bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bridging the Gap in Immobile Massive Rotator Cuff Tears
Authors: Rhee Yong Girl , Cho Nam Su , Lim Chan Teak , Yi Jin Woong , Vishvanathan Thimurayan 
Published: April 2008

Background Numerous operative techniques have been described for the treatment of massive rotator cuff tears with severe retraction where anatomical repair is impossible. Purpose To evaluate the outcome of massive rotator cuff tears repaired using the biceps interposition technique. Study Design Case series; Level of evidence, 4. Methods Between April 2000 and April 2004, 31 shoulders with irreparable massive rotator cuff tears and associated degenerative lesions of the biceps tendon were included for analysis. Open procedures were performed in 15 cases (open group), while 16 patients underwent arthroscopic procedures (arthroscopic group). The mean follow-up period was 32 months (range, 24-67 months). Results The overall University of California at Los Angeles score at the last follow-up was 31.1 points (range, 21-35). The clinical outcome was excellent in 15 (48.4%) and good in 13 (41.9%) cases. Three patients (9.7%) had poor outcome. There was 1 case of reoperation in the open group for a retear. The mean preoperative Constant score, which was 44.6 points (range, 8-70) in the open group and 51.8 points (range, 24-70) in the arthroscopic group, improved to 80.7 points (range, 37-88) in the former and 83.5 points (range, 57-96) in the latter. The University of California at Los Angeles score improved from preoperative means of 11.3 points (range, 6-16) and 13.6 points (range, 6-19) to 29.5 points (range, 9-33) and 32.6 points (range, 21-35), respectively. However, the differences between the scores in both the categories were not statistically significant ( P = .412 and .198, respectively). According to the postoperative repair integrity analyzed with use of magnetic resonance imaging in 14 of 16 cases with arthroscopic augmentation, 9 (64.3%) presented complete healing. Conclusion The biceps tendon interposition technique for massive rotator cuff tears offers a possible improvement in the clinical outcomes and is comparable to that of conventional repair. As well, the augmentation technique using the tenotomized biceps as potential graft for rotator cuff tears is particularly useful in bridging the gap in immobile massive rotator cuff tears with posterior defects and retraction.
Epidemiology of National Football League Training Camp Injuries from 1998 to 2007
Authors: Feeley Brian T. , Kennelly Steve , Barnes Ronnie P. , Muller Mark S. , Kelly Bryan T. , Rodeo Scott A. , Warren Russell F. 
Published: April 2008

Background Football is one of the leading causes of athletic-related injuries. Injury rates and patterns of the training camp period of the National Football League are unknown. Hypothesis Injury rates will vary with time, and injury patterns will differ between training camp practices and preseason games. Study Design Descriptive epidemiology study. Methods From 1998 to 2007, injury data were collected from 1 National Football League team during its training camp period. Injuries were recorded as a strain, sprain, concussion, contusion, fracture/dislocation, or other injury. The injury was further categorized by location on the body. Injury rates were determined based on the exposure of an athlete to a game or practice event. An athlete exposure was defined as 1 athlete participating in 1 practice or game. The injury rate was calculated as the ratio of injuries per 1000 athlete exposures. Results There were 72.8 (range, 58-109) injuries per year during training camp. Injuries were more common during weeks 1 and 2 than during weeks 3 to 5. The rate of injury was significantly higher during games (64.7/1000 athlete exposures) than practices (12.7/1000 athlete exposures, P < .01). The rate of season-ending injuries was also much higher in games (5.4/1000 athlete exposures) than practices (0.4/1000 athlete exposures). The most common injury during the training camp period was a knee sprain, followed by hamstring strains and contusions. Conclusion Muscle strains are the most common injury type in practices. Contact type injuries are most common during preseason games, and the number of significant injuries that occur during preseason games is high.
The Mycobacterium tuberculosis Rv2540c DNA sequence encodes a bifunctional chorismate synthase
Authors: Ely Fernanda , Nunes José ES , Schroeder Evelyn K , Frazzon Jeverson , Palma Mário S , Santos Diógenes S , Basso Luiz A 
Published: April 2008

