bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Epidemiology of Knee Injuries in English Professional Rugby Union
Authors: Dallalana Richard J. , Brooks John H. M. , Kemp Simon P. T. , Williams Andrew M. 
Published: February 2007

Background Detailed injury epidemiology is an invaluable tool for reducing risks associated with sporting injuries. Very little accurate injury surveillance data exist regarding knee injuries in professional rugby. Hypotheses (1) Knee injuries have a greater impact on the game than injuries to other body locations. (2) Anterior cruciate ligament and medial collateral ligament injuries cause the greatest days absent from training and match play. Study Design Descriptive epidemiology study. Methods Medical personnel prospectively reported time-loss injuries sustained by 546 professional rugby union players from 12 clubs in England over 2 seasons, and the knee injuries were evaluated. Results Injuries to the knee accounted for the highest number of days absent due to injury (7776 days, 21%) and were characteristically severe, with a disproportionately high number of days missed per injury (37 days). Anterior cruciate ligament injuries accounted for the greatest proportion of days missed of all knee injuries (29%), followed by medial collateral ligament injuries (25%). Most severe injuries occurred during contact, mostly during a tackle, and most commonly in the final 20 minutes of a match. Injuries tended to be more common in backs. Injuries sustained during training accounted for 16% of all knee injuries. Each club studied had a mean of 10 knee injuries per season resulting in a total of 353 days absent. Conclusions The incidence of knee injuries sustained during matches was higher than that reported in all other football codes, surpassed only by rugby union at the international level. Knee injuries accounted for the highest player absence due to injury; 5% of an average playing squad were absent at any one time due to knee injuries.
Increasing the Distance between the Posterior Cruciate Ligament and the Popliteal Neurovascular Bundle by a Limited Posterior Capsular Release during Arthroscopic Transtibial Posterior Cruciate Ligament Reconstruction
Authors: Ahn Jin Hwan , Wang Joon Ho , Lee Sang Hak , Yoo Jae Chul , Jeon Woo Joo 
Published: February 2007

Background During arthroscopic transtibial posterior cruciate ligament reconstruction, popliteal vessel injury is the most serious complication, and it rarely occurs. Purpose To evaluate the distance change between the posterior cruciate ligament and the neurovascular bundle by limited release of the posterior capsule during arthroscopic posterior cruciate ligament reconstruction. Study Design Controlled laboratory study. Methods The authors performed an arthroscopic posterior cruciate ligament reconstruction procedure on 10 fresh-frozen cadaveric knees. The experimental procedure included 4 steps. Before the procedure and just after each step, angiographic lateral radiographs were checked to find the relationship and the distances between the popliteal artery and the posterior cruciate ligament. Changes in the distances at each step were compared and analyzed by ANOVA with Bonferroni correction. Results The mean distance between the popliteal artery and the tibial insertion of the posterior cruciate ligament increased significantly (from 4.4 ± 3.2 mm to 14.7 ± 4.1 mm) after limited posterior capsular release (P < .01). The distance from the popliteal artery to the midsubstance of the posterior cruciate ligament at the level of the posterior trans-septal portal significantly increased (from 11.3 ± 3.9 mm to 17.6 ± 4.0 mm) just after distension of the knee joint with a pump (P < .01). Conclusion This study showed a significant increase in the distance from the popliteal artery to the posterior cruciate ligament through arthroscopic limited posterior capsular release during arthroscopic transtibial posterior cruciate ligament reconstruction. Clinical Relevance The results of this study support the claim that risk of iatrogenic popliteal vessel injury could be reduced by limited posterior capsular release during arthroscopic transtibial posterior cruciate ligament reconstruction.
I nterferon beta-1a slows progression of brain atrophy in relapsing-remitting multiple sclerosis predominantly by reducing gray matter atrophy
Authors: Zivadinov R. , Locatelli L. , Cookfair D. , Srinivasaraghavan B. , Bertolotto A. , Ukmar M. , Bratina A. , Maggiore C. , Bosco A. , Grop A. , Catalan M. , Zorzon M. 
Published: February 2007

Background Brain atrophy, as assessed by magnetic resonance imaging (MRI), has been correlated with disability in patients with multiple sclerosis (MS). Recent evidence indicates that both white matter (WM) and gray matter (GM) are subject to atrophy in patients with MS. Although neurological deficiencies in MS are primarily due to loss of WM, the clinical significance of GM atrophy has not been fully explored in MS. Methods We have undertaken a three-year, open-label study, comparing 26 patients who elected to receive intramuscular interferon beta-1a (IFN β-1a) therapy, with 28 patients who elected not to receive therapy. Both groups had quantitative cranial MRI scans at study entry and after three years, and standardized clinical assessments every six months. Brain parenchymal fraction (BPF), GM fraction (GMF), and WM fraction (WMF) percent changes were calculated, and T2- and T1-lesion volumes (LVs) assessed. Results After three years, mean percent (%) change in BPF favored the IFN β-1a treatment group (IFN β-1a —1.3% versus the control group —2.5%, P=0.009), as did the mean percent change in GMF (+0.2 versus —1.4%, P=0.014), and the mean percent change in T1-LV (—9.3 versus +91.6%, P=0.011). At the end of the study, there was a significant within-patient decrease in BPF for both groups (P=0.02 for the IFN β-1a treatment group, and P<0.001 for the control group), a significant within-patient decrease in WMF for the IFN β-1a treatment group (P=0.01), and a significant decrease in GMF for the control group (P=0.013) when compared with baseline. Conclusion Over a three-year period, treatment with IFN β-1a significantly slowed the progression of whole-brain and GM atrophy, and of T1-hypointense LV accumulation, when compared with the control group. Multiple Sclerosis 2007; 13: 490-501. http://msj.sagepub.com
Conceptual-level workflow modeling of scientific experiments using NMR as a case study
Authors: Verdi Kacy K , Ellis Heidi JC , Gryk Michael R 
Published: February 2007

