bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders
Authors: Gaiteri C. , Ding Y. , French B. , Tseng G. C. , Sibille E. 
Published: November 2013

AbstractIn a research environment dominated by reductionist approaches to brain disease mechanisms, gene network analysis provides a complementary framework in which to tackle the complex dysregulations that occur in neuropsychiatric and other neurological disorders. Gene–gene expression correlations are a common source of molecular networks because they can be extracted from high‐dimensional disease data and encapsulate the activity of multiple regulatory systems. However, the analysis of gene coexpression patterns is often treated as a mechanistic black box, in which looming ‘hub genes’ direct cellular networks, and where other features are obscured. By examining the biophysical bases of coexpression and gene regulatory changes that occur in disease, recent studies suggest it is possible to use coexpression networks as a multi‐omic screening procedure to generate novel hypotheses for disease mechanisms. Because technical processing steps can affect the outcome and interpretation of coexpression networks, we examine the assumptions and alternatives to common patterns of coexpression analysis and discuss additional topics such as acceptable datasets for coexpression analysis, the robust identification of modules, disease‐related prioritization of genes and molecular systems and network meta‐analysis. To accelerate coexpression research beyond modules and hubs, we highlight some emerging directions for coexpression network research that are especially relevant to complex brain disease, including the centrality–lethality relationship, integration with machine learning approaches and network pharmacology.
A Small‐Diameter NMR Logging Tool for Groundwater Investigations
Authors: Walsh David , Turner Peter , Grunewald Elliot , Zhang Hong , Butler James J. , Reboulet Ed , Knobbe Steve , Christy Tom , Lane John W. , Johnson Carole D. , Munday Tim , Fitzpatrick Andrew 
Published: November 2013

AbstractA small‐diameter nuclear magnetic resonance (NMR) logging tool has been developed and field tested at various sites in the United States and Australia. A novel design approach has produced relatively inexpensive, small‐diameter probes that can be run in open or PVC‐cased boreholes as small as 2 inches in diameter. The complete system, including surface electronics and various downhole probes, has been successfully tested in small‐diameter monitoring wells in a range of hydrogeological settings. A variant of the probe that can be deployed by a direct‐push machine has also been developed and tested in the field. The new NMR logging tool provides reliable, direct, and high‐resolution information that is of importance for groundwater studies. Specifically, the technology provides direct measurement of total water content (total porosity in the saturated zone or moisture content in the unsaturated zone), and estimates of relative pore‐size distribution (bound vs. mobile water content) and hydraulic conductivity. The NMR measurements show good agreement with ancillary data from lithologic logs, geophysical logs, and hydrogeologic measurements, and provide valuable information for groundwater investigations.
CO2 Capture and Geologic Storage: The Possibilities
Authors: Loáiciga Hugo A. 
Published: November 2013

AbstractCarbon dioxide (CO2) capture and geologic storage has been postulated as one possible method to stabilize the atmospheric concentration of CO2 by injecting and storing it in deep geologic formations. This issue paper analyzes the viability of capture and geologic storage of becoming an effective method to aid in stabilizing the atmospheric concentration of CO2. It is herein shown that such viability is contingent on overcoming major obstacles that are hydrogeological, technical, and economic in nature. Our analysis indicates that capture and geologic storage is likely to have negligible success in reducing the atmospheric buildup of CO2 in the coming decades. The magnitude of the anthropogenic emissions of CO2 indicates that a transition of the world economy away from reliance on fossil fuels might be the only path to stabilize its atmospheric concentration.
Optimising the retrieval of information on adverse drug effects
Authors: Golder Su 
Published: November 2013

AbstractPharmaceutical interventions have brought about many benefits to health, improving the population's well‐being and life expectancy. However, these interventions are not without potential harmful side‐effects and yet searching for the evidence on adverse effects is challenging. This article summarises a PhD whose main aim was to develop a better understanding of the implications of using different sources and approaches to identifying relevant data on adverse effects. The author is Su Golder, who has recently completed her PhD at the University of York and who has already published several articles on specific aspects of her research, including this journal. This article is the first in the Dissertations into Practice series to report on a PhD study, and it summarises her research in a way which emphasises the implications for practice.AM
Juvenile‐like (inflammatory/hyperplastic) mucosal polyps of the gastrointestinal tract in neurofibromatosis type 1
Authors: Agaimy Abbas , Schaefer Inga‐Marie , Kotzina Leopoldina , Knolle Jürgen , Baumann Irith , Ströbel Philipp , Vieth Michael 
Published: November 2013

