bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic characterization of complex inter‐recombinant HIV‐1 strains circulating in Spain and reliability of distinct rapid subtyping tools
Authors: Holguín Africa , Lospitao Eva , López Marisa , de Arellano Eva Ramírez , Pena María José , del Romero Jorge , Martín Cristina , Soriano Vincent 
Published: January 2008

AbstractGenetic recombination and high rate of mutation increase HIV‐1 diversity, allowing viruses to escape more easily from the host immune response or antiretroviral drugs. The recombinant nature of full‐length HIV‐1 genomic sequences derived from viruses infecting five epidemiologically unlinked individuals carrying HIV‐1 non‐B variants was investigated. Overlapping PCR amplifications followed by direct sequencing of viral products derived from plasma and phylogenetic analyses were carried out. Four viral sequences clustered with CRF06_cpx and one with CRF02_AG. However, subtyping of separate genes within the same genome revealed that four were recombinant forms involving different subtypes and/or CRFs with distinct breakpoints. Two specimens included CRF02_AG and CRF06_cpx sequences with several fragments from other HIV‐1 clades along their genomes. Three rapid subtyping tools (Stanford, NCBI, and REGA) showed discrepant results when interpreting these viral sequences. This is the first description of CRF02_AG/CRF06_ cpx recombinants in Spain. The results highlight the tremendous heterogeneity of HIV‐1 recombinant strains currently in circulation. J. Med. Virol. 80:383–391, 2008. © 2008 Wiley‐Liss, Inc.
Mumps virus reinfection is not a rare event confirmed by reverse transcription loop‐mediated isothermal amplification
Authors: Yoshida Naoko , Fujino Motoko , Miyata Akiko , Nagai Takao , Kamada Makoto , Sakiyama Hiroshi , Ihara Toshiaki , Kumagai Takuji , Okafuji Teruo , Okafuji Takao , Nakayama Tetsuo 
Published: January 2008

AbstractClinically apparent mumps reinfection is considered extremely rare, but several cases have been suspected of reinfection in an out‐patient clinic. In this study, virological examination, virus isolation, the reverse transcription loop‐mediated isothermal amplification (RT‐LAMP), and IgG and IgM EIA antibodies, were examined in order to identify mumps reinfection. Patients were divided into three categories; the reinfection group comprised 29 patients with a history of natural infection, the vaccine‐failure group consisted of 37 patients with an immunization history, and two patients had histories of both immunization and mumps infection. Another 25 patients were enrolled as a primary infection group. Mumps virus was isolated in 5 (17%) and the genome was detected in 12 (41%) of 29 in the reinfection group. Reinfection was confirmed in 21/28, demonstrating high avidity of IgG EIA. Mumps virus was isolated in 15 (41%) and there was a higher positivity of genome amplification in 25 (68%) of 37 patients in the vaccine‐failure group. Among these, 23 were confirmed as secondary vaccine failure by high avidity IgG EIA serology. In the primary infection group, the isolation rate and genome detection rate was higher in 16 (64%) and in 18 (72%) of 25 patients, respectively. There was no significant difference in virus load among the three groups but high mumps virus load was suspected in the IgM EIA‐positive group based on the shorter amplification time on RT‐LAMP. Mumps virus reinfection was confirmed by RT‐LAMP and an IgG avidity test and was not a rare event. J. Med. Virol. 80:517–523, 2008. © 2008 Wiley‐Liss, Inc.
Experimental investigation of key parameters on the effects of cavity surface roughness in microinjection molding
Authors: Zhang H.L. , Ong N.S. , Lam Y.C. 
Published: January 2008

