bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptidoglycan: a post-genomic analysis
Authors: Cayrou Caroline , Henrissat Bernard , Gouret Philippe , Pontarotti Pierre , Drancourt Michel 
Published: December 2012

Abstract

Background
To derive post-genomic, neutral insight into the peptidoglycan (PG) distribution among organisms, we mined 1,644 genomes listed in the Carbohydrate-Active Enzymes database for the presence of a minimal 3-gene set that is necessary for PG metabolism. This gene set consists of one gene from the glycosyltransferase family GT28, one from family GT51 and at least one gene belonging to one of five glycoside hydrolase families (GH23, GH73, GH102, GH103 and GH104).

Results
None of the 103 Viruses or 101 Archaea examined possessed the minimal 3-gene set, but this set was detected in 1/42 of the Eukarya members (Micromonas sp., coding for GT28, GT51 and GH103) and in 1,260/1,398 (90.1%) of Bacteria, with a 100% positive predictive value for the presence of PG. Pearson correlation test showed that GT51 family genes were significantly associated with PG with a value of 0.963 and a p value less than 10-3. This result was confirmed by a phylogenetic comparative analysis showing that the GT51-encoding gene was significantly associated with PG with a Pagel’s score of 60 and 51 (percentage of error close to 0%). Phylogenetic analysis indicated that the GT51 gene history comprised eight loss and one gain events, and suggested a dynamic on-going process.

Conclusions
Genome analysis is a neutral approach to explore prospectively the presence of PG in uncultured, sequenced organisms with high predictive values.
Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.)
Authors: Zhao Yongli , Williams Roxanne , Prakash C S , He Guohao 
Published: December 2012

Abstract

Background
Date palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding.

Results
In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins.

Conclusion
Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.
Hypertriglyceridemic-waist phenotype predicts diabetes: a cohort study in Chinese urban adults
Authors: Zhang Meilin , Gao Yuxia , Chang Hong , Wang Xuan , Liu Dongmei , Zhu Zongjian , Huang Guowei 
Published: December 2012

AbstractBackgroundHypertriglycedemic-waist (HTGW) phenotype is a simple and inexpensive screening parameter to identify people at increased risk for cardiovascular disease. We evaluated whether the HTGW phenotype predicts prediabetes and diabetes in Chinese urban adults.MethodsTwo thousand nine hundred and eight (2908) subjects including 1957 men and 951 women, aged 20 years and older, free of prediabetes and diabetes at baseline were enrolled in 2008 and followed for 3 years. Meanwhile, new cases of prediabetes and diabetes were identified via annual physical examination. Cox proportional hazards models were used to assess the association of HTGW phenotype with the incidence of prediabetes and diabetes.ResultsOne thousand five hundred and thirty-three (1533) new prediabetes and 90 new diabetes cases were diagnosed during the follow-up period. The accumulated incidence of prediabetes and diabetes was 52.7% and 3.1%, respectively. Compared with the normal waist normal triglyceride (NWNT) group, those in the HTGW group had higher incidence of prediabetes and diabetes for both men and women. The hazard ratio (HR) for developing prediabetes in the presence of HTGW phenotype at baseline was 1.51 (95% confidence interval [CI] =1.04-2.19) in women, not in men (HR=1.01; 95% CI = 0.82-1.24), after adjusting for age, body mass index, systolic blood pressure, total cholesterol and low density lipoprotein-cholesterol. The HR for developing diabetes were 4.46 (95% CI = 1.88-10.60) in men and 4.64 (95% CI = 1.20-17.97) in women for people who were HTGW phenotype at baseline, after adjusting for age, body mass index, systolic blood pressure, total cholesterol and low density lipoprotein-cholesterol.ConclusionsThe HTGW phenotype can be used as a simple screening approach to predict diabetes. By using this approach, it is possible to identify individuals at high-risk for diabetes, which is of great significance in reducing the incidence of diabetes among Chinese urban adults.
Risk factors for revision of primary total hip arthroplasty: a systematic review
Authors: Prokopetz Julian JZ , Losina Elena , Bliss Robin L , Wright John , Baron John A , Katz Jeffrey N 
Published: December 2012

Abstract

Background
Numerous papers have been published examining risk factors for revision of primary total hip arthroplasty (THA), but there have been no comprehensive systematic literature reviews that summarize the most recent findings across a broad range of potential predictors.

