bluuebunny/crossref_metadata_2025_split huggingface dataset:
CMView: Interactive contact map visualization and analysis
Authors: Vehlow Corinna , Stehr Henning , Winkelmann Matthias , Duarte José M. , Petzold Lars , Dinse Juliane , Lappe Michael 
Published: April 2011

Abstract
Summary: Contact maps are a valuable visualization tool in structural biology. They are a convenient way to display proteins in two dimensions and to quickly identify structural features such as domain architecture, secondary structure and contact clusters. We developed a tool called CMView which integrates rich contact map analysis with 3D visualization using PyMol. Our tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods. A unique feature is the interactive refinement of structural alignments based on user selected substructures.
Availability: CMView is freely available for Linux, Windows and MacOS. The software and a comprehensive manual can be downloaded from http://www.bioinformatics.org/cmview/. The source code is licensed under the GNU General Public License.
Contact: lappe@molgen.mpg.de, stehr@molgen.mpg.de
Inferring Boolean network structure via correlation
Authors: Maucher Markus , Kracher Barbara , Kühl Michael , Kestler Hans A. 
Published: April 2011

AbstractMotivation: Accurate, context-specific regulation of gene expression is essential for all organisms. Accordingly, it is very important to understand the complex relations within cellular gene regulatory networks. A tool to describe and analyze the behavior of such networks are Boolean models. The reconstruction of a Boolean network from biological data requires identification of dependencies within the network. This task becomes increasingly computationally demanding with large amounts of data created by recent high-throughput technologies. Thus, we developed a method that is especially suited for network structure reconstruction from large-scale data. In our approach, we took advantage of the fact that a specific transcription factor often will consistently either activate or inhibit a specific target gene, and this kind of regulatory behavior can be modeled using monotone functions.Results: To detect regulatory dependencies in a network, we examined how the expression of different genes correlates to successive network states. For this purpose, we used Pearson correlation as an elementary correlation measure. Given a Boolean network containing only monotone Boolean functions, we prove that the correlation of successive states can identify the dependencies in the network. This method not only finds dependencies in randomly created artificial networks to very high percentage, but also reconstructed large fractions of both a published Escherichia coli regulatory network from simulated data and a yeast cell cycle network from real microarray data.Contact: hans.kestler@uni-ulm.deSupplementary information: Supplementary data are available at Bioinformatics online.
Correcting errors in short reads by multiple alignments
Authors: Salmela Leena , Schröder Jan 
Published: April 2011

Abstract
Motivation: Current sequencing technologies produce a large number of erroneous reads. The sequencing errors present a major challenge in utilizing the data in de novo sequencing projects as assemblers have difficulties in dealing with errors.
Results: We present Coral which corrects sequencing errors by forming multiple alignments. Unlike previous tools for error correction, Coral can utilize also bases distant from the error in the correction process because the whole read is present in the alignment. Coral is easily adjustable to reads produced by different sequencing technologies like Illumina Genome Analyzer and Roche/454 Life Sciences sequencing platforms because the sequencing error model can be defined by the user. We show that our method is able to reduce the error rate of reads more than previous methods.
Availability: The source code of Coral is freely available at http://www.cs.helsinki.fi/u/lmsalmel/coral/.
Contact: leena.salmela@cs.helsinki.fi
Alignment-free detection of local similarity among viral and bacterial genomes
Authors: Domazet-Lošo Mirjana , Haubold Bernhard 
Published: April 2011

AbstractMotivation: Bacterial and viral genomes are often affected by horizontal gene transfer observable as abrupt switching in local homology. In addition to the resulting mosaic genome structure, they frequently contain regions not found in close relatives, which may play a role in virulence mechanisms. Due to this connection to medical microbiology, there are numerous methods available to detect horizontal gene transfer. However, these are usually aimed at individual genes and viral genomes rather than the much larger bacterial genomes. Here, we propose an efficient alignment-free approach to describe the mosaic structure of viral and bacterial genomes, including their unique regions.Results: Our method is based on the lengths of exact matches between pairs of sequences. Long matches indicate close homology, short matches more distant homology or none at all. These exact match lengths can be looked up efficiently using an enhanced suffix array. Our program implementing this approach, alfy (ALignment-Free local homologY), efficiently and accurately detects the recombination break points in simulated DNA sequences and among recombinant HIV-1 strains. We also apply alfy to Escherichia coli genomes where we detect new evidence for the hypothesis that strains pathogenic in poultry can infect humans.Availability: alfy is written in standard C and its source code is available under the GNU General Public License from http://guanine.evolbio.mpg.de/alfy/. The software package also includes documentation and example data.Contact: haubold@evolbio.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.
The Unfolded Protein Response Is Triggered by a Plant Viral Movement Protein
Authors: Ye Changming , Dickman Martin B. , Whitham Steven A. , Payton Mark , Verchot Jeanmarie 
Published: April 2011

