bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Coracoidal Insertion of the Coracoclavicular Ligaments
Authors: Salzmann Gian M. , Paul Jochen , Sandmann Gunther H. , Imhoff Andreas B. , Schöttle Philip B. 
Published: December 2008

Background Current surgical procedures restoring a dislocated acromioclavicular joint aim to perform an anatomically correct and biomechanically stable reconstruction. However, the coracoidal insertions for the coracoclavicular ligaments have not yet been defined. Purpose The objective was to evaluate dimension and orientation of the coracoclavicular footprints with respect to bony landmarks for use in anatomic reconstruction of the coracoclavicular ligament complex. Study Design Descriptive laboratory study. Methods Twenty-three (17 female, 6 male) fresh-frozen cadaveric human shoulders were dissected, and the coracoclavicular ligaments including the coracoid and the lateral clavicle were exposed. After measurement of bony coracoidal dimensions, the ligaments were dissected and the insertion sites as well as the footprint centers were identified and marked. Each coracoclavicular insertion dimension and its distance to the bony landmarks was recorded. Sex-related differences were calculated. Results The mean total coracoidal length was 43.1 ± 2.2 mm. The distance from the tip of the coracoid to the precipice, the point at which the undersurface of the coracoid changes from a horizontal to a vertical direction, measured 20.3 ± 2.6 mm. The mean distance from the conoidal center to the medial coracoidal boarder and to the precipice was 1.7 ± 0.7 mm and 16.4 ± 2.4 mm, respectively. The mean distance from the trapezoidal center to the medial border and to the precipice was 8.7 ± 3 mm and 10.9 ± 2.4 mm, respectively. The mean distance between the footprint centers was 10.1 ± 4.2 mm. Conclusion Reproducible dimensions and orientation of the coracoclavicular footprints are given. Clinical Relevance Coracoidal anatomic landmarks can be used intraoperatively for an anatomic reconstruction of the coracoclavicular ligaments.
Neurologic and Vascular Injuries Associated with Knee Ligament Injuries
Authors: Johnson Michael E. , Foster Lynanne , DeLee Jesse C. 
Published: December 2008

Background Multiple ligament knee injuries are commonly associated with neurovascular complications such as popliteal artery, common peroneal nerve, and tibial nerve injuries. Hypothesis While the importance of identifying these complications in association with bicruciate and triligamentous injuries has been well established, it is important to recognize that any biligamentous and some single ligament knee injuries present with neurological and vascular complications as well. Study Design Literature review. Conclusion Popliteal artery injuries require immediate intervention to help prevent limb loss. Peroneal and tibial nerve injuries can be a significant cause of morbidity and, therefore, require an understanding of their natural history, anatomy, and pathophysiologic implications to maximize functionality. Clinical Relevance This review explores the types, mechanisms, and classifications of common neurovascular complications of knee ligament injuries, discusses their diagnosis, and reviews the therapeutic options available to optimize patient outcomes.
Productivity of Rural Credit
Authors: Sriram M. S. 
Published: December 2008

The policy intervention in agriculture has been credit driven. This is even more pronounced in the recent interventions made by the State in the package announced for distressed farmers, in doubling agricultural credit, providing subvention and putting an upper cap on interest rates for agricultural loans. We use existing literature and data to argue that the causality of agricultural output with increased doses of credit cannot be clearly established. We argue that Indian agriculture is undergoing a fundamental change wherein the technology and inputs are moving out of the hands of the farmers to external suppliers. This, over a period of time may have resulted in the de–skilling of farmers and without adequate public investments in support services and without appropriate risk mitigation products, has created a near–crisis in agriculture. Thus, we argue that policy interventions have to be necessarily patient and holistic. Looking specifically at the rural financial markets using some primary data, we argue that it is necessary to understand the rural financial markets from the demand side. We conclude the article by identifying some directions in which the policy intervention could move, keeping the overall rural economy in view rather than being focussed only on agriculture.
Polyclonal T-cell reconstitution of X-SCID recipients after in utero transplantation of lymphoid-primed multipotent progenitors
Authors: Liuba Karina , Pronk Cornelis J. H. , Stott Simon R. W. , Jacobsen Sten-Eirik W. 
Published: December 2008

