bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the evolution of the snail superfamily from metazoan wide molecular phylogenies and expression data in annelids
Authors: Kerner Pierre , Hung Johanne , Béhague Julien , Le Gouar Martine , Balavoine Guillaume , Vervoort Michel 
Published: May 2009

Abstract

Background
An important issue concerning the evolution of duplicated genes is to understand why paralogous genes are retained in a genome even though the most likely fate for a redundant duplicated gene is nonfunctionalization and thereby its elimination. Here we study a complex superfamily generated by gene duplications, the snail related genes that play key roles during animal development. We investigate the evolutionary history of these genes by genomic, phylogenetic, and expression data studies.

Results
We systematically retrieved the full complement of snail related genes in several sequenced genomes. Through phylogenetic analysis, we found that the snail superfamily is composed of three ancestral families, snail, scratchA and scratchB. Analyses of the organization of the encoded proteins point out specific molecular signatures, indicative of functional specificities for Snail, ScratchA and ScratchB proteins. We also report the presence of two snail genes in the annelid Platynereis dumerilii, which have distinct expression patterns in the developing mesoderm, nervous system, and foregut. The combined expression of these two genes is identical to that of two independently duplicated snail genes in another annelid, Capitella spI, but different aspects of the expression patterns are differentially shared among paralogs of Platynereis and Capitella.

Conclusion
Our study indicates that the snail and scratchB families have expanded through multiple independent gene duplications in the different bilaterian lineages, and highlights potential functional diversifications of Snail and ScratchB proteins following duplications, as, in several instances, paralogous proteins in a given species show different domain organizations. Comparisons of the expression pattern domains of the two Platynereis and Capitella snail paralogs provide evidence for independent subfunctionalization events which have occurred in these two species. We propose that the snail related genes may be especially prone to subfunctionalization, and this would explain why the snail superfamily underwent so many independent duplications leading to maintenance of functional paralogs.
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE
Authors: Wang Xin , Zhao Yongjun , Wong Kim , Ehlers Peter , Kohara Yuji , Jones Steven J , Marra Marco A , Holt Robert A , Moerman Donald G , Hansen Dave 
Published: May 2009

Abstract

Background
Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis and entering meiosis, progressing through the various stages of meiotic prophase, adopting either a male (sperm) or female (oocyte) fate, and completing meiosis. Additionally, many of the factors needed to drive embryogenesis are synthesized in the germ line. To increase our understanding of the genes that might be necessary for the formation and function of the germ line, we have constructed a SAGE library from hand dissected C. elegans hermaphrodite gonads.

Results
We found that 4699 genes, roughly 21% of all known C. elegans genes, are expressed in the adult hermaphrodite germ line. Ribosomal genes are highly expressed in the germ line; roughly four fold above their expression levels in the soma. We further found that 1063 of the germline-expressed genes have enriched expression in the germ line as compared to the soma. A comparison of these 1063 germline-enriched genes with a similar list of genes prepared using microarrays revealed an overlap of 460 genes, mutually reinforcing the two lists. Additionally, we identified 603 germline-enriched genes, supported by in situ expression data, which were not previously identified. We also found >4 fold enrichment for RNA binding proteins in the germ line as compared to the soma.

Conclusion
Using multiple technological platforms provides a more complete picture of global gene expression patterns. Genes involved in RNA metabolism are expressed at a significantly higher level in the germ line than the soma, suggesting a stronger reliance on RNA metabolism for control of the expression of genes in the germ line. Additionally, the number and expression level of germ line expressed genes on the X chromosome is lower than expected based on a random distribution.
Identification and target prediction of miRNAs specifically expressed in rat neural tissue
Authors: Hua You-Jia , Tang Zhong-Yi , Tu Kang , Zhu Li , Li Yi-Xue , Xie Lu , Xiao Hua-Sheng 
Published: May 2009

Abstract

Background
MicroRNAs (miRNAs) are a large group of RNAs that play important roles in regulating gene expression and protein translation. Several studies have indicated that some miRNAs are specifically expressed in human, mouse and zebrafish tissues. For example, miR-1 and miR-133 are specifically expressed in muscles. Tissue-specific miRNAs may have particular functions. Although previous studies have reported the presence of human, mouse and zebrafish tissue-specific miRNAs, there have been no detailed reports of rat tissue-specific miRNAs. In this study, Home-made rat miRNA microarrays which established in our previous study were used to investigate rat neural tissue-specific miRNAs, and mapped their target genes in rat tissues. This study will provide information for the functional analysis of these miRNAs.