Methods
We performed a PubMed search for papers published between January, 2000 and November, 2010 that provided data on risk factors for revision of primary THA. We collected data on revision for any reason, as well as on revision for aseptic loosening, infection, or dislocation. For each risk factor that was examined in at least three papers, we summarize the number and direction of statistically significant associations reported.

Results
Eighty-six papers were included in our review. Factors found to be associated with revision included younger age, greater comorbidity, a diagnosis of avascular necrosis (AVN) as compared to osteoarthritis (OA), low surgeon volume, and larger femoral head size. Male sex was associated with revision due to aseptic loosening and infection. Longer operating time was associated with revision due to infection. Smaller femoral head size was associated with revision due to dislocation.

Conclusions
This systematic review of literature published between 2000 and 2010 identified a range of demographic, clinical, surgical, implant, and provider variables associated with the risk of revision following primary THA. These findings can inform discussions between surgeons and patients relating to the risks and benefits of undergoing total hip arthroplasty.
Violation of ethical principles in clinical research. Influences and possible solutions for Latin America
Authors: Cornejo Moreno Borys Alberto , Gómez Arteaga Gress Marissell 
Published: December 2012

Abstract

Background
Even though we are now well into the 21st century and notwithstanding all the abuse to individuals involved in clinical studies that has been documented throughout History, fundamental ethical principles continue to be violated in one way or another.

Discussion
Here are some of the main factors that contribute to the abuse of subjects participating in clinical trials: paternalism, improper use of informed consent, lack of strict ethical supervision, pressure exerted by health institutions to increase the production of scientific material, and the absence of legislation regarding ethics in terms of health care and research. Are researchers ready to respect fundamental ethical principles in light of the ample window of information provided by individual genomes, while defending the rights of the subjects participating in clinical studies as a major priority?

Summary
As one of the possible solutions to this problem, education regarding fundamental ethical principles is suggested for participants in research studies as an initial method of cognitive training in ethics, together with the promotion of ethical behavior in order to encourage the adoption of reasonable policies in the field of values, attitudes and behavior.
Why are the neurodegenerative disease-related pathways overrepresented in primary HIV-infected peripheral blood mononuclear cells: a genome-wide perspective
Authors: Zhou Li , Conceicao Viviane , Gupta Priyanka , Saksena Nitin K 
Published: December 2012

Abstract
We demonstrate for the first time that the genome-wide profiling of HIV-infected peripheral blood mononuclear cells (PBMCs) from HIV-patients free of neurologic disease show overrepresentation of neurodegenerative pathways (Alzheimer’s, Parkinson’s, ALS, Huntington’s and Prion Disease, etc.) in genome-wide microarray analysis, which suggests that this genome-wide representation of neurodegenerative diseases-related pathways in PBMCs could possibly be a subcellular manifestation of neurologic interference by HIV. Further, the cell-tagging analysis attested this belief showing the large majority of genes tagged with cells of monocyte and macrophage lineage, which are implicated in neuronal dysfunction in both viral and non-viral neurodegenerative diseases. Together, these findings suggest that the genomic interference of HIV with neurodegenerative pathways is not by chance, but may be an early sign of HIV-mediated sub-genomic and sub-cellular manifestation of neurologic disease. Moreover, these findings signify the utility of PBMC and genome-wide mapping of the host gene expression as a powerful tool in predicting possible early events in neurologic deterioration in HIV patients.
Investigation of biomaterials by human epithelial gingiva cells: an in vitro study
Authors: Neunzehn Jörg , Lüttenberg Beate , Wiesmann Hans-Peter 
Published: December 2012

Abstract

Introduction
In modern medicine and dentistry the use of biomaterials is a fast developing field of increasing interest. Especially in dentistry the interaction between biomaterials like implant materials and the soft tissue in the oral cavity is in the focus of daily research. In this context the high importance of testing materials and their surfaces concerning their biocompatibility towards corresponding cells is very likely. For this purpose this study investigates cells derived from human gingival biopsies on different materials and surfaces.

