bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservative Therapy is an Effective Option in Patients with Localized Infection After Penile Implant Surgery
Authors: Habous Mohamad , Farag Mohammed , Williamson Ben , Laban Osama , Mahmoud Saad , Abdelwahab Osama , Elkhouly Mohamed , Kamil Usama , Binsaleh Saleh , Tal Raanan , Ralph David , Mulhall John P. 
Published: May 2016

ABSTRACT

Introduction
Traditionally, penile implant (PI) infections have been managed by removal with immediate or delayed replacement. Recently, interest has been focused on conservative therapy (CT) using antibiotic therapy.

Aim
To investigate the success rate and predictive factors affecting the outcome of CT in PI infection patients.

Methods
Patients diagnosed with early, localized PI infection were considered candidates for CT. Exclusion criteria included temperature &gt;37.5°C, WBC &gt;13,000/μL, and appearance of any sign of sepsis. In patients with purulent drainage, culture swabs were taken and an antibiotic was chosen based on sensitivity results. Oral antibiotics were used until the local infection was completely resolved. Patients were evaluated weekly during this process.

Results
Thirty-seven patients were retrospectively reviewed and constituted the study population. Mean age was 58.1 (range 37–85; SD 9.9) years. All were diabetic. Mean BMI was 31.8 (range 24–47; SD 5.0). PI was malleable in 33 cases and inflatable in 4 cases. Culture results (n = 19) included Staphylococcus epidermidis (42 %), pseudomonas (21%), Escherichia coli (21%), and S aureus (16%). Four of 37 patients needed the PI removed due to CT failure and onset of systemic symptoms, at a mean time-point of 75 ± 1.8 days after CT commencement. In men who were cured, mean time to complete healing was 49 (range 29–97; SD 15.8) days. Two of 37 patients (5%) had PI removal because of persistent penile pain despite complete wound healing, at a mean time point of 128 ± 2.5 days after CT commencement. All men managed conservatively resumed sexual intercourse.

Conclusion
CT of localized PI infection appears to be a viable option for such patients, with the majority of patients retaining their implant and resuming sexual activity.
Information capacity of specific interactions
Authors: Huntley Miriam H. , Murugan Arvind , Brenner Michael P. 
Published: May 2016

Significance
The past 15 years have seen a proliferation of experimental techniques aimed at engineering self-assembled structures. These bottom–up techniques rely on specific interactions between components that arise from diverse physical mechanisms such as chemical affinities and shape complementarity attraction. Comparisons of specificity across such diverse systems, each with unique physics and constraints, can be difficult. Here we describe an information theoretic measure, capacity, to quantify specificity in a range of recent experimental systems. Capacity quantifies the maximal amount of information that can be encoded and then resolved by a system of specific interactions, as a function of experimentally tunable parameters. Our framework can be applied to specific interactions of diverse origins, from colloidal experiments to protein interactions.
Meaningful call combinations and compositional processing in the southern pied babbler
Authors: Engesser Sabrina , Ridley Amanda R. , Townsend Simon W. 
Published: May 2016

SignificanceHuman language is syntactic in its nature: meaningful words are assembled into larger meaningful phrases or sentences. How unique this ability is to humans remains surprisingly unclear. A considerable body of work has indicated that birds are capable of combining sounds into large, elaborate songs, but there is currently no evidence suggesting that these structures are syntactic. Here, we provide important evidence for this ability in a highly social bird. Specifically, pied babblers combine two functionally distinct vocalizations into a larger sequence, the function of which is related to the function of its parts. Our work adds important evidence to the variation and distribution of combinatorial vocal mechanisms outside humans and provides insights into potentially early forms of human syntactic communication.
Elucidation of tonic and activated B-cell receptor signaling in Burkitt’s lymphoma provides insights into regulation of cell survival
Authors: Corso Jasmin , Pan Kuan-Ting , Walter Roland , Doebele Carmen , Mohr Sebastian , Bohnenberger Hanibal , Ströbel Philipp , Lenz Christof , Slabicki Mikolaj , Hüllein Jennifer , Comoglio Federico , Rieger Michael A. , Zenz Thorsten , Wienands Jürgen , Engelke Michael , Serve Hubert , Urlaub Henning , Oellerich Thomas 
Published: May 2016