AbstractFor microinjection molding, it is envisaged that cavity surface roughness plays an important role in the cavity filling of polymer melt. This article presents an experimental investigation into the surface roughness effects on the flow area of a microthickness disk through injection molding. Three core inserts, each of which has different surface roughness on its two semicircular halves but with the same roughness mean lines, were machined and formed the mold cavity. The difference in flow area (or volume) between these two semicircular halves of the molded part was investigated by varying the mold and melt temperatures. Regressive analysis of the significance of mold and melt temperatures and cavity thickness on the surface roughness effects was carried out. Experimental results obtained indicated that the flow area on the smoother half is larger than that on the rougher half during cavity filling. For the same surface roughness, its effect on cavity filling is a function of mold temperature, melt temperature, and cavity thickness. An increase in mold temperature or melt temperature will result in smaller surface roughness effect on the flow area. When cavity thickness is reduced, the surface roughness effect will become more significant. Moreover, a larger difference in the surface roughness between the two semicircular halves of the insert will result in a larger difference in the flow area between the two halves of the molded part. POLYM. ENG. SCI., 2008. © 2008 Society of Plastics Engineers.
Influence of phase modifiers on morphology and properties of thermoplastic elastomers prepared from ethylene propylene diene rubber and isotactic polypropylene
Authors: Chakraborty Pinka , Ganguly Anirban , Mitra Suman , Bhowmick Anil K. 
Published: January 2008

AbstractA series of thermoplastic elastomers (TPEs) were prepared from a binary blend of ethylene propylene diene rubber (EPDM) and isotactic polypropylene (iPP) using different types of phase modifiers. The influence of sulphonated EPDM, maleated EPDM, styrene‐ethylene‐co‐butylene‐styrene block copolymer, maleated PP, and acrylated PP as phase modifiers showed improved physico‐mechanical properties (like maximum stress, elongation at break, moduli, and tension set). Scanning electron and atomic force microscopy studies revealed better morphologies obtained with these phase modified EPDM‐iPP blends. The dependence of the phase modifier type and concentration was optimized with respect to the improvement in physical properties and morphology of the blends. Physical properties, dynamic mechanical properties, and morphology of these blends were explained with the help of interaction parameter, melt viscosity, and crystallinity of the blends. Theoretical modeling showed that Kerner, Ishai‐Cohen, and Paul models predicted the right morphology–property correlation for the prepared TPEs. POLYM. ENG. SCI., 2008. © 2008 Society of Plastics Engineers.
Complications in Thyroid Surgery for Carcinoma: One Institution’s Surgical Experience
Authors: Toniato Antonio , Boschin Isabella Merante , Piotto Andrea , Pelizzo Maria Rosa , Guolo Annamaria , Foletto Mirto , Casalide Eric 
Published: January 2008

AbstractBackgroundThe purpose of this study was to evaluate the factors influencing morbidity after total thyroidectomy for carcinoma, such as the histotype, the extension of surgery, the primary surgery versus reoperation, and the surgeon’s experience.MethodsWe performed a retrospective analysis on inferior laryngeal nerve (ILN) injury and permanent hypoparathyroidism (HPT) rates in 504 consecutive patients with thyroid carcinoma who were operated on by the same surgeon from 1999 to 2006. The following parameters were assessed at univariate analysis: histotype, total thyroidectomy with or without central node dissection (level VI), primary surgery versus reoperation, and early (group 1: 1999–2002, 143 patients) and late (group 2: 2003–2006, 361 patients) experience.ResultsThe global incidence rates of ILN palsy and permanent HPT were 2.18% and 6.3%, respectively. The incidence of ILN damage after total thyroidectomy plus node dissection versus total thyroidectomy without node excision was 2.87% vs. 0.36% (p = 0.029). The incidence of permanent HPT in group 1 was 13.2% vs. 3.6% in group 2 (p = 0.0001). Moreover, the incidence rate of ILN palsy resulted higher in group 1 (2.8%) and in reoperation (3.4%), while the permanent HPT resulted higher in thyroidectomy with node dissection (6.8%) and reoperation (6.9%), although the difference was not significant.ConclusionsThe complications after total thyroidectomy were progressively reduced as a result of a more accurate technique. Nevertheless, our study showed that the incidence of complications is mostly related to the dissection of central lymph node (level VI) and the surgeon’s experience.
Petrous Carotid Artery’s In Situ Bypass: Anatomic Study
Authors: Keshelava Grigol , Mikadze Igor , Abzianidze Giorgi , Kakabadze Zurab 
Published: January 2008

