bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delivering Partner Services to Reduce Transmission and Promote Linkage to Care: Process Outcomes Varied for Chlamydial Infection, Gonorrhea, HIV, and Syphilis Cases
Authors: Martin Erika G. , Feng Wenhui , Qian Feng , Johnson Britney 
Published: October 2015

Context:
Partner services for HIV and sexually transmitted diseases, a public health intervention activity recommended by the Centers for Disease Control and Prevention, includes counseling, partner notification, linkage to care, and referral to other services.

Objective:
A time study of partner services case investigations documented differences in times to process HIV/sexually transmitted disease cases.

Setting:
Cases were from 9 local and regional sites in New York.

Participants:
Fifty-two partner services disease investigators documented 542 randomly selected cases (271 chlamydial infections, 162 gonorrhea, 48 HIV, and 61 syphilis cases) assigned between June and September 2014. Cases were the unit of the analysis and represented 6.9% of all partner services investigations in 2014.

Design:
Cases were selected via stratified random sampling of infections assigned to staff. For each case, disease investigators completed a standard time study form to document the time spent on specific tasks and other outcomes. Kruskal-Wallis tests for continuous variables and χ2 tests for categorical variables assessed variation in outcomes across infection type.

Main Outcome Measures:
Outcomes included minutes spent on specific tasks (such as medical provider and index case outreach, travel, and partner notification), days the case remained open, disposition codes, and number of partners reached.

Results:
Case processing times varied, with HIV and syphilis tasks taking more minutes (P < .001) and cases staying open for more days (P < .001). Partners were notified in 33% of cases overall, with more notifications in syphilis (44%). Most time (median = 77%) was spent on index cases and 2% (median) on partner notification, with a wide range across cases.

Conclusions:
Given their chronic resource constraints, public health agencies must identify efficient methods to allocate resources, including which infections to prioritize. Documenting how workers allocate time across cases is essential to improving the effectiveness and efficiency of this program and generating the data to model return on investment.
Contiguous and accuratede novoassembly of metazoan genomes with modest long read coverage
Authors: Chakraborty Mahul , Baldwin-Brown James G. , Long Anthony D. , Emerson J.J. 
Published: October 2015

AbstractGenome assemblies that are accurate, complete, and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements, and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standardDrosophila melanogasterreference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a “missing manual” that guides key decisions in building high qualityde novogenome assemblies, from DNA isolation to polishing the assembly.
Blood circulation in the tunicateCorella inflata(Corellidae)
Authors: Konrad Michael W. 
Published: October 2015

AbstractThe ascidian tunicateCorella inflatais relatively transparent compared to other solitary tunicates and the circulatory system can be visualized by injecting high molecular weight fluorescein labeled dextran into the beating heart or the large vessels at the ends of the heart. In addition, after staining with neutral red the movement of blood cells can be followed to further define and characterize the circulatory system. The heart is a gently curved tube with a constriction in the middle and extends across the width of the animal. As in other tunicates, pumping is peristaltic and periodically reverses direction. During the abvisceral directional phase blood leaves the anterior end of the heart in two asymmetric vessels that connect to the two sides of the branchial basket (or pharynx), in contrast to the direct connection between the heart and the endostyle seen in the commonly studied tunicateCiona intestinalis.InCorella inflatablood then flows in both transverse directions through a complex system of ducts in the branchial basket into large ventral and dorsal vessels and then to the visceral organs in the posterior of the animal. During the advisceral phase blood leaves the posterior end of the heart in vessels that repeatedly bifurcate to fan into the stomach and gonads. Blood speed, determined by following individual cells, is high and pulsatory near the heart, but decreases and becomes more constant in peripheral regions. Estimated blood flow volume during one directional phase is greater than the total volume of the animal. Circulating blood cells are confined to vessels or ducts in the visible parts of the animal and retention of high molecular weight dextran in the vessels is comparable to that seen in vertebrates. These flow patterns are consistent with a closed circulatory network.
Ecological diversification associated with the pharyngeal jaw diversity of Neotropical cichlid fishes
Authors: Burress Edward D. 
Published: October 2015

Summary

Innovations can facilitate bursts of diversification by increasing access to novel resources and the attainment of novel functional designs. Pharyngognathy, exhibited by highly diverse groups such as wrasses and cichlid fishes, is hypothesized to increase foraging capacity and efficiency.

Here, I test the hypothesis that pharyngeal jaw shape and tooth morphology are adaptive in an ecologically diverse radiation of Neotropical cichlid fishes that spans North, Central and South America.