Significance
B-cell receptor (BCR) signaling promotes the survival of malignant B cells, such as Burkitt’s lymphoma (BL) and the activated B-cell–like subtype of diffuse large B-cell lymphoma (ABC-DLBCL). In contrast to ABC-DLBCL, which depends on chronic activation of the BCR, BL cells rely on tonic BCR signaling that is antigen-independent. Elucidation and systematic comparison of tonic and activated BCR signaling led to the identification of novel signaling effectors, including ACTN4 and ARFGEF2, which were identified as regulators of BL-cell survival. Beyond its relevance to the understanding of BL pathogenesis and the development of targeted therapies, our study complements the general understanding of BCR-induced processes also in physiological settings.
Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers
Authors: Farley Emma K. , Olson Katrina M. , Zhang Wei , Rokhsar Daniel S. , Levine Michael S. 
Published: May 2016

Significance
Transcriptional enhancers are elements within the genome that control when and where genes are expressed. Although they were identified more than 3 decades ago, how DNA sequence encodes enhancer function remains unclear. Here we show that enhancer syntax (the order, orientation, and spacing of transcription factor binding sites) is important for tissue-specific gene expression. Surprisingly, enhancers with low-affinity binding sites can mediate robust tissue specific patterns of gene expression when they are organized with optimal syntax. Such enhancers may be a vastly underappreciated feature of the regulatory genome.
Clonal integration facilitates the colonization of drought environments by plant invaders
Authors: Lechuga-Lago Yaiza , Sixto-Ruiz Marta , Roiloa Sergio R. , González Luís 
Published: May 2016

Abstract
Biological invasion represents one of the main threats for biodiversity conservation at the global scale. Identifying the mechanisms underlying the process of biological invasions is a crucial objective in the prediction of scenarios of future invasions and the mitigation of their impacts. In this sense, some plant attributes might better explain the success of invasive plant species than others. Recently, clonal growth has been identified as an attribute that could contribute to the invasiveness of plants. In this experiment, we aim to determine the effect of physiological integration (one of the most striking attributes associated with clonal growth) in the performance (at morphological and physiological levels) of the aggressive invader Carpobrotus edulis , when occupying stressful environments. To achieve this objective we performed a greenhouse experiment in which apical ramets of C. edulis were water-stressed and the connection with the basal ramets was either left intact (physiological integration is allowed) or severed (physiological integration is impeded). Our results show that clonal integration allowed apical ramets to buffer drought stress in terms of photochemical activity, and as a consequence, to increase their growth in comparison with severed apical ramets. Interestingly, this increase in biomass was mainly due to the production of aboveground structures, increasing the spread along the soil surface, and consequently having important implications for the colonization success of new environments by this aggressive invader.
Effectiveness of cuticular transpiration barriers in a desert plant at
controlling water loss at high temperatures
Authors: Schuster Ann-Christin , Burghardt Markus , Alfarhan Ahmed , Bueno Amauri , Hedrich Rainer , Leide Jana , Thomas Jacob , Riederer Markus 
Published: May 2016

