcomes. We conducted several laboratory experiments and behavioural assays to relate patterns from the field to their likely causal processes.

Young crayfish typically hosted only two relatively small worm species. Older crayfish hosted two additional larger species. In laboratory experiments, young crayfish exhibited a directed grooming response to all worm species, but were unable to remove small species. Conversely, adult crayfish did not exhibit grooming responses to any worm species. Relaxed grooming allowed the colonization of large worm species and initiated symbiont–symbiont intraguild predation that reduced the abundance and altered the behaviour of small worm species. Thus, the dominant processes of symbiont community assembly shifted from host resistance to symbiont–symbiont interactions through host ontogeny and a concomitant transition towards mutualism.

This work shows that host resistance can have a prevailing influence over symbiont community assembly when symbiosis is disadvantageous to the host. However, when symbiosis is advantageous and resistance is relaxed, symbiont colonization rate and consequently abundance and diversity increases and interactions among symbionts become increasingly important to symbiont community assembly.
The role of water and fire in driving tree dynamics in Australian savannas
Authors: Strickland Christopher , Liedloff Adam C. , Cook Garry D. , Dangelmayr Gerhard , Shipman Patrick D. 
Published: February 2016

Summary

Ecologists rely on models to explore tree compositional changes especially when occurring over decades or centuries. In this article, we construct a theoretical, mathematical model to investigate the long‐term relationships between savanna stand structure, water resource availability and fire disturbance.

We show how dry season length, rather than mean annual precipitation, leads to savanna stability, and how the soil properties and variation in annual rainfall distribution determines a climatic equilibrium for woody total basal area, with fire disturbance acting as a perturbation away from this state. This leads to our premise that rainfall and tree population dynamics drives the savanna state leading to grasses and fire, rather than grasses promoting fire to drive the savannas.

The model predicts that savanna tree stands undergo cyclic variation in tree populations as a result of long‐term population cycles and germination events. This outcome is true regardless of the presence of fire, however, fire does introduce a more heterogeneous stand size structure.

Synthesis. Using a mathematically transparent model for water resource availability and stand structure in savannas, we demonstrate how seasonal rainfall distribution, specifically seasonal drought, acts as the primary determinant for stand structure through stand water dynamics, with frequent fire disturbance able to reduce the populations from the climatically induced state.
Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias
Authors: Ruiz‐Gutierrez Viviana , Hooten Mevin B. , Campbell Grant Evan H. 
Published: February 2016

Summary

Biological monitoring programmes are increasingly relying upon large volumes of citizen‐science data to improve the scope and spatial coverage of information, challenging the scientific community to develop design and model‐based approaches to improve inference.

Recent statistical models in ecology have been developed to accommodate false‐negative errors, although current work points to false‐positive errors as equally important sources of bias. This is of particular concern for the success of any monitoring programme given that rates as small as 3% could lead to the overestimation of the occurrence of rare events by as much as 50%, and even small false‐positive rates can severely bias estimates of occurrence dynamics.

We present an integrated, computationally efficient Bayesian hierarchical model to correct for false‐positive and false‐negative errors in detection/non‐detection data. Our model combines independent, auxiliary data sources with field observations to improve the estimation of false‐positive rates, when a subset of field observations cannot be validated a posteriori or assumed as perfect. We evaluated the performance of the model across a range of occurrence rates, false‐positive and false‐negative errors, and quantity of auxiliary data.

The model performed well under all simulated scenarios, and we were able to identify critical auxiliary data characteristics which resulted in improved inference. We applied our false‐positive model to a large‐scale, citizen‐science monitoring programme for anurans in the north‐eastern United States, using auxiliary data from an experiment designed to estimate false‐positive error rates. Not correcting for false‐positive rates resulted in biased estimates of occupancy in 4 of the 10 anuran species we analysed, leading to an overestimation of the average number of occupied survey routes by as much as 70%.

The framework we present for data collection and analysis is able to efficiently provide reliable inference for occurrence patterns using data from a citizen‐science monitoring programme. However, our approach is applicable to data generated by any type of research and monitoring programme, independent of skill level or scale, when effort is placed on obtaining auxiliary information on false‐positive rates.
Behavioral Pain Scale – translation, reliability, and validity in a Swedish context
Authors: Hylén M. , Akerman E. , Alm‐Roijer C. , Idvall E. 
Published: February 2016