Abstract

Background
Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration.

Results
We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy.

Conclusion
Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment.
Estimation of the real population and its impact on the utilisation of healthcare services in Mediterranean resort regions: an ecological study
Authors: Perea-Milla Emilio , Pons Sergi Mari , Rivas-Ruiz Francisco , Gallofre Anna , Jurado Enrique Navarro , Ales Marco A Navarro , Jimenez-Puente Alberto , Fernandez-Nieto Fidel , Cerda Joan C March , Carrasco Manuel , Martin Lydia , Cano Damian Lopez , Gutierrez Gonzalo E , Macías Rafael Cortes , Garcia-Ruiz Jose A 
Published: February 2007

Abstract
Background
The demographic structure has a significant influence on the use of healthcare services, as does the size of the population denominators. Very few studies have been published on methods for estimating the real population such as tourist resorts. The lack of information about these problems means there is a corresponding lack of information about the behaviour of populational denominators (the floating population or tourist load) and the effect of this on the use of healthcare services. The objectives of the study were: a) To determine the Municipal Solid Waste (MSW) ratio, per person per day, among populations of known size; b) to estimate, by means of this ratio, the real population in an area where tourist numbers are very significant; and c) to determine the impact on the utilisation of hospital emergency healthcare services of the registered population, in comparison to the non-resident population, in two areas where tourist numbers are very significant.

Methods
An ecological study design was employed. We analysed the Healthcare Districts of the Costa del Sol and the island of Menorca. Both are Spanish territories in the Mediterranean region.

Results
In the two areas analysed, the correlation coefficient between the MSW ratio and admissions to hospital emergency departments exceeded 0.9, with p < 0.001. On the basis of MSW generation ratios, obtained for a control zone and also measured in neighbouring countries, we estimated the real population. For the summer months, when tourist activity is greatest and demand for emergency healthcare at hospitals is highest, this value was found to be double that of the registered population.

Conclusion
The MSW indicator, which is both ecological and indirect, can be used to estimate the real population in areas where population levels vary significantly during the year. This parameter is of interest in planning and dimensioning the provision of healthcare services.
MDA-7/IL-24 suppresses human ovarian carcinoma growth in vitro and in vivo
Authors: Gopalan Began , Shanker Manish , Chada Sunil , Ramesh Rajagopal 
Published: February 2007

Abstract

Background
Previous studies showed that the human melanoma differentiation-associated gene-7 (mda-7), also known as interleukin-24 (IL-24), has potent antitumor activity against human and murine cancer cells. However, the majority of these studies were limited to in vitro testing. In the present study, we investigated the antitumor activity of mda-7/IL-24 against human ovarian cancer cells both in vitro and in vivo.

Results
In vitro, treatment of ovarian cancer cells with an adenoviral vector carrying the mda-7 gene (Ad-mda7) resulted in inhibition of cell proliferation and induction of cell cycle arrest, leading to apoptosis. We did not observe inhibitory activity in Ad-mda7-treated normal cells. In vivo, treatment of subcutaneous tumor xenografts with Ad-mda7 resulted in significant tumor growth inhibition when compared with that in control groups (p < 0.001). Molecular analysis of ovarian tumor tissue lysates treated with Ad-mda7 showed that MDA-7 protein expression was associated with activation of the caspase cascade.

Conclusion
Our results show that treatment of ovarian cancer cells with mda-7/IL-24 results in growth suppression both in vitro and in vivo.
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ
TM
Authors: Siepen Jennifer A , Swainston Neil , Jones Andrew R , Hart Sarah R , Hermjakob Henning , Jones Philip , Hubbard Simon J 
Published: February 2007

Abstract

Background
Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed.

Results
We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ
TM
reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ
TM
reported intensities from Mascot output, into a valid PRIDE XML entry.

Conclusion
We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ
TM
data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from http://www.mcisb.org/software/PrideWizard.
Effect of chloroquine on reducing HIV-1 replication in vitro and the DC-SIGN mediated transfer of virus to CD4+T-lymphocytes
Authors: Naarding Marloes A , Baan Elly , Pollakis Georgios , Paxton William A 
Published: February 2007

Abstract

Background
Chloroquine (CQ) has been shown to inhibit HIV-1 replication in vitro as well as in vivo and has been proposed to alter the glycosylation pattern of the gp120 envelope. These activities indicate that the compound can be used not only as an effective HIV-1 therapeutic agent but also as a modulator of the gp120 envelope protein structure enabling for the production of broader neutralizing Ab responses.