Abstract
Although successful in utero hematopoietic cell transplantation (IUHCT) of X-linked severe combined immune deficiency (X-SCID) with enriched stem and progenitor cells was achieved more than a decade ago, it remains applied only in rare cases. Although this in part reflects that postnatal transplantations have overall given good results, there are no direct comparisons between IUHCT and postnatal transplantations of X-SCID. The proposed tolerance of the fetal immune system to foreign human leukocyte antigen early in gestation, a main rationale behind IUHCT, has recently been challenged by evidence for a considerable immune barrier against in utero transplanted allogeneic bone marrow cells. Consequently, there is need for further exploring the application of purified stem and progenitor cells to overcome this barrier also in IUHCT. Herein, we demonstrate in a congenic setting that recently identified lymphoid-primed multipotent progenitors are superior to hematopoietic stem cells in providing rapid lymphoid reconstitution after IUHCT of X-SCID recipients, and sustain in the long-term B cells, polyclonal T cells, as well as short-lived B-cell progenitors and thymic T-cell precursors. We further provide evidence for IUHCT of hematopoietic stem cells giving superior B- and T-cell reconstitution in fetal X-SCID recipients compared with neonatal and adolescent recipients.
Functional analysis of novel SNPs and mutations in human and mouse genomes
Authors: Liu Chuan-Kun , Chen Yan-Hau , Tang Cheng-Yang , Chang Shu-Chuan , Lin Yi-Jung , Tsai Ming-Fang , Chen Yuan-Tsong , Yao Adam 
Published: December 2008

Abstract

Background
With the flood of information generated by the new generation of sequencing technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully designed presentation of results so researchers can focus more on thinking instead of typing and calculating.

Results
FANS http://fans.ngc.sinica.edu.tw/ harnesses the power of public information databases and powerful tools from six well established websites to enhance the efficiency of analysis of novel variations. FANS can process any point change in any coding region or GT-AG splice site to provide a clear picture of the disease risk of a prioritized variation by classifying splicing and functional alterations into one of nine risk subtypes with five risk levels.

Conclusion
FANS significantly simplifies the analysis operations to a four-step procedure while still covering all major areas of interest to researchers. FANS offers a convenient way to prioritize the variations and select the ones with most functional impact for validation. Additionally, the program offers a distinct improvement in efficiency over manual operations in our benchmark test.
WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding
Authors: Lee Yong Seok , Kim Tae-Hyung , Kang Tae-Wook , Chung Won-Hyong , Shin Gwang-Sik 
Published: December 2008

AbstractBackgroundIn the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting. In general, the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks) is used to estimate either negative or positive selection for an entire gene region of interest. However, since each amino acid in a region has a different function and structure, the type and strength of natural selection may be different for each amino acid. Specifically, domain sites on the protein are indicative of structurally and functionally important sites. Therefore, Window-sliding tools can be used to detect evolutionary forces acting on mutation sites.ResultsThis paper reports the development of a web-based tool, WSPMaker (Window-sliding Selection pressure Plot Maker), for calculating selection pressures (estimated by Ka/Ks) in the sub-regions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA with a user-defined window length. This enables the investigation of adaptive protein evolution and shows selective constraints of the overall/specific region(s) of two orthologous gene-coding DNA sequences. The method accommodates various evolutionary models and options such as the sliding window size. WSPmaker uses domain information from Pfam HMM models to detect highly conserved residues within orthologous proteins.ConclusionWSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs).
The value of position-specific scoring matrices for assessment of protein allegenicity
Authors: Lim Shen Jean , Tong Joo Chuan , Chew Fook Tim , Tammi Martti T 
Published: December 2008

Abstract

Background
Bioinformatics tools are commonly used for assessing potential protein allergenicity. While these methods have achieved good accuracies for highly conserved sequences, they are less effective when the overall similarity is low. In this study, we assessed the feasibility of using position-specific scoring matrices as a basis for predicting potential allergenicity in proteins.