Methods
Cells in this study were cultivated out of human biopsies by a grow out explant technique and were sub cultivated on titanium, zirconium dioxide and collagen membrane specimens. To characterise the cells on the material surfaces used in this study immunohistochemical and histological staining techniques as well as different methods of microscopy (light microscopy and SEM) were applied.

Results
With the aid of the explant technique and the chosen cell cultivation method it was possible to investigate the human gingiva derived cells on different materials. The data of the present study show that the human gingival cells attach and proliferate on all three tested materials by exhibiting characteristic gingival keratinocyte protein expression even after long periods of culture e.g. up to 70 days.

Conclusions
It could be shown that the three tested materials titanium, zirconium dioxide and collagen membrane (and their special surfaces) are good candidates for the application as materials in the dental gingival environment or, in the case of the collagen membrane as scaffold/cell-carrier for human gingival cells in tissue engineering.
On the group theoretical background of assigning stepwise mutations onto phylogenies
Authors: Fischer Mareike , Klaere Steffen , Thi Nguyen Minh Anh , Haeseler Arndt von 
Published: December 2012

AbstractBackgroundRecently one step mutation matrices were introduced to model the impact of substitutions on arbitrary branches of a phylogenetic tree on an alignment site. This concept works nicely for the four-state nucleotide alphabet and provides an efficient procedure conjectured to compute the minimal number of substitutions needed to transform one alignment site into another. The present paper delivers a proof of the validity of this algorithm. Moreover, we provide several mathematical insights into the generalization of the OSM matrix to multi-state alphabets. The construction of the OSM matrix is only possible if the matrices representing the substitution types acting on the character states and the identity matrix form a commutative group with respect to matrix multiplication. We illustrate this approach by looking at Abelian groups over twenty states and critically discuss their biological usefulness when investigating amino acids.
Open triple-branched stent graft placement for the surgical treatment of acute aortic arch dissection
Authors: Sun Xiaoning , Lu Shuyang , Yang Shouguo , Lai Hao , Chen Hao , Hong Tao , Wang Chunsheng 
Published: December 2012

Abstract

Background
The primary experience of open triple-branched stent graft placement for acute aortic arch dissection was reported.

Methods
Between January 2011 and October 2011, 13 well-selected patients (mea age, 46±8.2 years; approximate range, 30~58 years) with acute aortic arch dissection underwent open triple-branched stent graft placement for total arch reconstruction. The triple-branched stent graft was a branched 1-piece graft consisting of a self-expandable nitinol stent and polyester vascular graft fabric (Yuhengjia Sci Tech Corp Ltd, Beijing, China).During hypothermic circulatory arrest, through the transverse incision of the ascending aorta, the main graft of the triple-branched stent graft was inserted into the true lumen of the arch and proximal descending aorta, and then each sidearm graft was positioned one by one into the aortic branch. Once the main graft and sidearm grafts were properly positioned, the restraining strings were withdrawn and then the main graft and sidearm grafts were deployed. Enhanced electric beam computed tomography was performed in each patient before discharge to evaluate the postoperative time course of the residual false lumen.

Results
Open triple-branched stent graft placement was technically successful in all patients. The mean cardiopulmonary bypass time, aortic cross-clamp time and arrest time were 138.40±47.75 min, 70.60±28.94 min and 28.60±12.48 min, respectively. All patients were discharged from hospital. Their computed tomographic scans postoperatively showed that all stent grafts were fully opened and not kinked, there was no blood flow surrounding the triple-branched stent graft.