AbstractThe purpose of our study was to reveal the possibility of cervical‐to‐petrous carotid artery in situ bypass with maximum preservation of cranial nerves. Four human cadavers prepared in formalin were investigated. Eight surgical approaches were used (bilateral exposure on each cadaver). The skin incision started from the level of the temporomandibular joint. The VII, IX, X, and XII cranial nerves, starting from the stylomastoid angle, were maximally preserved. Resection of the styloid process, subluxation of the mandibular joint, and milling of tympanic bone revealed the petrous carotid artery. Exposure of the carotid bifurcation was performed with a mini‐skin incision. After dividing the petrous internal carotid artery (ICA) and the cervical ICA, the cervical ICA was dilated using a Fogarty catheter to simulate aneurysmal dilatation. The patient’s saphenous vein after stripping was utilized for the bypass. The vein was passed into the lumen of the dilated cervical ICA, and a cervical‐to‐petrous carotid bypass was performed. In each case, the described technique made it possible to expose the intrapetrous carotid artery adequately. In two cases it was impossible to make a luxation, and therefore the mandibular branch was resected. The vertical segment’s mean length was 12 mm (range 10–15 mm). In all cases, the VII, IX, X, and XII cranial nerves were preserved maximally. The main points of the approach are luxation of the mandibular articulation and milling of the tympanic bone. Our study in cadavers suggests the possibility of petrous carotid artery bypass without exposing the cervical ICA.
Minimizing Disparities in Surgical Care: A Research Focus for the Future
Authors: Ryoo Joan J. , Ko Clifford Y. 
Published: January 2008

AbstractThe wide array of questions and opportunities for surgical health services research offers important prospects for inquiry into surgical disparities. In this essay we discuss research that directly or indirectly addresses disparities in surgery, highlighting the strengths and the future directions such research efforts intimate as potential foci of collective attention. We then consider possible research approaches—including community‐based participatory models—for confronting disparity and the potential role of research in quality improvement to help achieve the ultimate aim, an optimal level of health care for all.
Effect of uniaxial stretching on rat bone mesenchymal stem cell: Orientation and expressions of collagen types I and III and tenascin‐C
Authors: Zhang Lei , Kahn Cyril J.F. , Chen Huai‐Qing , Tran Nguyen , Wang Xiong 
Published: January 2008

AbstractBone marrow mesenchymal stem cells (BMSC) have the potential to differentiate into a variety of cell types like osteoblasts, chondroblasts, adipocytes, etc. It is well known that mechanical forces regulate the biological function of cells. The aim of this study was to investigate the effect of uniaxial stretching on the orientation and biological functions of BMSC. Rat BMSCs were harvested from femoral and tibial bone marrow by density gradient centrifugation. Cells from passages 1–6 were characterized by flow cytometry using monoclonal antibodies. The recovered cells were stably positive for the markers CD90 and CD44 and negative for CD34 and CD45. A cyclic 10% uniaxial stretching at 1 Hz was applied on rat BMSC for different time‐courses. The length, width, and orientation of the cells were subsequently determined. Expression of collagen types I and III and tenascin‐C mRNAs was measured by real‐time RT‐PCR, and the synthesis of these receptors was determined by radioimmunoassay. Results showed that uniaxial stretching lengthened and rearranged the cells. Compared with control groups, expression of collagen types I and III mRNAs was up‐regulated after 12‐h of stretching, while significant increase in synthesis of the two collagen protein types was not observed until after 24‐h stretching. The expression of tenascin‐C mRNA was significantly increased after a 24‐h stretching. These data suggest that cyclic stretching promotes the synthesis of collagen types I and III and tenascin‐C by the rat BMSC.
Preliminary note on an “international magnetic standard”
Authors: Bauer L. A. 
Published: February 2008

