bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis
Authors: Meyer Hanna , Weidmann Hendrikje , Lalk Michael 
Published: July 2013

Abstract

Background

Bacillus subtilis (B. subtilis) has become widely accepted as a model organism for studies on Gram-positive bacteria. A deeper insight into the physiology of this prokaryote requires advanced studies of its metabolism. To provide a reliable basis for metabolome investigations, a validated experimental protocol is needed since the quality of the analytical sample and the final data are strongly affected by the sampling steps. To ensure that the sample analyzed precisely reflects the biological condition of interest, outside biases have to be avoided during sample preparation.

Results
Procedures for sampling, quenching, extraction of metabolites, cell disruption, as well as metabolite leakage were tested and optimized for B. subtilis. In particular the energy status of the bacterial cell, characterized by the adenylate energy charge, was used to evaluate sampling accuracy. Moreover, the results of the present study demonstrate that the cultivation medium can affect the efficiency of the developed sampling procedure.

Conclusion
The final workflow presented here allows for the reproducible and reliable generation of physiological data. The method with the highest qualitative and quantitative metabolite yield was chosen, and when used together with complementary bioanalytical methods (i.e., GC-MS, LC-MS and 1H-NMR) provides a solid basis to gather information on the metabolome of B. subtilis.
Importance of leptin signaling and signal transducer and activator of transcription-3 activation in mediating the cardiac hypertrophy associated with obesity
Authors: Leifheit-Nestler Maren , Wagner Nana-Maria , Gogiraju Rajinikanth , Didié Michael , Konstantinides Stavros , Hasenfuss Gerd , Schäfer Katrin 
Published: July 2013

Abstract

Background
The adipokine leptin and its receptor are expressed in the heart, and leptin has been shown to promote cardiomyocyte hypertrophy in vitro. Obesity is associated with hyperleptinemia and hypothalamic leptin resistance as well as an increased risk to develop cardiac hypertrophy and heart failure. However, the role of cardiac leptin signaling in mediating the cardiomyopathy associated with increased body weight is unclear, in particular, whether it develops subsequently to cardiac leptin resistance or overactivation of hypertrophic signaling pathways via elevated leptin levels.

Methods
The cardiac phenotype of high-fat diet (HFD)-induced obese wildtype (WT) mice was examined and compared to age-matched genetically obese leptin receptor (LepR)-deficient (LepRdb/db) or lean WT mice. To study the role of leptin-mediated STAT3 activation during obesity-induced cardiac remodeling, mice in which tyrosine residue 1138 within LepR had been replaced with a serine (LepRS1138) were also analyzed.

Results
Obesity was associated with hyperleptinemia and elevated cardiac leptin expression in both diet-induced and genetically obese mice. Enhanced LepR and STAT3 phosphorylation levels were detected in hearts of obese WT mice, but not in those with LepR mutations. Moreover, exogenous leptin continued to induce cardiac STAT3 activation in diet-induced obese mice. Although echocardiography revealed signs of cardiac hypertrophy in all obese mice, the increase in left ventricular (LV) mass and diameter was significantly more pronounced in LepRS1138 animals. LepRS1138 mice also exhibited an increased activation of signaling proteins downstream of LepR, including Jak2 (1.8-fold), Src kinase (1.7-fold), protein kinase B (1.3-fold) or C (1.6-fold). Histological analysis of hearts revealed that the inability of leptin to activate STAT3 in LepRdb/db and LepRS1138 mice was associated with reduced cardiac angiogenesis as well as increased apoptosis and fibrosis.

Conclusions
Our findings suggest that hearts from obese mice continue to respond to elevated circulating or cardiac leptin, which may mediate cardioprotection via LepR-induced STAT3 activation, whereas signals distinct from LepR-Tyr1138 promote cardiac hypertrophy. On the other hand, the presence of cardiac hypertrophy in obese mice with complete LepR signal disruption indicates that additional pathways also play a role.
Simulation of normal and pathological gaits using a fusion knowledge strategy
Authors: Martínez Fabio , Cifuentes Christian , Romero Eduardo 
Published: July 2013

