bluuebunny/crossref_metadata_2025_split huggingface dataset:
Venipuncture Nerve Injuries in the Upper Extremity From More Than 1 Million Procedures
Authors: Tsukuda Yukinori , Funakoshi Tadanao , Nasuhara Yasuyuki , Nagano Yusuke , Shimizu Chikara , Iwasaki Norimasa 
Published: June 2016

Objectives
The purpose of this study was to investigate the nerve injury rate for 1 million venipunctures and the efficacy of attempts to avoid severe nerve injury.

Methods
We collected data for outpatients from whom a venipuncture blood sample was obtained in our hospital from 2005 to 2014. Every venipuncture procedure for outpatients was performed by a trained nurse or clinical technologist at the center for blood sampling in our hospital. In addition, a series of lectures by a specialist is held in our hospital at various times. All complaints related to venipuncture blood sampling were reported to our division of hospital safety management and were followed up using the guidelines for injuries related to the venipuncture.

Results
The number of venipuncture-related complications was 293 (0.027%, 1/3700) of 1,082,053 during the 10 years. A total of 40 of the 1,082,053 venipunctures were referred to the department of orthopedic surgery, and 16 (0.0015%, 1/67,000) were diagnosed with obvious nerve injuries. The average duration of the treatment was 46.4 days (range, 1–126 days); 69% of the patients recovered within 5 weeks, and all patients recovered within 18 weeks.

Conclusions
Although it is impossible to completely prevent venipuncture-related complications, appropriate venipuncture skills and risk management decrease the incidence of chronic or permanent nerve injury risk after venipuncture.
A Multi-State Model Examining Patterns of Transitioning Among States of Engagement in Care in HIV-Positive Individuals Initiating Combination Antiretroviral Therapy
Authors: Gillis Jennifer , Loutfy Mona , Bayoumi Ahmed M. , Antoniou Tony , Burchell Ann N. , Walmsley Sharon , Cooper Curtis , Klein Marina B. , Machouf Nima , Montaner Julio S. G. , Rourke Sean B. , Tsoukas Christos , Hogg Robert , Raboud Janet ,   the CANOC Collaboration
Published: June 2016

Background:
Common measures of engagement in care fail to acknowledge that infrequent follow-up may occur either intentionally among patients with sustained virologic suppression or unintentionally among patients with poor clinical outcomes.

Methods:
Five states of HIV care were defined within the Canadian Observational Cohort Collaboration following combination antiretroviral therapy (cART) initiation: (1)
guidelines
HIV care [suppressed viral load (VL) and CD4 >200 cells per cubic millimeter, no gaps in cART >3 months, no gaps in CD4 or VL measurement >6 months], (2)
successful
care with
decreased
frequency of follow-up (as above except no gaps in CD4 or VL measurement >12 months), (3)
suboptimal
care (unsuppressed VL, CD4 <200 cells per cubic millimeter on 2 consecutive visits, ≥1 gap in cART >3 months, or ≥1 gap in CD4 or VL measurement >12 months), (4)
loss to follow-up
(no contact for 18 months), and (5)
death
. Multi-state models were used to determine factors associated with transitioning among states.

Results:
In total, 7810 participants were included. Younger age, female gender, Indigenous ethnicity, and people who have injected drugs were associated with increased likelihoods of transitioning from guidelines to suboptimal care and decreased likelihoods of transitioning from suboptimal to guidelines care. One-fifth of individuals in successful, decreased follow-up after cART initiation (mean sojourn time 0.72 years) were in suboptimal care in subsequent years.

Conclusions:
Using routinely collected data, we have developed a flexible framework that characterizes patient transitions among states of HIV clinical care. We have demonstrated that multi-state models provide a useful approach to supplement “cascade of care” work.
Effect of HIV Infection on Human Papillomavirus Types Causing Invasive Cervical Cancer in Africa
Authors: Clifford Gary M. , de Vuyst Hugo , Tenet Vanessa , Plummer Martyn , Tully Stephen , Franceschi Silvia 
Published: June 2016

Objectives:
HIV infection is known to worsen the outcome of cervical human papillomavirus (HPV) infection and may do so differentially by HPV type.

Design:
Twenty-one studies were included in a meta-analysis of invasive cervical cancers (ICC) among women infected with HIV in Africa.

