bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
Authors: Zhang Xiujun , Zhao Xing-Ming , He Kun , Lu Le , Cao Yongwei , Liu Jingdong , Hao Jin-Kao , Liu Zhi-Ping , Chen Luonan 
Published: November 2011

Abstract
Motivation: Reconstruction of gene regulatory networks (GRNs), which explicitly represent the causality of developmental or regulatory process, is of utmost interest and has become a challenging computational problem for understanding the complex regulatory mechanisms in cellular systems. However, all existing methods of inferring GRNs from gene expression profiles have their strengths and weaknesses. In particular, many properties of GRNs, such as topology sparseness and non-linear dependence, are generally in regulation mechanism but seldom are taken into account simultaneously in one computational method.
Results: In this work, we present a novel method for inferring GRNs from gene expression data considering the non-linear dependence and topological structure of GRNs by employing path consistency algorithm (PCA) based on conditional mutual information (CMI). In this algorithm, the conditional dependence between a pair of genes is represented by the CMI between them. With the general hypothesis of Gaussian distribution underlying gene expression data, CMI between a pair of genes is computed by a concise formula involving the covariance matrices of the related gene expression profiles. The method is validated on the benchmark GRNs from the DREAM challenge and the widely used SOS DNA repair network in Escherichia coli. The cross-validation results confirmed the effectiveness of our method (PCA-CMI), which outperforms significantly other previous methods. Besides its high accuracy, our method is able to distinguish direct (or causal) interactions from indirect associations.
Availability: All the source data and code are available at: http://csb.shu.edu.cn/subweb/grn.htm.
Contact: lnchen@sibs.ac.cn; zpliu@sibs.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Mitochondrial DNA diversity patterns in Pakistani buffalo
Authors: Babar M. E. , Hussain T. , Imran M. , Nagarajan M. , Kumar S. 
Published: November 2011

SummaryThe Indian subcontinent is considered to be the likely centre of river buffalo domestication, based on population dynamics, archaeological evidence and genetic diversity. Recent studies on mitochondrial DNA diversity have drawn useful conclusions about the domestication history of Bubalus bubalis. The conclusions of these studies are, however, incomplete, unless samples can also be analysed from Pakistan, which contains the second largest buffalo population of the world. Here, we report the results of the first study on mitochondrial D‐loop sequence diversity in five breeds of Pakistani buffalo. Analysis of sequence variations in 503‐bp of the D‐loop region of 123 animals revealed 52 haplotypes, including 40 singletons. Multidimensional display of breed pairwise FST values revealed no strong clustering of breeds. Bayesian, maximum parsimony, neighbour joining and UPGMA trees revealed a topology consistent with domestication as well as subsequent introgression of multiple maternal lineages from the wild stocks. Reduced median network analysis provided evidence of population expansion from more than one set of haplotypes. The study also confirmed that Pakistani buffalo are of the river type. The observed mitochondrial D‐loop sequence diversity suggests that Pakistani areas bordering India might have contributed to the initiation of domestication of the present‐day river buffalo.
A spatial analytical approach for selecting reintroduction sites for burbot in English rivers
Authors: WORTHINGTON T. , KEMP P. S. , OSBORNE P. E. , DILLEN A. , COECK J. , BUNZEL‐DRÜKE M. , NAURA M. , GREGORY J. , EASTON K. 
Published: November 2011

Summary1. Availability of suitable habitat is a prerequisite for species reintroduction success, and to ensure population persistence, investigations of a species’ habitat utilisation throughout its life history should be conducted as part of a feasibility study.2. Habitat utilisation models for burbot, Lota lota, developed using data from field studies conducted in France and Germany and information from the literature were used to assess the feasibility of reintroducing burbot into rivers of its former native range in eastern England.3. Per cent tree roots, aquatic vegetation and flow types were important predictors of adult burbot abundance. Furthermore, the habitat utilisation models were supplemented with information from the literature, which suggested that off‐channel habitat such as wetlands and backwaters is important for spawning and nursery stages.4. An assessment of the habitat availability in the rivers of the burbot’s former native range using variables related to spawning and nursery and adult life stages showed that although adult habitat was widely distributed, the availability of spawning and nursery habitat was less abundant, potentially limiting successful reestablishment.5. Potential suitable habitat was concentrated in the central and southern areas of the species’ former English distribution. Overall, rivers of the burbot’s former range potentially afford suitable habitat to sustain a reintroduced population. However, sites should be preferentially selected on the basis of having appropriate spawning and nursery areas.
Histological and immunohistological findings in biliary intraepithelial neoplasia arising from a background of chronic biliary disease compared with liver cirrhosis of non‐biliary aetiology
Authors: Aishima Shinichi , Iguchi Tomohiro , Fujita Nobuhiro , Taketomi Akinobu , Maehara Yoshihiko , Tsuneyoshi Masazumi , Oda Yoshinao 
Published: November 2011