Abstract

Background
Gait distortion is the first clinical manifestation of many pathological disorders. Traditionally, the gait laboratory has been the only available tool for supporting both diagnosis and prognosis, but under the limitation that any clinical interpretation depends completely on the physician expertise. This work presents a novel human gait model which fusions two important gait information sources: an estimated Center of Gravity (CoG) trajectory and learned heel paths, by that means allowing to reproduce kinematic normal and pathological patterns. The CoG trajectory is approximated with a physical compass pendulum representation that has been extended by introducing energy accumulator elements between the pendulum ends, thereby emulating the role of the leg joints and obtaining a complete global gait description. Likewise, learned heel paths captured from actual data are learned to improve the performance of the physical model, while the most relevant joint trajectories are estimated using a classical inverse kinematic rule. The model is compared with standard gait patterns, obtaining a correlation coefficient of 0.96. Additionally,themodel simulates neuromuscular diseases like Parkinson (phase 2, 3 and 4) and clinical signs like the Crouch gait, case in which the averaged correlation coefficient is 0.92.
MORPH-PRO: a novel algorithm and web server for protein morphing
Authors: Castellana Natalie E , Lushnikov Andrey , Rotkiewicz Piotr , Sefcovic Natasha , Pevzner Pavel A , Godzik Adam , Vyatkina Kira 
Published: July 2013

AbstractBackgroundProteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations.ResultsWe present a novel, efficient morphing algorithm,Morph-Probased on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test this by using the intermediate structures of a c-Jun N-terminal kinase (JNK1) conformational change in a virtual docking experiment. The structures are shown to dock with higher score to known JNK1-binding ligands than structures solved using X-Ray crystallography. This experiment demonstrates the potential applications of the intermediate structures in modeling or virtual screening efforts.ConclusionsVisualization of protein conformational changes is important for characterization of protein function. Furthermore, the intermediate structures produced by our algorithm are good approximations to true structures. We believe there is great potential for these computationally predicted structures in protein-ligand docking experiments and virtual screening. TheMorph-Proweb server can be accessed athttp://morph-pro.bioinf.spbau.ru.
Dysphagia caused by focal guttural pouch mycosis: mononeuropathy of the pharyngeal ramus of the vagal nerve in a 20-year-old pony mare
Authors: Eichentopf Annemarie , Snyder Alice , Recknagel Stephan , Uhlig Albrecht , Waltl Veronika , Schusser Gerald Fritz 
Published: July 2013

AbstractA 20-year-old pony mare was presented to the equine hospital with a ten-day history of dysphagia, regurgitation and coughing. An obstruction of the oesophagus was excluded via endoscopy, but the proximal oesophagus appeared to be distended and circular contractions were missing. A guttural pouch endoscopy revealed a single, black-mottled plaque on the pharyngeal ramus of the vagus nerve in the left guttural pouch, causing a local swelling of this nerve. The pharyngeal ramus seemed to be atrophic distal to the lesion. A biopsy was taken from the lesion and histopathological findings proved the reasonable suspicion of a guttural pouch mycosis with a high degree of purulent-necrotic inflammation and invasion of fungal hyphae. There were no signs of neoplasia, such as melanoma. Daily guttural pouch irrigations with a clotrimazole emulsion (20 g Canesten®Gyn4solved in 500 ml water), led to a good recovery of the mucosa above the nerve. Periodic endoscopic examination of the left guttural pouch showed that local thickening and distal atrophy of this pharyngeal ramus did not improve, neither did the clinical symptoms. Due to progressive weight loss, acute respiratory distress and aspiration pneumonia, the 20-year-old pony mare unfortunately had to be euthanized three weeks after discharge. This case report emphasizes the enormous importance of a single nerve for the realization of the swallowing process. The one-sided loss of function of the pharyngeal branch of the vagal nerve cannot be compensated neither by the remaining ipsilateral nerves nor by the contralateral normal functioning glossopharyngeal and vagal nerves and thus inevitably leads to severe dysphagia.
Versican is upregulated in circulating monocytes in patients with systemic sclerosis and amplifies a CCL2-mediated pathogenic loop
Authors: Masuda Ayako , Yasuoka Hidekata , Satoh Takashi , Okazaki Yuka , Yamaguchi Yukie , Kuwana Masataka 
Published: July 2013

Abstract
Introduction
Altered phenotypes of circulating monocytes of patients with systemic sclerosis (SSc) have been reported, but the role of these alterations in the pathogenesis of SSc remains unclear. This study was undertaken to identify molecules that are preferentially expressed by SSc monocytes, and to investigate the roles of these molecules in the pathogenic process of SSc.

