bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental evidence for asymmetric mate preference and aggression: behavioral interactions in a woodrat (Neotoma) hybrid zone
Authors: Shurtliff Quinn R , Murphy Peter J , Yeiter Jaclyn D , Matocq Marjorie D 
Published: October 2013

AbstractBackgroundFemale mate preferences may be under strong selection in zones of contact between closely related species because of greater variation in available mates and the potential costs of hybridization. We studied female mate preferences experimentally in a zone of secondary contact between Desert and Bryant’s Woodrat (Neotoma lepidaandN. bryanti) in the southern foothills of the Sierra Nevada of California. We tested female preference for conspecific versus heterospecific males in paired choice trials in which females could interact freely with males, but males could not interact directly with each other. We compared preferences of females from both allopatric and sympatric sites.ResultsWe did not find evidence of the process of reinforcement as assortative preferences were not stronger in sympatry than in allopatry. Mate preferences, however, were asymmetric, withN. lepidafemales mating preferentially with conspecifics andN. bryantifemales showing no preference by species. Sympatric females were less likely to mate than allopatric females, due in part to an increase in aggressive interactions. However, even in the absence of aggression, courtship led to mating less often in sympatric females, suggesting they were choosier or had lower sexual motivation than allopatric females.ConclusionsPatterns of mate choice in this woodrat system appear to be strongly impacted by body size and aggressive behavior. In particular, females of the smaller-bodied species rarely interact with the relatively large heterospecific males. In contrast females of the larger-bodied species accept the relatively small heterospecific males. For sympatric animals, rates of aggression were markedly higher than for allopatric animals and reduced affiliative and reproductive behavior in our trials. Sympatric animals are larger and more aggressive, traits that are likely under strong ecological selection across the sharp resource gradient that characterizes the contact zone. However, our results suggest that these traits that are likely favored in competitive interactions between the species also impact reproductive interactions. Combined with our previous findings of post-zygotic isolation in this system, this study suggests that multiple isolating mechanisms contribute to the rate of genetic exchange between these species when they come into contact, and that these mechanisms are the result of selection on traits that are important in a range of ecological and reproductive interactions.
InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data
Authors: Xiong Wenwei , He Limei , Li Yubin , Dooner Hugo K , Du Chunguang 
Published: October 2013

Abstract

Background
The advent of next-generation high-throughput technologies has revolutionized whole genome sequencing, yet some experiments require sequencing only of targeted regions of the genome from a very large number of samples. These regions can be amplified by PCR and sequenced by next-generation methods using a multidimensional pooling strategy. However, there is at present no available generalized tool for the computational analysis of target-enriched NGS data from multidimensional pools.

Results
Here we present InsertionMapper, a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. InsertionMapper consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. We illustrate InsertionMapper with an example from our project 'New reverse genetics resources for maize’, which aims to sequence-index a collection of 15,000 independent insertion sites of the transposon Ds in maize. Identified sequences are validated by PCR assays. This pipeline tool is applicable to similar scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

Conclusions
InsertionMapper is proven efficacious for the identification of target-enriched sequences from multidimensional high throughput sequencing data. With adjustable parameters and experiment configurations, this tool can save great computational effort to biologists interested in identifying their sequences of interest within the huge output of modern DNA sequencers. InsertionMapper is freely accessible at https://sourceforge.net/p/insertionmapper and http://bo.csam.montclair.edu/du/insertionmapper.
Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks
Authors: Brion Christian , Ambroset Chloé , Sanchez Isabelle , Legras Jean-Luc , Blondin Bruno 
Published: October 2013

Abstract

Background
Variation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast (Saccharomyces cerevisiae) properties. However, the molecular bases of this variation of gene expression are unknown. We addressed these questions by carrying out an integrated genetical-genomic study in fermentation conditions. We report here quantitative trait loci (QTL) mapping based on expression profiling in a segregating population generated by a cross between a derivative of the popular wine strain EC1118 and the laboratory strain S288c.

Results
Most of the fermentation traits studied appeared to be under multi-allelic control. We mapped five phenotypic QTLs and 1465 expression QTLs. Several expression QTLs overlapped in hotspots. Among the linkages unraveled here, several were associated with metabolic processes essential for wine fermentation such as glucose sensing or nitrogen and vitamin metabolism. Variations affecting the regulation of drug detoxification and export (TPO1, PDR12 or QDR2) were linked to variation in four genes encoding transcription factors (PDR8, WAR1, YRR1 and HAP1). We demonstrated that the allelic variation of WAR1 and TPO1 affected sorbic and octanoic acid resistance, respectively. Moreover, analysis of the transcription factors phylogeny suggests they evolved with a specific adaptation of the strains to wine fermentation conditions. Unexpectedly, we found that the variation of fermentation rates was associated with a partial disomy of chromosome 16. This disomy resulted from the well known 8–16 translocation.

