julilili42/papers huggingface dataset:
The role of epiphytism in architecture and evolutionary constraint within mycorrhizal networks of tropical orchids
2012-07-05

Abstract Characterizing the architecture of bipartite networks is increasingly used as a framework to study biotic interactions within their ecological context and to assess the extent to which evolutionary constraint shape them. Orchid mycorrhizal symbioses are particularly interesting as they are viewed as more beneficial for plants than for fungi, a situation expected to result in an asymmetry of biological constraint. This study addressed the architecture and phylogenetic constraint in these associations in tropical context. We identified a bipartite network including 73 orchid species and 95 taxonomic units of mycorrhizal fungi across the natural habitats of Reunion Island. Unlike some recent evidence for nestedness in mycorrhizal symbioses, we found a highly modular architecture that largely reflected an ecological barrier between epiphytic and terrestrial subnetworks. By testing for phylogenetic signal, the overall signal was stronger for both partners in the epiphytic subnetwork. Moreover, in the subnetwork of epiphytic angraecoid orchids, the signal in orchid phylogeny was stronger than the signal in fungal phylogeny. Epiphytic associations are therefore more conservative and may co‐evolve more than terrestrial ones. We suggest that such tighter phylogenetic specialization may have been driven by stressful life conditions in the epiphytic niches. In addition to paralleling recent insights into mycorrhizal networks, this study furthermore provides support for epiphytism as a major factor affecting ecological assemblage and evolutionary constraint in tropical mycorrhizal symbioses.
CySBML: a Cytoscape plugin for SBML
2012-07-05

Abstract Summary: CySBML is a plugin designed to work with Systems Biology Markup Language (SBML) in Cytoscape having the following features: SBML import, support of the SBML layout and qualitative model packages, navigation in network layouts based on SBML structure, access to MIRIAM and SBO-based annotations and SBML validation. CySBML includes an importer for BioModels to load SBML from standard repositories. Availability and implementation: Freely available for non-commercial purposes through the Cytoscape plugin manager or for download at http://sourceforge.net/projects/cysbml/. Contact: cysbml-team@lists.sourceforge.net Supplementary Information: Tutorial, usage guide, installation instructions and additional figures are available for download at http://www.charite.de/sysbio/people/koenig/software/cysbml/.
AMP‐activated protein kinase in BK‐channel regulation and protection against hearing loss following acoustic overstimulation
2012-07-05

The energy‐sensing AMP‐activated serine/threonine protein kinase (AMPK) confers cell survival in part by stimulation of cellular energy production and limitation of cellular energy utilization. AMPK‐sensitive functions further include activities of epithelial Na + channel ENaC and voltage‐gated K + channel KCNE1/KCNQ1. AMPK is activated by an increased cytosolic Ca 2+ concentration. The present study explored whether AMPK regulates the Ca 2+ ‐sensitive large conductance and voltage‐gated potassium (BK) channel. cRNA encoding BK channel was injected into Xenopus oocytes with and without additional injection of wild‐type AMPK (AMPKα1+AMPKβ1+AMPKγ1), constitutively active AMPK γR70Q , or inactive AMPK αK45R . BK‐channel activity was determined utilizing the 2‐electrode voltage‐clamp. Moreover, BK‐channel protein abundance in the cell membrane was determined by confocal immunomicroscopy. As BK channels are expressed in outer hair cells (OHC) of the inner ear and lack of BK channels increases noise vulnerability, OHC BK‐channel expression was examined by immunohistochemistry and hearing function analyzed by auditory brain stem response measurements in AMPK α 1‐deficient mice ( ampk –/– ) and in wild‐type mice ( ampk +/+ ). As a result, coexpression of AMPK or AMPK γR70Q but not of AMPK αK45R significantly enhanced BK‐channel‐mediated currents and BK‐channel protein abundance in the oocyte cell membrane. BK‐channel expression in the inner ear was lower in ampk –/– mice than in ampk +/+ mice. The hearing thresholds prior to and immediately after an acoustic overexposure were similar in ampk –/– and ampk +/+ mice. However, the recovery from the acoustic trauma was significantly impaired in ampk –/– mice compared to ampk +/+ mice. In summary, AMPK is a potent regulator of BK channels. It may thus participate in the signaling cascades that protect the inner ear from damage following acoustic overstimulation.—Föller, M., Jaumann, M., Dettling, J., Saxena, A., Pakladok, T., Munoz, C., Ruth, P., Sopjani, M., Seebohm, G., Rüttiger, L., Knipper, M., Lang, F. AMP‐activated protein kinase in BK‐channel regulation and protection against hearing loss following acoustic overstimulation. FASEB J. 26, 4243–4253 (2012). www.fasebj.org
Flows in networks with delay in the vertices
2012-07-05