Abstract

Background
The emergence of multi- and extensively-drug resistant Mycobacterium tuberculosis strains has created an urgent need for new agents to treat tuberculosis (TB). The enzymes of shikimate pathway are attractive targets to the development of antitubercular agents because it is essential for M. tuberculosis and is absent from humans. Chorismate synthase (CS) is the seventh enzyme of this route and catalyzes the NADH- and FMN-dependent synthesis of chorismate, a precursor of aromatic amino acids, naphthoquinones, menaquinones, and mycobactins. Although the M. tuberculosis Rv2540c (aroF) sequence has been annotated to encode a chorismate synthase, there has been no report on its correct assignment and functional characterization of its protein product.

Results
In the present work, we describe DNA amplification of aroF-encoded CS from M. tuberculosis (Mt CS), molecular cloning, protein expression, and purification to homogeneity. N-terminal amino acid sequencing, mass spectrometry and gel filtration chromatography were employed to determine identity, subunit molecular weight and oligomeric state in solution of homogeneous recombinant Mt CS. The bifunctionality of Mt CS was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. The flavin reductase activity was characterized, showing the existence of a complex between FMNox and Mt CS. FMNox and NADH equilibrium binding was measured. Primary deuterium, solvent and multiple kinetic isotope effects are described and suggest distinct steps for hydride and proton transfers, with the former being more rate-limiting.

Conclusion
This is the first report showing that a bacterial CS is bifunctional. Primary deuterium kinetic isotope effects show that C4-proS hydrogen is being transferred during the reduction of FMNox by NADH and that hydride transfer contributes significantly to the rate-limiting step of FMN reduction reaction. Solvent kinetic isotope effects and proton inventory results indicate that proton transfer from solvent partially limits the rate of FMN reduction and that a single proton transfer gives rise to the observed solvent isotope effect. Multiple isotope effects suggest a stepwise mechanism for the reduction of FMNox. The results on enzyme kinetics described here provide evidence for the mode of action of Mt CS and should thus pave the way for the rational design of antitubercular agents.
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
Authors: Vijaya Satya Ravi , Zavaljevski Nela , Kumar Kamal , Reifman Jaques 
Published: April 2008

Abstract

Background
We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment.

Results
The algorithmic improvements result in significant reduction in runtimes, with the updated pipeline being nearly up to five-times faster than the previous version. The improvements in specificity assessment, based on multiple specificity criteria, result in robust and consistent evaluation of cross-hybridization with nontarget sequences. In addition, the multiple criteria provide finer control on the number of resulting fingerprints, which helps in obtaining a larger number of fingerprints with high specificity. Simulation tests for Francisella tularensis and Yersinia pestis, using a well-established hybridization model to estimate cross-hybridization with nontarget sequences, show that the improved specificity criteria yield a larger number of fingerprints as compared to using a single specificity criterion.

Conclusion
The faster runtimes, achieved as the result of algorithmic improvements, are critical for extending the pipeline to process multiple target genomes. The larger numbers of identified fingerprints, obtained by considering broader specificity criteria, are essential for designing probes for hard-to-distinguish target sequences.
ConStruct: Improved construction of RNA consensus structures
Authors: Wilm Andreas , Linnenbrink Kornelia , Steger Gerhard 
Published: April 2008

Abstract

Background
Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone.

Results
We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation.
One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and suboptimal secondary structures as well as tertiary interaction can be predicted. We demonstrate CONSTRUCT's ability to guide the user in correcting an initial alignment, and show an example for optimal secondary consensus structure prediction on very hard to align SECIS elements. Moreover we use CONSTRUCT to predict tertiary interactions from sequences of the internal ribosome entry site of CrP-like viruses. In addition we show that alignments specifically designed for benchmarking can be easily be optimized using CONSTRUCT, although they share very little sequence identity.