Conclusions
This large data set made it possible to decipher the effects of genetic variation on gene expression during fermentation and certain wine fermentation properties. Our findings shed a new light on the adaptation mechanisms required by yeast to cope with the multiple stresses generated by wine fermentation. In this context, the detoxification and export systems appear to be of particular importance, probably due to nitrogen starvation. Furthermore, we show that the well characterized 8–16 translocation located in SSU1, which is associated with sulfite resistance, can lead to a partial chromosomic amplification in the progeny of strains that carry it, greatly improving fermentation kinetics. This amplification has been detected among other wine yeasts.
Down-regulation of microglial activity attenuates axotomized nigral dopaminergic neuronal cell loss
Authors: Song Dae-Yong , Yu Ha-Nul , Park Chae-Ri , Lee Jin-Sook , Lee Ji-Yong , Park Byung-Gu , Woo Ran-Sook , Han Jung-Tae , Cho Byung-Pil , Baik Tai-Kyoung 
Published: October 2013

Abstract

Background
There is growing evidence that inflammatory processes of activated microglia could play an important role in the progression of nerve cell damage in neurodegenerative disorders such as Parkinson’s disease and Alzheimer’s disease which harbor features of chronic microglial activation, though the precise mechanism is unknown. In this study, we presented in vivo and ex vivo experimental evidences indicating that activated microglia could exacerbate the survival of axotomized dopaminergic neurons and that appropriate inactivation of microglia could be neuroprotective.

Results
The transection of medial forebrain bundle (MFB) of a rat induced loss of dopaminergic neurons in a time-dependent manner and accompanied with microglial activation. Along with microglial activation, production of reactive oxygen species (ROS) was upregulated and TH/OX6/hydroethidine triple-immunofluorescence showed that the microglia mainly produced ROS. When the activated microglial cells that were isolated from the substantia nigra of the MFB axotomized animal, were transplanted into the substantia nigra of which MFB had been transected at 7 days ago, the survival rate of axotomized dopaminergic neurons was significantly reduced as compared with sham control. Meanwhile, when the microglial activation was attenuated by administration of tuftsin fragment 1-3 (microglia inhibitory factor) into the lateral ventricle using mini-osmotic pump, the survival rate of axotomized dopaminergic neurons was increased.

Conclusion
The present study suggests that activated microglia could actively produce and secrete unfavorable toxic substances, such as ROS, which could accelerate dopaminergic neuronal cell loss. So, well-controlled blockade of microglial activation might be neuroprotective in some neuropathological conditions.
Assessment of the caudate nucleus and its relation to route learning in both congenital and late blind individuals
Authors: Voss Patrice , Fortin Madeleine , Corbo Vincent , Pruessner Jens C , Lepore Franco 
Published: October 2013

Abstract

Background
In the absence of visual input, the question arises as to how complex spatial abilities develop and how the brain adapts to the absence of this modality. As such, the aim of the current study was to investigate the relationship between visual status and an important brain structure with a well established role in spatial cognition and navigation, the caudate nucleus. We conducted a volumetric analysis of the caudate nucleus in congenitally and late blind individuals, as well as in matched sighted control subjects.

Results
No differences in the volume of the structure were found either between congenitally blind (CB) and matched sighted controls or between late blind (LB) and matched sighted controls. Moreover, contrary to what was expected, no significant correlation was found between caudate volume and performance in a spatial navigation task. Finally, consistent with previously published reports, the volume of the caudate nucleus was found to be negatively correlated with age in the sighted; however such correlations were not significant in the blind groups.

Conclusion
Although there were no group differences, the absence of an age-volume correlation in the blind suggests that visual deprivation may still have an effect on the developmental changes that occur in the caudate nucleus.
Listening in on difficult conversations: an observational, multi-center investigation of real-time conversations in medical oncology
Authors: Kimball Brittany C , James Katherine M , Yost Kathleen J , Fernandez Cara A , Kumbamu Ashok , Leppin Aaron L , Robinson Marguerite E , Geller Gail , Roter Debra L , Larson Susan M , Lenz Heinz-Josef , Garcia Agustin A , Braddock Clarence H , Jatoi Aminah , de Nuncio María Luisa Zúñiga , Montori Victor M , Koenig Barbara A , Tilburt Jon C 
Published: October 2013

Abstract

Background
The quality of communication in medical care has been shown to influence health outcomes. Cancer patients, a highly diverse population, communicate with their clinical care team in diverse ways over the course of their care trajectory. Whether that communication happens and how effective it is may relate to a variety of factors including the type of cancer and the patient’s position on the cancer care continuum. Yet, many of the routine needs of cancer patients after initial cancer treatment are often not addressed adequately. Our goal is to identify areas of strength and areas for improvement in cancer communication by investigating real-time cancer consultations in a cross section of patient-clinician interactions at diverse study sites.