AimsDiffuse neurofibromatosis/ganglioneuromatosis, solitary/plexiform neurofibroma, periampullary carcinoids and gastrointestinal stromal tumour (GIST) are the main gastrointestinal manifestations of neurofibromatosis type 1 (NF‐1, von Recklinghausen disease). Inflammatory (juvenile‐like) polyps have not been recognised to date as specific gastrointestinal (GI) manifestations ofNF‐1.Methods and resultsWe describe four males aged 23–65 years withNF‐1 and inflammatory (juvenile‐like) gastrointestinal polyps, and review the literature for similar cases. Two patients had single polyps (sigmoid colon and antrum, respectively), one had two polyps (left colon), and one had three polyps (distal oesophagus and colon). Histological appearances were variable, ranging from juvenile‐like to granulation tissue‐rich, predominantly inflammatory and hyperplastic. Three lesions showed obliterative vasculopathic changes. None had neurofibromatous or ganglioneuromatous polyps. A review of the literature disclosed 11 similar cases. Most patients presented with severe gastrointestinal symptoms and/or anaemia.ConclusionsNF‐1‐associated inflammatory polyps probably represent specificGImanifestations of this disorder, and should be considered, particularly in patients withGIsymptoms. They should be distinguished from inflammatory fibroid polyps and from juvenile‐like changes associated with ganglioneuroma/ganglioneuromatosis and neurofibroma/neurofibromatosis. Their aetiology remains obscure, but different mechanisms, includingNF‐1inactivation,NF‐1‐associated vasculopathy, and localised mucosal prolapse/damage caused by motility disorders, might be involved.
T cell receptor (TCR) V gene usage in patients with systemic necrotizing vasculitis
Authors: GISCOMBE R , GRUNEWALD J , NITYANAND S , LEFVERT A K 
Published: November 2013

SUMMARYWegener's granulomatosis (WG) and polyarteritis nodosa (PAN) are systemic necrotizing vasculitides of unknown etiology. These disorders run a fatal course if untreated. T lymphocytes are implicated in the pathogenesis of WG, since they have been found to infiltrate affected organs, and sIL-2R correlates with disease activity. To elucidate further the role of T cells in necrotizing vasculitis, we have used a panel of 12 TCR V-specific MoAbs to investigate the number of cells expressing certain Vα and Vβ gene segments in the CD4+ and CD8+ subsets of altogether 11 patients with WG or PAN. In the group of patients, we found abnormal expansions of T cells using particular TCR Vα or β gene products. These T cell expansions were more numerous, of a dramatically higher magnitude, and frequently more often found in the CD4 subset, compared with T cell expansions identified in healthy individuals. In long-term studies of the T cell expansions for up to 18 months, a heterogeneous pattern was revealed, with no obvious correlation to clinical features such as disease activity or treatment. Studies of TCR V gene usage in this group of patients may help in understanding the pathogenesis of necrotizing vasculitis, and in the identification of unknown antigens, and may open the possibility to a highly selective immunotherapy by targeting disease-mediating T cells.
Thermodynamic Properties of LaCrO4, La2CrO6, and La2Cr3O12, and Subsolidus Phase Relations in the System Lanthanum–Chromium–Oxygen
Authors: Kallarackel Thomas Jacob , Gupta Sapna , Singh Prabhakar 
Published: November 2013

In the system La–Cr–O, there are three ternary oxides (LaCrO4, La2Cr3O12, and La2CrO6) that contain Cr in higher valence states (V or VI). On heating, LaCrO4 decomposes to LaCrO3, La2Cr3O12 to a mixture of LaCrO4 and Cr2O3, and La2CrO6 to LaCrO3 and La2O3 with loss of oxygen. The oxygen potentials corresponding to these decomposition reactions are determined as a function of temperature using solid‐state cells incorporating yttria‐stabilized zirconia as the electrolyte. Measurements are made from 840 K to the decomposition temperature of the ternary oxides in pure oxygen. The standard Gibbs energies of formation of the three ternary oxides are derived from the reversible electromotive force (EMF) of the three cells. The standard enthalpy of formation and standard entropy of the three ternary oxides at 298.15 K are estimated. Subsolidus phase relations in the system La–Cr–O are computed from thermodynamic data and displayed as isothermal sections at several temperature intervals. The decomposition temperatures in air are 880 (±3) K for La2Cr3O12, 936 (±3) K for LaCrO4, and 1056 (±4) K for La2CrO6.
Theoretical Prediction and Experimental Investigation on the Thermal and Mechanical Properties of Bulk β‐Yb2Si2O7
Authors: Zhou Yan‐Chun , Zhao Cen , Wang Feng , Sun Yin‐Jie , Zheng Li‐Ya , Wang Xiao‐Hui 
Published: November 2013

