bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment
Authors: Exarchos Konstantinos P , Exarchos Themis P , Rigas Georgios , Papaloukas Costas , Fotiadis Dimitrios I 
Published: May 2011

Abstract

Background
In peptides and proteins, only a small percentile of peptide bonds adopts the cis configuration. Especially in the case of amide peptide bonds, the amount of cis conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline cis formations (cis-nonPro).

Results
In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the cis-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with cis-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between cis-nonPro and trans-nonPro formations.

Conclusions
In terms of functional implications, we observe a significant association of cis-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.
The addition of a pH-sensitive gel improves microemulsion stability for the targeted removal of colonic ammonia
Authors: Wang Ai-Hong , Duan Zhi-Jun , Tian Ge , Lu Dan , Zhang Wen-Jun , He Gao-Hong , Fang Gui-Hua 
Published: May 2011

Abstract

Background
We prepared an oral W/O microemulsion for the removal of colonic ammonia (ME-RCA). The effect of this microemulsion was influenced by the digestion process in the gastrointestinal tract. In this paper, we aim to show that stability was improved by using a microemulsion-based gel for the removal of colonic ammonia (MBG-RCA).

Methods
MBG-RCA was prepared by adding sodium alginate to the ME-RCA. MBG-RCA and ME-RCA were passed through a simulated gastrointestinal environment, and the amount of colonic ammonia present was then determined by titration with a standard solution of hydrochloric acid. The pH of the gastrointestinal fluid was measured using a pH test paper and the size and form of the microemulsions were examined under the microscope. 18 healthy rats were randomly divided into three groups, fasted for 24 hours and allowed to drink normally. Three-way pipes were placed at the gastroduodenal junction in Group I, and at the terminal ileum in Group II. After the intragastric administration of ME-RCA, the stomach contents in Group I, the effluent from the terminal ileum in Group II and discharge from the anus in Group III were collected. The pH values of the gastrointestinal juice were measured by the pH test paper and those of the colon were determined by a universal indicator. These animal experiments were also used to test the effect of MBG-RCA.

Results
MBG-RCA showed a better removal rate of artificial colonic ammonia than ME-RCA (P < 0.05). The decrease in pH value of the artificial small intestinal fluid due to ME-RCA did not occur when MBG-RCA was used. In the simulated gastrointestinal process, MBG-RCA maintained greater stability and released the emulsion (ME-RCA) in the colonic fluid. In the gastrointestinal tract of normal SD rats, ME-RCA decreased in size and lost its stable form after entering the small intestine, while MBG-RCA remained stable and intact emulsion-drops were observed from the anus. Neither substance had any effect on the pH of the stomach or colon of normal rats (partly because normal rats were fasted for 24 hours and allowed to drink normally, which resulted in a low level of ammonia production in the colon). Unlike ME-RCA, MBG-RCA did not reduce the pH of the small intestine.

Conclusions
MBG-RCA was more stable in the gastrointestinal tract and more effective at removing colonic ammonia when a higher concentration of ammonia was present. This made it possible to achieve the targeted removal of colonic ammonia and is a promising method to prevent hepatic encephalopathy (HE) in future studies.
Age, gender and disability predict future disability in older people: the Rotterdam Study
Authors: Taş Ümit , Steyerberg Ewout W , Bierma-Zeinstra Sita MA , Hofman Albert , Koes Bart W , Verhagen Arianne P 
Published: May 2011

Abstract

Background
To develop a prediction model that predicts disability in community-dwelling older people. Insight in the predictors of disability is needed to target preventive strategies for people at increased risk.

Methods
Data were obtained from the Rotterdam Study, including subjects of 55 years and over. Subjects who had complete data for sociodemographic factors, life style variables, health conditions, disability status at baseline and complete data for disability at follow-up were included in the analysis. Disability was expressed as a Disability Index (DI) measured with the Health Assessment Questionnaire.
We used a multivariable polytomous logistic regression to derive a basic prediction model and an extended prediction model. Finally we developed readily applicable score charts for the calculation of outcome probabilities.

Results
Of the 5027 subjects included, 49% had no disability, 18% had mild disability, 16% had severe disability and 18% had deceased at follow-up after six years. The strongest predictors were age and prior disability. The contribution of other predictors was relatively small. The discriminative ability of the basic model was high; the extended model did not enhance predictive ability.