Method:
Type-specific HPV DNA prevalence was compared with data from a similar meta-analysis of HIV-negative ICC using prevalence ratios (PR).

Results:
HPV detection was similar in 770 HIV-positive (91.2%) and 3846 HIV-negative (89.6%) ICC, but HIV-positive ICC harbored significantly more multiple HPV infections (PR = 1.75, 95% confidence intervals: 1.18 to 2.58), which were significantly more prevalent in ICC tested from cells than from biopsies. HPV16 was the most frequently detected type in HIV-positive ICC (42.5%), followed by HPV18 (22.2%), HPV45 (14.4%), and HPV35 (7.1%). Nevertheless, HIV-positive ICC were significantly less frequently infected with HPV16 than HIV-negative ICC (PR = 0.88, 95% confidence intervals: 0.79 to 0.99). Other high-risk types were significantly more prevalent in HIV-positive ICC, but only for HPV18 was there a significantly higher prevalence of both single and multiple infections in HIV-positive ICC. Increases for other high-risk types were primarily accounted for by multiple infections. The proportion of HPV-positive ICC estimated attributable to HPV16/18 (71.8% in HIV positive, 73.4% in HIV negative) or HPV16/18/31/33/45/52/58 (88.8%, 89.5%) was not affected by HIV.

Conclusions:
HIV alters the relative carcinogenicity of HPV types, but prophylactic HPV16/18 vaccines may nevertheless prevent a similar proportion of ICC, irrespective of HIV infection.
Retreat Site Selection inVaejovis carolinianusPopulations of Tennessee’s Upper Cumberland Region
Authors: Baggett Bob A 
Published: June 2016

Abstract:My study examined Tennessee’s only native scorpion species,Vaejovis carolinianus. Little is known about its ecology, so the objectives of my study were to determine if: (1)V. carolinianusselected cover objects based on surface area; (2)V. carolinianuspreferred moister soils under the cover object; and (3) length of time in captivity altered the preferences. Scorpions were captured from two different locations: (1) a roadcut parallel to State Highway 96 near Edgar Evins State Park; (2) France Mountain in Overton County. In laboratory trials, scorpions were allowed to choose among three retreat sites and three soil moisture levels. Transects were established at both field locations to count and measure rocks that may serve as retreat sites. Surface area trials indicated thatV. carolinianusselected large objects as retreat sites most often, but overall retreat site selection did not differ from that expected based on random choice weighted by cover object size. Soil moisture trial results varied, with no statistical significance in the results from the Highway 96 and 2013 France Mountain populations. The 2014 France Mountain population did show statistically significant differences. The surface area trials did not exhibit a time in captivity effect, but the soil moisture trials indicated a time in captivity effect between the 2013 and 2014 France Mountain populations. Based on test results, it appearsV. carolinianusselected larger rocks as cover sites, perhaps due to chance or perhaps to escape sunlight and heat, for predator avoidance, or for higher soil moisture levels.
Ecological Representations
Authors: Golonka Sabrina , Wilson Andrew D 
Published: June 2016

AbstractMainstream cognitive science and neuroscience both rely heavily on the notion of representation in order to explain the full range of our behavioral repertoire. The relevant feature of representation is its ability todesignate(stand in for) spatially or temporally distant properties, When we organize our behavior with respect to mental or neural representations, we are (in principle) organizing our behavior with respect to the property it designates. While representational theories are a potentially a powerful foundation for a good cognitive theory, problems such as grounding and system-detectable error remain unsolved. For these and other reasons, ecological explanations reject the need for representations and do not treat the nervous system as doing any mediating work. However, this has left us without a straight-forward vocabulary to engage with so-called ‘representation-hungry’ problems or the role of the nervous system in cognition.In an effort to develop such a vocabulary, here we show that James J Gibson’s ecological information functions to designate the ecologically-scaled dynamical world to an organism. We then show that this designation analysis of information leads to an ecological conceptualization of the neural activity caused by information, which in turn we argue can together support intentional behavior with respect to spatially and temporally distal properties. Problems such as grounding and error detection are solved via law-based specification. This analysis extends the ecological framework into the realm of ‘representation-hungry’ problems, making it as powerful a potential basis for theories of behavior as traditional cognitive approaches. The resulting analysis does, according to some definitions, allow information and the neural activity to be conceptualized as representations; however, the key work is done by information and the analysis remains true to Gibson’s ecological ontology.
Visualizing tumor evolution with the fishplot package for R
Authors: Miller Christopher A. , McMichael Joshua , Dang Ha X. , Maher Christopher A. , Ding Li , Ley Timothy J. , Mardis Elaine R. , Wilson Richard K. 
Published: June 2016