Conclusion
CONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints. It combines several algorithms for prediction of secondary consensus structure and even tertiary interactions. The CONSTRUCT package can be downloaded from the URL listed in the Availability and requirements section of this article.
Hybridization produces novelty when the mapping of form to function is many to one
Authors: Parnell Nicholas F , Hulsey C Darrin , Streelman J Todd 
Published: April 2008

Abstract

Background
Evolutionary biologists want to explain the origin of novel features and functions. Two recent but separate lines of research address this question. The first describes one possible outcome of hybridization, called transgressive segregation, where hybrid offspring exhibit trait distributions outside of the parental range. The second considers the explicit mapping of form to function and illustrates manifold paths to similar function (called many to one mapping, MTOM) when the relationship between the two is complex. Under this scenario, functional novelty may be a product of the number of ways to elicit a functional outcome (i.e., the degree of MTOM). We fuse these research themes by considering the influence of MTOM on the production of transgressive jaw biomechanics in simulated hybrids between Lake Malawi cichlid species.

Results
We characterized the component links and functional output (kinematic transmission, KT) of the 4-bar mechanism in the oral jaws of Lake Malawi cichlids. We demonstrated that the input and output links, the length of the lower jaw and the length of the maxilla respectively, have consistent but opposing relationships with KT. Based on these data, we predicted scenarios in which species with different morphologies but similar KT (MTOM species) would produce transgressive function in hybrids. We used a simple but realistic genetic model to show that transgressive function is a likely outcome of hybridization among Malawi species exhibiting MTOM. Notably, F2 hybrids are transgressive for function (KT), but not the component links that contribute to function. In our model, transgression is a consequence of recombination and assortment among alleles specifying the lengths of the lower jaw and maxilla.

Conclusion
We have described a general and likely pervasive mechanism that generates functional novelty. Simulations of hybrid offspring among Lake Malawi cichlids exhibiting MTOM produce transgressive function in the majority of cases, and at appreciable frequency. Functional transgression (i) is a product of recombination and assortment between alleles controlling the lengths of the lower jaw and the maxilla, (ii) occurs in the absence of transgressive morphology, and (iii) can be predicted from the morphology of parents. Our genetic model can be tested by breeding Malawi cichlid hybrids in the laboratory and examining the resulting range of forms and functions.
Transcriptome analysis identifies pathways associated with enhanced maternal performance in QSi5 mice
Authors: Ramanathan Palaniappan , Martin Ian C , Gardiner-Garden Margaret , Thomson Peter C , Taylor Rosanne M , Ormandy Christopher J , Moran Christopher , Williamson Peter 
Published: April 2008

AbstractBackgroundHighly fecund mouse strains provide an ideal model to understand the factors affecting maternal performance. The QSi5 inbred strain of mice was selected for high fecundity and low inter-litter interval, and is very successful at weaning large numbers of offspring when compared to other inbred strains.ResultsPost-natal pup weight gain was used to estimate mammary gland output and to compare the performance of QSi5 mice to CBA mice. Cumulative litter weights and individual pup weight gain was significantly higher throughout the first eight days of lactation in QSi5 mice compared to CBA mice. Morphometric analysis of mammary glands during pregnancy in QSi5 mice revealed a 150 percent greater ductal side branching compared to CBA mice (P< 0.001). Ontology and pathway classification of transcript profiles from the two strains identified an enrichment of genes involved in a number of pathways, including the MAPK, tight junction, insulin signalling andWntsignalling. Eleven of these genes, including six genes from the MAPK signalling pathway, were identified as associated with postnatal growth. Further, positive mediators of Wnt signalling, includingWnt4, Csnk2a1andSmad4, were over-represented in the QSi5 strain profile, while negative regulators, includingDkkl1, Ppp2r1aandNlk, were under-represented. These findings are consistent with the role of Wnt and MAPK signalling pathway in ductal morphogenesis and lobuloalveolar development suggesting enhanced activity in QSi5 mice. A similar pattern of phenotype concordance was seen amongst 12 genes from the tight junction pathway, but a pattern did not emerge from the insulin signalling genes. Amongst a group of differentially expressed imprinted genes, two maternal imprinted genes that suppress growth inducedviathe IGF signalling pathway,Grb10andIgf2r, were under-represented in QSi5 mice. WhereasPeg3andPlagl1, both paternally imprinted genes that enhance neonatal growth, were over-represented in QSi5 mice.ConclusionWe propose that the combined action of at least three major signalling pathways involved in mammary gland development and milk secretion, namely Wnt, MAPK and tight junction pathways, contribute to the superior maternal performance phenotype in QSi5 mice. Additionally, favourable expression patterns of the imprinted genesPeg3, Plagl1, Grb10andIgf2rmay also contribute.
Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities
Authors: Williams Bryony AP , Lee Renny CH , Becnel James J , Weiss Louis M , Fast Naomi M , Keeling Patrick J 
Published: April 2008