Methods
We analyzed circulating CD14+ monocytes isolated from 36 patients with SSc and 32 healthy control subjects. The monocytes' gene expression profiles were assessed by Oligo GEArray® (SABiosciences, Frederic, MA, USA) and semiquantitative or quantitative PCR; their protein expression was evaluated in culture supernatants of unstimulated monocytes by immunoblotting or ELISA, and by immunocytostaining. Monocyte chemoattractant activity of CCL2 was assessed in a TransWell® system (Corning Incorporated, Corning, NY, USA) in the presence or absence of chondroitin sulfate (CS).

Results
A step-wise approach to profiling gene expression identified that versican and CCL2 were upregulated in SSc monocytes. Subsequent analysis of proteins expressed in monocyte culture supernatants confirmed enhanced production of versican and CCL2 in SSc monocytes compared with control monocytes. CCL2 bound to CS chains of versican and colocalized with versican in the monocytes' Golgi apparatus. Finally, CCL2 had a greater ability to mediate monocyte migration when bound to CS chains, because this binding provided efficient formation of CCL2 gradients and protection from protease attack.

Conclusion
Circulating monocytes with elevated versican and CCL2 levels may contribute to the fibrotic process in a subset of SSc patients by amplifying a positive feedback loop consisting of versican, CCL2, and the influx of monocytes.
Relationship between extravascular lung water and severity categories of acute respiratory distress syndrome by the Berlin definition
Authors: Kushimoto Shigeki , Endo Tomoyuki , Yamanouchi Satoshi , Sakamoto Teruo , Ishikura Hiroyasu , Kitazawa Yasuhide , Taira Yasuhiko , Okuchi Kazuo , Tagami Takashi , Watanabe Akihiro , Yamaguchi Junko , Yoshikawa Kazuhide , Sugita Manabu , Kase Yoichi , Kanemura Takashi , Takahashi Hiroyuki , Kuroki Yuuichi , Izumino Hiroo , Rinka Hiroshi , Seo Ryutarou , Takatori Makoto , Kaneko Tadashi , Nakamura Toshiaki , Irahara Takayuki , Saito Nobuyuki ,   the PiCCO Pulmonary Edema Study Group
Published: July 2013

Abstract
Introduction
The Berlin definition divides acute respiratory distress syndrome (ARDS) into three severity categories. The relationship between these categories and pulmonary microvascular permeability as well as extravascular lung water content, which is the hallmark of lung pathophysiology, remains to be elucidated. The aim of this study was to evaluate the relationship between extravascular lung water, pulmonary vascular permeability, and the severity categories as defined by the Berlin definition, and to confirm the associated predictive validity for severity.

Methods
The extravascular lung water index (EVLWi) and pulmonary vascular permeability index (PVPI) were measured using a transpulmonary thermodilution method for three consecutive days in 195 patients with an EVLWi of ≥10 mL/kg and who fulfilled the Berlin definition of ARDS. Collectively, these patients were seen at 23 ICUs. Using the Berlin definition, patients were classified into three categories: mild, moderate, and severe.

Results
Compared to patients with mild ARDS, patients with moderate and severe ARDS had higher acute physiology and chronic health evaluation II and sequential organ failure assessment scores on the day of enrollment. Patients with severe ARDS had higher EVLWi (mild, 16.1; moderate, 17.2; severe, 19.1; P <0.05) and PVPI (2.7; 3.0; 3.2; P <0.05). When categories were defined by the minimum PaO2/FIO2 ratio observed during the study period, the 28-day mortality rate increased with severity categories: moderate, odds ratio: 3.125 relative to mild; and severe, odds ratio: 4.167 relative to mild. On independent evaluation of 495 measurements from 195 patients over three days, negative and moderate correlations were observed between EVLWi and the PaO2/FIO2 ratio (r = -0.355, P<0.001) as well as between PVPI and the PaO2/FIO2 ratio (r = -0.345, P <0.001). ARDS severity was associated with an increase in EVLWi with the categories (mild, 14.7; moderate, 16.2; severe, 20.0; P <0.001) in all data sets. The value of PVPI followed the same pattern (2.6; 2.7; 3.5; P <0.001).