AbstractBackgroundMassively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. Easily interpretable data visualizations can greatly aid these studies, especially in cases with multiple timepoints. Current data visualization methods are typically manual and laborious, and often only approximate subclonal fractions.ResultsWe have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication.ConclusionsThe simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. Fishplot is available athttps://github.com/chrisamiller/fishplot
Uniparental inheritance promotes adaptive evolution in cytoplasmic genomes
Authors: Christie Joshua R. , Beekman Madeleine 
Published: June 2016

1AbstractEukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes—specifically their organization into host cells and their uniparental (maternal) inheritance—enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller’s ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes—despite their asexual mode of reproduction—can readily undergo adaptive evolution.
Modelling the effects of bacterial cell state and spatial location on tuberculosis treatment: Insights from a hybrid multiscale cellular automaton model
Authors: Bowness Ruth , Chaplain Mark A. J. , Powathil Gibin G. , Gillespie Stephen H. 
Published: June 2016

AbstractIf improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection.We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment. The individual elements (bacteria, macrophages and T cells) are modelled using cellular automaton (CA) rules, and the evolution of oxygen, drugs and chemokine dynamics are incorporated in order to study the effects of the microenvironment in the pathological lesion. We allow bacteria to switch states depending on oxygen concentration, which affects how they respond to treatment. This is the first multiscale model of its type to consider both oxygen-driven phenotypic switching of theMycobacterium tuberculosisand antibiotic treatment. Using this model, we investigate the role of bacterial cell state and of initial bacterial location on treatment outcome. We demonstrate that when bacteria are located further away from blood vessels, less favourable outcomes are more likely, i.e. longer time before infection is contained/cleared, treatment failure or later relapse. We also show that in cases where bacteria remain at the end of simulations, the organisms tend to be slower-growing and are often located within granulomas, surrounded by caseous material.
Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells
Authors: Shinkai Soya , Nozaki Tadasu , Maeshima Kazuhiro , Togashi Yuichi 
Published: June 2016

AbstractThe mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory. We analytically show that the mean-squared displacement (MSD) of nucleosome fluctuations within CDs is subdiffusive. The diffusion coefficient and the subdiffusive exponent depend on the structural information of CDs. This analytical result enabled us to extract information from the single-nucleosome imaging data for HeLa cells. Our observation that the MSD is lower at the nuclear periphery region than the interior region indicates that CDs in the heterochromatin-rich nuclear periphery region are more compact than those in the euchromatin-rich interior region with respect to the fractal dimensions as well as the size. Finally, we evaluated that the average size of CDs is in the range of 100-500 nm and that the relaxation time of nucleosome movement within CDs is a few seconds. Our results provide physical and dynamic insights into the genome architecture in living cells.Author SummaryThe mammalian genome is partitioned into topological chromatin domains (CDs) in the living cell nuclei. Gene expression is highly regulated within CDs according to their structure, whereas chromatin itself is highly dynamic. This raises the following question: how is the CD structure in such dynamic chromatin? We developed a conceptual framework that unifies chromatin dynamics and structure. Using a polymer model with a fractal domain structure in a viscoelastic medium, we analytically show that nucleosome movement is subdiffusive and depends on CD structure. Hence, structural information can be extracted based on nucleosome movement in living cells with single-particle tracking experiments. This framework provides physical insights into the relationship between dynamic genome organization and gene expression.
A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference
Authors: Maciuca Sorina , del Ojo Elias Carlos , McVean Gil , Iqbal Zamin 
Published: June 2016