Aishima S, Iguchi T, Fujita N, Taketomi A, Maehara Y, Tsuneyoshi M & Oda Y (2011) Histopathology59, 867–875Histological and immunohistological findings in biliary intraepithelial neoplasia arising from a background of chronic biliary disease compared with liver cirrhosis of non‐biliary aetiologyAims:  Hitherto, biliary intraepithelial neoplasia (BilIN) has been described in chronic biliary disease but rarely in non‐biliary liver cirrhosis (LC). Intraepithelial neoplasia of the pancreas shows alterations in the expression of cell cycle and mucin core proteins. The aim of this study was to evaluate BilIN and reactive biliary lesions in biliary disease and non‐biliary LC.Methods and results:  BilIN was found in 51% (33 of 65) of liver tissue cases of biliary disease, and in 11% (34 of 310) of the LC group. Immunohistologically, MUC5AC, an ‘early phase’ protein, and Ki67, reflecting ‘late phase’ expression, were identified with increasing degrees of dysplasia in both groups, but that expression was significantly higher in the biliary disease group. ‘Early phase’ cell cycle proteins, p16 (decrease) and p21 (increase) altered in both biliary and LC groups with increasing degrees of dysplasia.Conclusions:  We found BilIN in the large bile ducts of hepatitis B virus‐ and hepatitis C virus‐related LC as well as in cases related to a biliary aetiology. The LC group was significantly less likely to show changes in the expression of MUC5AC and proliferative activity than the biliary group. Alterations in p16 and p21 reflected increasing degrees of dysplasia in both groups.
Minimizing damage during FIB sample preparation of soft materials
Authors: BASSIM N.D. , DE GREGORIO B.T. , KILCOYNE A.L.D. , SCOTT K. , CHOU T. , WIRICK S. , CODY G. , STROUD R.M. 
Published: November 2011

SummaryAlthough focused ion beam (FIB) microscopy has been used successfully for milling patterns and creating ultra‐thin electron and soft X‐ray transparent sections of polymers and other soft materials, little has been documented regarding FIB‐induced damage of these materials beyond qualitative evaluations of microstructure. In this study, we sought to identify steps in the FIB preparation process that can cause changes in chemical composition and bonding in soft materials. The impact of various parameters in the FIB‐scanning electron microscope (SEM) sample preparation process, such as final milling voltage, temperature, ion beam overlap and mechanical stability of soft samples, was evaluated using two test‐case materials systems: polyacrylamide, a low melting‐point polymer, and Wyodak lignite coal, a refractory organic material. We evaluated changes in carbon bonding in the samples using X‐ray absorption near‐edge structure spectroscopy (XANES) at the carbon K edge and compared these samples with thin sections that had been prepared mechanically using ultramicrotomy. Minor chemical changes were induced in the coal samples during FIB‐SEM preparation, and little effect was observed by changing ion‐beam parameters. However, polyacrylamide was particularly sensitive to irradiation by the electron beam, which drastically altered the chemistry of the sample, with the primary damage occurring as an increase in the amount of aromatic carbon bonding (C=C). Changes in temperature, final milling voltage and beam overlap led to small improvements in the quality of the specimens. We outline a series of best practices for preparing electron and soft X‐ray transparent samples, with respect to preserving chemical structure and mechanical stability of soft materials using the FIB.
The contribution of protein kinase C and CPI‐17 signaling pathways to hypercontractility in murine experimental colitis
Authors: Ihara E. , Chappellaz M. , Turner S. R. , Macdonald J. A. 
Published: November 2011

AbstractBackground  Colonic smooth muscle contractility is altered in colitis, and several protein kinase pathways can mediate colonic smooth muscle contraction. In the present study, we investigated whether protein kinase C (PKC) pathways also play a role in colonic hypercontractility observed during TH2 colitis in BALB/c mice.Methods  Colitis was induced in BALB/c mice by provision of 5% dextran sodium sulfate (DSS) for 7 days. Changes in smooth muscle contractility were examined using dissected circular smooth muscle preparations from the distal colon. The contribution of conventional and novel PKC isozymes to the hypercontractile response was examined with pharmacological PKC inhibitors. Western blot analyses were used to examine protein expression and phosphorylation changes.Key Results  Colonic smooth muscle was associated with inflammation‐induced hypercontractility and altered PKC expression. Carbachol‐induced peak (phasic) and sustained (tonic) contractions were increased. Chelerythrine was the most effective PKC inhibitor of both phasic and tonic contractions. There was no general difference in the percent contribution of conventional and novel PKC isozymes toward the DSS‐induced hypercontractility, but inhibition of sustained force with GF109203x was higher for inflamed muscle. The CPI‐17 phosphorylation was equally suppressed in both normal and DSS conditions by Gö6976 and chelerythrine, but only for the phasic component of contraction.Conclusions & Inferences  The outcomes suggest that both conventional and novel PKC isozymes contribute to the phasic and tonic contractile components of BALB/c colonic circular smooth muscle under normal conditions, with novel PKC isozymes having a greater contribution to the tonic contraction. However, no effect of inflammation was observed on the relative contribution of PKC and CPI‐17 toward the observed hypercontractility.
Identification of genomic deletions spanning the PCDH19 gene in two unrelated girls with intellectual disability and seizures
Authors: Vincent AK , Noor A , Janson A , Minassian BA , Ayub M , Vincent JB , Morel CF 
Published: November 2011