Results
Two simple methods for predicting potential allergenicity in proteins, based on general and group-specific allergen profiles, are presented. Testing results indicate that the performances of both methods are comparable to the best results of other methods. The group-specific profile approach, with a sensitivity of 84.04% and specificity of 96.52%, gives similar results as those obtained using the general profile approach (sensitivity = 82.45%, specificity = 96.92%).

Conclusion
We show that position-specific scoring matrices are highly promising for constructing computational models suitable for allergenicity assessment. These data suggest it may be possible to apply a targeted approach for allergenicity assessment based on the profiles of allergens of interest.
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research
Authors: Lin Hong Huang , Zhang Guang Lan , Tongchusak Songsak , Reinherz Ellis L , Brusic Vladimir 
Published: December 2008

Abstract

Background
Initiation and regulation of immune responses in humans involves recognition of peptides presented by human leukocyte antigen class II (HLA-II) molecules. These peptides (HLA-II T-cell epitopes) are increasingly important as research targets for the development of vaccines and immunotherapies. HLA-II peptide binding studies involve multiple overlapping peptides spanning individual antigens, as well as complete viral proteomes. Antigen variation in pathogens and tumor antigens, and extensive polymorphism of HLA molecules increase the number of targets for screening studies. Experimental screening methods are expensive and time consuming and reagents are not readily available for many of the HLA class II molecules. Computational prediction methods complement experimental studies, minimize the number of validation experiments, and significantly speed up the epitope mapping process. We collected test data from four independent studies that involved 721 peptide binding assays. Full overlapping studies of four antigens identified binding affinity of 103 peptides to seven common HLA-DR molecules (DRB1*0101, 0301, 0401, 0701, 1101, 1301, and 1501). We used these data to analyze performance of 21 HLA-II binding prediction servers accessible through the WWW.

Results
Because not all servers have predictors for all tested HLA-II molecules, we assessed a total of 113 predictors. The length of test peptides ranged from 15 to 19 amino acids. We tried three prediction strategies – the best 9-mer within the longer peptide, the average of best three 9-mer predictions, and the average of all 9-mer predictions within the longer peptide. The best strategy was the identification of a single best 9-mer within the longer peptide. Overall, measured by the receiver operating characteristic method (AROC), 17 predictors showed good (AROC > 0.8), 41 showed marginal (AROC > 0.7), and 55 showed poor performance (AROC < 0.7). Good performance predictors included HLA-DRB1*0101 (seven), 1101 (six), 0401 (three), and 0701 (one). The best individual predictor was NETMHCIIPAN, closely followed by PROPRED, IEDB (Consensus), and MULTIPRED (SVM). None of the individual predictors was shown to be suitable for prediction of promiscuous peptides. Current predictive capabilities allow prediction of only 50% of actual T-cell epitopes using practical thresholds.

Conclusion
The available HLA-II servers do not match prediction capabilities of HLA-I predictors. Currently available HLA-II prediction servers offer only a limited prediction accuracy and the development of improved predictors is needed for large-scale studies, such as proteome-wide epitope mapping. The requirements for accuracy of HLA-II binding predictions are stringent because of the substantial effect of false positives.
A protein interaction based model for schizophrenia study
Authors: Hsu Pei-Chun , Yang Ueng-Cheng , Shih Kuan-Hui , Liu Chih-Min , Liu Yu-Li , Hwu Hai-Gwo 
Published: December 2008

Abstract

Background
Schizophrenia is a complex disease with multiple factors contributing to its pathogenesis. In addition to environmental factors, genetic factors may also increase susceptibility. In other words, schizophrenia is a highly heritable disease. Some candidate genes have been deduced on the basis of their known function with others found on the basis of chromosomal location. Individuals with multiple candidate genes may have increased risk. However it is not clear what kind of gene combinations may produce the disease phenotype. Their collective effect remains to be studied.