AbstractInfection with Potato virus X (PVX) in Nicotiana benthamiana plants leads to increased transcript levels of several stress-related host genes, including basic-region leucine zipper 60 (bZIP60), SKP1, ER luminal binding protein (BiP), protein disulfide isomerase (PDI), calreticulin (CRT), and calmodulin (CAM). bZIP60 is a key transcription factor that responds to endoplasmic reticulum (ER) stress and induces the expression of ER-resident chaperones (BiP, PDI, CRT, and CAM). SKP1 is a component of SCF (for SKP1-Cullin-F box protein) ubiquitin ligase complexes that target proteins for proteasomal degradation. Expression of PVX TGBp3 from a heterologous vector induces the same set of genes in N. benthamiana and Arabidopsis (Arabidopsis thaliana) leaves. Virus-induced gene silencing was employed to knock down the expression of bZIP60 and SKP1, and the number of infection foci on inoculated leaves was reduced and systemic PVX accumulation was altered. Silencing bZIP60 led to the suppression of BiP and SKP1 transcript levels, suggesting that bZIP60 might be an upstream signal transducer. Overexpression of TGBp3 led to localized necrosis, but coexpression of TGBp3 with BiP abrogated necrosis, demonstrating that the unfolded protein response alleviates ER stress-related cell death. Steady-state levels of PVX replicase and TGBp2 (which reside in the ER) proteins were unaltered by the presence of TGBp3, suggesting that TGBp3 does not contribute to their turnover. Taken together, PVX TGBp3-induced ER stress leads to up-regulation of bZIP60 and unfolded protein response-related gene expression, which may be important to regulate cellular cytotoxicity that could otherwise lead to cell death if viral proteins reach high levels in the ER.
GUN4-Porphyrin Complexes Bind the ChlH/GUN5 Subunit of Mg-Chelatase and Promote Chlorophyll Biosynthesis inArabidopsis
Authors: Adhikari Neil D. , Froehlich John E. , Strand Deserah D. , Buck Stephanie M. , Kramer David M. , Larkin Robert M. 
Published: April 2011

AbstractThe GENOMES UNCOUPLED4 (GUN4) protein stimulates chlorophyll biosynthesis by activating Mg-chelatase, the enzyme that commits protoporphyrin IX to chlorophyll biosynthesis. This stimulation depends on GUN4 binding the ChlH subunit of Mg-chelatase and the porphyrin substrate and product of Mg-chelatase. After binding porphyrins, GUN4 associates more stably with chloroplast membranes and was proposed to promote interactions between ChlH and chloroplast membranes—the site of Mg-chelatase activity. GUN4 was also proposed to attenuate the production of reactive oxygen species (ROS) by binding and shielding light-exposed porphyrins from collisions with O2. To test these proposals, we first engineered Arabidopsis thaliana plants that express only porphyrin binding–deficient forms of GUN4. Using these transgenic plants and particular mutants, we found that the porphyrin binding activity of GUN4 and Mg-chelatase contribute to the accumulation of chlorophyll, GUN4, and Mg-chelatase subunits. Also, we found that the porphyrin binding activity of GUN4 and Mg-chelatase affect the associations of GUN4 and ChlH with chloroplast membranes and have various effects on the expression of ROS-inducible genes. Based on our findings, we conclude that ChlH and GUN4 use distinct mechanisms to associate with chloroplast membranes and that mutant alleles of GUN4 and Mg-chelatase genes cause sensitivity to intense light by a mechanism that is potentially complex.
Serum fetuin‐A concentrations are elevated in subjects with impaired glucose tolerance and newly diagnosed type 2 diabetes
Authors: Ou Horng‐Yih , Yang Yi‐Ching , Wu Hung‐Tsung , Wu Jin‐Shang , Lu Feng‐Hwa , Chang Chih‐Jen 
Published: April 2011