Vincent AK, Noor A, Janson A, Minassian BA, Ayub M, Vincent JB, Morel CF. Identification of genomic deletions spanning the PCDH19 gene in two unrelated girls with intellectual disability and seizures.Recently, missense and truncating mutations in the gene PCDH19 have been reported to cause female‐restricted epilepsy with mental retardation (EFMR). EFMR (MIM#300088) is an X‐linked disorder characterized by early onset seizures and intellectual disability (ID). Interestingly, unlike typical X‐linked mode of inheritance, the phenotype is restricted to females, and males are unaffected carriers. PCDH19 is highly expressed in brain, and the encoded protein belongs to the cadherin superfamily. Here we report two unrelated female patients with deletions spanning PCDH19 identified by copy number variation (CNV) analysis and validated by qPCR. In one, we have identified a 3 Mb interstitial deletion at Xq21.33‐q22.1 which spans PCDH19, LOC442459 & TNMD. This patient had her first seizure at 8 months old, and also has ID and aggressive behavior. In another female patient we identified a de novo 603 kb heterozygous deletion in a female patient with fits (since 1 year of age), ID, hyperactivity and aggressive behavior. The deletion spans the entire PCDH19 gene (also TNMD, SRPX2, TSPAN6 and SYTL4). In conclusion, our results suggest that deletions at PCDH19 also cause EFMR.
Overweight and obesity in pediatric liver transplant recipients: Prevalence and predictors before and after transplant, United Network for Organ Sharing Data, 1987–2010
Authors: Perito Emily Rothbaum , Glidden Dave , Roberts John Paul , Rosenthal Philip 
Published: November 2011

Perito ER, Glidden D, Roberts JP, Rosenthal P. Overweight and obesity in pediatric liver transplant recipients: Prevalence and predictors before and after transplant, United Network for Organ Sharing Data, 1987–2010.  Pediatr Transplantation 2012: 16: 41–49. © 2011 John Wiley & Sons A/S.Abstract:  Obesity is extremely common in adult liver transplant recipients and healthy U.S. children. Little is known about the prevalence or risk factors for post‐transplant obesity in pediatric liver transplant recipients. UNOS data on all U.S. liver transplants 1987–2010 in children 6 months–20 yr at transplant were analyzed. Subjects were categorized as underweight, normal weight, overweight, or obese by CDC guidelines. Predictors of weight status at and after transplant were identified using multivariate logistic regression. Of 3043 children 6–24 months at transplant, 14% were overweight. Of 4658 subjects 2–20 yr at transplant, 16% were overweight and 13% obese. Children overweight/obese at transplant were more likely to be overweight/obese at one, two, and five yr after transplant in all age groups after adjusting for age, ethnicity, primary diagnosis, year of transplant, and transplant type. Weight status at transplant was not associated with overweight/obesity by 10 yr after transplant. The prevalence of post‐transplant obesity remained high in long‐term follow‐up, from 20% to 50% depending on age and weight status at transplant. Weight status at transplant is the strongest predictor of post‐transplant overweight/obesity. To optimize long‐term outcomes in pediatric liver transplant recipients, monitoring for obesity and its comorbidities is important.
Acute humoral rejection in pediatric renal transplant recipients receiving steroid minimization immunosuppression
Authors: Butani Lavjay , Gallay Brian J. 
Published: November 2011