I partitioned species into generalized trophic guilds using published stomach content analyses and quantified shape variation of the lower pharyngeal jaw (LPJ) using geometric morphometrics. Additionally, I tested for convergence in LPJ shape and trophic guild by mapping the phylogeny onto the principal components and testing for shifts towards similar evolutionary regimes.

Major LPJ shape variation included the length and orientation (i.e. narrow or wide) of the lateral processes and length of the medial process, which varied based on the proportion of fishes and plants consumed. Pharyngeal tooth number, diversity and the frequency of tooth types were not evenly distributed among trophic guilds. There were seven distinct evolutionary regimes that converged upon four optima.

Pharyngeal jaw diversification is associated with the exploitation of novel resources among Neotropical cichlids such that pharyngeal specialization has increased access to otherwise poorly accessible resources, such as resources that are difficult to crush (e.g. hard‐shelled organisms) and assimilate (e.g. algae).
Influences of sampling effort on detected patterns and structuring processes of a Neotropical plant–hummingbird network
Authors: Vizentin‐Bugoni Jeferson , Maruyama Pietro K. , Debastiani Vanderlei J. , Duarte L. da S. , Dalsgaard Bo , Sazima Marlies 
Published: October 2015

Summary

Virtually all empirical ecological interaction networks to some extent suffer from undersampling. However, how limitations imposed by sampling incompleteness affect our understanding of ecological networks is still poorly explored, which may hinder further advances in the field.

Here, we use a plant–hummingbird network with unprecedented sampling effort (2716 h of focal observations) from the Atlantic Rainforest in Brazil, to investigate how sampling effort affects the description of network structure (i.e. widely used network metrics) and the relative importance of distinct processes (i.e. species abundances vs. traits) in determining the frequency of pairwise interactions.

By dividing the network into time slices representing a gradient of sampling effort, we show that quantitative metrics, such as interaction evenness, specialization (H2′), weighted nestedness (wNODF) and modularity (Q; QuanBiMo algorithm) were less biased by sampling incompleteness than binary metrics. Furthermore, the significance of some network metrics changed along the sampling effort gradient. Nevertheless, the higher importance of traits in structuring the network was apparent even with small sampling effort.

Our results (i) warn against using very poorly sampled networks as this may bias our understanding of networks, both their patterns and structuring processes, (ii) encourage the use of quantitative metrics little influenced by sampling when performing spatio‐temporal comparisons and (iii) indicate that in networks strongly constrained by species traits, such as plant–hummingbird networks, even small sampling is sufficient to detect their relative importance for the frequencies of interactions. Finally, we argue that similar effects of sampling are expected for other highly specialized subnetworks.
Community structure influences species’ abundance along environmental gradients
Authors: Eloranta Antti P. , Helland Ingeborg P. , Sandlund Odd T. , Hesthagen Trygve , Ugedal Ola , Finstad Anders G. 
Published: October 2015

Summary

Species’ response to abiotic environmental variation can be influenced by local community structure and interspecific interactions, particularly in restricted habitats such as islands and lakes. In temperate lakes, future increase in water temperature and run‐off of terrestrial (allochthonous) dissolved organic carbon (DOC) are predicted to alter community composition and the overall ecosystem productivity. However, little is known about how the present community structure and abiotic environmental variation interact to affect the abundance of native fish populations.

We used a space‐for‐time approach to study how local community structure interact with lake morphometric and climatic characteristics (i.e. temperature and catchment productivity) to affect brown trout (Salmo trutta L.) yield in 283 Norwegian lakes located in different biogeographical regions.

Brown trout yield (based on data from standardized survey gill net fishing; g 100 m−2 gill net night−1) was generally lower in lakes where other fish species were present than in lakes with brown trout only. The yield showed an overall negative relationship with increasing temperature and a positive relationship with lake shoreline complexity. Brown trout yield was also negatively correlated with DOC load (measured using Normalized Difference Vegetation Index as a proxy) and lake size and depth (measured using terrain slope as a proxy), but only in lakes where other fish species were present. The observed negative response of brown trout yield to increasing DOC load and proportion of the pelagic open‐water area is likely due to restricted (littoral) niche availability and competitive dominance of more pelagic fishes such as Arctic charr (Salvelinus alpinus (L.)).

Our study highlights that, through competitive interactions, the local community structure can influence the response of a species’ abundance to variation in abiotic conditions. Changes in biomass and niche use of top predators (such as the brown trout), associated with predicted changes in direct and indirect climatic factors, may have further influences on the structure and function of temperate lake ecosystems.
Top predators and habitat complexity alter an intraguild predation module in pond communities
Authors: Anderson Thomas L. , Semlitsch Raymond D. 
Published: October 2015

Summary

Predator diversity and habitat complexity frequently influence species interactions at lower trophic levels, yet their joint investigation has been performed infrequently despite the demonstrated importance of each individual factor.