Conclusions
Severity categories of ARDS described by the Berlin definition have good predictive validity and may be associated with increased extravascular lung water and pulmonary vascular permeability.

Trial registration
UMIN-CTR ID UMIN000003627
Storage of bronchoalveolar lavage fluid and accuracy of microbiologic diagnostics in the ICU: a prospective observational study
Authors: Kneidinger Nikolaus , Warszawska Joanna , Schenk Peter , Fuhrmann Valentin , Bojic Andja , Hirschl Alexander , Herkner Harald , Madl Christian , Makristathis Athanasios 
Published: July 2013

Abstract
Introduction
Early initiation of appropriate antimicrobial treatment is a cornerstone in managing pneumonia. Because microbiologic processing may not be available around the clock, optimal storage of specimens is essential for accurate microbiologic identification of pathogenetic bacteria. The aim of our study was to determine the accuracy of two commonly used storage approaches for delayed processing of bronchoalveolar lavage in critically ill patients with suspected pneumonia.

Methods
This study included 132 patients with clinically suspected pneumonia at two medical intensive care units of a tertiary care hospital. Bronchoalveolar lavage samples were obtained and divided into three aliquots: one was used for immediate culture, and two, for delayed culture (DC) after storage for 24 hours at 4°C (DC4) and -80°C (DC-80), respectively.

Results
Of 259 bronchoalveolar lavage samples, 84 (32.4%) were positive after immediate culture with 115 relevant culture counts (≥104 colony-forming units/ml). Reduced (<104 colony-forming units/ml) or no growth of four and 57 of these isolates was observed in DC4 and DC-80, respectively. The difference between mean bias of immediate culture and DC4 (-0.035; limits of agreement, -0.977 to 0.906) and immediate culture and DC-80 (-1.832; limits of agreement, -4.914 to 1.267) was -1.788 ± 1.682 (P < 0.0001). Sensitivity and negative predictive value were 96.5% and 97.8% for DC4 and 50.4% and 75.4% for DC-80, respectively; the differences were statistically significant (P < 0.0001).

Conclusions
Bronchoalveolar lavage samples can be processed for culture when stored up to 24 hours at 4°C without loss of diagnostic accuracy. Delayed culturing after storage at -80°C may not be reliable, in particular with regard to Gram-negative bacteria.
Stimulant treatment for attention-deficit hyperactivity disorder and risk of developing substance use disorder
Authors: Groenman Annabeth P. , Oosterlaan Jaap , Rommelse Nanda N. J. , Franke Barbara , Greven Corina U. , Hoekstra Pieter J. , Hartman Catharina A. , Luman Marjolein , Roeyers Herbert , Oades Robert D. , Sergeant Joseph A. , Buitelaar∗ Jan K. , Faraone∗ Stephen V. 
Published: July 2013

BackgroundAttention-deficit hyperactivity disorder (ADHD) is linked to increased risk for substance use disorders and nicotine dependence.AimsTo examine the effects of stimulant treatment on subsequent risk for substance use disorder and nicotine dependence in a prospective longitudinal ADHD case–control study.MethodAt baseline we assessed ADHD, conduct disorder and oppositional defiant disorder. Substance use disorders, nicotine dependence and stimulant treatment were assessed retrospectively after a mean follow-up of 4.4 years, at a mean age of 16.4 years.ResultsStimulant treatment of ADHD was linked to a reduced risk for substance use disorders compared with no stimulant treatment, even after controlling for conduct disorder and oppositional defiant disorder (hazard ratio (HR) = 1.91, 95% Cl 1.10−3.36), but not to nicotine dependence (HR = 1.12, 95% Cl 0.45−2.96). Within the stimulant-treated group, a protective effect of age at first stimulant use on substance use disorder development was found, which diminished with age, and seemed to reverse around the age of 18.ConclusionsStimulant treatment appears to lower the risk of developing substance use disorders and does not have an impact on the development of nicotine dependence in adolescents with ADHD.
Tumor angiogenesis is caused by single melanoma cells in a reactive oxygen species and NF-κB dependent manner
Authors: Schaafhausen Maximilian K. , Yang Wan-Jen , Centanin Lazaro , Wittbrodt Joachim , Bosserhoff Anja , Fischer Andreas , Schartl Manfred , Meierjohann Svenja 
Published: July 2013