Butani L, Gallay BJ. Acute humoral rejection in pediatric renal transplant recipients receiving steroid minimization immunosuppression.Abstract:  SM protocols have increasingly gained acceptance owing to their favorable side effect profile with comparable cellular rejection rates. After encountering SM patients with AHR, we performed a case‐control study to identify predictors associated with AHR in this cohort. Patients with (n = 4) and without (n = 19) biopsy proven AHR on a SM regimen were compared using the Student’s t‐tests. The median age at transplant was 13.8 yr. Compared to controls, the AHR cohort was older (15.9 vs. 12.1 yr, p = 0.01). Children with AHR had a lower mean tacrolimus trough level and were more likely to have a sub‐therapeutic trough at six months (3.5 vs. 5.5 ng/mL, p = 0.05); mean MMF doses were lower at all times points except three months in the AHR group (not statistically significant). This occurred in spite of higher MPA trough levels at all study points in the AHR group (significant at 3 [p = 0.019] and 6 [p = 0.03] months). Children receiving a SM regimen have a lower safety net and may benefit from more intensive monitoring of tacrolimus exposure. MMF dose modifications based on MPA trough determinations should be resisted in the setting of SM.
The role of autophagy in unilateral ureteral obstruction rat model
Authors: KIM WAN‐YOUNG , NAM SUN AH , SONG HO CHEOL , KO JUN SUNG , PARK SANG HEE , KIM HONG LIM , CHOI EUY JIN , KIM YONG‐SOO , KIM JIN , KIM YONG KYUN 
Published: November 2011

ABSTRACT:Aim:  Autophagy is a cellular process of degradation of damaged cytoplasmic components and regulates cell death or proliferation. Unilateral ureteral obstruction (UUO) is a model of progressive renal fibrosis in the obstructed kidney. And UUO is followed by compensatory cellular proliferation in the contralateral kidney. We investigate the role of autophagy in the obstructed kidney and contralateral kidney after UUO.Methods:  To obtain the evidence and the patterns of autophagy during UUO, the rats were sacrificed 3, 7 and 14 days after UUO. To examine the efficacy of the autophagy inhibitors, 3‐methyladenine (3‐MA), the rats were treated daily with intraperitoneal injection of 3‐MA (30 mg/kg per day) for 7 days.Results:  After UUO, autophagy was induced in the obstructed kidney in a time‐dependent manner. Inhibition of autophagy by 3‐MA enhanced tubular cell apoptosis and tubulointerstitial fibrosis in the obstructed kidney after UUO. In the contralateral kidney, autophagy was also induced and prolonged during UUO. Inhibition of autophagy by 3‐MA increased the protein expression of proliferating cell nuclear antigen significantly in the contralateral kidney after UUO. The Akt‐mammalian target of rapamycin (mTOR) signalling pathway was involved in the induction of autophagy after UUO in both kidneys.Conclusion:  Our present results support that autophagy induced by UUO has a renoprotective role in the obstructed kidney and regulatory role of compensatory cellular proliferation in the contralateral kidney through Akt‐mTOR signalling pathway.
Losing anti‐predatory behaviour: A cost of translocation
Authors: WHITWELL SARAH M. , AMIOT CHRISTOPHE , MCLEAN IAN G. , LOVEGROVE TIM G. , ARMSTRONG DOUG P. , BRUNTON DIANNE H. , JI WEIHONG 
Published: November 2011

AbstractTranslocation of endangered species to habitats where exotic predators have been removed is now a common conservation practice around the world. Many of these translocated populations have thrived, and they are often used as sources for the harvesting of individuals for translocations to sites where exotic predators still exist, albeit at reduced densities. This study investigates how isolation from exotic predators affects the ability of individuals to recognize such predators using the North Island robin (Petroica longipes) as a model. The study was carried out in three robin populations in the North Island, New Zealand: a translocated population on Tiritiri Matangi Island, where exotic mammalian predators are absent; a population reintroduced from Tiritiri Matangi Island to Wenderholm Regional Park, a mainland site where these mammals are controlled to low densities; and a mainland population at Benneydale where exotic predatory mammals are common. The response intensity of robins to a model stoat was high at Benneydale and low at Tiritiri Matangi and Wenderholm. This result indicates that isolation from mammalian predators on Tiritiri Matangi has suppressed the ability of North Island robins to recognize these predators. It is possible that the low predatory mammal densities at Wenderholm have reduced robin contact with stoats, therefore reduced the opportunity for robins to learn to recognize stoats. Thus, translocation of individuals from populations without predators to places where key predators still exist could be unsuccessful if translocated individuals fail to perform appropriate anti‐predator behaviours.
Energetic and biomechanical constraints on animal migration distance
Authors: Hein Andrew M. , Hou Chen , Gillooly James F. 
Published: November 2011

Ecology Letters(2011)AbstractAnimal migration is one of the great wonders of nature, but the factors that determine how far migrants travel remain poorly understood. We present a new quantitative model of animal migration and use it to describe the maximum migration distance of walking, swimming and flying migrants. The model combines biomechanics and metabolic scaling to show how maximum migration distance is constrained by body size for each mode of travel. The model also indicates that the number of body lengths travelled by walking and swimming migrants should be approximately invariant of body size. Data from over 200 species of migratory birds, mammals, fish, and invertebrates support the central conclusion of the model – that body size drives variation in maximum migration distance among species through its effects on metabolism and the cost of locomotion. The model provides a new tool to enhance general understanding of the ecology and evolution of migration.