SummaryObjective  Hepatic steatosis is associated with an increased risk of diabetes. Although the levels of serum fetuin‐A, a liver‐derived glycoprotein that impairs insulin signalling, are positively correlated with hepatic steatosis, the levels of fetuin‐A in subjects with impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and newly diagnosed type 2 diabetes (NDD) have not been established. The aim of this study is to investigate the relationship among serum fetuin‐A concentrations, IFG, IGT and NDD in Chinese subjects without nonalcoholic fatty liver disease (NAFLD).Design  A total of 360 age‐ and sex‐matched subjects with normal glucose tolerance (NGT), IFG, IGT and NDD were recruited in this case–control study.Measurements  Each subject was assessed by abdominal ultrasound to exclude the presence of NAFLD. Serum fetuin‐A concentrations were measured by enzyme‐linked immunosorbent assay and compared between NGT, IFG, IGT and NDD groups. The association with clinical and metabolic parameters was also examined.Results  Serum fetuin‐A concentrations were higher in NDD and IGT groups than NGT groups (341 ± 88, 335 ± 90, and 300 ± 75 μg/ml). In multiple linear regression analysis, IGT (P < 0·01) and NDD (P < 0·05) were the positively associated factors of serum fetuin‐A concentrations, but age (P < 0·05) was a negatively associated factor after adjusting for age, anthropometric indices, lipid profile, estimated glomerular filtration rate (eGFR), adiponectin, C‐reactive protein (CRP) and homeostasis model assessment (HOMA‐IR).Conclusions  IGT and NDD are positively associated with serum fetuin‐A concentrations in subjects without NAFLD independent of cardiometabolic risk factors.
Aircraft‐derived regional scale CO2 fluxes from vegetated drained thaw‐lake basins and interstitial tundra on the Arctic Coastal Plain of Alaska
Authors: ZULUETA ROMMEL C. , OECHEL WALTER C. , LOESCHER HENRY W. , LAWRENCE WILLIAM T. , PAW U KYAW THA 
Published: April 2011

AbstractThe landscape surface of the Barrow Peninsula of Alaska is a mosaic of small ponds, thaw lakes, different aged vegetated drained thaw‐lake basins (VDTLBs), and interstitial tundra which have been dynamically formed by both short‐ and long‐term processes. We used a combination of tower‐ and aircraft‐based eddy covariance measurements to characterize the spatial and temporal patterns of CO2, latent, and sensible heat fluxes along with MODIS NDVI, and were able to scale the aircraft‐based CO2 fluxes to the 1802 km2 Barrow Peninsula region. During typical 2006 summer conditions, the midday hourly CO2 flux over the region was −2.04 × 105 kg CO2 h−1. The CO2 fluxes among the interstitial tundra, Ancient, and Old VDTLBs, as well as between the Medium and Young VDTLBs were not significantly different. Combined, the interstitial tundra and Old and Ancient VDTLBs represent∼67% of the Barrow Peninsula surface area, accounting for ∼59% of the regional flux signal. Although the Medium and Young VDTLBs represent ∼11% of the surface area, they account for a large portion, ∼35%, of the total regional flux. The remaining ∼22% of the surface area are lakes and contributed the remaining ∼6% of the total regional flux. Previous studies treated vegetated areas of the region as a single surface type with measurements from a few study sites; doing so could underestimate the regional flux by ∼22%. Here, we demonstrate that aircraft‐based systems have the ability to cover large spatial scales while measuring the turbulent fluxes across a number of surfaces and combined with ground‐ and satellite‐based measurements provide a valuable tool for both scaling and validation of regional‐scale fluxes.
An exploratory study of religious involvement as a moderator between anxiety, depressive symptoms and quality of life outcomes of older adults
Authors: Huang Chiung‐Yu , Hsu Mei‐Chi , Chen Tai‐Jui 
Published: April 2011