Results
In order to obtain as complete a picture of specific miRNA expression in rat neural tissues as possible, customized miRNA microarrays with 152 selected miRNAs from miRBase were used to detect miRNA expression in 14 rat tissues. After a general clustering analysis, 14 rat tissues could be clearly classified into neural and non-neural tissues based on the obtained expression profiles with p values < 0.05. The results indicated that the miRNA profiles were different in neural and non-neural tissues. In total, we found 30 miRNAs that were specifically expressed in neural tissues. For example, miR-199a was specifically expressed in neural tissues. Of these, the expression patterns of four miRNAs were comparable with those of Landgraf et al., Bak et al., and Kapsimani et al. Thirty neural tissue-specific miRNAs were chosen to predict target genes. A total of 1,475 target mRNA were predicted based on the intersection of three public databases, and target mRNA's pathway, function, and regulatory network analysis were performed. We focused on target enrichments of the dorsal root ganglion (DRG) and olfactory bulb. There were four Gene Ontology (GO) functions and five KEGG pathways significantly enriched in DRG. Only one GO function was significantly enriched in the olfactory bulb. These targets are all predictions and have not been experimentally validated.

Conclusion
Our work provides a global view of rat neural tissue-specific miRNA profiles and a target map of miRNAs, which is expected to contribute to future investigations of miRNA regulatory mechanisms in neural systems.
A probable aculeacin A acylase from the Ralstonia solanacearum GMI1000 is N-acyl-homoserine lactone acylase with quorum-quenching activity
Authors: Chen Chin-Nung , Chen Chii-Jaan , Liao Chen-Ting , Lee Chia-Yin 
Published: May 2009

Abstract

Background
The infection and virulence functions of diverse plant and animal pathogens that possess quorum sensing systems are regulated by N-acylhomoserine lactones (AHLs) acting as signal molecules. AHL-acylase is a quorum quenching enzyme and degrades AHLs by removing the fatty acid side chain from the homoserine lactone ring of AHLs. This blocks AHL accumulation and pathogenic phenotypes in quorum sensing bacteria.

Results
An aac gene of undemonstrated function from Ralstonia solanacearum GMI1000 was cloned, expressed in Escherichia coli; it inactivated four AHLs that were tested. The sequence of the 795 amino acid polypeptide was considerably similar to the AHL-acylase from Ralstonia sp. XJ12B with 83% identity match and shared 39% identity with an aculeacin A acylase precursor from the gram-positive actinomycete Actinoplanes utahensis. Aculeacin A is a neutral lipopeptide antibiotic and an antifungal drug. An electrospray ionisation mass spectrometry (ESI-MS) analysis verified that Aac hydrolysed the amide bond of AHL, releasing homoserine lactone and the corresponding fatty acids. However, ESI-MS analysis demonstrated that the Aac could not catalyze the hydrolysis of the palmitoyl moiety of the aculeacin A. Moreover, the results of MIC test of aculeacin A suggest that Aac could not deacylate aculeacin A. The specificity of Aac for AHLs showed a greater preference for long acyl chains than for short acyl chains. Heterologous expression of the aac gene in Chromobacterium violaceum CV026 effectively inhibited violacein and chitinase activity, both of which were regulated by the quorum-sensing mechanism. These results indicated that Aac could control AHL-dependent pathogenicity.