Abstract
Maintaining the integrity of the cuticular transpiration barrier even at elevated temperatures is of vital importance especially for hot-desert plants. Currently, the temperature dependence of the leaf cuticular water permeability and its relationship with the chemistry of the cuticles are not known for a single desert plant. This study investigates whether (i) the cuticular permeability of a desert plant is lower than that of species from non-desert habitats, (ii) the temperature-dependent increase of permeability is less pronounced than in those species and (iii) whether the susceptibility of the cuticular permeability barrier to high temperatures is related to the amounts or properties of the cutin or the cuticular waxes. We test these questions with Rhazya stricta using the minimum leaf water vapour conductance ( g min ) as a proxy for cuticular water permeability. g min of R. stricta (5.41 × 10 −5 m s −1 at 25 °C) is in the upper range of all existing data for woody species from various non-desert habitats. At the same time, in R. stricta , the effect of temperature (15–50 °C) on g min (2.4-fold) is lower than in all other species (up to 12-fold). Rhazya stricta is also special since the temperature dependence of g min does not become steeper above a certain transition temperature. For identifying the chemical and physical foundation of this phenomenon, the amounts and the compositions of cuticular waxes and cutin were determined. The leaf cuticular wax (251.4 μg cm −2 ) is mainly composed of pentacyclic triterpenoids (85.2% of total wax) while long-chain aliphatics contribute only 3.4%. In comparison with many other species, the triterpenoid-to-cutin ratio of R. stricta (0.63) is high. We propose that the triterpenoids deposited within the cutin matrix restrict the thermal expansion of the polymer and, thus, prevent thermal damage to the highly ordered aliphatic wax barrier even at high temperatures.
Computational approach to dendritic spine taxonomy and shape transition analysis
Authors: Kusmierczyk Tomasz , Lukasik Michal , Magnowska Marta , Roszkowska Matylda , Bokota Grzegorz , Plewczynski Dariusz 
Published: May 2016

AbstractThe common approach in morphological analysis of dendritic spines is to categorize spines into subpopulations based on whether they are stubby, mushroom, thin, or filopodia. Corresponding cellular models of synaptic plasticity, long-term potentiation, and long-term depression associate synaptic strength with either spine enlargement or spine shrinkage. Although a variety of automatic spine segmentation and feature extraction methods were developed recently, no approaches allowing for an automatic and unbiased distinction between dendritic spine subpopulations and detailed computational models of spine behavior exist.We propose an automatic and statistically based method for the unsupervised construction of spine shape taxonomy based on arbitrary features. The taxonomy is then utilized in the newly introduced computational model of behavior, which relies on transitions between shapes. Models of different populations are compared using supplied bootstrap-based statistical tests.We compared two populations of spines at two time points. The first population was stimulated with long-term potentiation, and the other in the resting state was used as a control. The comparison of shape transition characteristics allowed us to identify differences between population behaviors. Although some extreme changes were observed in the stimulated population, statistically significant differences were found only when whole models were compared. Therefore, we hypothesize that the learning process is related to the subtle changes in the whole ensemble of different dendritic spine structures, but not at the level of single shape classes.The source code of our software is freely available for non-commercial use1.
Data-Driven Phenotypic Categorization for Neurobiological Analyses: Beyond DSM-5 Labels
Authors: Van Dam Nicholas T. , O’Connor David , Marcelle Enitan T. , Ho Erica J. , Craddock R. Cameron , Tobe Russell H. , Gabbay Vilma , Hudziak James J. , Castellanos F. Xavier , Leventhal Bennett L. , Milham Michael P. 
Published: May 2016