Conclusion
Open triple-branched stent graft placement is a new effective technique for total arch reconstruction in acute arch dissection.
Changes in mean scrotal circumference in performance tested Swedish beef bulls over time
Authors: Eriksson Pernilla , Lundeheim Nils , Söderquist Lennart 
Published: December 2012

AbstractBackgroundThere is a growing interest in beef cattle breeding in Sweden. The majority of the females are bred naturally, which is why it is important to choose healthy fertile bulls to obtain good reproduction and profitability. The breeding soundness evaluation includes measurement of scrotal circumference (SC). Our aim was to analyze if the SC of performance tested beef bulls has changed over the years. In total, 1332 bulls (Angus, Charolais, Hereford and Simmental) from 13 batches (1997-2010) were included in the study. Case book entries from final evaluation of the bulls, 11-13 months old, were compiled and analyzed.ResultsAn overall mean SC of 34.7 cm independent of breed and age was found which is above the set minimum level. Only eleven bulls did not reach the minimum level. An increase in SC of 0.06-0.07 cm/year was shown for all breeds. In all (1997-2010), the increase of the average SC (independent of breed and age) was approximately 1 cm. The positive trend was apparent for all breeds but only statistically significant for the Charolais breed.ConclusionsIn conclusion, our results indicated an increase in the SC over time, which improves the possibilities to obtain performance tested beef sires in Sweden with the potential for achieving better fertility results.
Development of a surgical safety checklist for the performance of radical nephrectomy and tumor thrombectomy
Authors: Joshi Shivam , Gorin Michael A , Ayyathurai Rajinikanth , Ciancio Gaetano 
Published: December 2012

Abstract

Background
The surgical management of renal cell carcinoma with invasion of the renal vein or inferior vena cava is associated with significant rates of perioperative morbidity and mortality. In this report we propose a surgical checklist aimed at reducing adverse events associated with the resection of these tumors.

Methods
This review describes the development of an evidence- and experience-based surgical checklist aimed at improving the perioperative safety of patients undergoing radical nephrectomy and tumor thrombectomy.

Results
Reducing the risk of complications during the surgical management of renal tumors with venous invasion begins with appropriate pre-operative imaging aimed at defining the cranial extent of the tumor thrombus, thus facilitating accurate preoperative planning. Other key elements of the checklist are aimed at ensuring clear and precise pre-, intra- and postoperative communication between members of the multidisciplinary-care team.

Conclusion
A standardized surgical checklist may help to increase the perioperative safety of patients undergoing radical nephrectomy and tumor thrombectomy. Future validation studies are required to determine the clinical feasibility and post-implementation safety profile of this new checklist.
Support for calcium channel gene defects in autism spectrum disorders
Authors: Lu Ake Tzu-Hui , Dai Xiaoxian , Martinez-Agosto Julian A , Cantor Rita M 
Published: December 2012

Abstract

Background
Alternation of synaptic homeostasis is a biological process whose disruption might predispose children to autism spectrum disorders (ASD). Calcium channel genes (CCG) contribute to modulating neuronal function and evidence implicating CCG in ASD has been accumulating. We conducted a targeted association analysis of CCG using existing genome-wide association study (GWAS) data and imputation methods in a combined sample of parent/affected child trios from two ASD family collections to explore this hypothesis.

Methods
A total of 2,176 single-nucleotide polymorphisms (SNP) (703 genotyped and 1,473 imputed) covering the genes that encode the α1 subunit proteins of 10 calcium channels were tested for association with ASD in a combined sample of 2,781 parent/affected child trios from 543 multiplex Caucasian ASD families from the Autism Genetics Resource Exchange (AGRE) and 1,651 multiplex and simplex Caucasian ASD families from the Autism Genome Project (AGP). SNP imputation using IMPUTE2 and a combined reference panel from the HapMap3 and the 1,000 Genomes Project increased coverage density of the CCG. Family-based association was tested using the FBAT software which controls for population stratification and accounts for the non-independence of siblings within multiplex families. The level of significance for association was set at 2.3E-05, providing a Bonferroni correction for this targeted 10-gene panel.