Conclusion
This is the first study to find an AHL-acylase in a phytopathogen. Our data provide direct evidence that the functioning of the aac gene (NP520668) of R. solanacearum GMI1000 is via AHL-acylase and not via aculeacin A acylase. Since Aac is a therapeutic potential quorum-quenching agent, its further biotechnological applications in agriculture, clinical and bio-industrial fields should be evaluated in the near future.
Expression patterns of Neil3 during embryonic brain development and neoplasia
Authors: Hildrestrand Gunn A , Neurauter Christine G , Diep Dzung B , Castellanos Cesilie G , Krauss Stefan , Bjørås Magnar , Luna Luisa 
Published: May 2009

Abstract

Background
The base excision repair pathway is responsible for repairing small DNA base lesions caused by endogenous and exogenous damaging agents. Repair is initiated by DNA glycosylases that recognize and remove the lesions. NEIL3 is one of 11 mammalian DNA glycosylases identified to date and it was discovered on the basis of sequence homology to the E. coli Fpg and Nei glycosylases. Difficulties in purifying the protein have limited its biochemical characterization and in contrast to the other glycosylases, its function remains unclear.

Results
In this study we describe the expression pattern of Neil3 during mouse embryonic development with special focus on brain development. We have also looked at the expression of NEIL3 in several normal and tumor tissues. Quantitative real-time PCR and in situ hybridization revealed that Neil3 was highly expressed at embryonic days 12–13, when neurogenesis starts. The expression decreased during development and in the adult brain,Neil3 could not be detected in any of the brain areas examined by quantitative real-time PCR. During embryogenesis and in newborn mice specific expression was observed in areas known to harbour neural stem and progenitor cells such as the subventricular zone and the dentate gyrus. Finally, NEIL3 expression was higher in tumors compared to normal tissues, except for testis and pancreas.

Conclusion
Our findings indicate that mammalian NEIL3 is specifically expressed in brain areas where neurogenesis takes place during development and that its expression is tightly regulated both temporally and spatially. In addition, NEIL3 seems to be upregulated in tumor tissues compared to normal tissues. Altogether, mammalian NEIL3 seems to be highly expressed in cells with high proliferative potential.
Seroprevalence of Immunoglobulin G antibodies against pertussis toxin among asymptomatic medical students in the west of Iran: a cross sectional study
Authors: Hashemi Seyyed Hamid , Ranjbar Mitra , Hajilooi Mehrdad , Seif-Rabiei Mohammad-Ali , Bolandi Mahnaz , Moghimi Javad 
Published: May 2009

AbstractBackgroundPertussis is a highly communicable, vaccine-preventable respiratory infection. Immune response against this disease can be induced by infection or vaccination. Protection after childhood vaccination is minimal after ten years. Our aim was to assess pertussis immunity state in a population of healthy young medical students.MethodsIn this seroepidemiological survey, blood samples were obtained from 163 first-year medical students in Hamedan University, Iran. Serum level of IgG against pertussis toxin (IgG-PT) was measured by Enzyme-Linked Immunosorbent Assay (ELISA) method. For qualitative assessment, IgG-PT levels more than 24 unit (U)/ml were considered positive. Data was analysed qualitatively and quantitatively considering gender and age groups.ResultsThere were 83 males and 80 females, with a mean age of 19.48 years, Prevalence of IgG-PT was 47.6% with mean level of 71.7 u/ml (95% confidence interval: 68.1–75.3). No statistically significant difference was observed with respect to sero-positivity of IgG-PT between males and females (45 cases (54%) vs. 34 cases (42%); P = 0.06). Mean IgG-PT levels in males and females were 84 U/ml and 58.8 U/ml, respectively (P = 0.91).ConclusionA considerable proportion of our study population with a positive history of childhood vaccination for pertussis was not serologically immune to pertussis. A booster dose of acellular pertussis vaccine may be indicated in Iranian, medical students regarding their serologic conditions and outstanding role in health care systems.
Caesarean section in four South East Asian countries: reasons for, rates, associated care practices and health outcomes
Authors: Festin Mario R , Laopaiboon Malinee , Pattanittum Porjai , Ewens Melissa R , Henderson-Smart David J , Crowther Caroline A ,   The SEA-ORCHID Study Group
Published: May 2009