AbstractWe show how positional markers can be used to encode genetic variation within aBurrows-Wheeler Transform (BWT), and use this to construct a generalisation ofthe traditional “reference genome”, incorporating known variation within aspecies. Our goal is to support the inference of the closest mosaic of previouslyknown sequences to the genome(s) under analysis.Our scheme results in an increased alphabet size, and by using a wavelet tree encoding of the BWT we reduce the performance impact on rank operations. We give a specialised form of the backward search that allows variation-aware exact matching. We implement this, and demonstrate the cost of constructing an index of the whole human genome with 8 million genetic variants is 25GB of RAM. We also show that inferring a closer reference can close large kilobase-scale coverage gaps inP. falciparum.
Genome resources for climate-resilient cowpea, an essential crop for food security
Authors: Muñoz-Amatriaín María , Mirebrahim Hamid , Xu Pei , Wanamaker Steve I. , Luo MingCheng , Alhakami Hind , Alpert Matthew , Atokple Ibrahim , Batieno Benoit Joseph , Boukar Ousmane , Bozdag Serdar , Cisse Ndiaga , Drabo Issa , Ehlers Jeffrey D. , Farmer Andrew , Fatokun Christian , Gu Yong Q. , Guo Yi-Ning , Huynh Bao-Lam , Jackson Scott A. , Kusi Francis , Lawley Cynthia T. , Lucas Mitchell R. , Ma Yaqin , Timko Michael P. , Wu Jiajie , You Frank , Roberts Philip A. , Lonardi Stefano , Close Timothy J. 
Published: June 2016

SUMMARYCowpea (Vigna unguiculataL. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crop plants. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include bacterial artificial chromosome (BAC) libraries and a BAC-based physical map, assembled sequences from 4,355 BACs, as well as a whole-genome shotgun (WGS) assembly. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for over 50,000 SNPs, which was then applied to five biparental RIL populations to produce a consensus genetic map containing 37,372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The genomes of West African breeding lines and landraces have regions of marked depletion of diversity, some of which coincide with QTL that may be the result of artificial selection or environmental adaptation. The new publicly available resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
Firm’s strategic orientation, market context, and performance
Authors: Pehrsson Anders 
Published: June 2016

PurposeThe purpose of this paper is to extend the understanding of relationships between entrepreneurial orientation (EO) and performance, and between market orientation (MO) and performance in different market contexts that set boundaries for performance.Design/methodology/approachThe paper presents a review of studies containing empirical research incorporating EO, MO, market context and firm performance.FindingsPatterns regarding content of previous studies of the issue are outlined, and crucial research gaps are identified. These concern a lack of focus on relationships between EO/MO and performance of foreign units.Research limitations/implicationsFirst, further studies on international strategy need to develop EO/MO components that are consistent with foreign units’ value-adding roles. Second, the impact of dynamism originating from competitors in foreign markets needs attention. Third, direct impacts of market dynamism on performance of foreign units, and moderating roles of EO/MO need to be studied.Practical implicationsInternational competitiveness of the firm as a whole would benefit from higher performance of foreign units that may be achieved through aligning EO/MO with local market contexts.Originality/valueMeta-analyses show that it is difficult to establish universal direct relationship between EO/MO and performance and that the importance of market context is underestimated. The paper provides opportunities for further studies that may clarify underlying contingency mechanisms.
Hanging on to wisdom of the “old”
Authors: Beal Brian 
Published: June 2016

Purpose
The purpose of this paper is to shed light on developments in Norwegian companies’ active ageing policies, and hence offer insight into what characterizes those Norwegian companies offering measures to retain their older workers.

Design/methodology/approach
The research questions are investigated using data from two surveys carried out among a representative sample of Norwegian companies in 2005 and 2010. The two data sets are analyzed both separately and jointly, being merged to obtain a pooled cross-section data set. Both multivariate logistic and linear regression are applied.

Findings
The proportion of companies in Norway offering retention measures, as well as the extensiveness of their retention efforts (the number of different measures offered), has increased considerably from 2005 to 2010. What characterizes these companies however are surprisingly similar in 2005 and 2010. Their retention efforts seem to be part of a holistic approach to active ageing. Offering a number of different retention measures is more common among companies having initiated “measures to facilitate lifelong learning” and “measures to prevent health problems or reduced work capacity”.

Originality/value
The employers’ perspective has received little attention in previous research and the authors are the first to report on developments in Norwegian companies’ retention efforts over time. Knowledge about what characterizes employers offering such measures will be important for future efforts to increase employments rates among older workers, which is an aim for most European countries.