Abstract Our goal is to show asynchronous exponential growth (AEG) for a flow in a network with delay in the vertices. For this purpose we show first that its wellposedness can be characterized via an appropriate operator being the generator of a strongly continuous semigroup. We investigate the long term behavior of the system via the spectrum of this generator using techniques from operator matrices, Hille‐Yosida operators and positive semigroups. Finally, we apply our results to deduce that our problem has (AEG).
Digital planning of high tibial osteotomy. Interrater reliability by using two different software
2012-07-06

Abstract Purpose The purpose of the study was to determine the interrater reliability as well as the correlation of mediCAD ® and PreOPlan ® in deformity analysis and digital planning of osteotomies. Methods Digital radiographs were obtained from 81 patients planned to undergo an open wedge high tibial osteotomy. The JPEG files of the radiographs were imported to landmark‐based software. Deformity analysis and planning of correction were performed by 1 experienced and 2 unexperienced observers. Osteotomy planning was aimed at correction to the predefined mechanical tibiofemoral angle of 3° valgus leg alignment. The interrater reliability of measurements was assessed using intraclass correlation coefficients (ICCs) and the confidence interval. Results The ICC of PreOPlan ® was from 0.841 (mechanical lateral distal femur angle) to 0.993 (wedge‐angle) and from 0.896 (joint line convergence angle) to 0.995 (mechanical tibiofemoral angle) of mediCAD ® . The ICC of height of wedge‐base was 0.979 with PreOPlan ® and 0.969 with mediCAD ® . Comparing PreOPlan ® and mediCAD ® , the ICC of the height of wedge‐base of the observers was 0.966, 0.956 and 0.969, respectively. Conclusions The results show a high interrater reliability of digital planning software. Experience of the observer had no influence on results. Furthermore, a high interrater reliability and correlation of digital planning specific parameters was found. Surgeons need to master limb geometry measurements and osteotomy planning on digital radiographs as digital planning reports are used for intercolleagual correspondence, teaching purposes and as medicolegal documents. The digital planning software tested agrees with the actual demands and could be recommended for deformity analysis and planning of osteotomies. Level of evidence Diagnostic studies, Level I.
The Arabidopsis B‐type response regulator 18 homomerizes and positively regulates cytokinin responses
2012-07-06

Summary In higher plants, the two‐component system (TCS) is a signaling mechanism based on a His‐to‐Asp phosphorelay. The Arabidopsis TCS involves three different types of proteins, namely the histidine kinases (AHKs), the histidine phosphotransfer proteins (AHPs) and the response regulators (ARRs). The ARRs comprise three different families, namely A, B and C types, according to their protein structure. While some members of the B‐type family of ARRs have been studied extensively and reported to act as DNA‐binding transcriptional regulators, very limited information is available for other B‐type ARRs such as ARR18. In this study, we characterize in detail the molecular and functional properties of ARR18. ARR18 acts as a transcriptional regulator in plant cells and forms homodimers in planta as shown by FRET–FLIM studies. As demonstrated by mutational analysis, the aspartate at position 70 (D70) in the receiver domain of ARR18 acts as crucial phosphorylation site. The modification of D70 affects the response regulator’s ability to homodimerize and to activate its target genes. Furthermore, physiological investigations of Arabidopsis lines ectopically expressing ARR18 introduce ARR18 as a new member within the cytokinin‐regulated response pathway regulating root elongation.
Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities
2012-07-06