Abstract

Background
Caesarean section is a commonly performed operation on women that is globally increasing in prevalence each year. There is a large variation in the rates of caesarean, both in high and low income countries, as well as between different institutions within these countries. This audit aimed to report rates and reasons for caesarean and associated clinical care practices amongst nine hospitals in the four South East Asian countries participating in the South East Asia-Optimising Reproductive and Child Health in Developing countries (SEA-ORCHID) project.

Methods
Data on caesarean rates, care practices and health outcomes were collected from the medical records of the 9550 women and their 9665 infants admitted to the nine participating hospitals across South East Asia between January and December 2005.

Results
Overall 27% of women had a caesarean section, with rates varying from 19% to 35% between countries and 12% to 39% between hospitals within countries. The most common indications for caesarean were previous caesarean (7.0%), cephalopelvic disproportion (6.3%), malpresentation (4.7%) and fetal distress (3.3%). Neonatal resuscitation rates ranged from 7% to 60% between countries. Prophylactic antibiotics were almost universally given but variations in timing occurred between countries and between hospitals within countries.

Conclusion
Rates and reasons for caesarean section and associated clinical care practices and health outcomes varied widely between the four South East Asian countries.
Rasch model analysis of the Depression, Anxiety and Stress Scales (DASS)
Authors: Shea Tracey L , Tennant Alan , Pallant Julie F 
Published: May 2009

Abstract

Background
There is a growing awareness of the need for easily administered, psychometrically sound screening tools to identify individuals with elevated levels of psychological distress. Although support has been found for the psychometric properties of the Depression, Anxiety and Stress Scales (DASS) using classical test theory approaches it has not been subjected to Rasch analysis. The aim of this study was to use Rasch analysis to assess the psychometric properties of the DASS-21 scales, using two different administration modes.

Methods
The DASS-21 was administered to 420 participants with half the sample responding to a web-based version and the other half completing a traditional pencil-and-paper version. Conformity of DASS-21 scales to a Rasch partial credit model was assessed using the RUMM2020 software.

Results
To achieve adequate model fit it was necessary to remove one item from each of the DASS-21 subscales. The reduced scales showed adequate internal consistency reliability, unidimensionality and freedom from differential item functioning for sex, age and mode of administration. Analysis of all DASS-21 items combined did not support its use as a measure of general psychological distress. A scale combining the anxiety and stress items showed satisfactory fit to the Rasch model after removal of three items.

Conclusion
The results provide support for the measurement properties, internal consistency reliability, and unidimensionality of three slightly modified DASS-21 scales, across two different administration methods. The further use of Rasch analysis on the DASS-21 in larger and broader samples is recommended to confirm the findings of the current study.
Evaluation of uptake and attitude to voluntary counseling and testing among health care professional students in Kilimanjaro region, Tanzania
Authors: Charles Mgosha P , Kweka Eliningaya J , Mahande Aneth M , Barongo Longin R , Shekalaghe Seif , Nkya Hassan M , Lowassa Asanterabi , Mahande Michael J 
Published: May 2009

Abstract

Background
Voluntary counseling and testing (VCT) is a corner stone for successful implementation of prevention, care and support services among HIV negative and positive individuals. VCT is also perceived to be an effective strategy in risk reduction among sexually active young people.. This study aimed to assess the acceptability of VCT and its actual uptake among young health care professional students at KCM College of Tumaini University and Allied health schools.

Methods
This was a cross-sectional study. A structured questionnaire was used among health care professional students aged 18–25 years who were enrolled in degrees, diplomas and certificates courses at Kilimanjaro Christian Medical College and all other Allied health schools

Results
A total of 309 students were recruited, among these 197 (63.8%) were females. All respondents were aware of the benefits of VCT. Only 107 (34.6%) of students have had VCT done previously. About 59 (19.1%) of the students had negative for health care professional to attend VCT. Risk perception among the students was low (37.2%) even though they were found to have higher risk behaviors that predispose them to get HIV infection.