Conclusion
As prior disability status predicts future disability status, interventive strategies should be aimed at preventing disability in the first place.
Single nucleotide polymorphisms at the TRAF1/C5 locus are associated with rheumatoid arthritis in a Han Chinese population
Authors: Zhu Jing , Zhang Dinging , Wu Fengxia , He Fei , Liu Xiaoqi , Wu Lijun , Zhou Bin , Liu Jianping , Lu Fang , Liu Jian , Luo Ruijun , Long Wubin , Yang Minghui , Ma Shi , Wu Xiaodan , Shi Yi , Wu Tong , Lin Ying , Yang Jiyun , Yuan Guohua , Yang Zhenglin 
Published: May 2011

AbstractBackgroundGenetic variants inTRAF1C5andPTPN22genes have been shown to be significantly associated with arthritis rheumatoid in Caucasian populations. This study investigated the association between single nucleotide polymorphisms (SNPs) inTRAF1/C5andPTPN22genes and rheumatoid arthritis (RA) in a Han Chinese population. We genotyped SNPs rs3761847 and rs7021206 at theTRAF1/C5locus and rs2476601 SNP in thePTPN22gene in a Han Chinese cohort composed of 576 patients with RA and 689 controls. The concentrations of anti-cyclic citrullinated peptide antibodies (CCP) and rheumatoid factor (RF) were determined for all affected patients. The difference between the cases and the controls was compared usingχ2analysis.ResultsSignificant differences in SNPs rs3761847 and rs7021206 atTRAF1/C5were observed between the case and control groups in this cohort; the allelic p-value was 0.0018 with an odds ratio of 1.28 for rs3761847 and 0.005 with an odds ratio of 1.27 for rs7021206. This significant association between rs3761847 and RA was independent of the concentrations of anti-CCP and RF. No polymorphism of rs2476601 was observed in this cohort.ConclusionsWe first demonstrated that genetic variants at theTRAF1/C5locus are significantly associated with RA in Han Chinese, suggesting thatTRAF1/C5may play a role in the development of RA in this population, which expands the pathogenesis role ofTRAF1/C5in a different ethnicity.
Varicella-zoster virus infections in immunocompromised patients - a single centre 6-years analysis
Authors: Wiegering Verena , Schick Judith , Beer Meinrad , Weissbrich Benedikt , Gattenlöhner Stefan , Girschick Hermann J , Liese Johannes , Schlegel Paul G , Eyrich Matthias 
Published: May 2011

AbstractBackgroundInfection with varicella-zoster virus (VZV) contemporaneously with malignant disease or immunosuppression represents a particular challenge and requires individualized decisions and treatment. Although the increasing use of varicella-vaccines in the general population and rapid initiation of VZV-immunoglobulins and acyclovir in case of exposure has been beneficial for some patients, immunocompromised individuals are still at risk for unfavourable courses.MethodsIn this single center, 6-year analysis we review incidence, hospitalization and complication rates of VZV-infections in our center and compare them to published data. Furthermore, we report three instructive cases.ResultsHospitalization rate of referred children with VZV-infections was 45%, among these 17% with malignancies and 9% under immunosuppressive therapy. Rate of complications was not elevated in these two high-risk cohorts, but one ALL-patient died due to VZV-related complications. We report one 4-year old boy with initial diagnosis of acute lymphoblastic leukemia who showed a rapidly fatal outcome of his simultaneous varicella-infection, one 1.8-year old boy with an identical situation but a mild course of his disease, and an 8.5-year old boy with a steroid-dependent nephrotic syndrome. This boy developed severe hepatic involvement during his varicella-infection but responded to immediate withdrawl of steroids and administration of acyclovir plus single-dose cidofovir after nonresponse to acyclovir after 48 h.ConclusionOur data show that patients with malignant diseases or immunosuppressive therapy should be hospitalized and treated immediately with antiviral agents. Despite these measures the course of VZV-infections can be highly variable in these patients. We discuss aids to individual decision-making for these difficult situations.
Breast cancer screening in the Czech Republic: time trends in performance indicators during the first seven years of the organised programme
Authors: Majek Ondrej , Danes Jan , Skovajsova Miroslava , Bartonkova Helena , Buresova Lucie , Klimes Daniel , Brabec Petr , Kozeny Pavel , Dusek Ladislav 
Published: May 2011

Abstract

Background
The Czech Breast Cancer Screening Programme (CBCSP) was initiated in September 2002 by establishing a network of accredited centres. The aim of this article is to describe progress in the programme quality over time after the inception of the organised programme.

Methods
The CBCSP is monitored using an information system consisting of three principal components: 1) the national cancer registry, 2) a screening registry collecting data on all screening examinations, further assessments and final diagnoses at accredited programme centres, and 3) administrative databases of healthcare payers. Key performance indicators from the European Guidelines have been adopted for continuous monitoring.