Methods/design
In this paper we describe the rationale and approach for an ongoing observational study involving three institutions that will utilize quantitative and qualitative methods and employ a short-term longitudinal, prospective follow-up component to investigate decision-making, key topics, and clinician-patient-companion communication dynamics in clinical oncology.

Discussion
Through a comprehensive, real-time approach, we hope to provide the fundamental groundwork from which to promote improved patient-centered communication in cancer care.
Mental state deterioration after switching from brand-name to generic olanzapine in an adolescent with bipolar affective disorder, autism and intellectual disability: a case study
Authors: Samuel Rani , Attard Azizah , Kyriakopoulos Marinos 
Published: October 2013

Abstract

Background
The appropriateness of use of generic instead of brand-name medication remains unresolved and controversial in several areas of medicine. Some evidence suggestive of variations in bioavailability and clinical effectiveness between different formulations make policy decisions occasionally difficult. The use of generic olanzapine is a widely acceptable practice on the basis of quality, safety and efficacy data and has been adopted in several countries.

Case presentation
The case of a 14 year old boy with bipolar affective disorder, autism and intellectual disability who had brand-name to generic olanzapine switch associated with rapid deterioration of his mental state is described. This clinical change was not related to any physical illness or other medication adjustment and resolved as rapidly when generic olanzapine was switched back to the brand-name formulation.

Conclusions
Caution should be exercised when policy for switching from brand-name to generic psychotropic medications are made, especially when using medications off label, in extremes of age and in those patients with co-morbid complicating factors such as intellectual disability.
Obesity prevalence and unfavorable health risk behaviors among German kindergarten teachers: cross-sectional results of the kindergarten teacher health study
Authors: Hoffmann Sascha W , Tug Suzan , Simon Perikles 
Published: October 2013

Abstract

Background
The aim of the study was to investigate obesity status and associated health risk behaviors in a sample of German kindergarten teachers. At present, such data are not available, despite the fact that kindergarten teachers educate children at a formative time in their lives.

Methods
Kindergarten teachers aged 18–62 years (n = 313) were invited to participate in the Kindergarten Teacher Health Study (KTHS) by completing a self-reported questionnaire. We analyzed their obesity status, health risk behaviors (i.e., habitual physical activity, screen time activities, eating behavior patterns, smoking), and their general ability to identify overweight children and the associated health risks of overweight and obesity based on special age- and sex-specific silhouettes. After adjusting for covariates, bivariate correlations were conducted for associations between body mass index (BMI) and health risk behaviors, while analyses of variance (ANOVAs) were used to analyze differences of health risk behaviors between BMI groups. Logistic regression analyses were conducted to predict determinants of kindergarten teachers who did not correctly identify the overweight silhouettes and their associated physical and mental health risks. Additionally, data regarding kindergarten teachers’ weight status and smoking behavior were compared with nationally representative data from the 2009 Microcensus (n = 371310) using the Mann–Whitney U-test.

Results
The prevalence rates of overweight and obesity were 41.2% and 17.9%, respectively. The prevalence of obesity was significantly higher in kindergarten teachers (p < 0.001) compared to national Microcensus data. Only 44.6% of teachers were able to identify overweight children correctly. The fact that being overweight is associated with physical and mental health risks was only reported by 40.1% and 21.2% of teachers, respectively. Older kindergarten teachers were more likely to misclassify the overweight silhouettes, while younger, normal-weight, and overweight kindergarten teachers were more likely to underestimate the associated health risks. Obese kindergarten teachers reported spending more time in front of computer and television screens than their normal-weight counterparts, especially on weekends. In addition, obese kindergarten teachers reported eating less often with their families and more frequently reported watching television during meals.

Conclusions
Advanced monitoring and multifaceted interventions to improve the health behaviors of kindergarten teachers should be given high priority. Because kindergarten teachers’ behavioral modeling presumably mediates children’s health behaviors, additional research is needed about kindergarten teachers’ health and its proposed interaction with children’s health.
Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
Authors: Baumann Tobias , Arndt Katja M , Müller Kristian M 
Published: October 2013

Abstract

Background
DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning.

Results
A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5′ end. Treatment of such PCR products with endonuclease V generates 3′ protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions.

