bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virological Blips and Predictors of Post Treatment Viral Control After Stopping ART Started in Primary HIV Infection
Authors: Fidler Sarah , Olson Ashley D. , Bucher Heiner C. , Fox Julie , Thornhill John , Morrison Charles , Muga Roberto , Phillips Andrew , Frater John , Porter Kholoud ,   on behalf of CASCADE Collaboration in EuroCoord
Published: November 2016

Background:
Few individuals commencing antiretroviral therapy (ART) in primary HIV infection (PHI) maintain undetectable viremia after treatment cessation. Associated factors remain unclear given the importance of the phenomenon to cure research.

Methods:
Using CASCADE data of seroconverters starting ART in PHI (≤6 months from seroconversion), we estimated proportions experiencing viral blips (>400 copies followed by <400 copies HIV-RNA/mL without alteration of regimen) while on ART. We used Cox models to examine the association between time from ART stop to loss of control (2 consecutive measurements >1000 copies per milliliter) and magnitude and frequency of blips while on ART, time from seroconversion to ART, time on ART, adjusting for mean number of HIV-RNA measurements/year while on ART, and other confounders.

Results:
Seven hundred seventy-eight seroconverters started ART in PHI with ≥3 HIV-RNA measurements. Median interquartile range (IQR) ART duration was 16.2 (8.0–35.9) months, within which we observed 13% with ≥1 blip. Of 228 who stopped ART, 119 rebounded; time to loss of control was associated with longer interval between seroconversion and ART initiation [hazard ratio (HR) = 1.16 per month; 1.04, 1.28], and blips while on ART (HR = 1.71 per blip; 95% confidence interval = 0.94 to 3.10). Longer time on ART (HR = 0.84 per additional month; 0.76, 0.92) was associated with lower risk of losing control. Of 228 stopping ART, 22 (10%) maintained post treatment control (PTC), ie, HIV-RNA <50 copies per milliliter ≥24 months after ART cessation.

Conclusion:
HIV viral blips on therapy are associated with subsequent viral rebound on stopping ART among individuals treated in PHI. Longer duration on ART is associated with a greater chance of PTC.
Clinical Significance of Late Phase of Lung Perfusion Blood Volume (Lung Perfusion Blood Volume) Quantified by Dual-Energy Computed Tomography in Patients With Pulmonary Thromboembolism
Authors: Koike Hirofumi , Sueyoshi Eijun , Sakamoto Ichiro , Uetani Masataka 
Published: November 2016

Purpose:
Using dual-energy computed tomography (DECT), we quantified the lung perfusion blood volume (PBV) in the late phase, which may reflect both the pulmonary artery and systemic collateral flow. We then investigated the clinical significance of late-phase lung PBV values.

Materials and Methods:
We retrospectively studied 206 patients (266 scans) who underwent early-phase and late-phase DECT. The patients were divided into 2 groups depending on whether or not they had pulmonary thromboembolism (PTE) (n=94 and 112). Patients with PTE were further divided into 2 subgroups, depending on whether they had acute PTE or chronic PTE (n=66 and 28). Pulmonary artery enhancement (PAenh) was measured on DECT. We then calculated the [lung PBV/PAenh] ratio in all patients during both the early and late phases for adjustment of timing.

Results:
The [late-phase lung PBV/PAenh] ratio was 0.092±0.029 in the group with PTE and 0.108±0.030 in the group without PTE, showing a significant difference between the 2 groups (P<0.0001). The [early-phase lung PBV values/PAenh]/[late-phase lung PBV values/PAenh] ratio was 0.68±0.19 and 0.84±0.20, respectively, also showing a significant difference between the 2 groups (P<0.0001). Finally, the [early-phase lung PBV/PAenh]/[late-phase lung PBV/PAenh] ratio was 0.71±0.19 in patients with acute PTE and 0.56±0.16 in patients with chronic PTE, and there was a significant difference between these 2 subgroups (P=0.0004).