The thermal and mechanical properties of β‐Yb2Si2O7 were investigated using a combination of first‐principles calculations and experimental investigations. Theoretically, anisotropic chemical bonding and elastic properties, weak interatomic (010) and (001) planes in the crystal structure, damage tolerance, and low thermal conductivity are predicted. Experimentally, preferred orientation, superior mechanical properties, and damage tolerant behavior for hot‐pressed bulk β‐Yb2Si2O7 are approved. Slipping along the weakly bonded {010}, {001}, or {100} planes, grain delamination, buckling, and kinking of nanolaminated grains are identified as main mechanisms for damage tolerance. The anisotropic linear thermal expansion coefficients (CTEs) are: αa = (3.57 ± 0.18) × 10−6 K−1, αb = (2.49 ± 0.14) × 106 K−1, and αc = (1.48 ± 0.22) × 10−6 K−1 (673–1273 K). A low thermal conductivity of ~2.1 W (m·K)−1 at 1273 K has been confirmed. The unique combination of these properties endow it a potential candidate for thermal barrier coating (TBC)/environmental barrier coating of silicon‐based ceramics.
Correlations Between Microstructure and Mechanical Properties of Air Plasma‐Sprayed Thermal Barrier Coatings Exposed to a High Temperature
Authors: Osorio Julián D. , Maya Deiby , Barrios Augusto C. , Lopera Adrián , Jiménez Freddy , Meza Juan M. , Hernández‐Ortiz Juan P. , Toro Alejandro 
Published: November 2013

An indentation method is used to study the variations in Young's modulus, hardness and fracture toughness of air plasma‐sprayed thermal barrier coatings at a high temperature. The coatings were exposed to 1100°C during 1700 h. A sudden increase in Young's modulus for the first 600 h was observed, while the hardness increased after 800 h as a consequence of sintering. Conversely, there was a reduction of 25% in fracture toughness after 1700 h, evidencing the thermal barrier coating degradation. The evolution of these mechanical properties was correlated with microstructural changes. After 1700 h, the thermally grown oxide thickness reached 6.8 μm, the volumetric percentage of porosity was reduced from 6.8% to 4.7% and the amount of monoclinic phase increased to 23.4 wt%. These characteristics are closely related to the stress distribution in the top coat, which promotes cracks nucleation and propagation, compromising the coating durability.
Role of diet and nutritional management in non‐alcoholic fatty liver disease
Authors: Fan Jian‐Gao , Cao Hai‐Xia 
Published: November 2013

AbstractNon‐alcoholic fatty liver disease (NAFLD) encompasses a spectrum ranging from simple steatosis to non‐alcoholic steatohepatitis, which causes an increased risk of cirrhosis, type 2 diabetes, and cardiovascular complications. With the worldwide growing incidence of obesity, sedentary lifestyle, and unhealthy dietary pattern, NAFLD has currently been recognized as a major health burden. Dietary patterns and nutrients are the important contributors to the development, progression, and treatment of NAFLD and associated metabolic comorbidities. Generally, hypercaloric diet, especially rich in trans/saturated fat and cholesterol, and fructose‐sweetened beverages seem to increase visceral adiposity and stimulate hepatic lipid accumulation and progression into non‐alcoholic steatohepatitis, whereas reducing caloric intake, increasing soy protein and whey consumption, and supplement of monounsaturated fatty acids, omega‐3 fatty acids, and probiotics have preventive and therapeutic effects. In addition, choline, fiber, coffee, green tea, and light alcohol drinking might be protective factors for NAFLD. Based on available data, at least 3–5% of weight loss, achieved by hypocaloric diet alone or in conjunction with exercise and behavioral modification, generally reduces hepatic steatosis, and up to 10% weight loss may be needed to improve hepatic necroinflammation. A sustained adherence to diet rather than the actual diet type is a major predictor of successful weight loss. Moreover, a healthy diet has benefits beyond weight reduction on NAFLD patients whether obese or of normal weight. Therefore, nutrition serves as a major route of prevention and treatment of NAFLD, and patients with NAFLD should have an individualized diet recommendation.
Non‐nutritional effects of food: An underutilized and understudied therapeutic tool in chronic gastrointestinal diseases
Authors: Gibson Peter R , Muir Jane G 
Published: November 2013