The success of genome-wide association studies (GWAS) in deciphering the genetic architecture of complex diseases has fueled the expectations whether the individual risk can also be quantified based on the genetic architecture. So far, disease risk prediction based on top-validated single-nucleotide polymorphisms (SNPs) showed little predictive value. Here, we applied a support vector machine (SVM) to Parkinson disease (PD) and type 1 diabetes (T1D), to show that apart from magnitude of effect size of risk variants, heritability of the disease also plays an important role in disease risk prediction. Furthermore, we performed a simulation study to show the role of uncommon (frequency 1-5%) as well as rare variants (frequency <1%) in disease etiology of complex diseases. Using a cross-validation model, we were able to achieve predictions with an area under the receiver operating characteristic curve (AUC) of ~0.88 for T1D, highlighting the strong heritable component (∼90%). This is in contrast to PD, where we were unable to achieve a satisfactory prediction (AUC ~0.56; heritability ~38%). Our simulations showed that simultaneous inclusion of uncommon and rare variants in GWAS would eventually lead to feasible disease risk prediction for complex diseases such as PD. The used software is available at http://www.ra.cs.uni-tuebingen.de/software/MACLEAPS/.
The importance of low-risk HPV infection for the risk of abnormal cervical cytology/histology in more than 40 000 Danish women
2012-07-06

Objectives To estimate the age and type-specific distribution of low-risk (LR) human papillomavirus (HPV) types in cervical samples from women in the general population and to assess the distribution of LR-HPV without the coexistence of high-risk HPV types in different cytology and histology categories. Methods In a cross-sectional study, liquid-based cytology samples (SurePath) were collected over a 3-year period. The samples were HPV tested by Hybrid Capture II (HC2; Digene) and genotyped using a PCR-based assay (INNO-LiPAv2; Innogenetics Inc.). A total of 40 382 women (14–95 years of age) were included in the study. By linkage with the nationwide Pathology Data Bank, the HPV test results were directly linked to cytological diagnoses made from the same samples and to subsequent histology results. Results Overall, 2790 women (6.9%) tested positive for LR-HPV types, with HPV6 and HPV70 being the most frequent types detected, whereas HPV11 was uncommon. The highest prevalence was observed in the youngest age group (≤19 years). The LR-HPV prevalence was 6.3% in women with normal cytology, 33.1% in atypical squamous cells of undetermined significance (ASCUS), 19.6% in low-grade squamous intraepithelial lesion and 12.7% in those with high-grade squamous intraepithelial lesion. When considering women with LR-HPV alone, the prevalence was 2.0% (normal cytology), 11.3% (ASCUS), 2.6% (low-grade squamous intraepithelial lesion) and 0.7% in women with high-grade squamous intraepithelial lesion, respectively. A similar pattern was observed in relation to the histological diagnoses with the majority of LR-HPV infections detected in CIN1 lesions (24.7%). Conclusions LR-HPV types alone are relatively common in ASCUS, whereas LR-HPV types without coexisting high-risk HPV types are virtually never detected in severe cervical lesions.
CbrA Is a Flavin Adenine Dinucleotide Protein That Modifies the Escherichia coli Outer Membrane and Confers Specific Resistance to Colicin M
2012-07-06

ABSTRACT Colicin M (Cma) is a protein toxin produced by Escherichia coli that kills sensitive E. coli cells by inhibiting murein biosynthesis in the periplasm. Recombinant plasmids carrying cbrA (formerly yidS ) strongly increased resistance of cells to Cma, whereas deletion of cbrA increased Cma sensitivity. Transcription of cbrA is positively controlled by the two-component CreBC system. A Δ creB mutant was highly Cma sensitive because little CbrA was synthesized. Treatment of CbrA-overproducing cells by osmotic shock failed to render cells Cma sensitive because the cells were resistant to osmotic shock. In a natural environment with a growth-limiting nutrient supply, cells producing CbrA defend themselves against colicin M synthesized by competing cells. Isolated CbrA is a protein with noncovalently bound flavin adenine dinucleotide. Sequence comparison and structure prediction assign the closest relative of CbrA with a known crystal structure as digeranylgeranyl-glycerophospholipid reductase of Thermoplasma acidophilum . CbrA is found in Escherichia coli , Citrobacter , and Salmonella bongori but not in other enterobacteria. The next homologs with the highest identity (over 50%) are found in the anaerobic Clostridium botulinum group 1 and a few other Firmicutes .
Evaluation of the performance of evolutionary algorithms for optimization of low-enthalpy geothermal heating plants
2012-07-07