Conclusions:
It may be useful to determine late-phase lung PBV values in patients with PTE, because this parameter may reflect the systemic collateral flow, which is increased in chronic PTE.
Resilience, Invariability, and Ecological Stability across Levels of Organization
Authors: Haegeman Bart , Arnoldi Jean-François , Wang Shaopeng , de Mazancourt Claire , Montoya José M. , Loreau Michel 
Published: November 2016

AbstractEcological stability is a bewildering broad concept. The most common stability measures are asymptotic resilience, widely used in theoretical studies, and measures based on temporal variability, commonly used in empirical studies. We construct measures of invariability, defined as the inverse of variability, that can be directly compared with asymptotic resilience. We show that asymptotic resilience behaves like the invariability of the most variable species, which is often a rare species close to its extinction boundary. Therefore, asymptotic resilience displays complete loss of stability with changes in community composition. In contrast, mean population invariability and ecosystem invariability are insensitive to rare species and quantify stability consistently whether details of species composition are considered or not. Invariability provides a consistent framework to predict diversity-stability relationships that agree with empirical data at population and ecosystem levels. Our findings can enhance the dialogue between theoretical and empirical stability studies.
Genetic overlap between in-scanner head motion and the default network connectivity
Authors: Zhou Yuan , Chen Jie , Luo Yu L.L. , Zheng Dang , Rao Li-Lin , Li Xinying , Zhang Jianxin , Li Shu , Friston Karl , Zuo Xi-Nian 
Published: November 2016

AbstractThe association between in-scanner head motion and intrinsic functional connectivity (iFC) may confound explanations for individual differences in functional connectomics. However, the etiology of the correlation between head motion and iFC has not been established. This study aimed to investigate genetic and environmental contributions on the association between head motion and iFC using a twin dataset (175 same-sex twin pairs, aged 14-23 years, 48% females). After establishing that both head motion and default network iFC are moderately heritable, we found large genetic correlations (-0.52 to -0.73) between head motion and the default network iFCs. Common genes can explain 48% - 61% of the negative phenotypic correlation between the two phenotypes. These results advance our understanding of the relationship between head motion and iFC, and may have profound implications for interpreting individual differences in default network connectivity in clinical research and brain-behavior association.
Genetic variation for mitochondrial function in the New Zealand freshwater snailPotamopyrgus antipodarum
Authors: Sharbrough Joel , Cruise Jennifer L. , Beetch Megan , Enright Nicole M. , Neiman Maurine 
Published: November 2016

ABSTRACTThe proteins responsible for mitochondrial function are encoded by two different genomes with distinct inheritance regimes, rendering rigorous inference of genotype-phenotype connections intractable for all but a few model systems. Asexual organisms provide a powerful means for addressing these challenges because offspring produced without recombination inherit both nuclear and mitochondrial genomes from a single parent. As such, these offspring inherit mitonuclear genotypes that are identical to the mitonuclear genotypes of their parents and siblings and different from those of other asexual lineages. Here, we compared mitochondrial function across distinct asexual lineages ofPotamopyrgus antipodarum,a New Zealand freshwater snail model for understanding the evolutionary consequences of asexuality. Our analyses revealed substantial phenotypic variation across asexual lineages at three levels of biological organization: mitogenomic, organellar, and organismal. These data demonstrate that different asexual lineages have different mitochondrial function phenotypes and that there exists heritable variation (that is, the raw material for evolution) for mitochondrial function inP. antipodarum.The discovery of this variation combined with the methods developed here sets the stage to useP. antipodarumto study central evolutionary questions involving mitochondrial function, including whether mitochondrial mutation accumulation influences the maintenance of sexual reproduction in natural populations.
EMDUNIFRAC: EXACT LINEAR TIME COMPUTATION OF THE UNIFRAC METRIC AND IDENTIFICATION OF DIFFERENTIALLY ABUNDANT ORGANISMS
Authors: McClelland Jason , Koslicki David 
Published: November 2016