We investigated how different top predators and varying habitat complexity influence the function of an intraguild predation module consisting of two larval salamanders, intraguild predator Ambystoma annulatum and intraguild prey A. maculatum.

We manipulated predator food webs and habitat complexity in outdoor mesocosms.

Top predators significantly influenced body condition and survival of A. annulatum, but habitat complexity had minimal effects on either response.

A three‐way interaction among the covariates top predator identity, habitat complexity and A. annulatum survival influenced body condition and survival of A. maculatum via a density‐mediated indirect effect. Different top predator combinations had variable effects in different habitat complexity treatments on intraguild predator (A. annulatum) survival that subsequently influenced intraguild prey (A. maculatum) body condition and survival.

Future work should consider how different top predators influence other food web components, which should vary due to predator attributes and the physical environments in which they co‐occur.
Nefopam analgesia and its role in multimodal analgesia: A review of preclinical and clinical studies
Authors: Girard Philippe , Chauvin Marcel , Verleye Marc 
Published: October 2015

SummaryNefopam is a non‐opioid, non‐steroidal, centrally acting analgesic drug used to prevent postoperative pain, primarily in the context of multimodal analgesia. This paper reviews preclinical and clinical studies in which nefopam has been combined with opioids, non‐steroidal anti‐inflammatory compounds, and paracetamol. This report focuses on the literature during the last decade and discusses the translational efforts between animal and clinical studies in the context of multimodal or balanced analgesia. In preclinical rodent models of acute and inflammatory pain, nefopam combinations including opioids revealed a synergistic interaction or enhanced morphine analgesia in six out of seven studies. Nefopam combinations including non‐steroidal anti‐inflammatory drugs (NSAIDs) (aspirin, ketoprofen or nimesulide) or paracetamol likewise showed enhanced analgesic effects for the associated compound in all instances. Clinical studies have been performed in various types of surgeries involving different pain intensities. Nefopam combinations including opioids resulted in a reduction in morphine consumption in 8 out of 10 studies of severe or moderate pain. Nefopam combinations including NSAIDs (ketoprofen or tenoxicam) or paracetamol also demonstrated a synergic interaction or an enhancement of the analgesic effect of the associated compound. In conclusion, this review of nefopam combinations including various analgesic drugs (opioids, NSAIDs and paracetamol) reveals that enhanced analgesia was demonstrated in most preclinical and clinical studies, suggesting a role for nefopam in multimodal analgesia based on its distinct characteristics as an analgesic. Further clinical studies are needed to evaluate the analgesic effects of nefopam combinations including NSAIDs or paracetamol.
Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis
Authors: Casaburi Giorgio , Duscher Alexandrea A. , Reid R. Pamela , Foster Jamie S. 
Published: October 2015

SummaryModern stromatolites represent ideal ecosystems to understand the biological processes required for the precipitation of carbonate due to their long evolutionary history and occurrence in a wide range of habitats. However, most of the prior molecular work on stromatolites has focused on understanding the taxonomic complexity and not fully elucidating the functional capabilities of these systems. Here, we begin to characterize the microbiome associated with stromatolites of Little Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct whole shotgun sequencing. The metagenomic analysis of the Little Darby stromatolites revealed many shared taxa and core pathways associated with biologically induced carbonate precipitation, suggesting functional convergence within Bahamian stromatolites. A comparison of the Little Darby stromatolites with other lithifying microbial ecosystems also revealed that although factors, such as geographic location and salinity, do drive some differences within the population, there are extensive similarities within the microbial populations. These results suggest that for stromatolite formation, ‘who’ is in the community is not as critical as metabolic activities and environmental interactions. Together, these analyses help improve our understanding of the similarities among lithifying ecosystems and provide an important first step in characterizing the shared microbiome of modern stromatolites.
Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes
Authors: Clerissi Camille , Desdevises Yves , Romac Sarah , Audic Stéphane , de Vargas Colomban , Acinas Silvia G , Casotti Raffaella , Poulain Julie , Wincker Patrick , Hingamp Pascal , Ogata Hiroyuki , Grimsley Nigel 
Published: October 2015

SummaryHigh‐throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey–predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.
IL‐17 Induces Fetal Loss in a CBA/J×BALB/c Mouse Model, and an Anti‐IL‐17 Antibody Prevents Fetal Loss in a CBA/J ×DBA/2 Mouse Model
Authors: Xu Wang‐Ming , Xiao Zhuo‐Ni , Wang Xiao‐Bo , Huang Ying 
Published: October 2015