AbstractBackgroundData-driven approaches can capture behavioral and biological variation currently unaccounted for by contemporary diagnostic categories, thereby enhancing the ability of neurobiological studies to characterize brain-behavior relationships.MethodsA community-ascertained sample of individuals (N=347, ages 18–59) completed a battery of behavioral measures, psychiatric assessment, and resting state functional magnetic resonance imaging (R-fMRI) in a cross-sectional design. Bootstrap-based exploratory factor analysis was applied to 49 phenotypic subscales from 10 measures. Hybrid Hierarchical Clustering was applied to resultant factor scores to identify nested groups. Adjacent groups were compared via independent samples t-tests and chi-square tests of factor scores, syndrome scores, and psychiatric prevalence. Multivariate Distance Matrix Regression examined functional connectome differences between adjacent groups.ResultsReduction yielded six factors, which explained 77.8% and 65.4% of the variance in exploratory and constrained exploratory models, respectively. Hybrid Hierarchical Clustering of these 6 factors identified 2, 4, and 8 nested groups (i.e., phenotypic communities). At the highest clustering level, the algorithm differentiated functionally adaptive and maladaptive groups. At the middle clustering level, groups were separated by problem type (maladaptive groups; internalizing vs. externalizing problems) and behavioral type (adaptive groups; sensation-seeking vs. extraverted/emotionally stable). Unique phenotypic profiles were also evident at the lowest clustering level. Group comparisons exhibited significant differences in intrinsic functional connectivity at the highest clustering level in somatomotor, thalamic, basal ganglia, and limbic networks.ConclusionsData-driven approaches for identifying homogenous subgroups, spanning typical function to dysfunction not only yielded clinically meaningful groups, but captured behavioral and neurobiological variation among healthy individuals as well.
Refined biomimetic model of chronic pain is healed with erythropoietin
Authors: Hannaman Mary R. , Fitts Douglas A. , Doss Rose M. , Weinstein David E. , Bryant Joseph L. 
Published: May 2016

AbstractHumans suffering with chronic pain may have no evidence of a lesion or disease. They are managed with a morass of drugs and invasive procedures. In many, their persistent pain occurs after the healing of a soft tissue injury, with a neural source hypothesized. Opiates, commonly used to mitigate their symptoms, can cause an increase in neuropathic pain over time. Current animal models of neuropathic pain commonly create direct neural damage with open surgeries using ligatures, neurectomies, chemicals or other forms of intentional trauma. However, we have observed clinically that after an injury in humans, the naturally occurring process of tissue repair can cause chronic neural pain. We show here how the refined biomimetic NeuroDigm GELTM Model, in the mature male rat, gradually induces neuropathic pain behavior with a nonsurgical percutaneous injection of tissue-derived hydrogel in the tunnel of the distal tibial nerve. This perineural model creates a mononeuritis with the biogenic matrix induction of tissue remodeling, the last stage of tissue repair. Repeated behavioral analgesic testing over 5 months in the model implied a unique predictive validity for all analgesics tested. Morphine, initially effective, had an increase in pain behavior over time, suggesting an opioid-induced hyperalgesia, as seen in humans. Celecoxib produced no analgesia, while gabapentin and duloxetine at low doses had profound analgesia. Histology reveals focal neural remodeling, with neural regeneration, as in human biopsies. For the first time, targeted erythropoietin appears to heal neural pain, by extinguishing bilateral pain behavior present for over 4 months.translational model, neuropathic pain, erythropoietin, neural regeneration, soft tissue injuries, neuritis, tissue repair, hydrogel, animal model of disease, neural remodeling, age, opioid-induced hyperalgesia, morphine resistance, analgesics, refined pain model, matrix remodeling, neuroinflammation, predictive validity, habituation, estrogen
Simple settlement decisions explain common dispersal patterns in territorial species
Authors: Gilroy James J. , Lockwood Julie L. 
Published: May 2016