Abstract

Background
Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but genomes of different species range in size from 2.3 Mb to 19.5 Mb and the nature of the larger genomes remains unknown.

Results
Here we have undertaken genome sequence surveys of two diverse microsporidia, Brachiola algerae and Edhazardia aedis. In both species we find very large intergenic regions, many transposable elements, and a low gene-density, all in contrast to the small, model microsporidian genomes. We also find no recognizable genes that are not also found in other surveyed or sequenced microsporidian genomes.

Conclusion
Our results demonstrate that microsporidian genome architecture varies greatly between microsporidia. Much of the genome size difference could be accounted for by non-coding material, such as intergenic spaces and retrotransposons, and this suggests that the forces dictating genome size may vary across the phylum.
Lsa21, a novel leptospiral protein binding adhesive matrix molecules and present during human infection
Authors: Atzingen Marina V , Barbosa Angela S , De Brito Thales , Vasconcellos Silvio A , de Morais Zenáide M , Lima Dirce MC , Abreu Patricia AE , Nascimento Ana LTO 
Published: April 2008

Abstract

Background
It has been well documented over past decades that interaction of pathogens with the extracellular matrix (ECM) plays a primary role in host cell attachment and invasion. Adherence to host tissues is mediated by surface-exposed proteins expressed by the microorganisms during infection. The mechanisms by which pathogenic leptospires invade and colonize the host remain poorly understood since few virulence factors contributing to the pathogenesis of the disease have been identified. Whole-genome sequencing analysis of L. interrogans allowed identification of a repertoire of putative leptospiral surface proteins.

Results
Here, we report the identification and characterization of a new leptospiral protein that exhibits extracellular matrix-binding properties, called as Lsa21 (leptospiral surface adhesin, 21 kDa). Compatible with its role in adhesion, the protein was shown to be surface-exposed by indirect immunofluorescence. Attachment of Lsa21 to laminin, collagen IV, and plasma fibronectin was specific and dose dependent. Laminin oxidation by sodium metaperiodate reduced the protein-laminin interaction in a concentration-dependent manner, indicating that laminin sugar moieties are crucial for this interaction. The gene coding for Lsa21 is present in pathogenic strains belonging to the L. interrogans species but was not found in the saprophytic L. biflexa serovar Patoc strain Patoc 1. Loss of gene expression occurs upon culture attenuation of pathogenic strains. Environmental factors such as osmolarity and temperature affect Lsa21 expression at the transcriptional level. Moreover, anti-Lsa21 serum labeled liver and kidney tissues of human fatal cases of leptospirosis.

Conclusion
Our data suggest a role of Lsa21 in the pathogenesis of leptospirosis.
Isolation of neuronal chromatin from brain tissue
Authors: Jiang Yan , Matevossian Anouch , Huang Hsien-Sung , Straubhaar Juerg , Akbarian Schahram 
Published: April 2008

Abstract

Background
DNA-protein interactions in mature brain are increasingly recognized as key regulators for behavioral plasticity and neuronal dysfunction in chronic neuropsychiatric disease. However, chromatin assays typically lack single cell resolution, and therefore little is known about chromatin regulation of differentiated neuronal nuclei that reside in brain parenchyma intermingled with various types of non-neuronal cells.

