bluuebunny/crossref_metadata_2025_split huggingface dataset:
Case‐Matched Comparison of the Retroperitoneal Approach With Laparotomy for Necrotizing Pancreatitis
Authors: van Santvoort Hjalmar C. , Besselink Marc G. , Bollen Thomas L. , Buskens Erik , van Ramshorst Bert , Gooszen Hein G. ,   Dutch Acute Pancreatitis Study Group
Published: June 2007

AbstractBackgroundMinimally invasive necrosectomy through a retroperitoneal approach is gaining popularity for the treatment of necrotizing pancreatitis. There is, however, no substantial evidence from comparative studies in favor of this technique over laparotomy. The aim of this case‐matched study was to perform the first head‐to‐head comparison of necrosectomy by the retroperitoneal approach with laparotomy in patients with necrotizing pancreatitis.MethodsBetween 2001 and 2005, there were 15 of 841 consecutive acute pancreatitis patients who underwent necrosectomy by the retroperitoneal approach using a small flank incision. These patients were matched for the presence of preoperative organ failure, status of infection, timing of surgery, age, and computed tomography severity index score with 15 of 46 patients treated with necrosectomy by laparotomy and continuous postoperative lavage (CPL).MethodsIn addition to all matched preoperative characteristics, there were no significant differences in sex, preoperative intensive care unit (ICU) admission, preoperative ICU stay, preoperative APACHE‐II scores, and preoperative multiple organ failure (MOF). Postoperative complications requiring reintervention occurred in six patients in each group (p = 1.000). Postoperative new‐onset MOF occurred in 10 patients in the laparotomy/CPL group versus 2 patients in the retroperitoneal approach group (p = 0.008). Six patients died in the laparotomy/CPL group versus 1 patient in the retroperitoneal approach group (p = 0.080).ConclusionsThe less postoperative organ failure and the trend toward lower mortality may point to a benefit of the retroperitoneal approach over laparotomy. A randomized controlled design is, however, still required to answer definitively the question of which operative technique is preferably for patients with (infected) necrotizing pancreatitis.
Spawning sockeye salmon fossils in Pleistocene lake beds of Skokomish Valley, Washington
Authors: Smith Gerald R. , Montgomery David R. , Peterson N. Phil , Crowley Bruce 
Published: June 2007

AbstractAn assemblage of fossil sockeye salmon was discovered in Pleistocene lake sediments along the South Fork Skokomish River, Olympic Peninsula, Washington. The fossils were abundant near the head of a former glacial lake at 115 m elevation. Large adult salmon are concentrated in a sequence of death assemblages that include individuals with enlarged breeding teeth and worn caudal fins indicating migration, nest digging, and spawning prior to death. The specimens were 4 yr old and 45–70 cm in total length, similar in size to modern sockeye salmon, not landlocked kokanee. The fossils possess most of the characteristics of sockeye salmon, Oncorhynchus nerka, but with several minor traits suggestive of pink salmon, O. gorbuscha. This suggests the degree of divergence of these species at about 1 million yr ago, when geological evidence indicates the salmon were deposited at the head of a proglacial lake impounded by the Salmon Springs advance of the Puget lobe ice sheet. Surficial geology and topography record a complicated history of glacial damming and river diversion that implies incision of the modern gorge of the South Fork Skokomish River after deposition of the fossil-bearing sediments.
A Content-Centric Organization of the Genetic Code
Authors: Yu Jun 
Published: June 2007