ABSTRACTBoth the weighted and unweighted Unifrac distances have been very successfully employed to assess if two communities differ, but do not give any information abouthowtwo communities differ. We take advantage of recent observations that the Unifrac metric is equivalent to the so-calledearth mover’s distance(also known as the Kantorovich-Rubinstein metric) to develop an algorithm that not only computes the Unifrac distance in linear time and space, but also simultaneously finds which operational taxonomic units are responsible for the observed differences between samples. This allows the algorithm, called EMDUnifrac, to determinewhygiven samples are different, not justifthey are different, and with no added computational burden. EMDUnifrac can be utilized on any distribution on a tree, and so is particularly suitable to analyzing both operational taxonomic units derived from amplicon sequencing, as well as community profiles resulting from classifying whole genome shotgun metagenomes. The EMDUnifrac source code (written in python) is freely available at:https://github.com/dkoslicki/EMDUnifrac.
Mathematical models of SIR disease spread with combined non-sexual and sexual transmission routes
Authors: Miller Joel C 
Published: November 2016

AbstractThe emergence of diseases such as Zika and Ebola has highlighted the need to understand the role of sexual transmission in the spread of diseases with a primarily non-sexual transmission route. In this paper we develop a number of low-dimensional models which are appropriate for a range of assumptions for how a disease will spread if it has sexual transmission through a sexual contact network combined with some other transmission mechanism, such as direct contact or vectors. The equations derived provide exact predictions for the dynamics of the corresponding simulations in the large population limit.
Test-retest reliability of functional connectivity networks during naturalistic fMRI paradigms
Authors: Wang Jiahui , Ren Yudan , Hu Xintao , Thai Nguyen Vinh , Guo Lei , Han Junwei , Guo Christine Cong 
Published: November 2016

AbstractFunctional connectivity analysis has become a powerful tool for probing the human brain function and its breakdown in neuropsychiatry disorders. So far, most studies adopted resting state paradigm to examine functional connectivity networks in the brain, thanks to its low demand and high tolerance that are essential for clinical studies. However, the test-retest reliability of resting state connectivity measures is moderate, potentially due to its low behavioral constraint. On the other hand, naturalistic neuroimaging paradigms, an emerging approach for cognitive neuroscience with high ecological validity, could potentially improve the reliability of functional connectivity measures. To test this hypothesis, we characterized the test-retest reliability of functional connectivity measures during a natural viewing condition, and benchmarked it against resting state connectivity measures acquired within the same functional magnetic resonance imaging (fMRI) session. We found that the reliability of connectivity and graph theoretical measures of brain networks is significantly improved during natural viewing conditions over resting state conditions, with an average increase of almost 50% across various connectivity measures. Not only sensory networks for audio-visual processing become more reliable, higher order brain networks, such as default mode and attention networks, also appear to show higher reliability during natural viewing. Our results support the use of natural viewing paradigms in estimating functional connectivity of brain networks, and have important implications for clinical application of fMRI.
Modeling disease spread in populations with birth, death, and concurrency
Authors: Miller Joel C. , Slim Anja C. 
Published: November 2016

AbstractThe existence of sexual partnerships that overlap in time (concurrent relationships) is believed by some to be a significant contributing factor to the spread of HIV, although this is controversial. We derive an analytic model which allows us to investigate and compare disease spread in populations with and without concurrency. We can identify regions of parameter space in which its impact is negligible, and other regions in which it plays a major role. We also see that the impact of concurrency on the initial growth phase can be much larger than its impact on the equilibrium size. We see that the effect of concurrency saturates, which leads to the perhaps surprising conclusion that interventions targeting concurrency may be most effective in populations with low to moderate levels of concurrency.Author SummaryWe consider the spread of an infectious disease through a population modeled by a dynamic network with demographic turnover. We develop a stochastic model of the disease and derive governing equations that exactly predict the large population (deterministic) limit of the stochastic model. We use this to investigate the role of concurrency and find that interventions targeting concurrency may be most effective in populations with lower levels of concurrency.Our model is not intended to be an accurate representation of any single population. Rather it is intended to give general insights for intervention design and to provide a framework which can be further specialized to particular populations.This model is the first model to allow for analytic investigation of the impact of concurrent partnerships in a population exhibiting demographic turnover. Thus it will be useful for investigating the “concurrency hypothesis.”
Proteotype profiling unmasks a viral signaling network essential for poxvirus assembly and transcriptional competence
Authors: Novy Karel , Kilcher Samuel , Omasits Ulrich , Ernst Bleck Christopher Karl , Beerli Corina , Syedbasha Mohammedyaseen , Maiolica Alessio , Mercer Jason , Wollscheid Bernd 
Published: November 2016