Melanomas have a high angiogenic potential, but respond poorly to medical treatment and metastasize very early. To understand the early events in tumor angiogenesis, animal models with high tumor- and blood vessel resolution are required which provide the opportunity to test small molecule inhibitors for modulating the angiogenic tumor programme. We have established a transgenic melanoma angiogenesis model in the small laboratory fish species Japanese medaka. Here, pigment cells are transformed by an oncogenic receptor tyrosine kinase in fishes expressing GFP throughout their vasculature. We show that angiogenesis occurs in a reactive oxygen species- and NF-κB-dependent, but hypoxia-independent manner. Intriguingly, we observed that blood vessel sprouting is induced even by single transformed pigment cells. The oncogenic receptor as well as human melanoma cells harbouring other oncogenes caused the production of pro-angiogenic factors, most prominently angiogenin, via NF-κB signalling. Inhibiting NF-κB prevented tumor angiogenesis and led to the regression of existing tumor blood vessels.
In conclusion, our high resolution medaka melanoma model discloses that ROS and NF-κB signaling from single tumor cells causes hypoxia-independent angiogenesis, thus demonstrating that the intrinsic malignant tumor cell features are sufficient to initiate and maintain a pro-angiogenic signaling threshold.
Dynamic Characteristics and Speed Control Strategy of Cellulose Hydrolysis Reactor at High Solids Loading
Authors: Huang Juan , Zhang Jian , He Yanqing , Bao Jie , Dai Gance 
Published: July 2013

Abstract
This article put emphasis on systematic research and development on cellulose hydrolysis reactor. The simultaneous saccharification and fermentation of lignocellulosic was carried out in a 5-L reactor at high solids loading of corn stover (25%, w/w). The dynamic characteristics of reactive system were examined. The experimental results showed that the lignocellulosic biomass experienced a series of morphology evolution and viscosity variation. This evolution was a typical event caused by solid reactive processing, and it constituted the basis of a new geometrical configuration of reactor (specifically hybrid impeller). The minimum rotational speed of the impeller was proposed based on the Coutte flow analogy and the yield stress concept. The macroscopic performance of the reactor changed significantly with time. In view of this effect, the operating strategy of the impeller was determined.
Geographic ranges of reef corals (Cnidaria: Anthozoa: Scleractinia) in the Indo‐Pacific
Authors: Hughes Terry P. , Connolly Sean R. , Keith Sally A. 
Published: July 2013

AbstractInformation on geographic ranges and the location of range boundaries of individual species is key to studies of biogeography, evolution, macroecology, and conservation biology. Traditionally, marine biogeography has emphasized patterns in contours of species or generic richness, based on counts of species collected from different locations. To understand more fully why these and other patterns occur requires data on the geographic extent of individual species, and how their ranges overlap. We compiled a spatial database of geographic range boundaries from the primary literature and from our own records for Indo‐Pacific reef‐building scleractinian corals (726 species in 17 families: Acroporidae, Agariciidae, Astrocoeniidae, Caryophylliidae, Dendrophylliidae, Euphyllidae, Faviidae, Fungiidae, Meandrinidae, Merulinidae, Oculinidae, Pocilloporidae, Poritidae, Mussidae, Pectiniidae, Siderastreidae, and Trachyphylliidae). Corals have strongly skewed range distributions, with many species being pandemics. The data show little support for Rapoport's Rule (smaller ranges near the equator) or for the more general hypothesis that range sizes are smaller, on average, where species richness peaks. The unusual disparity between species richness and endemicity in locations such as the Coral Triangle hotspot challenges conservation priorities that tend to focus on hotspots and neglect depauperate locations. The empirically observed locations of ranges diverge from predictions of mid‐domain models in ways that are consistent with the hypothesis that westward‐flowing equatorial currents influence the species distributions of Indo‐Pacific corals. The spatial database also can be used to examine species turnover at faunal boundaries, facilitating new studies that can explore barriers to dispersal and the evolution of geographic range size.