AbstractThe use of diet has traditionally been used to improve the nutrition of patients. However, diet also can be utilized to modify disease processes and manage symptoms independently of its nutritional role. There are few chronic gastrointestinal conditions where dietary modification is utilized therapeutically and backed by a high degree of evidence. This is not due to a lack of ideas but is more likely to lie in the difficulties associated with translating those ideas into evidence‐based practice. Long lead‐in times and low incidence hinders interventional studies of prevention for many conditions. The design and execution of dietary clinical trials is challenging and funding them even more so. The knowledge base of doctors in nutrition and food composition is often poor, and attitudes toward the success of and adherence to dietary therapies create additional problems. However, ideas can be successfully translated into evidence‐based practice, as exemplified but the low fermentable, oligo‐, di‐, and mono‐saccharides and polyols (FODMAP) (poorly‐absorbed short‐chain carbohydrates) diet for patients with functional bowel symptoms. Showing efficacy is, however, insufficient for non‐nutritional dietary manipulations. Adverse effects, such as nutritional adequacy of the diet and effect on pathogenesis of other diseases, must also be carefully addressed. The physiological principles upon which the diet is based should be matched to the physiology associated with the condition being targeted, as it can be hazardous to extrapolate findings in healthy persons. There is a need for greater attention to the evaluation of dietary therapies for many chronic gastrointestinal disorders.
Distribution of interferon lambda‐3 gene polymorphisms in Australian patients with previously untreated genotype 1 chronic hepatitis C: Analysis from the PREDICT and CHARIOT studies
Authors: Roberts Stuart K , Mitchell Joanne , Leung Reynold , Booth David , Bollipo Steven , Ostapowicz George , Sloss Andrew , McCaughan Geoffrey W , Dore Gregory J , Thompson Alexander , Crawford Darrell HG , Sievert William , Weltman Martin , Cheng Wendy , George Jacob ,   Australian Liver Association Clinical Research Network
Published: November 2013

AbstractBackground and AimsThe aim of this study was to examine the distribution of interferon lambda‐3 (IFN‐λ3) gene polymorphisms in previously untreated Australian patients with genotype 1 (Gt1) chronic hepatitis C (CHC) and to compare the IFN‐λ3 genotype frequency among the different ethnic populations.MethodsThis was a prospective, multicenter, observational study undertaken by the Australian Liver Association Clinical Research Network. Eligible subjects had Gt1 CHC and were being considered for and/or undergoing treatment. IFN‐λ3 single nucleotide polymorphisms were genotyped by the Applied Biosystems's Taqman single nucleotide polymorphism genotyping assay.ResultsBetween May 2012 and June 2012, 1132 patients were recruited from 38 treatment clinics across Australia. Also, 561 subjects from the CHARIOT (collaborative group hepatitis C study using high dose Pegasys RBV Induction dose in genotype one) study of high‐dose interferon who had baseline serum available were retrospectively tested. The overall frequency of IFN‐λ3 rs12979860 CC/CT/TT genotypes was 36%, 52%, and 12%, and that of rs8099917 TT/TG/GG genotypes was 54%, 41%, and 5%, respectively. The prevalence of the favorable IFN‐λ3 rs12979860 CC and rs8099917 TT genotypes in Causcasians, Asians, Aboriginals, Maori/Pacific Islanders, and Mediterraneans was 32% and 52%, 80% and 86%, 33% and 63%, 77% and 88%, and 19% and 29%, respectively. Compared with Caucasians, the frequency of IFN‐λ3 CC was significantly higher among Asians (P < 0.0001) and Maori/Pacific Islander subjects (P < 0.0001).ConclusionsThe distribution of IFN‐λ3 polymorphisms among untreated patients with Gt1 CHC in Australia appears similar to that reported from North America. The frequency of the favorable response alleles varies considerably according to ethnicity, being more common in self‐reported Asians and Maori/Pacific Islanders than Caucasians, Aboriginals, and Mediterraneans.
Role of glycine N‐methyltransferase in experimental ulcerative colitis
Authors: Chou Wen‐Yueh , Zhao Jin‐Feng , Chen Yi‐Ming Arthur , Lee Kuan‐I , Su Kuo‐Hui , Shyue Song‐Kun , Lee Tzong‐Shyuan 
Published: November 2013