Abstract
The codon table for the canonical genetic code can be rearranged in such a way that the code is divided into four quarters and two halves according to the variability of their GC and purine contents, respectively. For prokaryotic genomes, when the genomic GC content increases, their amino acid contents tend to be restricted to the GC-rich quarter and the purine-content insensitive half, where all codons are fourfold degenerate and relatively mutation-tolerant. Conversely, when the genomic GC content decreases, most of the codons retract to the AU-rich quarter and the purine-content sensitive half; most of the codons not only remain encoding physicochemically diversified amino acids but also vary when transversion (between purine and pyrimidine) happens. Amino acids with sixfold-degenerate codons are distributed into all four quarters and across the two halves; their fourfold-degenerate codons are all partitioned into the purine-insensitive half in favorite of robustness against mutations. The features manifested in the rearranged codon table explain most of the intrinsic relationship between protein coding sequences (the informational content) and amino acid compositions (the functional content). The renovated codon table is useful in predicting abundant amino acids and positioning the amino acids with related or distinct physicochemical properties.
A Brief Review of Short Tandem Repeat Mutation
Authors: Fan Hao , Chu Jia-You 
Published: June 2007

Abstract
Short tandem repeats (STRs) are short tandemly repeated DNA sequences that involve a repetitive unit of 1–6 bp. Because of their polymorphisms and high mutation rates, STRs are widely used in biological research. Strand-slippage replication is the predominant mutation mechanism of STRs, and the stepwise mutation model is regarded as the main mutation model. STR mutation rates can be influenced by many factors. Moreover, some trinucleotide repeats are associated with human neurodegenerative diseases. In order to deepen our knowledge of these diseases and broaden STR application, it is essential to understand the STR mutation process in detail. In this review, we focus on the current known information about STR mutation.
Alternative Splicing and Expression Profile Analysis of Expressed Sequence Tags in Domestic Pig
Authors: Zhang Liang , Tao Lin , Ye Lin , He Ling , Zhu Yuan-Zhong , Zhu Yue-Dong , Zhou Yan 
Published: June 2007

Abstract
Domestic pig (Sus scrofa domestica) is one of the most important mammals to humans. Alternative splicing is a cellular mechanism in eukaryotes that greatly increases the diversity of gene products. Expression sequence tags (ESTs) have been widely used for gene discovery, expression profile analysis, and alternative splicing detection. In this study, a total of 712,905 ESTs extracted from 101 different non-normalized EST libraries of the domestic pig were analyzed. These EST libraries cover the nervous system, digestive system, immune system, and meat production related tissues from embryo, newborn, and adult pigs, making contributions to the analysis of alternative splicing variants as well as expression profiles in various stages of tissues. A modified approach was designed to cluster and assemble large EST datasets, aiming to detect alternative splicing together with EST abundance of each splicing variant. Much efforts were made to classify alternative splicing into different types and apply different filters to each type to get more reliable results. Finally, a total of 1,223 genes with average 2.8 splicing variants were detected among 16,540 unique genes. The overview of expression profiles would change when we take alternative splicing into account.
Comparative Analysis of the 100 kb Region Containing the Pi-k
h Locus Between Indica and Japonica Rice Lines
Authors: Kumar S.P. , Dalal V. , Singh N.K. , Sharma T.R. 
Published: June 2007

Abstract
We have recently cloned a pathogen inducible blast resistance gene Pi-kh from the indica rice line Tetep using a positional cloning approach. In this study, we carried out structural organization analysis of the Pi-kh locus in both indica and japonica rice lines. A 100 kb region containing 50 kb upstream and 50 kb downstream sequences flanking to the Pi-kh locus was selected for the investigation. A total of 16 genes in indica and 15 genes in japonica were predicted and annotated in this region. The average GC content of indica and japonica genes in this region was 53.15% and 49.3%, respectively. Both indica and japonica sequences were polymorphic for simple sequence repeats having mono-, di-, tri-, tetra-, and pentanucleotides. Sequence analysis of the specific blast resistant Pi-kh allele of Tetep and the susceptible Pi-kh allele of the japonica rice line Nipponbare showed differences in the number and distribution of motifs involved in phosphorylation, resulting in the resistance phenotype in Tetep.
Generation of Synthetic Transcriptome Data with Defined Statistical Properties for the Development and Testing of New Analysis Methods
Authors: Brysbaert Guillaume , Noth Sebastian , Benecke Arndt 
Published: June 2007