BackgroundAssessing pain in the intensive care unit (ICU) is challenging. Due to intubation and sedation, communication can be limited. International guidelines recommend assessing pain with instruments based on behavioral parameters when critically ill patients are unable to self‐report their pain level. One of the recommended instruments, the Behavioral Pain Scale (BPS), has shown good validity and reliability in international studies. The aim of this study was to translate and adapt the BPS for critically ill intubated and non‐intubated patients in a Swedish ICU context and to assess inter‐rater reliability and discriminant validity.MethodsThe BPS (both for intubated and non‐intubated patients) was translated and adapted into Swedish using a translation method consisting of ten steps. The Swedish version was then tested for inter‐rater reliability and discriminant validity on 20 critically ill patients (10 intubated and 10 non‐intubated) before and directly after a potentially painful procedure (repositioning).ResultsThe Swedish version of the BPS showed inter‐rater reliability with a percentage agreement of 85% when tested on a sample of critically ill patients. The instrument also showed discriminant validity between assessments at rest and after repositioning.ConclusionResults of the Swedish version of the BPS support its use in critically ill patients who cannot self‐report their pain level. Still, additional studies are needed to further explore its reliability and validity in the Swedish ICU context.
Characterization of white matter integrity deficits in cocaine‐dependent individuals with substance‐induced psychosis compared with non‐psychotic cocaine users
Authors: Willi Taylor S. , Barr Alasdair M. , Gicas Kristina , Lang Donna J. , Vila‐Rodriguez Fidel , Su Wayne , Thornton Allen E. , Leonova Olga , Giesbrecht Chantelle J. , Procyshyn Ric M. , Rauscher Alexander , MacEwan William G. , Honer William G. , Panenka William J. 
Published: February 2016

AbstractWith sufficient drug exposure, some individuals develop transient psychotic symptoms referred to as ‘substance‐induced psychosis’ (SIP), which closely resemble the symptoms observed in schizophrenia spectrum disorders. The comparability in psychotic presentation between SIP and the schizophrenias suggests that similar underlying neural deficits may contribute to the emergence of psychosis across these disorders. Only a small number of studies have investigated structural alterations in SIP, and all have been limited to volumetric imaging methods, with none controlling for the effects of chronic drug exposure. To investigate white matter abnormalities associated with SIP, diffusion tensor imaging was employed in a group of individuals with cocaine‐associated psychosis (CAP; n = 24) and a cocaine‐dependent non‐psychotic (CDN) group (n = 43). Tract‐based spatial statistics was used to investigate group differences in white matter diffusion parameters. The CAP group showed significantly lower fractional anisotropy values than the CDN group (p < 0.05) in voxels within white matter tracts of fronto‐temporal, fronto‐thalamic and interhemispheric pathways. The greatest differences in white matter integrity were present in the corpus callosum, corona radiata, bilateral superior longitudinal fasciculi and bilateral inferior longitudinal fasciculi. Additionally, the CAP group had voxels of significantly higher radial diffusivity in a subset of the previously mentioned pathways. These results are the first description of white matter integrity abnormalities in a SIP sample and indicate that differences in these pathways may be a shared factor in the expression of different forms of psychosis.
Should Deceased Donation be Morally Preferred in Uterine Transplantation Trials?
Authors: Williams Nicola 
Published: February 2016

AbstractIn recent years much research has been undertaken regarding the feasibility of the human uterine transplant (UTx) as a treatment for absolute uterine factor infertility (AUFI). Should it reach clinical application this procedure would allow such individuals what is often a much‐desired opportunity to become not only social mothers (via adoption or traditional surrogacy arrangements), or genetic and social mothers (through gestational surrogacy) but mothers in a social, genetic and gestational sense. Like many experimental transplantation procedures such as face, hand, corneal and larynx transplants, UTx as a therapeutic option falls firmly into the camp of the quality of life (QOL) transplant, undertaken with the aim, not to save a life, but to enrich one. However, unlike most of these novel procedures – where one would be unlikely to find a willing living donor or an ethics committee that would sanction such a donation – the organs to be transplanted in UTx are potentially available from both living and deceased donors.In this article, in the light of the recent nine‐case research trial in Sweden which used uteri obtained from living donors, and the assertions on the part of a number of other research teams currently preparing trials that they will only be using deceased donors, I explore the question of whether, in the case of UTx, there exist compelling moral reasons to prefer the use of deceased donors despite the benefits that may be associated with the use of organs obtained from the living.
Mechanisms of late Quaternary fault throw‐rate variability along the north central Gulf of Mexico coast: implications for coastal subsidence
Authors: Shen Zhixiong , Dawers Nancye H. , Törnqvist Torbjörn E. , Gasparini Nicole M. , Hijma Marc P. , Mauz Barbara 
Published: January 2016

AbstractQuaternary sea‐level cycles have caused dramatic depocentre shifts near the mouths of major rivers. The effects of these shifts on fault activity in passive margin settings is poorly known, as no studies have constrained passive margin fault throw‐rate variability over 103 to 105 year time scales. Here we present 11 mean throw rates for the Tepetate–Baton Rouge fault zone along the northern Gulf of Mexico coast in southern Louisiana. These data were obtained by optically stimulated luminescence dating over time scales spanning the last interglacial to the late Holocene. The mean throw rate is ca. 0.22 mm year−1 during the late Holocene, ca. 0.03 mm year−1 during the last glacial and at least 0.07 mm year−1 during the last interglacial. Throw rates averaged over the late Pleistocene to present are spatially uniform within our study area. The temporal variability in throw rates suggests that shifts of the Mississippi River depocentre relative to this fault zone, driven by Quaternary sea‐level cycles, may have imposed a significant control on fault activity. The late Holocene throw rate is at least in the order of magnitude smaller than the rates of land‐surface subsidence in the Mississippi Delta, indicating that this fault zone is not a dominant contributor to subsidence in this region.
The Importance of Ficus (Moraceae) Trees for Tropical Forest Restoration
Authors: Cottee‐Jones H. Eden W. , Bajpai Omesh , Chaudhary Lal B. , Whittaker Robert J. 
Published: February 2016