AbstractBackground and AimInflammatory bowel diseases (IBDs) are chronic inflammatory disorders with unclear etiology and mechanism(s). Glycine N‐methyltransferase (GNMT) plays a central role in inflammatory diseases such as hepatitis and atherosclerosis. However, little is known about the impact of GNMT and the involved mechanism in the pathogenesis of IBD. In the current study, we investigated the role of GNMT in the mouse model of dextran sulfate sodium (DSS)‐induced colitis.MethodsProtein expression was determined by Western blotting or immunohistochemistry. Histopathology was examined by hematoxylin and eosin staining. Levels of pro‐inflammatory cytokines were evaluated by ELISA kits.ResultsGNMT was expressed in the epithelium of the colon under normal conditions, and with DSS treatment, its expression was predominant in infiltrated leukocytes of lesions. Mice with genetic deletion of GNMT (GNMT−/−) showed increased susceptibility to DSS induction of colitis, as revealed by the progression of colitis. Additionally, severe colonic inflammation, including increased crypt loss, leukocyte infiltration, and hemorrhage, was greater with DSS treatment in GNMT−/− than wild‐type mice. Furthermore, the expression of adhesion molecule and inflammatory mediators in the colon was significantly higher with DSS treatment in GNMT−/− than wild‐type mice. Moreover, loss of GNMT decreased cell apoptosis in colitis lesions with DSS treatment.ConclusionsCollectively, our findings suggest that GNMT may be a crucial molecule in the pathogenesis of DSS‐induced colitis. This finding may provide new information for a potential therapeutic target in treating IBD.
Relationship between serum circulating insulin‐like growth factor‐1 and liver fat in the United States
Authors: Runchey Shauna S , Boyko Edward J , Ioannou George N , Utzschneider Kristina M 
Published: November 2013

AbstractBackground and AimNonalcoholic fatty liver disease (NAFLD), circulating insulin‐like growth factor‐1 (IGF‐1), and IGF‐1/IGF‐binding protein‐3 (IGFBP‐3) concentrations are associated with adiposity and insulin resistance. We aimed to determine whether serum IGF‐1, IGFBP‐3, and IGF‐1/IGFBP‐3 are associated with presence or severity of NAFLD independent of potential confounding.MethodsWe performed a cross‐sectional analysis of data from the Third National Health and Nutrition Examination Survey, 1988–1994, a representative sample of the United States adult population. Among participants who had a fasting blood draw and ultrasound examination, we excluded those with missing data, viral hepatitis, iron overload, excessive alcohol intake, pregnancy, or taking glucose‐lowering therapy, yielding 4172 adults for this analysis.ResultsIn logistic regression analyses adjusted for age, gender, and race/ethnicity, higher IGF‐1 and IGF‐1/IGFBP‐3 quartiles were associated with lower likelihood of NAFLD and lower grade steatosis. These associations became non‐significant when further adjusted for adiposity (body mass index, waist circumference) with the exception of the association between IGF‐1/IGFBP‐3 and severity of NAFLD which remained significant after adjustment for homeostasis model assessment for insulin resistance (HOMA‐IR) (odds ratio [95% CI]: Q3: 0.71 [0.53–0.96], Q4: 0.62 [0.43–0.89]) and adiposity (Q4: 0.67 [0.47–0.96]). Full adjustment (age, gender, race/ethnicity, adiposity, HOMA‐IR, A1C%) further attenuated associations between IGF‐1 or IGF‐1/IGFBP‐3 and liver fat such that they were no longer significant.ConclusionsAdiposity explains much of the observed association between IGF‐1 or IGF‐1/IGFBP‐3 and liver fat. These findings do not support a direct role for the growth hormone‐IGF‐1/IGFBP‐3 axis in the pathophysiology of NAFLD.