Abstract
We have previously developed a combined signal/variance distribution model that accounts for the particular statistical properties of datasets generated on the Applied Biosystems AB1700 transcriptome system. Here we show that this model can be efficiently used to generate synthetic datasets with statistical properties virtually identical to those of the actual data by aid of the JAVA application ace.map creator 1.0 that we have developed. The fundamentally different structure of AB1700 transcriptome profiles requires re-evaluation, adaptation, or even redevelopment of many of the standard microarray analysis methods in order to avoid misinterpretation of the data on the one hand, and to draw full benefit from their increased specificity and sensitivity on the other hand. Our composite data model and the ace.map creator 1.0 application thereby not only present proof of the correctness of our parameter estimation, but also provide a tool for the generation of synthetic test data that will be useful for further development and testing of analysis methods.
Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics
Authors: Tamaki Satoshi , Arakawa Kazuharu , Kono Nobuaki , Tomita Masaru 
Published: June 2007

Abstract
Annotations of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http://restauro-g.iab.keio.ac.jp/ under the GNU General Public License.
Genetic Polymorphisms of Nine X-STR Loci in Four Population Groups from Inner Mongolia, China
Authors: Hou Qiao-Fang , Yu Bin , Li Sheng-Bin 
Published: June 2007

Abstract
Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance betweent Mongol and Han (Xi’an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.
Genetic Analysis of 15 STR Loci in Chinese Han Population from West China
Authors: Deng Ya-Jun , Yan Jiang-Wei , Yu Xiao-Guang , Li Yuan-Zhe , Mu Hao-Fang , Huang Yan-Qing , Shi Xiao-Tie , Sun Wei-Min 
Published: June 2007

Abstract
Allele frequencies for 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were obtained from 7,636 unrelated individuals of Chinese Han population living in Qinghai and Chongqing, China. Totally 206 alleles were observed, with the corresponding allele frequencies ranging from 0.0001–0.4982. Chi-square test showed that all of the STR loci agreed with the Hardy-Weinberg equilibrium. We also compared our data with previously published population data of other ethnics or areas. The results are valuable for human identification and paternity testing in Chinese Han population.
Genetic structure analyses of different populations of grass carp (Ctenopharyngodon idella) using the TRAP technique
Authors: Zhi-Wei Zhang , Zhe-Ming Cao , Jing-Song Zhou , Ting-Ting Wu 
Published: June 2007

AbstractTarget region amplified polymorphism (TRAP) was used to compare genetic structures among three populations of grass carp (Ctenopharyngodon idella) – one wild and two cultured populations. Seven out of 15 primer combinations produced good amplification patterns and provided 103 amplified loci from the three populations. Numbers of polymorphic loci in the wild population were higher, indicating a decrease in genetic polymorphism in the two cultured populations. Compared with the wild population, only 39.98% loci gene frequency remained unchanged in the cultured samples, showing a genetic structure change in cultured populations. The genetic distances between wild and cultured populations were 0.0421 and 0.0809. With primer combination Ga5-800-E5, we detected a region in the electrophoretic pattern in which the number of amplified loci apparently decreased in cultured populations. These results establish a good scientific basis for developing molecular markers that can help in distinguishing wild from cultured populations.
Transcription factor AP‐1, and the role of Fra‐2
Authors: FOLETTA VICTORIA C 
Published: June 2007

SummaryTranscription factors function to regulate gene transcription. They may be constitutively expressed or may only be activated during specific situations. Activator protein‐1 (AP‐1) is an inducible transcription factor, and is comprised of multiple protein complexes that include the gene products of the fos and jun gene families. Numerous cellular and viral genes contain AP‐1 binding sites within their promoters and, accordingly, AP‐1 has been shown to play a role in the regulation of both basal and inducible transcription of these genes, fos‐related antigen‐2 (fra‐2) has been found to have both similar and unique properties to that of other fos gene members in terms of its regulation and expression. The analysis and determination of the function of Fra‐2 will provide further information on the role of AP‐1.
Gonadotropin‐releasing hormone agonist influences absolute levels of lymphocyte subsets in vivo in male mice
Authors: RAO LV , CLEVELAND RP , KIMMEL RJ , ATAYA KM 
Published: June 2007