Results
Breast cancer incidence in the Czech Republic has steadily been increasing, however with a growing proportion of less advanced stages. The mortality rate has recently stabilised. The screening registry includes 2,083,285 records on screening episodes between 2002 and 2008. In 2007-2008, 51% of eligible women aged 45-69 were screened. In 2008, the detection rates were 6.1 and 3.7 per 1,000 women in initial and subsequent screening respectively. Corresponding recall rates are 3.9% and 2.2%, however, it is necessary to pay attention to further assessment performed during the screening visits. Benign to malignant open biopsy ratio was 0.1. Of invasive cases detected in screening, 35.6% was less than 10 mm in diameter. Values of early performance indicators, as measured by both crude and standardized estimates, are generally improving and fulfil desirable targets set by European Guidelines.

Conclusions
Mammography screening in the Czech Republic underwent successful transformation from opportunistic prevention to an organised programme. Values of early indicators confirm continuous improvement in different aspects of process quality. Further stimulation of participation through invitation system is necessary to exploit the full potential of screening mammography at the population level.
Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G
Authors: Bracken Colten D , Neighbor Amber M , Lamlenn Kenneth K , Thomas Geoffrey C , Schubert Heidi L , Whitby Frank G , Howard Bruce R 
Published: May 2011

Abstract

Background
Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea.

Results
We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A.

Conclusions
The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated.
Quantum dots: a new tool for anti-malarial drug assays
Authors: Ku Min-Je , Dossin Fernando M , Choi Youngseon , Moraes Carolina B , Ryu Jiyoung , Song Rita , Freitas-Junior Lucio H 
Published: May 2011

Abstract

Background
Malaria infects over 300 million people every year and one of the major obstacles for the eradication of the disease is parasite's resistance to current chemotherapy, thus new drugs are urgently needed. Quantum dot (QD) is a fluorescent nanocrystal that has been in the spotlight as a robust tool for visualization of live cell processes in real time. Here, a simple and efficient method using QD to directly label Plasmodium falciparum-infected erythrocytes (iRBCs) was searched in order to use the QD as a probe in an anti-malarial drug-screening assay.

Methods
A range of QDs with different chemical coatings were tested for their ability to specifically bind iRBCs by immunofluorescence assay (IFA). One QD was selected and used to detect parasite growth and drug sensitivity by flow cytometry.

Results
PEGylated-cationic QD (PCQD) was found to specifically label infected erythrocytes preferentially with late stage parasites. The detection of QD-labelled infected erythrocytes by flow cytometry was sensitive enough to monitor chloroquine anti-malarial toxicity with a drug incubation period as short as 24 h (EC50 = 113nM). A comparison of our assay with another widely used anti-malarial drug screening assay, the pLDH assay, showed that PCQD-based assay had 50% improved sensitivity in detecting drug efficacy within a parasite life cycle. An excellent Z-factor of 0.8 shows that the QD assay is suitable for high-throughput screening.

Conclusions
This new assay can offer a rapid and robust platform to screen novel classes of anti-malarial drugs.
Respondent-driven sampling on the Thailand-Cambodia border. I. Can malaria cases be contained in mobile migrant workers?
Authors: Khamsiriwatchara Amnat , Wangroongsarb Piyaporn , Thwing Julie , Eliades James , Satimai Wichai , Delacollette Charles , Kaewkungwal Jaranit 
Published: May 2011

Abstract

Background
Reliable information on mobility patterns of migrants is a crucial part of the strategy to contain the spread of artemisinin-resistant malaria parasites in South-East Asia, and may also be helpful to efforts to address other public health problems for migrants and members of host communities. In order to limit the spread of malarial drug resistance, the malaria prevention and control programme will need to devise strategies to reach cross-border and mobile migrant populations.

Methodology
The Respondent-driven sampling (RDS) method was used to survey migrant workers from Cambodia and Myanmar, both registered and undocumented, in three Thai provinces on the Thailand-Cambodia border in close proximity to areas with documented artemisinin-resistant malaria parasites. 1,719 participants (828 Cambodian and 891 Myanmar migrants) were recruited. Subpopulations of migrant workers were analysed using the Thailand Ministry of Health classification based on length of residence in Thailand of greater than six months (long-term, or M1) or less than six months (short-term, or M2). Key information collected on the structured questionnaire included patterns of mobility and migration, demographic characteristics, treatment-seeking behaviours, and knowledge, perceptions, and practices about malaria.

Results
Workers from Cambodia came from provinces across Cambodia, and 22% of Cambodian M1 and 72% of Cambodian M2 migrants had been in Cambodia in the last three months. Less than 6% returned with a frequency of greater than once per month. Of migrants from Cambodia, 32% of M1 and 68% of M2 were planning to return, and named provinces across Cambodia as their likely next destinations. Most workers from Myanmar came from Mon state (86%), had never returned to Myanmar (85%), and only 4% stated plans to return.