Results
Four SNPs in three CCGs were associated with ASD. One, rs10848653, is located in CACNA1C, a gene in which rare de novo mutations are responsible for Timothy syndrome, a Mendelian disorder that features ASD. Two others, rs198538 and rs198545, located in CACN1G, and a fourth, rs5750860, located in CACNA1I, are in CCGs that encode T-type calcium channels, genes with previous ASD associations.

Conclusions
These associations support a role for common CCG SNPs in ASD.
Rnd3 induces stress fibres in endothelial cells through RhoB
Authors: Gottesbühren Undine , Garg Ritu , Riou Philippe , McColl Brad , Brayson Daniel , Ridley Anne J. 
Published: December 2012

Summary
Rnd proteins are atypical Rho family proteins that do not hydrolyse GTP and are instead regulated by expression levels and post-translational modifications. Rnd1 and Rnd3/RhoE induce loss of actin stress fibres and cell rounding in multiple cell types, whereas responses to Rnd2 are more variable. Here we report the responses of endothelial cells to Rnd proteins. Rnd3 induces a very transient decrease in stress fibres but subsequently stimulates a strong increase in stress fibres, in contrast to the reduction observed in other cell types. Rnd2 also increases stress fibres whereas Rnd1 induces a loss of stress fibres and weakening of cell–cell junctions. Rnd3 does not act through any of its known signalling partners and does not need to associate with membranes to increase stress fibres. Instead, it acts by increasing RhoB expression, which is then required for Rnd3-induced stress fibre assembly. Rnd2 also increases RhoB levels. These data indicate that the cytoskeletal response to Rnd3 expression is dependent on cell type and context, and identify regulation of RhoB as a new mechanism for Rnd proteins to affect the actin cytoskeleton.
Human IGF1 extends lifespan and enhances resistance to Plasmodium falciparum infection in the malaria vector Anopheles stephensi
Authors: Drexler Anna , Nuss Andrew , Hauck Eric , Glennon Elizabeth , Cheung Kong , Brown Mark , Luckhart Shirley 
Published: December 2012

SUMMARY
The highly conserved insulin/insulin-like growth factor (IGF) signaling (IIS) pathway regulates metabolism, development, lifespan and immunity across a wide range of organisms. Previous studies have shown that human insulin ingested in the blood meal can activate mosquito IIS, resulting in attenuated lifespan and increased malaria parasite infection. Because human IGF1 is present at higher concentrations in blood than insulin and is functionally linked with lifespan and immune processes, we predicted that human IGF1 ingested in a blood meal would affect lifespan and malaria parasite infection in the mosquito Anopheles stephensi. Here we demonstrate that physiological levels of ingested IGF1, like insulin, can persist intact in the blood-filled midgut for up to 30 h and disseminate into the mosquito body, and that both peptides activate IIS in mosquito cells and midgut. At these same levels, ingested IGF1 alone extended average mosquito lifespan by 23% compared with controls and, more significantly, when ingested in infected blood meals, reduced the prevalence of Plasmodium falciparum-infected mosquitoes by &gt;20% and parasite load by 35–50% compared with controls. Thus, the effects of ingested IGF1 on mosquito lifespan and immunity are opposite to those of ingested insulin. These results offer the first evidence that insect cells can functionally discriminate between mammalian insulin and IGF1. Further, in light of previous success in genetically targeting IIS to alter mosquito lifespan and malaria parasite transmission, this study indicates that a more complete understanding of the IIS-activating ligands in blood can be used to optimize transgenic strategies for malaria control.