Aims.  The aims of this study were to examine the relationships among religion, religious involvement, anxiety, depressive symptoms and quality of life in older adults with psychological problems and whether religious involvement moderated anxiety and depressive symptoms on the outcome of quality of life. Evidence for the mechanism through which religious involvement exerts its moderated effect on anxiety and depressive symptoms was provided.Background.  Older adults suffering from stress may consequently have anxiety or depressive symptoms and their quality of life is also influenced. The meanings of religious involvement are well documented but less is known about moderating characteristics that determine which older adults with psychological problems are most likely to benefit.Design.  A correlational, cross‐sectional study.Methods.  The study was conducted in 2007–2008 with a purposive sample of 115 older adults who were 60 years of age or older at a psychiatric centre in Taiwan. Three reliable and valid questionnaires and a demographic sheet were administered.Results.  Approximately 75% of older adults had mild to severe anxiety; 76·5% had depressive symptoms; and 67·8% of participants who had depressive symptoms also had comorbid anxiety. Findings indicated that there was a significant moderating effect for religious involvement on the quality of life outcome. Religious involvement significantly moderated anxiety and depressive symptoms on quality of life. Moreover, religious participants had a better quality of life and had lower anxiety and depressive symptoms than non‐religious participants.Conclusion.  Testing for moderating effects provides important information regarding the benefits of religious involvement. The current study reveals that religious participants have lower levels of depressive symptoms and anxiety and better quality of life than non‐religious ones. Religious involvement plays a role in buffering the relationship between psychological problems and quality of life.Relevance to clinical practice.  Nurses can encourage individuals with health problems to participate in religious involvement, which may help individuals to experience a feeling of support and enhance their quality of life.
Pharmacokinetic study of Rhizoma Curcumae Oil and Rhizoma Curcumae Oil‐β‐cyclodextrin inclusion complex in pigs after oral administration
Authors: YONG‐XUE S. , YONGJIN L. , DONGPING Z. , GANG W. , ZHICHANG L. , HAIYAN Z. 
Published: April 2011

Yong‐Xue, S., Yongjin, L., Dongping, Z., Gang, W., Zhichang, L., Haiyan, Z. Pharmacokinetic study of Rhizoma Curcumae Oil and Rhizoma Curcumae Oil‐β‐cyclodextrin inclusion complex in pigs after oral administration. J. vet. Pharmacol. Therap. 35, 47–51.Pharmacokinetics of Rhizoma Curcumae oil‐pure drug (RCO‐PD) and its β‐cyclodextrin inclusion complex (RCO‐βCD) were studied in a randomized two‐way crossover design following a single oral administration of the two formulations. Germacrone concentrations in plasma were determined by high‐performance liquid chromatography with UV detector. The concentrations vs. time data were analyzed by a noncompartmental pharmacokinetic method. The result showed that germacrone in both groups was rapidly absorbed followed by a slow elimination. The main parameters in RCO‐PD group were as follows: t1/2λz 6.63 ± 1.08 h, Cmax 2.50 ± 0.34 μg/mL, MRT 7.19 ± 0.93 h, and AUC0–∞ 13.92 ± 2.75 mg/L·h, while in RCO‐βCD group, t1/2λz 6.77 ± 0.67 h, Cmax 2.98 ± 0.24 μg/mL, MRT 8.87 ± 0.76 h, and AUC0–∞ 21.60 ± 1.95 mg/L·h, respectively. The above results indicated that Cmax, Tmax, AUC0–t, AUC0−∞, and MRT in RCO‐βCD group were significantly different from RCO‐PD group, and the relative bioavailability of RCO‐βCD group is significantly higher while compared to RCO‐PD group (F = 156%, with its 90% confidence interval of 145–169%).
A nationwide investigation on gestational age specific birthweight and mortality among Japanese twins
Authors: Tobe Ruoyan Gai , Mori Rintaro , Shinozuka Norio , Kubo Takahiko , Itabashi Kazuo 
Published: April 2011