Conclusions
The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
Biological properties of carotenoids extracted from Halobacterium halobium isolated from a Tunisian solar saltern
Authors: Abbes Molka , Baati Houda , Guermazi Sonda , Messina Concetta , Santulli Andrea , Gharsallah Neji , Ammar Emna 
Published: October 2013

Abstract

Background
Bioactive molecules have received increasing attention due to their nutraceutical attributes and anticancer, antioxidant, antiproliferative and apoptosis-inducing properties. This study aimed to investigate the biological properties of carotenoids extracted from Archaea.

Methods
Halophilic Archaea strains were isolated from the brine of a local crystallizer pond (TS7) of a solar saltern at Sfax, Tunisia. The most carotenoid-producing strain (M8) was investigated on heptoma cell line (HepG2), and its viability was assessed by the MTT-test. The cells were incubated with different sub-lethal extract rates, with carotenoid concentrations ranging from 0.2 to 1.5 μM. Antioxidant activity was evaluated through exposing the cells to sub-lethal extract concentrations for 24 hours and then to oxidative stress induced by 60 μM arachidonic acid and 50 μM H2O2.

Results
Compared to non-treated cells, bacterial carotenoid extracts inhibited HepG2 cell viability (50%). A time and dose effect was observed, with cell viability undergoing a significant (P < 0.05) decrease with extract concentration. After exposure to oxidative stress, control cells underwent a significant (P < 0.05) decrease in viability as compared to the non-treated cells.

Conclusions
The bacterial extracts under investigation were noted to exhibit the strongest free radical scavenging activity with high carotenoid concentrations. The carotenoid extract also showed significant antiproliferative activity against HepG2 human cancer cell lines.
The role of profilin-1 in endothelial cell injury induced by advanced glycation end products (AGEs)
Authors: Li Zhenyu , Zhong Qiaoqing , Yang Tianlun , Xie Xiumei , Chen Meifang 
Published: October 2013

Abstract

Background
Accumulation of advanced glycation end products (AGEs) in the vasculature triggers a series of morphological and functional changes contributing to endothelial hyperpermeability. The reorganisation and redistribution of the cytoskeleton regulated by profilin-1 mediates endothelial cell contraction, which results in vascular hyperpermeability. This study aimed to investigate the pivotal role of profilin-1 in the process of endothelial cell damage induced by AGEs.

Methods
Human umbilical vein endothelial cells (HUVECs) were incubated with AGEs. The mRNA and protein expression of profilin-1 was determined using real-time PCR and western blotting analyses. The levels of intercellular adhesion molecule-1 (ICAM-1), nitric oxide (NO) and reactive oxygen species (ROS), as well as the activities of nuclear factor-κB (NF-κB) and protein kinase C (PKC), were detected using the appropriate kits. The levels of asymmetric dimethylarginine (ADMA) were determined using HPLC. The distribution of the cytoskeleton was visualised using immunofluorescent staining.

Results
Compared with the control, incubation of endothelial cells with AGEs (200 μg/ml) for 4 or 24 h significantly up-regulated the mRNA and protein expression of profilin-1, markedly increased the levels of ICAM-1 and ADMA and decreased the production of NO (P<0.05, P<0.01), which was significantly attenuated by pretreatment with DPI (an antioxidant), GF 109203X (PKC inhibitor) or BAY-117082 (NF-κB inhibitor). DPI (10 μmol/L) markedly decreased the elevated levels of ROS induced by AGEs (200 μg/ml, 24 h); however, GF 109203X (10 μmol/L) and BAY-117082 (5 μmol/L) exhibited no significant effect on the formation of ROS by AGEs. Immunofluorescent staining indicated that AGEs markedly increased the expression of profilin-1 in the cytoplasm and the formation of actin stress fibres, resulting in the rearrangement and redistribution of the cytoskeleton. This effect was significantly ameliorated by DPI, GF 109203X, BAY-117082 or siRNA treatment of profilin-1. Incubation with DPI and GF 109203X markedly inhibited the activation of PKC triggered by AGEs, and DPI and BAY-117082 significantly decreased the activity of NF-κB mediated by AGEs. Disruption of profilin-1 gene expression attenuated the extent of endothelial abnormalities by reducing ICAM-1 and ADMA levels and elevating NO levels (P<0.05, P<0.01), but this disruption had no effect on the activities of NF-κB and PKC (P>0.05).

Conclusions
These findings suggested that profilin-1 might act as an ultimate and common cellular effector in the process of metabolic memory (endothelial abnormalities) mediated by AGEs via the ROS/PKC or ROS/NF-қB signalling pathways.