Results
Most pathways except metabolic pathways are rich in protein-protein interactions (PPIs). Thus, the PPI network contains pathway information, even though the upstream-downstream relation of PPI is yet to be explored. Here we have constructed a PPI sub-network by extracting the nearest neighbour of the 36 reported candidate genes described in the literature. Although these candidate genes were discovered by different approaches, most of the proteins formed a cluster. Two major protein interaction modules were identified on the basis of the pairwise distance among the proteins in this sub-network. The large and small clusters might play roles in synaptic transmission and signal transduction, respectively, based on gene ontology annotation. The protein interactions in the synaptic transmission cluster were used to explain the interaction between the NRG1 and CACNG2 genes, which was found by both linkage and association studies. This working hypothesis is supported by the co-expression analysis based on public microarray gene expression.

Conclusion
On the basis of the protein interaction network, it appears that the NRG1-triggered NMDAR protein internalization and the CACNG2 mediated AMPA receptor recruiting may act together in the glutamatergic signalling process. Since both the NMDA and AMPA receptors are calcium channels, this process may regulate the influx of Ca2+. Reducing the cation influx might be one of the disease mechanisms for schizophrenia. This PPI network analysis approach combined with the support from co-expression analysis may provide an efficient way to propose pathogenetic mechanisms for various highly heritable diseases.
MiRTif: a support vector machine-based microRNA target interaction filter
Authors: Yang Yuchen , Wang Yu-Ping , Li Kuo-Bin 
Published: December 2008

Abstract

Background
MicroRNAs (miRNAs) are a set of small non-coding RNAs serving as important negative gene regulators. In animals, miRNAs turn down protein translation by binding to the 3' UTR regions of target genes with imperfect complementary pairing. The identification of microRNA targets has become one of the major challenges of miRNA research. Bioinformatics investigations on miRNA target have resulted in a number of target prediction tools. Although these tools are capable of predicting hundreds of targets for a given miRNA, many of them suffer from high false positive rates, indicating the need for a post-processing filter for the predicted targets. Once trained with experimentally validated true and false targets, machine learning methods appear to be ideal approaches to distinguish the true targets from the false ones.

Results
We present a miRNA target filtering system named MiRTif (miRNA:target interaction filter). The system is a support vector machine (SVM) classifier trained with 195 positive and 38 negative miRNA:target interaction pairs, all experimentally validated. Each miRNA:target interaction pair is divided into a seed and a non-seed region. The encoded feature vector contains various k-gram frequencies in the seed, the non-seed and the entire regions. Informative features are selected based on their discriminating abilities. Prediction accuracies are assessed using 10-fold cross-validation experiments. Our system achieves AUC (area under the ROC curve) of 0.86, sensitivity of 83.59%, and specificity of 73.68%. More importantly, the system correctly predicts majority of the false positive miRNA:target interactions (28 out of 38). The possibility of over-fitting due to the relatively small negative sample set has also been investigated using a set of non-validated and randomly selected targets (from miRBase).

Conclusion
MiRTif is designed as a post-processing filter that takes miRNA:target interactions predicted by other target prediction softwares such as TargetScanS, PicTar and miRanda as inputs, and determines how likely the given interaction is a real or a pseudo one. MiRTif can be accessed from http://bsal.ym.edu.tw/mirtif.
Human neural progenitors express functional lysophospholipid receptors that regulate cell growth and morphology
Authors: Hurst Jillian H , Mumaw Jennifer , Machacek David W , Sturkie Carla , Callihan Phillip , Stice Steve L , Hooks Shelley B 
Published: December 2008

Abstract

Background
Lysophospholipids regulate the morphology and growth of neurons, neural cell lines, and neural progenitors. A stable human neural progenitor cell line is not currently available in which to study the role of lysophospholipids in human neural development. We recently established a stable, adherent human embryonic stem cell-derived neuroepithelial (hES-NEP) cell line which recapitulates morphological and phenotypic features of neural progenitor cells isolated from fetal tissue. The goal of this study was to determine if hES-NEP cells express functional lysophospholipid receptors, and if activation of these receptors mediates cellular responses critical for neural development.