SummaryTobe RG, Mori R, Shinozuka N, Kubo T, Itabashi K. A nationwide investigation on gestational age specific birthweight and mortality among Japanese twins. Paediatric and Perinatal Epidemiology 2011; 25: 228–235.Gestational age specific birthweight has been used as an important indicator to identify the health status of neonates and to provide appropriate neonatal care services to those at high risk. To identify the gestational age specific birthweight of twins born in secondary and tertiary hospitals in Japan and to explore factors affecting mortality, we used a nationwide obstetric database in Japan. Liveborn twins from 2001 to 2005 in the database, which was established with the national Perinatal Health Care Project, were enrolled (n = 22 240). Obstetric data from the medical records were collected and analysed. Approximately 60% of liveborn twins were delivered between weeks 33 and 38, most frequently at 36 and 37 weeks. The mean birthweight of liveborn twins was 2084 g and the mean gestational age was 34.9 weeks. Intrauterine growth differed by parity, mode of delivery, birth order, chorionicity and sex. Using logistic regression, lower gestational age, small for gestational age, monochorionic twins and vaginal delivery tended to have higher risks of mortality.
Relative and absolute addressability of global disease burden in maternal and perinatal health by investment in R&D
Authors: Fisk Nicholas M. , McKee Martin , Atun Rifat 
Published: April 2011

SummaryMaternal and perinatal disease accounts for nearly 10% of the global burden of disease, with only modest progress towards achievement of the Millennium Development Goals. Despite a favourable new global health landscape in research and development (R&D) to produce new drugs for neglected diseases, R&D investment in maternal/perinatal health remains small and non‐strategic. Investment in obstetric R&D by industry or the not‐for‐profit sector has lagged behind other specialties, with the number of registered pipeline drugs only 1–5% that for other major disease areas. Using a Delphi exercise with maternal/perinatal experts in global and translational research, we estimate that equitable pharmaceutical R&D and public sector research funding over the next 10–20 years could avert 1.1% and 1.9% of the global disease burden, respectively. In contrast, optimal uptake of existing research would prevent 3.0%, justifying the current focus on health service provision. Although R&D predominantly occurs in high‐income countries, more than 98% of the estimated reduction in disease burden in this field would be in developing countries. We conclude that better pharmaceutical and public sector R&D would prevent around 1/3 and 2/3, respectively, of the disease burden addressable by optimal uptake of existing research. Strengthening R&D may be an important complementary strategy to health service provision to address global maternal and perinatal disease burden.
The relationship between adenosine triphosphate within CD4+ T lymphocytes and acute rejection after liver transplantation
Authors: Dong Jia‐Yong , Yin Hao , Li Rui‐Dong , Ding Guo‐Shan , Fu Zhi‐Ren , Wu You‐Min , Wang Zheng‐Xin 
Published: April 2011

Dong J‐Y, Yin H, Li R‐D, Ding G‐S, Fu Z‐R, Wu Y‐M, Wang Z‐X. The relationship between adenosine triphosphate within CD4+ T lymphocytes and acute rejection after liver transplantation. Clin Transplant 2011: 25: E292–E296. © 2011 John Wiley & Sons A/S.Abstract:  Background:  There have been increasing interests in the relationship between CD4+ T lymphocytes and acute rejection (AR) in transplantation. In this study, we explore the role of CD4+ T lymphocytes after liver transplantation.Methods:  From February to October 2009, 87 patients underwent liver transplantation. They were divided into the AR group and non‐acute rejection (NAR) group, with 56 healthy individuals in the control group. Blood specimens were collected preoperatively and at one, two, and four wk postoperatively for all groups and also on the day when AR occurred and one wk after intravenous glucocorticoid therapy for the AR group. Adenosine triphosphate (ATP) levels were measured using the ImmuKnow™ test kits for immune cell functions.Results:  After transplantation, the ATP levels within CD4+ T lymphocytes were significantly elevated in the two groups when compared with the preoperative levels. It peaked in the AR group and was significantly higher than that of the NAR group (p < 0.05). By ROC curve analysis, the obvious elevation of the ATP value one wk after transplantation had better sensitivity and specificity in diagnosing the AR. The ATP sensitivity rate for early AR was 85.7% and specificity rate 80.9% when the cutoff value was 407 μg/L. The ATP value collected on the day of AR occurrence has apparently positive correlation with the rejection acting index (RAI) (p < 0.01). After the intravenous glucocorticoid therapy, all the ARs were reversed and the ATP value declined significantly compared with the control group and that on the day when AR occurred (p < 0.01).Conclusions:  During the early postoperative period (especially at first week after liver transplantation), the elevation of ATP levels within CD4+ T lymphocytes has good sensitivity and specificity in diagnosing the AR at early stage. And the degree of AR has positive relationship with ATP value. After the intravenous glucocorticoid therapy, the obvious declination of AR might be used in evaluating the effectiveness of anti‐rejection treatment.