AbstractTo orchestrate context-dependent signaling programs poxviruses encode two dual-specificity enzymes, the F10 kinase and the H1 phosphatase. These signaling mediators are essential for poxvirus production, yet their substrate profiles and systems level functions remain enigmatic. Using a phosphoproteomic screen of cells infected with wildtype, F10, and H1 mutant viruses we systematically defined the viral signaling network controlled by these enzymes. Quantitative cross-comparison revealed 33 F10 and/or H1 phosphosites within 17 viral proteins. Using this proteotype dataset to inform genotype-phenotype relationships we found that H1-deficient virions harbor a hidden hyper-cleavage phenotype driven by reversible phosphorylation of the virus protease I7 (S134). Quantitative phospho-proteotyping further revealed that the phosphorylation-dependent activity of the viral early transcription factor, A7 (Y367), underlies the transcription-deficient phenotype of H1 mutant virions. Together these results highlight the utility of combining quantitative proteotype screens with mutant viruses to uncover novel proteotype-phenotype-genotype relationships that are masked by classical genetic studies.
Challenging the conceptual framework of maintenance hosts for influenza A viruses in wild birds
Authors: Caron Alexandre , Cappelle Julien , Gaidet Nicolas 
Published: November 2016

Summary

The conceptual framework considering Anseriformes and Charadriiformes as the main maintenance hosts for influenza A viruses (IAV) in wild birds has shaped IAV research and surveillance over the last decades.

We challenge this framework by reviewing the world‐wide surveillance data on non‐Anseriformes and non‐Charadriiformes (NANC) species, generally considered as playing little role in IAV maintenance, available in literature and online data bases (close to 200 sources).

Globally, we found an IAV infection rate of 1·51% (95% CI, 1·44–1·59%) for c. 101 000 birds tested from NANC species. If Anseriformes have, as expected, a higher infection rate than any other bird orders, eight bird orders have an infection rate higher or close to the Charadriiformes infection rate, challenging the status of Charadriiformes.

We interpret the attention paid in favour of Charadriiformes by an extrapolation bias from data collected in hotspots of IAV infection in Charadriiformes (e.g. Delaware Bay, USA).

The growing data on IAV in wild birds world‐wide, summarised here, support two non‐exclusive hypotheses: (i) the quality of the diagnostic tools and techniques used explain the patterns observed; (ii) IAV maintenance is determined by complex multi‐host systems composed of multiple bird species, dependent on the ecosystem and its bird diversity and composition.

Synthesis and applications. Our results have two main implications. First, new research and surveillance should be designed in order to understand influenza A viruses ecology in wild birds across the world, along with appropriate diagnostic tools and new hypotheses and dedicated protocols. This should be done in line with our new conceptual framework that conveys less a priori than its predecessor. Second, our results call for more bridging between biological and epidemiological sciences in order to tackle disease ecology in multi‐host systems.
A cadaver study comparing three fibreoptic‐assisted techniques for converting a supraglottic airway to a cuffed tracheal tube
Authors: Olesnicky B. L. , Rehak A. , Bestic W. B. , Brock J. T. , Watterson L. 
Published: November 2016