The intercomparisons of magnetic instruments made by the various investigators during the past fifteen to twenty years have served to call attention to the discrepancies existing between the determination of the magnetic elements by various observatory and magnetic survey instruments. These discrepancies frequently exceed the errors of observation. At the recent meeting of the International Meteorological Conference held at Innsbruck in 1905, renewed consideration was given this important matter by its Committee on Terrestrial Magnetism.The extensive magnetic operations of the Carnegie Institution of Washington have necessitated giving the adoption of an “International Standard” correct to within at least the allowable error of field observations early consideration. In the course of the work thus far executed, comparisons have been obtained between the following magnetic observatories: Cheltenham (Maryland), Toronto ‐ Agincourt (Canada), Baldwin (Kansas), Mexico (Mexico), Havana (Cuba), Sitka (Alaska), Honolulu (Hawaii), Apia (Samoa), Tokio (Japan), Zi‐ka‐wei (China), Hongkong (China), Christchurch (New Zealand, Sydney and Melbourne (Australia). Further comparisons will be obtained in 1908–9 in Europe, Africa and Asia in the course of magnetic work to be executed during this period.
Sur le champ électrique de l'atmosphère à Rio de Janeiro
Authors: Morize Par H. 
Published: February 2008

Depuis longtemps déjà, des tentatives ont été faites à l'Observatoire de Rio de Janeiro, dans le but d'obtenir des données continues sur le potentiel électrique de l'atmosphère; mais, par suite de ressources insuffisantes, aussi bien en matériel qu'en personnel, les résultats obtenus n'ont servi qu'à montrer les difficultés à vaincre.Ce n'est qu'en 1909, après l'acquisition d'un électromètre enregistreur de Benndorf et d'un disque radioactif Armet de Lisle, que les observations régulières ont pû commencer. Les difficultés rencontrées ont été tout d'abord le manque d'une place appropriée et l'inconstance de l'isolement, due à l'élévation du degré hygrométrique de l'air, et à de petites araignées qui établissent des courts‐circuits difficiles à localiser. Une autre cause, heureusement peu fréquente, provient de petites étincelles qui passent de la borne d'entrée à la caisse extérieure de l'appareil, quand, durant des orages, le potentiel devient très élevé. Ces étincelles lèchent la surface de l'isolateur d'ambre et laissent une couche d'oxyde presqu'invisible, qui lui fait perdre ses qualités isolantes, jusqu'à ce qu'un nettoyage complet l'ait enlevée.
Atmospheric potential‐gradient results at Cebu during solar eclipse, May 9, 1929
Authors: Deppermann C. E. 
Published: February 2008

The accompanying figure is a reproduction of the atmospheric‐electric curves taken with the Wulf electrometer of the Weather Bureau, Central Office, Manila, at Sogod, Cebu, Philippine Islands, on the day of the total eclipse of the Sun, May 9, 1929, together with the two curves for the days preceding.First contact was calculated as 14h 10m 29s and was correct practically to the second; totality began at 15h 29m 47s and lasted for 3 minutes and 38 seconds; last contact was at 16h 42m 7s.
A machine-learning approach to combined evidence validation of genome assemblies
Authors: Choi Jeong-Hyeon , Kim Sun , Tang Haixu , Andrews Justen , Gilbert Don G. , Colbourne John K. 
Published: January 2008