SummaryDispersal is one of the least‐understood aspects of animal behaviour. For example, little is known of the mechanisms that determine how individuals express different dispersal behaviours in response to different circumstances. Uncovering these mechanisms is important for our understanding of spatial population dynamics.Using agent‐based simulations, we examine how simple decision rules generate individual‐level dispersal plasticity, and how this can influence population‐scale dispersal dynamics. We model a territorial, monogamous population inhabiting a completely homogeneous environment. Dispersal variability therefore emerges solely as a result of between‐individual interactions (competition, settlement, reproduction), which are governed by simple decision‐making algorithms.We show that complex dispersal dynamics, including sex biases and strong density dependence, emerge naturally from simple rule‐based behaviours. Dispersal is particularly sensitive to the inclusion of mate availability as a criterion for settlement: if neither sex evaluates mate availability, dispersal distances tend to decline at low densities, leading to a strong Allee effect from reduced pairing success. If one sex evaluates mate availability (females), Allee effects are largely avoided, but female‐biased dispersal generates increasingly male‐biased adult sex ratios at low densities. Sex biases are eliminated if both sexes evaluate mate availability, but population growth rates tend to be reduced due to survival costs and reduced pairing success.Our models suggest that simple decision mechanisms can explain several dynamic patterns that are commonly observed among territorial species. Importantly, these patterns emerge in the absence of environmental heterogeneity or between‐individual variation in dispersal phenotypes, two conditions that are often invoked to explain dispersal heterogeneity in nature. This has implications for studies seeking to examine the causes of dispersal variability in wild populations, suggesting that observed patterns could be largely driven by the social and demographic conditions experienced by sampled individuals.Further insights could be gained by examining how selection operates on decision rules in different life‐history and environmental circumstances, and how this might interact with selection on other demographic traits. Uncovering the decision rules used during settlement should be a priority for those wishing to understand and predict dispersal patterns in nature.
Trade‐offs and mixed infections in an obligate‐killing insect pathogen
Authors: Redman Elizabeth M. , Wilson Kenneth , Cory Jenny S. 
Published: May 2016

Summary

Natural populations of pathogens are frequently composed of numerous interacting strains. Understanding what maintains this diversity remains a key focus of research in disease ecology. In addition, within‐host pathogen dynamics can have a strong impact on both infection outcome and the evolution of pathogen virulence, and thus, understanding the impact of pathogen diversity is important for disease management.

We compared eight genetically distinguishable variants from Spodoptera exempta nucleopolyhedrovirus (SpexNPV) isolated from the African armyworm, Spodoptera exempta. NPVs are obligate killers, and the vast majority of transmission stages are not released until after the host has died.

The NPV variants differed significantly in their virulence and could be clustered into two groups based on their dose–response curves. They also differed in their speed of kill and productivity (transmission potential) for S. exempta. The mixed‐genotype wild‐type (WT) SpexNPV, from which each variant was isolated, was significantly more virulent than any individual variant and its mean mortality rate was within the fastest group of individual variants. However, the WT virus produced fewer new infectious stages than any single variant, which might reflect competition among the variants.

A survival analysis, combining the mortality and speed of kill data, confirmed the superiority of the genetically mixed WT virus over any single variant. Spodoptera exempta larvae infected with WT SpexNPV were predicted to die 2·7 and 1·9 times faster than insects infected with isolates from either of the two clusters of genotypes.

Theory suggests that there are likely to be trade‐offs between pathogen fitness traits. Across all larvae, there was a negative linear relationship between virus yield and speed of kill, such that more rapid host death carried the cost of producing fewer transmission stages. We also found a near‐significant relationship for the same trend at the intervariant level. However, there was no evidence for a significant relationship between the induced level of mortality and transmission potential (virus yield) or speed of kill.
Secretion of small proteins is species‐specific withinAspergillussp
Authors: Valette Nicolas , Benoit‐Gelber Isabelle , Falco Marcos Di , Wiebenga Ad , de Vries Ronald P. , Gelhaye Eric , Morel‐Rouhier Mélanie 
Published: May 2016

SummarySmall secreted proteins (SSP) have been defined as proteins containing a signal peptide and a sequence of less than 300 amino acids. In this analysis, we have compared the secretion pattern ofSSPs among eight aspergilli species in the context of plant biomass degradation and have highlighted putative interesting candidates that could be involved in the degradative process or in the strategies developed by fungi to resist the associated stress that could be due to the toxicity of some aromatic compounds or reactive oxygen species released during degradation. Among these candidates, for example, some stress‐related superoxide dismutases or some hydrophobic surface binding proteins (HsbA) are specifically secreted according to the species . Since these latter proteins are able to recruit lytic enzymes to the surface of hydrophobic solid materials and promote their degradation, a synergistic action of HsbA with the degradative system may be considered and need further investigations. TheseSSPs could have great applications in biotechnology by optimizing the efficiency of the enzymatic systems for biomass degradation.