Results
Here, we describe a protocol to selectively tag neuronal nuclei from adult brain – either by (anti-NeuN) immunolabeling or transgene-derived histone H2B-GFP fusion protein – for subsequent fluorescence-activated sorting and chromatin immunoprecipitation (ChIP). To illustrate an example, we compared histone H3 lysine 4 and 9 methylation marks at select gene promoters in neuronal, non-neuronal and unsorted chromatin from mouse forebrain and human cerebral cortex, and provide evidence for neuron-specific histone methylation signatures.

Conclusion
With the modifications detailed in this protocol, the method can be used to collect nuclei from specific subtypes of neurons from any brain region for subsequent ChIP with native/un-fixed or crosslinked chromatin preparations. Starting with the harvest of brain tissue, ChIP-ready neuronal nuclei can be obtained within one day.
The SNF1-type serine-threonine protein kinase SAPK4regulates stress-responsive gene expression in rice
Authors: Diédhiou Calliste J , Popova Olga V , Dietz Karl-Josef , Golldack Dortje 
Published: April 2008

Abstract

Background
Plants respond to extracellularly perceived abiotic stresses such as low temperature, drought, and salinity by activation of complex intracellular signaling cascades that regulate acclimatory biochemical and physiological changes. Protein kinases are major signal transduction factors that have a central role in mediating acclimation to environmental changes in eukaryotic organisms. In this study, we characterized the function of the sucrose nonfermenting 1-related protein kinase2 (SnRK2) SAPK4 in the salt stress response of rice.

Results
Translational fusion of SAPK4 with the green fluorescent protein (GFP) showed subcellular localization in cytoplasm and nucleus. To examine the role of SAPK4 in salt tolerance we generated transgenic rice plants with over-expression of rice SAPK4 under control of the CaMV-35S promoter. Induced expression of SAPK4 resulted in improved germination, growth and development under salt stress both in seedlings and mature plants. In response to salt stress, the SAPK4-overexpressing rice accumulated less Na+ and Cl- and showed improved photosynthesis. SAPK4-regulated genes with functions in ion homeostasis and oxidative stress response were identified: the vacuolar H+-ATPase, the Na+/H+ antiporter NHX1, the Cl- channel OsCLC1 and a catalase.

Conclusion
Our results show that SAPK4 regulates ion homeostasis and growth and development under salinity and suggest function of SAPK4 as a regulatory factor in plant salt stress acclimation. Identification of signaling elements involved in stress adaptation in plants presents a powerful approach to identify transcriptional activators of adaptive mechanisms to environmental changes that have the potential to improve tolerance in crop plants.
Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference
Authors: Liu Chen , Chen Yaohui , Yu Xianjun , Jin Chen , Xu Jin , Long Jiang , Ni Quanxing , Fu Deliang , Jin Hong , Bai Chen 
Published: April 2008

Abstract

Background
Methyl-CpG binding domain protein 1 (MBD1), a suppressor of gene transcription, may be involved in inactivation of tumor suppressor genes during tumorigenesis. Over-expression of MBD1 has been reported in human pancreatic carcinomas.

Methods
In this study, we established a MBD1-knock-down pancreatic cancer cell line (BxPC-3) using stable RNA interference, to compare the proteomic changes between control and MBD1-knock-down cells using two-dimensional gel electrophoresis and mass spectrometry.

Results
We identified five proteins that were up-regulated and nine proteins that were down-regulated. Most of the identified proteins are involved in tumorigenesis, some are prognostic biomarkers for human malignant tumors.

Conclusion
Our data suggest that these differential proteins may be associated with the function of MBD1, and provide some insight into the functional mechanism of MBD1 in the development of pancreatic cancer.