Abstract
Motivation: While it is common to refer to ‘the genome sequence’ as if it were a single, complete and contiguous DNA string, it is in fact an assembly of millions of small, partially overlapping DNA fragments. Sophisticated computer algorithms (assemblers and scaffolders) merge these DNA fragments into contigs, and place these contigs into sequence scaffolds using the paired-end sequences derived from large-insert DNA libraries. Each step in this automated process is susceptible to producing errors; hence, the resulting draft assembly represents (in practice) only a likely assembly that requires further validation. Knowing which parts of the draft assembly are likely free of errors is critical if researchers are to draw reliable conclusions from the assembled sequence data.
Results: We develop a machine-learning method to detect assembly errors in sequence assemblies. Several in silico measures for assembly validation have been proposed by various researchers. Using three benchmarking Drosophila draft genomes, we evaluate these techniques along with some new measures that we propose, including the good-minus-bad coverage (GMB), the good-to-bad-ratio (RGB), the average Z-score (AZ) and the average absolute Z-score (ASZ). Our results show that the GMB measure performs better than the others in both its sensitivity and its specificity for assembly error detection. Nevertheless, no single method performs sufficiently well to reliably detect genomic regions requiring attention for further experimental verification. To utilize the advantages of all these measures, we develop a novel machine learning approach that combines these individual measures to achieve a higher prediction accuracy (i.e. greater than 90%). Our combined evidence approach avoids the difficult and often ad hoc selection of many parameters the individual measures require, and significantly improves the overall precisions on the benchmarking data sets.
Availability: http://people.cgb.indiana.edu/jeochoi/gav/
Contact: jeochoi@indiana.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
Authors: Hong Fangxin , Breitling Rainer 
Published: January 2008

AbstractMotivation: The proliferation of public data repositories creates a need for meta-analysis methods to efficiently evaluate, integrate and validate related datasets produced by independent groups. A t-based approach has been proposed to integrate effect size from multiple studies by modeling both intra- and between-study variation. Recently, a non-parametric ‘rank product’ method, which is derived based on biological reasoning of fold-change criteria, has been applied to directly combine multiple datasets into one meta study. Fisher's Inverse χ2 method, which only depends on P-values from individual analyses of each dataset, has been used in a couple of medical studies. While these methods address the question from different angles, it is not clear how they compare with each other.Results: We comparatively evaluate the three methods; t-based hierarchical modeling, rank products and Fisher's Inverse χ2 test with P-values from either the t-based or the rank product method. A simulation study shows that the rank product method, in general, has higher sensitivity and selectivity than the t-based method in both individual and meta-analysis, especially in the setting of small sample size and/or large between-study variation. Not surprisingly, Fisher's χ2 method highly depends on the method used in the individual analysis. Application to real datasets demonstrates that meta-analysis achieves more reliable identification than an individual analysis, and rank products are more robust in gene ranking, which leads to a much higher reproducibility among independent studies. Though t-based meta-analysis greatly improves over the individual analysis, it suffers from a potentially large amount of false positives when P-values serve as threshold. We conclude that careful meta-analysis is a powerful tool for integrating multiple array studies.Contact: fxhong@jimmy.harvard.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Reconstruction of genetic association networks from microarray data: a partial least squares approach
Authors: Pihur Vasyl , Datta Somnath , Datta Susmita 
Published: January 2008

AbstractMotivation: Gene association/interaction networks provide vast amounts of information about essential processes inside the cell. A complete picture of gene–gene associations/interactions would open new horizons for biologists, ranging from pure appreciation to successful manipulation of biological pathways for therapeutic purposes. Therefore, identification of important biological complexes whose members (genes and their products proteins) interact with each other is of prime importance. Numerous experimental methods exist but, for the most part, they are costly and labor intensive. Computational techniques, such as the one proposed in this work, provide a quick ‘budget’ solution that can be used as a screening tool before more expensive techniques are attempted. Here, we introduce a novel computational method based on the partial least squares (PLS) regression technique for reconstruction of genetic networks from microarray data.Results: The proposed PLS method is shown to be an effective screening procedure for the detection of gene–gene interactions from microarray data. Both simulated and real microarray experiments show that the PLS-based approach is superior to its competitors both in terms of performance and applicability.Availability: R code is available from the supplementary web-site whose URL is given below.Contact: susmita.datta@louisville.eduSupplementary information: Supplementary information are available at http://www.susmitadatta.org/Supp/GeneNet/supp.htm.
PGMapper: a web-based tool linking phenotype to genes
Authors: Xiong Qing , Qiu Yuhui , Gu Weikuan 
Published: January 2008

Abstract
Summary: With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species.
Availability: Available online at http://www.genediscovery.org/pgmapper/index.jsp
Contact: wgu@utmem.edu; qxiong1@utmem.edu