SummaryAfter rescuing an airway with a supraglottic airway device, a method to convert it to a cuffed tracheal tube is often needed. The best method to do this has never been directly studied. We compared three techniques for conversion of a standard LMA® Unique airway to a cuffed endotracheal tube using a fibrescope. The primary endpoint was time to intubation, with secondary endpoints of success rate, perceived difficulty and preferred technique. We also investigated the relationship between level of training and prior training and experience with the techniques on the primary outcome. The mean (95% CI) time to intubation using a direct tracheal tube technique of 37 (31–42) s was significantly shorter than either the Aintree intubation catheter technique at 70 (60–80) s, or a guidewire technique at 126 (110–141) s (p < 0.001). Most (13/24) participants rated the tracheal tube as their preferred technique, while 11/24 preferred the Aintree technique. In terms of perceived difficulty, 23/24, 21/24 and 9/24 participants rated the tracheal tube technique, Aintree technique and guidewire technique, respectively, as either very easy or easy. There was no relationship between prior training, prior experience or level of training on time to completion of any of the techniques. We conclude the tracheal tube and Aintree techniques both provide a rapid and easy method for conversion of a supraglottic airway device to a cuffed tracheal tube. The guidewire technique cannot be recommended.
Risk stratification: a tool to predict the course of active surveillance for localized prostate cancer?
Authors: Herden Jan , Heidenreich Axel , Weissbach Lothar 
Published: November 2016

ObjectiveTo investigate a cohort of patients undergoing active surveillance (AS) for localized prostate cancer (PCa) with regard to possible differences in discontinuation rates, subsequent therapies, reasons for intervention and pathological findings after deferred surgery after patient stratification into very‐low‐risk, low‐risk and intermediate‐/high‐risk PCa groups.Patients and MethodsThe HAROW study was a non‐interventional, observational, outcomes research study on the management of localized PCa in the community setting. A total of 468 patients were prospectively enrolled in the HAROW study, with a mean follow‐up of 28.5 months. Treating urologists reported clinical variables, information on therapy and clinical course of disease at 6‐month intervals.ResultsOf 468 patients under AS, 244 were stratified into very‐low‐risk, 142 into low‐risk and 82 into intermediate‐/high‐risk groups. Of these patients, 112 discontinued AS. Discontinuation rates were 25.4% in the very‐low‐risk, 21.1% in the low‐risk and 24.4% in the intermediate‐/high‐risk groups (P = 0.633). The main reasons for intervention were biopsy upgrade and/or prostate‐specific antigen elevation in the very‐low‐ and low‐risk groups, and patient preference in the intermediate‐/high‐risk group (P < 0.05). No significant differences were found regarding subsequent therapies and pathological findings after deferred surgery.ConclusionOur results show no differences in the outcome of risk‐stratified patients in the specified risk groups managed with AS, while switching to an invasive treatment on the patient′s request was more frequent in the intermediate‐/high‐risk group.
Genetic diversity and structure of the Australian flora
Authors: Broadhurst Linda , Breed Martin , Lowe Andrew , Bragg Jason , Catullo Renee , Coates David , Encinas‐Viso Francisco , Gellie Nick , James Elizabeth , Krauss Siegfried , Potts Brad , Rossetto Maurizio , Shepherd Mervyn , Byrne Margaret 
Published: November 2016

AbstractAimTo investigate the relationships between species attributes and genetic parameters in Australian plant species and to determine the associations in relation to predictions from population theory and previous global analyses.LocationContinent of Australia.MethodsWe assembled a dataset of all known population genetic analyses of Australian plants based on neutral markers and catalogued them according to key species attributes, including range, abundance, range disjunction, biome and growth form; and genetic parameters, mean number of alleles per locus, observed and expected heterozygosity and population differentiation. We determined relationships between species attributes and genetic parameters using a maximum‐likelihood, multimodel inference approach.ResultsWe found many associations that were consistent with predictions. Species attributes with greatest effect on genetic diversity were range size, growth form, abundance and biome. The most important attributes influencing genetic differentiation were range disjunction and abundance. We found unexpected results in the effects of biome and growth form on genetic diversity, with greater diversity in the eastern biome of Australia, and lower diversity in shrubs compared to trees.Main conclusionsOur analysis of genetic diversity of Australian plants showed associations consistent with predictions based on population genetics theory, with strong effects of range size, abundance and growth form. We identified a striking effect of range disjunction on population genetic differentiation, an effect that has received little attention in the literature. We also found some notable differences to global predictions, which were most likely explained by confounding effects across variables. This highlights that caution is needed when extrapolating trends from global analyses to regional floras. Identifying associations between species attributes and patterns of genetic diversity enables broadscale predictions to facilitate the inclusion of genetic considerations into conservation decision‐making.