Conclusion
Information on migratory patterns of migrants from Myanmar and Cambodia along the malaria endemic Thailand-Cambodian border within the artemisinin resistance containment zone will help target health interventions, including treatment follow-up and surveillance.
Identification of the protease cleavage sites in a reconstituted Gag polyprotein of an HERV-K(HML-2) element
Authors: George Maja , Schwecke Torsten , Beimforde Nadine , Hohn Oliver , Chudak Claudia , Zimmermann Anja , Kurth Reinhard , Naumann Dieter , Bannert Norbert 
Published: May 2011

Abstract

Background
The human genome harbors several largely preserved HERV-K(HML-2) elements. Although this retroviral family comes closest of all known HERVs to producing replication competent virions, mutations acquired during their chromosomal residence have rendered them incapable of expressing infectious particles. This also holds true for the HERV-K113 element that has conserved open reading frames (ORFs) for all its proteins in addition to a functional LTR promoter. Uncertainty concerning the localization and impact of post-insertional mutations has greatly hampered the functional characterization of these ancient retroviruses and their proteins. However, analogous to other betaretroviruses, it is known that HERV-K(HML-2) virions undergo a maturation process during or shortly after release from the host cell. During this process, the subdomains of the Gag polyproteins are released by proteolytic cleavage, although the nature of the mature HERV-K(HML-2) Gag proteins and the exact position of the cleavage sites have until now remained unknown.

Results
By aligning the amino acid sequences encoded by the gag-pro-pol ORFs of HERV-K113 with the corresponding segments from 10 other well-preserved human specific elements we identified non-synonymous post-insertional mutations that have occurred in this region of the provirus. Reversion of these mutations and a partial codon optimization facilitated the large-scale production of maturation-competent HERV-K113 virus-like particles (VLPs). The Gag subdomains of purified mature VLPs were separated by reversed-phase high-pressure liquid chromatography and initially characterized using specific antibodies. Cleavage sites were identified by mass spectrometry and N-terminal sequencing and confirmed by mutagenesis. Our results indicate that the gag gene product Pr74Gag of HERV-K(HML-2) is processed to yield p15-MA (matrix), SP1 (spacer peptide of 14 amino acids), p15, p27-CA (capsid), p10-NC (nucleocapsid) and two C-terminally encoded glutamine- and proline-rich peptides, QP1 and QP2, spanning 23 and 19 amino acids, respectively.

Conclusions
Expression of reconstituted sequences of original HERV elements is an important tool for studying fundamental aspects of the biology of these ancient viruses. The analysis of HERV-K(HML-2) Gag processing and the nature of the mature Gag proteins presented here will facilitate further studies of the discrete functions of these proteins and of their potential impact on the human host.
Changes in white adipose tissue metabolism induced by resveratrol in rats
Authors: Alberdi Goiuri , Rodríguez Víctor M , Miranda Jonatan , Macarulla María T , Arias Noemí , Andrés-Lacueva Cristina , Portillo María P 
Published: May 2011

Abstract

Background
A remarkable range of biological functions have been ascribed to resveratrol. Recently, this polyphenol has been shown to have body fat lowering effects. The aim of the present study was to assess some of the potential underlying mechanisms of action which take place in adipose tissue.

Methods
Sixteen male Sprague-Dawley rats were randomly divided into two groups: control and treated with 30 mg resveratrol/kg body weight/d. All rats were fed an obesogenic diet and after six weeks of treatment white adipose tissues were dissected. Lipoprotein lipase activity was assessed by fluorimetry, acetyl-CoA carboxylase by radiometry, and malic enzyme, glucose-6P-dehydrogenase and fatty acid synthase by spectrophotometry. Gene expression levels of acetyl-CoA carboxylase, fatty acid synthase, lipoprotein lipase, hormone-sensitive lipase, adipose triglyceride lipase, PPAR-gamma, SREBP-1c and perilipin were assessed by Real time RT-PCR. The amount of resveratrol metabolites in adipose tissue was measured by chromatography.

Results
There was no difference in the final body weight of the rats; however, adipose tissues were significantly decreased in the resveratrol-treated group. Resveratrol reduced the activity of lipogenic enzymes, as well as that of heparin-releasable lipoprotein lipase. Moreover, a significant reduction was induced by this polyphenol in hormone-sensitive lipase mRNA levels. No significant changes were observed in other genes. Total amount of resveratrol metabolites in adipose tissue was 2.66 ± 0.55 nmol/g tissue.

Conclusions
It can be proposed that the body fat-lowering effect of resveratrol is mediated, at least in part, by a reduction in fatty acid uptake from circulating triacylglycerols and also in de novo lipogenesis.