AbstractForest restoration is an increasingly important tool to offset and indeed reverse global deforestation rates. One low cost strategy to accelerate forest recovery is conserving scattered native trees that persist across disturbed landscapes and which may act as seedling recruitment foci. Ficus trees, which are considered to be critically important components of tropical ecosystems, may be particularly attractive to seed dispersers in that they produce large and nutritionally rewarding fruit crops. Here, we evaluate the effectiveness of remnant Ficus trees in inducing forest recovery compared to other common trees. We studied the sapling communities growing under 207 scattered trees, and collected data on seed rain for 55 trees in a modified landscape in Assam, India. We found that Ficus trees have more sapling species around them (species richness = 140.1 ± 9.9) than non‐Ficus trees (79.5 ± 12.9), and significantly more saplings of shrub and large tree species. Sapling densities were twice as high under Ficus trees (median = 0.06/m2) compared to non‐Ficus (0.03/m2), and seed rain densities of non‐parent trees were significantly higher under Ficus trees (mean = 12.73 ± 3/m2/wk) than other fruit or non‐zoochorous trees (2.19 ± 0.97/m2/wk). However, our regression model found that canopy area, used as a proxy for tree size, was the primary predictor of sapling density, followed by remnant tree type. These results suggest that large trees, and in particular large Ficus trees, may be more effective forest restoration agents than other remnant trees in disturbed landscapes, and therefore the conservation of these trees should be prioritized.
Oxytocin Receptor Genetic and Epigenetic Variations: Association With Child Abuse and Adult Psychiatric Symptoms
Authors: Smearman Erica L. , Almli Lynn M. , Conneely Karen N. , Brody Gene H. , Sales Jessica M. , Bradley Bekh , Ressler Kerry J. , Smith Alicia K. 
Published: January 2016

Childhood abuse can alter biological systems and increase risk for adult psychopathology. Epigenetic mechanisms, alterations in DNA structure that regulate the gene expression, are a potential mechanism underlying this risk. While abuse associates with methylation of certain genes, particularly those in the stress response system, no study to date has evaluated abuse and methylation of the oxytocin receptor (OXTR). However, studies support a role for OXTR in the link between abuse and adverse adult outcomes, showing that abuse can confer greater risk for psychiatric symptoms in those with specific OXTR genotypes. This study therefore sought to (a) assess the role of epigenetics in the link between abuse and psychopathology and (b) begin to integrate the genetic and epigenetic literature by exploring associations between OXTR genotypes and DNA CpG methylation. Data on 18 OXTR CpG sites, 44 single nucleotide polymorphisms, childhood abuse, and adult depression and anxiety symptoms were assessed in 393 African American adults (age = 41 ± 12.8 years). Overall, 68% of genotypes were associated with methylation of nearby CpG sites, with a subset surviving multiple test correction. Child abuse associated with higher methylation of two CpG sites yet did not survive correction or serve as a mediator of psychopathology. However, abuse interacted with CpG methylation to predict psychopathology. These findings suggest a role for OXTR in understanding the influence of early environments on adult psychiatric symptoms.
Diagnosis of Autism Spectrum Disorders Using Temporally Distinct Resting‐State Functional Connectivity Networks
Authors: Wee Chong‐Yaw , Yap Pew‐Thian , Shen Dinggang 
Published: January 2016

SummaryIntroductionResting‐state functional magnetic resonance imaging (R‐fMRI) is dynamic in nature as neural activities constantly change over the time and are dominated by repeating brief activations and deactivations involving many brain regions. Each region participates in multiple brain functions and is part of various functionally distinct but spatially overlapping networks. Functional connectivity computed as correlations over the entire time series always overlooks interregion interactions that often occur repeatedly and dynamically in time, limiting its application to disease diagnosis.AimsWe develop a novel framework that uses short‐time activation patterns of brain connectivity to better detect subtle disease‐induced disruptions of brain connectivity. A clustering algorithm is first used to temporally decompose R‐fMRItime series into distinct clusters with similar spatial distribution of neural activity based on the assumption that functionally distinct networks should be largely temporally distinct as brain states do not simultaneously coexist in general. A Pearson correlation‐based functional connectivity network is then constructed for each cluster to allow for better exploration of spatiotemporal dynamics of individual neural activity. To reduce significant intersubject variability and to remove possible spurious connections, we use a group‐constrained sparse regression model to construct a backbone sparse network for each cluster and use it to weight the corresponding Pearson correlation network.ResultsThe proposed method outperforms the conventional static, temporally dependent fully connected correlation‐based networks by at least 7% on a publicly available autism dataset. We were able to reproduce similar results using data from other centers.ConclusionsBy combining the advantages of temporal independence and group‐constrained sparse regression, our method improves autism diagnosis.