SummaryOur earlier studies have demonstrated that gonadotropin‐releasing hormone (GnRH) agonists suppress immune system function in female mice. No systematic studies regarding the effect of gender on immune system function following GnRH agonist treatment, however, have been reported. This study, therefore, investigated sequential changes in lymphocyte subsets in 3‐ and 10‐week‐old male mice following agonist or placebo administration. Changes in immunophenotypic expression of lymphocytes from thymus, bone marrow, spleen, and blood were analysed at periodic intervals. Upon agonist administration, plasma testosterone levels were significantly increased in pre‐pubertal mice, but were significantly decreased in post‐pubertal males. Absolute thymic weights, thymocytes and T subsets were significantly increased from the third week regardless of gonadal status. Blood lymphocyte subsets showed a decreasing trend after agonist administration in pre‐pubertal males, whereas no differences were observed in post‐pubertal males. No significant differences were observed in spleen cells after agonist administration. These studies, together with earlier observations in female mice indicate that GnRH agonist effects on the immune system, are independent of steroid hormone levels. In contrast to suppressive effects in females, GnRH agonists induce no change or ultimately enhanced lymphocyte counts in males, indicating differential effects on the immune system between males and females. This may have important implications for the treatment of various diseases.
Control of scarring in adult wounds using antisense transforming growth factor‐β1 oligodeoxynucleotides
Authors: CHOI BYUNG‐MIN , KWAK HYUN‐JEONG , JUN CHANG‐DUK , PARK SEOK‐DON , KIM KI‐YOUNG , KIM HYUNG‐RYUN , CHUNG HUN‐TAEG 
Published: June 2007

SummaryAdult wounds heal with scar formation, whereas fetal wounds heal without scarring and with a lesser inflammatory and cytokine response. We reasoned that a strategy employing antisense oligodeoxynucleotides (ODN) complementary to transforming growth factor (TGF)‐β1 mRNA might decrease the scarring of dermal wounds in the mouse. To evaluate this concept, we tested the effects of antisense ODN targeted to TGF‐β1 mRNA by topical application of the ODN on the skin wound. Phosphorothioation of ODN to retard their degradation. When antisense TGF‐βl ODN were applied on the wound site, there was a marked reduction of scarring compared with a control wound site. This effect of antisense TGF‐β1 ODN on scar formation was associated with decreased expression of the TGF‐β1 gene. However, sense TGF‐pl ODN had no effect on the expression of the TGF‐β1 gene. In addition, control wounds healed with excessive fibrosis compared with the antisense‐treated wounds. In conclusion, our results indicate that antisense TGF‐β1 ODN could be used for ameliorating scar formation during wound healing.
Molecular cloning and characterization of tumour necrosis factor alpha (TNF‐α) from the Australian common brushtail possum, Trichosurus vulpecula
Authors: WEDLOCK D NEIL , ALDWELL FRANK E , BUDDLE BRYCE M 
Published: June 2007