Conclusion
Awareness of VCT services and willingness to test is high among students; however its uptake is low. In order to promote these services, a comprehensive training module on VCT needs to be included in their training curricula. In particular, more emphasis should focus on the benefits of VCT and to help the students to internalize the risk of HIV so that they can take preventive measures.
Education level and physical functional limitations among Japanese community residents-gender difference in prognosis from stroke
Authors: Honjo Kaori , Iso Hiroyasu , Ikeda Ai , Inoue Manami , Tsugane Shoichiro ,   The JPHC Study Group
Published: May 2009

Abstract

Background
Little research has been conducted to examine the relationship between education level and functional limitations among Japanese community residents. We sought to examine the association between education level and physical functional limitations among Japanese men and women, and whether that association was modified by gender and history of stroke.

Methods
We examined prevalence of physical functional limitation by educational level using the data from a total of 29,134 Japanese men and women aged 50–69 years living in communities in 2000. The information of educational level (junior high school graduates, senior high school graduates, college and/or higher education) and physical functional limitations (no need for assistance, need for assistance when going outdoors, and need for assistance to carry out indoor activities) were obtained by self-administrated questionnaire.

Results
The proportions of the subjects reported their highest level of schooling were 48% for junior high school, 39% for high school, and 13% for college. Three hundred and twenty eight subjects (1% of total subjects) reported having some physical functional limitations. Multinomial logistic regression analyses showed that the odds ratio of needing assistance to carry out indoor activities were 4.84(95%CI:3.61,6.50) for lowest education level group and 2.21(95%CI:1.00,4.86) for middle education level group compared to highest education level group. The corresponding odds ratios of needing assistance when going outdoors were 2.36(95%CI: 2.03,2.72) and 1.08(95%CI:0.73,1.60), respectively. Further, the significant excess prevalence of having functional limitations associated with the low education level was identified for men regardless of history of stroke and for women without history of stroke.

Conclusion
Low education level was associated with the higher prevalence of physical functional limitations for both genders. That association among persons with history of stroke was observed for men but not for women probably due to gender differences in stroke subtypes and social support.
Negative pressure wound therapy for soft tissue injuries around the foot and ankle
Authors: Lee Hyun-Joo , Kim Joon-Woo , Oh Chang-Wug , Min Woo-Kie , Shon Oog-Jin , Oh Jong-Keon , Park Byung-Chul , Ihn Joo-Chul 
Published: May 2009

Abstract

Background
This study was performed to evaluate the results of negative pressure wound therapy (NPWT) in patients with open wounds in the foot and ankle region.

Materials and methods
Using a NPWT device, 16 patients were prospectively treated for soft tissue injuries around the foot and ankle. Mean patient age was 32.8 years (range, 3–67 years). All patients had suffered an acute trauma, due to a traffic accident, a fall, or a crush injury, and all had wounds with underlying tendon or bone exposure. Necrotic tissues were debrided before applying NPWT. Dressings were changed every 3 or 4 days and treatment was continued for 18.4 days on average (range, 11–29 days).

Results
Exposed tendons and bone were successfully covered with healthy granulation tissue in all cases except one. The sizes of soft tissue defects reduced from 56.4 cm2 to 42.9 cm2 after NPWT (mean decrease of 24%). In 15 of the 16 cases, coverage with granulation tissue was achieved and followed by a skin graft. A free flap was needed to cover exposed bone and tendon in one case. No major complication occurred that was directly attributable to treatment. In terms of minor complications, two patients suffered scar contracture of grafted skin.

Conclusion
NPWT was found to facilitate the rapid formation of healthy granulation tissue on open wounds in the foot and ankle region, and thus, to shorten healing time and minimize secondary soft tissue defect coverage procedures.