In this paper, we present the application of Evolutionary Algorithms (EAs) and linear programming for minimizing thermal impacts in the ground by operating a low-enthalpy geothermal plant with a field of multiple borehole heat exchangers (BHEs). The new methodology is demonstrated on two synthetic case studies with 36 BHEs that are grounded in reality and operated to produce given seasonal heating energy demand. We compare the performance of six different Evolutionary Algorithms (EAs) (two Differential Evolution variants, Particle Swarm Optimization, two Evolution Strategy based Algorithms, real valued Genetic Algorithm) and Monte-Carlo random search to find the optimal BHE positions. Additionally, linear programming is applied to adjust the energy extraction (loads) for the individual BHEs in the field. Both optimization steps are applied separately and in combination, and the achieved system improvements are compared to the conditions for the non-optimized case. The EAs were able to find constellations that cause less pronounced temperature changes in the subsurface (18% - 25%) than those associated with non-optimized BHE fields. Further, we could show that exclusive optimization of BHE energy extraction rates delivers slightly better results than the optimization of BHE positions. Combining both optimization approaches is the best choice and, ideally, adjusts the geothermal plant.
Guided evolution in XCSF
2012-07-07

High-dimensional problems are challenging for iterative, online (Michigan-style) Learning Classifier Systems, especially because of the large size of the evolutionary search space. The present work proposes to guide mutation toward most suitable classifier condition structures. Focusing on XCSF, we introduce a guided mutation operator: Each classifier stores a finite set of matched samples. Mutation uses those samples to optimize classifier condition shapes by means of an accuracy-weighted covariance matrix. While this approach does not necessarily produce an optimal shape, it is sufficient to discriminate relevant from irrelevant dimensions. Regular evolutionary operators handle the fine tuning. We show that guided XCSF does not only drastically speed up learning, but it also solves higher-dimensional problems than regular XCSF. Experiments illustrate that guided XCSF quickly detects the intrinsic structure of non-linear, oblique, fully sampled, ten-dimensional approximation tasks. The results show that guided XCSF strongly outperforms regular XCSF as well as a statistics-based machine learning approach, the so called Locally Weighted Projection Regression algorithm.
Filtering sensory information with XCSF
2012-07-07

It was previously shown that the control of a robot arm can be efficiently learned using the XCSF classifier system. So far, however, the predictive knowledge about how actual motor activity changes the state of the arm system has not been exploited. In this paper, we exploit the forward velocity kinematics knowledge of XCSF to alleviate the negative effect of noisy sensors for successful learning and control. We incorporate Kalman filtering for estimating successive arm positions iteratively combining sensory readings with XCSF-based predictions of hand position changes over time. The filtered arm position is used to improve both trajectory planning and further learning of the forward velocity kinematics. We test the approach on a simulated, kinematic robot arm model. The results show that the combination can improve learning and control performance significantly. However, it also shows that variance estimates of XCSF predictions maybe underestimated, in which case self-delusional spiraling effects hinder effective learning. Thus, we introduce a heuristic parameter, which limits the influence of XCSF's predictions on its own further learning input. As a result, we obtain drastic improvements in noise tolerance coping with more than ten times higher noise levels.
Relationship Between Job Satisfaction and Job Performance: Job Ambivalence as a Moderator
2012-07-09

Based on research regarding the role of attitudinal ambivalence in the validity of attitudes in predicting behavior, we propose job ambivalence as a promising concept for job satisfaction research. In particular, we argue that job ambivalence (i.e., coexistence of positive and negative evaluations of one's job) may moderate the relationship between job satisfaction and job performance. Results of a study conducted with managers of an IT company show, as predicted, that job satisfaction is a better predictor of job performance (i.e., higher satisfaction related to higher performance) when individuals experience low job ambivalence, as compared to when individuals experience high job ambivalence. Implications for future research are discussed.
Yersinia enterocolitica YopT and Clostridium difficile Toxin B Induce Expression of GILZ in Epithelial Cells
2012-07-09