Results
Our results demonstrate that Lysophosphatidic Acid (LPA) and Sphingosine-1-phosphate (S1P) receptors are functionally expressed in hES-NEP cells and are coupled to multiple cellular signaling pathways. We have shown that transcript levels for S1P1 receptor increased significantly in the transition from embryonic stem cell to hES-NEP. hES-NEP cells express LPA and S1P receptors coupled to Gi/o G-proteins that inhibit adenylyl cyclase and to Gq-like phospholipase C activity. LPA and S1P also induce p44/42 ERK MAP kinase phosphorylation in these cells and stimulate cell proliferation via Gi/o coupled receptors in an Epidermal Growth Factor Receptor (EGFR)- and ERK-dependent pathway. In contrast, LPA and S1P stimulate transient cell rounding and aggregation that is independent of EGFR and ERK, but dependent on the Rho effector p160 ROCK.

Conclusion
Thus, lysophospholipids regulate neural progenitor growth and morphology through distinct mechanisms. These findings establish human ES cell-derived NEP cells as a model system for studying the role of lysophospholipids in neural progenitors.
Abelson tyrosine kinase links PDGFbeta receptor activation to cytoskeletal regulation of NMDA receptors in CA1 hippocampal neurons
Authors: Beazely Michael A , Weerapura Manjula , MacDonald John F 
Published: December 2008

AbstractBackgroundWe have previously demonstrated that PDGF receptor activation indirectly inhibits N-methyl-D-aspartate (NMDA) currents by modifying the cytoskeleton. PDGF receptor ligand is also neuroprotective in hippocampal slices and cultured neurons. PDGF receptors are tyrosine kinases that control a variety of signal transduction pathways including those mediated by PLCγ. In fibroblasts Src and another non-receptor tyrosine kinase, Abelson kinase (Abl), control PDGF receptor regulation of cytoskeletal dynamics. The mechanism whereby PDGF receptor regulates cytoskeletal dynamics in central neurons remains poorly understood.ResultsIntracellular applications of active Abl, but not heat-inactivated Abl, decreased NMDA-evoked currents in isolated hippocampal neurons. This mimics the effects of PDGF receptor activation in these neurons. The Abl kinase inhibitor, STI571, blocked the inhibition of NMDA currents by Abl. We demonstrate that PDGF receptors can activate Abl kinase in hippocampal neurons via mechanisms similar to those observed previously in fibroblasts. Furthermore, PDGFβ receptor activation alters the subcellular localization of Abl. Abl kinase is linked to actin cytoskeletal dynamics in many systems. We show that the inhibition of NMDA receptor currents by Abl kinase is blocked by the inclusion of the Rho kinase inhibitor, Y-27632, and that activation of Abl correlates with an increase in ROCK tyrosine phosphorylation.ConclusionThis study demonstrates that PDGFβ receptors act via an interaction with Abl kinase and Rho kinase to regulated cytoskeletal regulation of NMDA receptor channels in CA1 pyramidal neurons.
Spontaneous intramural jejunal haematoma: a case report
Authors: Birla Rashmi P , Mahawar Kamal K , Saw Elena YW , Tabaqchali Mohamed A , Woolfall Philip 
Published: December 2008

Abstract

Background
Spontaneous intramural intestinal haematoma is a rare complication of anticoagulation therapy. A misdiagnosis may lead to an unnecessary and even hazardous surgical intervention.

Case presentation
An 85 year old lady presented to us with acute abdomen. She was on Warfarin and was found to have grossly deranged clotting parameters. Computed Tomography Scan revealed a long loop of markedly thick-walled proximal jejunum. A diagnosis of spontaneous intramural jejunal haematoma was made.

Conclusion
She was successfully treated with conservative management with Vitamin K and blood products.