SummaryImmune responses in the Australian common brushtail possum (Trichosurus vulpecula) and in particular the role of cytokines are poorly understood. We have undertaken to isolate cytokine genes using reverse transcriptase‐polymerase chain reaction (RT‐PCR) and in this study describe the molecular cloning of TNF‐α. Primers were designed from consensus sequences at the N‐terminus end of eutherian mammalian TNF‐α and the possum cDNA, derived from spleen RNA, identified by RT‐PCR. The complete cDNA encoding possum TNF‐α was amplified from lymphocyte RNA by 5′ and 3′ rapid amplification of cDNA ends (RACE). The nucleotide sequence of the protein coding region of this cDNA shared 66‐69% identity with other mammalian TNF‐α genes. The predicted protein of 233 amino acids shared 56‐58% identity with eutherian mammalian TNF‐α. Possum TNF‐α was expressed in both Saceharomyces cerevisiae and Escherichia coli by constructing expression plasmid derivatives of the vectors pYES2 and pGEX‐2T respectively. Cell extracts prepared from transformants and the purified GST/TNF‐α fusion protein exhibited cytotoxic activity on the TNF‐α‐sensitive murine fibroblast L929 cells and stimulated proliferation of possum thymocyte cells. The induction of possum TNF‐α mRNA in alveolar macrophages was analysed by RT‐PCR using possumspecific TNF‐α primers. Macrophages cultured in the presence of LPS showed enhanced transcription of TNF‐α mRNA. This is the first report of the cloning and sequence analysis of the cDNA encoding a marsupial cytokine gene.
Uncontrolled triggering of programmed cell death (apoptosis) in haematopoietic stem cells: A new hypothesis for the pathogenesis of aplastic anaemia
Authors: LAVEDER FRANCESCO , MARCOLONGO RENZO 
Published: June 2007

SummaryThe cause of bone marrow failure in aplastic anaemia (AA) is still unknown: however, it is clear that acquired AA is a heterogeneous disease including basically different pathophysiological conditions. Causative agents, clinically associated with AA, possibly exert their action through restricted pathways. Some theoretical and experimental data show that programmed cell death (PCD) or apoptosis is physiologically important in normal haematopoiesis and could be involved in the pathophysiological events responsible for the development of AA. Therefore, it is intriguing to hypothesize that the pathogenetic mechanism underlying most cases of acquired AA could be represented by an excessive and/or uncontrolled triggering of PCD in haematopoietic stem cells. Investigations to test this hypothesis are proposed.
Antigen presentation in allergic sensitization
Authors: MUDDE GEERT C , REISCHL ILONA G , CORVAIA NATHALIE , HREN ANDREA , POELLABAUER EVA‐MARIA 
Published: June 2007

SummaryIgE antibodies, when cross‐linked by allergen on the surface of effector cells such as mast cells and basophils, are known to be directly responsible for immediate type hypersensitivity reactions. In addition, IgE may be involved in other, indirect, mechanisms, fundamental to the pathogenesis of allergic diseases, such as enhancement of the antigen capturing capacity of antigen presenting cells. IgE mediated antigen presentation could lead to a continuous activation of the immune system by very low concentrations of allergen. As a result, Th2 cell populations may expand and may induce more B cells to switch to IgE production. Subsequently, the overproduction of IgE and Th2 cells in a patient may explain the clinical observation that certain allergic patients deteriorate from sensitivity to a single group of allergens to sensitivity to multiple groups of allergens. Therefore, control of IgE production is not only important for the treatment of allergic symptoms, but may also regulate deterioration of allergy via the mechanism of CD23/IgE mediated allergen presentation by native B cells. The role that monocytes, which have recently been found to express FCERL play in the pathogenesis of allergy, remains speculative. We hypothesize that their role may be to remove IgE from the circulation and re‐direct the immune response from naive B cells. IgG antibodies which cannot be used for antigen uptake by B cells also direct the immune response to monocytes.
Peptide‐mediated regulation of the allergic immune response
Authors: HOYNE GERARD F , LAMB JONATHAN R 
Published: June 2007

SummaryA major key to successful immunotherapy may depend on altering the qualitative nature of the immune response in allergic patients. In this review we examine how immune responses to environmental allergens are regulated, and the mechanisms used by the immune system to prevent allergic sensitization. We also discuss future prospects of using allergen‐derived peptides in immunotherapy and the possibility of‘reprogramming’the immune responses by immunizing under conditions that promote Th1 responses instead of Th2 responses.