Glucocorticoid induced-leucine zipper (GILZ) has been shown to be induced in cells by different stimuli such as glucocorticoids, IL-10 or deprivation of IL-2. GILZ has anti-inflammatory properties and may be involved in signalling modulating apoptosis. Herein we demonstrate that wildtype Yersinia enterocolitica which carry the pYV plasmid upregulated GILZ mRNA levels and protein expression in epithelial cells. Infection of HeLa cells with different Yersinia mutant strains revealed that the protease activity of YopT, which cleaves the membrane-bound form of Rho GTPases was sufficient to induce GILZ expression. Similarly, Clostridium difficile toxin B, another bacterial inhibitor of Rho GTPases induced GILZ expression. YopT and toxin B both increased transcriptional activity of the GILZ promoter in HeLa cells. GILZ expression could not be linked to the inactivation of an individual Rho GTPase by these toxins. However, forced expression of RhoA and RhoB decreased basal GILZ promoter activity. Furthermore, MAPK activation proved necessary for profound GILZ induction by toxin B. Promoter studies and gel shift analyses defined binding of upstream stimulatory factor (USF) 1 and 2 to a canonical c-Myc binding site (E-box) in the GILZ promoter as a crucial step of its trans-activation. In addition we could show that USF-1 and USF-2 are essential for basal as well as toxin B induced GILZ expression. These findings define a novel way of GILZ promoter trans-activation mediated by bacterial toxins and differentiate it from those mediated by dexamethasone or deprivation of IL-2.
Storage, patterns, and control of soil organic carbon and nitrogen in the northeastern margin of the Qinghai–Tibetan Plateau
2012-07-10

This study tested the hypothesis that soil organic carbon (SOC) and total nitrogen (TN) spatial distributions show clear relationships with soil properties and vegetation composition as well as climatic conditions. Further, this study aimed to find the corresponding controlling parameters of SOC and TN storage in high-altitude ecosystems. The study was based on soil, vegetation and climate data from 42 soil pits taken from 14 plots. The plots were investigated during the summers of 2009 and 2010 at the northeastern margin of the Qinghai–Tibetan Plateau. Relationships of SOC density with soil moisture, soil texture, biomass and climatic variables were analyzed. Further, storage and vertical patterns of SOC and TN of seven representative vegetation types were estimated. The results show that significant relationships of SOC density with belowground biomass (BGB) and soil moisture (SM) can be observed. BGB and SM may be the dominant factors influencing SOC density in the topsoil of the study area. The average densities of SOC and TN at a depth of 1 m were about 7.72 kg C m ^−2 and 0.93 kg N m ^−2 . Both SOC and TN densities were concentrated in the topsoil (0–20 cm) and fell exponentially as soil depth increased. Additionally, the four typical vegetation types located in the northwest of the study area were selected to examine the relationship between SOC and environmental factors (temperature and precipitation). The results indicate that SOC density has a negative relationship with temperature and a positive relationship with precipitation diminishing with soil depth. It was concluded that SOC was concentrated in the topsoil, and that SOC density correlates well with BGB. SOC was predominantly influenced by SM, and to a much lower extent by temperature and precipitation. This study provided a new insight in understanding the control of SOC and TN density in the northeastern margin of the Qinghai–Tibetan Plateau.
Wavelength-Dependent Pathways of Poly-3-hexylthiophene Photo-Oxidation
2012-07-10

The photodegradation kinetics of regioregular poly-3-hexylthiophene (P3HT) thin films (∼150 nm) upon illumination with both visible light of 525 nm and UV light of 365 nm has been studied using UV/vis and FTIR spectroscopy in order to probe both the disruption of the π-conjugated system and the chemical product evolution. Reaction effectiveness and product evolution turn out to depend strongly on the wavelength of the incident light. Under UV light, the π-conjugated system and the hexyl side chain are degraded almost simultaneously, involving Norrish-type reactions that lead to complete disintegration of the alkyl chains. Under visible light only the π-conjugated system is destroyed, whereas the aliphatic side chains are hardly affected. While the reaction under UV light is consistent with a radical reaction starting at the α-carbon of the alkyl side chain, the reaction under visible illumination is more likely to involve a photosensitized species that primarily attacks the π-conjugated system of the polymer.
Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
2012-07-11

Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in command-line mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.].