ProblemMany researchers have demonstrated that the expression of interleukin‐17(IL‐17) is higher in spontaneous abortion. However, whether Th17 cells are an independent factor in inducing abortion is not known.Method of studyThis study investigated the effect of exogenous recombinant IL‐17 and an anti‐IL‐17 antibody in a normal and an abortion mouse model using flow cytometry, enzyme‐linked immunosorbent assay, real‐time PCR, and Western blot.ResultsTh17 cells and the related factors, IL‐17 and RORγt, were significantly upregulated in abortion mice, and Treg cells and the related factor, Foxp3, were downregulated. Intraperitoneal injection of recombinant IL (rIL)‐17 induced fetal loss in a normal mouse model, and an anti‐IL‐17 antibody prevented fetal loss in an abortion mouse model.ConclusionThis study confirmed an imbalance of the Th17/Treg paradigm in abortion mice and IL‐17 as a risk factor of fetal loss. An anti‐IL‐17 antibody may prevent abortion.
Parental smoking and development of allergic sensitization from birth to adolescence
Authors: Thacher J. D. , Gruzieva O. , Pershagen G. , Neuman Å. , van Hage M. , Wickman M. , Kull I. , Melén E. , Bergström A. 
Published: October 2015

AbstractBackgroundThe relation between secondhand tobacco smoke (SHS) exposure and the development of allergic sensitization in children is unclear. The aim of this study was to determine whether maternal smoking during pregnancy and postnatal SHS exposure contributes to the development of allergic sensitization in children and adolescents up to 16 years of age.MethodsWe included 3316 children from a birth cohort followed up for 16 years. SHS exposure and symptoms of allergic disease were assessed using repeated parental questionnaires. Serum immunoglobulin E against eight common inhalant and six food allergens was assessed at ages 4, 8, and 16 years with ImmunoCAP. The association between SHS exposure and sensitization was explored using logistic regression and generalized estimating equations.ResultsExposure to SHS in infancy without prior exposure in utero was associated with an excess risk of food sensitization at age 4 years (OR 1.47, 95% CI 1.08–2.00), with comparable ORs at ages 8 and 16 years. In longitudinal analyses, an overall association was indicated between SHS in infancy and food sensitization up to age 16 years (OR 1.24, 95% CI 0.98–1.56). Maternal smoking during pregnancy was unrelated to sensitization up to 16 years of age. When sensitization was combined with concurrent symptoms of allergic disease, SHS in infancy was associated with an overall elevated risk of eczema with sensitization (OR 1.62, 95% CI 1.20–2.18).ConclusionsSHS exposure in infancy appears to increase the risk of sensitization to food allergens up to age 16 years, as well as eczema in combination with sensitization.
Collision of lymphoepithelioma‐like carcinoma and adenocarcinoma of the lung: a case report
Authors: Chan Jammy Kin Iong , Tai Wai Meng , Wen Jian Ming 
Published: October 2015

AbstractWe report a rare case of collision of lymphoepithelioma‐like carcinoma (LELC) and adenocarcinoma (AC) in the lung. A 59‐year‐old woman had a history of fever and cough. A mass was found by X‐ray in the left upper lung. Magnetic resonance imaging (MRI) shows a dumbbell‐like mass in the fore and tongue segment of the left upper lung with irregular spiculate margin. Positron emission tomography/computed tomography (PET/CT) (18F‐FDG) shows strong concentration of radioactivity (SUVmax 6.9–12.3 cm) in the lung mass only. The patient subsequently underwent resection of left upper lung and associated hilar lymph nodes. Histological examination revealed it was a collision carcinoma comprising LELC and AC. The hilar lymph nodes were tumuor free. The immunoreactions, Epstein–Barr early RNA in situ hybridization and molecular analyses, such as EGFR mutation, c‐Met, anaplastic lymphoma kinase were different in both tumuor components, indicating they derived from different cell origin. This rare case was discussed.
Keratoacanthoma: a distinct entity?
Authors: Gleich Tobias , Chiticariu Elena , Huber Marcel , Hohl Daniel 
Published: October 2015

AbstractKeratoacanthoma (KA) are common but exceptional benign tumors, often appearing on sun‐exposed areas of light skinned people and showing spontaneous resolution. The goal of this study was to review existing literature, to point out the etiological complexity of KA biology and to answer the controversial debate if or not KA is a distinct entity or a variant of squamous cell carcinoma (SCC). Relying on recent results, we highlight that KA is an individual lesion with a unique molecular signature caused by alterations in the TGFβ signalling pathway. These recent findings will help to understand the nature of KA and to develop new reliable diagnostic tools, simplifying the discrimination of the histologically similar KA and SCC.