Results
We confirm here that HIV-1 replication on CD4+ T-lymphocytes can be reduced in the presence of CQ and show that the reduced replication is producer cell mediated, with viruses generated in the presence of CQ not being inhibited for subsequent infectivity and replication. By analysing the gp120 envelope protein sequences from viruses cultured long-term in the absence or presence of CQ we demonstrate variant evolution patterns. One noticeable change is the reduction in the number of potential N-linked glycosylation sites in the V3 region as well as within the 2G12 Ab binding and neutralization epitope. We also demonstrate that HIV-1 produced in the presence of CQ has a reduced capacity for transfer by Raji-DC-SIGN cells to CD4+ T-lymphocytes, indicating another means whereby virus transmission or replication may be reduced in vivo.

Conclusion
These results indicate that CQ should be considered as an HIV-1 therapeutic agent with its influence exerted through a number of mechanisms in vivo, including modulation of the gp120 structure.
Quantification of human bocavirus in lower respiratory tract infections in China
Authors: Lin Feng , Zeng Aiping , Yang Ningmin , Lin Haiyan , Yang En , Wang Shengqi , Pintel David , Qiu Jianming 
Published: February 2007

Abstract
A quantitative PCR method was established to quantify human bocavirus (HBoV) genomic copies in clinical specimens from children with lower respiratory tract infections (LRTI) in China. A total of 257 respiratory tract specimens were tested, and 7 (2.7%) of these (all sputum samples) were positive, with genomic copies that ranged from 8.0 × 103 to 8.0 × 109 in the samples. The main clinical symptom of patients who were positive for HBoV DNA was a pneumonia-like syndrome represented by high fever and cough. Our results suggest that HBoV may be an important etiological agent of LRTI in children in China.
DFT/Ab initio Study on the Pathways for the Reaction of CH3SH with NO3 Radical
Authors: Uchimaru Tadafumi , El-Nahas Ahmed M , Sugie Masaaki , Tokuhashi Kazuaki , Sekiya Akira 
Published: February 2007

Abstract
Pathways for hydrogen abstraction (H-abstraction) by the NO3 radical from the SH and the CH sites of the CH3SH molecule have been found for the reaction of CH3SH + NO3. Energy evaluations of the stationary points indicate that H-abstraction exclusively occurs from the SH site via a reactant complex [CH3S(H)–ONO2] possessing a two-center three-electron (2c–3e) S–O bond. Two oxygen atoms of the NO3 radical are involved separately in the 2c–3e S–O bond and in H-abstraction from the SH site.
Effect of Blockade of TNF-α and Interleukin-1 Action on Bone Resorption in Early Postmenopausal Women
Authors: Charatcharoenwitthaya Natthinee , Khosla Sundeep , Atkinson Elizabeth J , McCready Louise K , Riggs B Lawrence 
Published: February 2007

Abstract
After acute estrogen withdrawal in postmenopausal women, administration of anakinra or etanercept, specific blockers of IL-1 and TNF-α, respectively, reduced the rise in bone resorption markers to about one half of that in controls. This is consistent with an important role for these immune cytokines in mediating the effect of estrogen deficiency on bone.
Introduction: Studies in rodents have implicated increased production of interleukin (IL)-1β and TNF-α as mediators of bone loss after ovariectomy, but their roles are unclear in humans whose immune system differs markedly from that of rodents.
Materials and Methods: We administered transdermal estradiol, 0.1 mg/d, for 60 days to 42 early postmenopausal women. Estrogen treatment was discontinued, and subjects were randomly assigned to intervention groups receiving 3 wk of injections with 0.9% saline, anakinra 100 mg/d, or etanercept 25 mg/twice weekly. Bone turnover was assessed by measuring serum carboxyl-terminal telopeptide of type 1 collagen (CTX) and amino-terminal telopeptide of type 1 collagen (NTX), markers for bone resorption, and serum amino-terminal propeptide of type 1 collagen (P1NP), a marker for bone formation. Results were expressed as percent change in markers from baseline (last 2 days of estrogen treatment and days 20 and 21 of intervention).
Results: The percent changes from baseline during intervention for serum CTX, urine NTX, and serum PINP, respectively, were 43.3 ± 8.0%, 12.0 ± 7.1%, and −41.0 ± 2.5% for the control group; 25.9 ± 6.3%, 9.5 ± 4.0%, and −37.8 ± 3.0% for the anakinra group; and 21.7 ± 5.0%, 0.32 ± 3.82%, and −34.5 ± 3.9% for the etanercept group. Compared with the control group, the blunting of the increase in serum CTX fell just below the level of significance (p = 0.10) after anakinra treatment, whereas the blunting of the increase in serum CTX (p = 0.034) and in urine NTX (p = 0.048) were significant after etanercept treatment. Other changes were not significant.
Conclusions: The data are consistent with a role for TNF-α, and possibly for IL-1β, in mediating increased bone resorption during estrogen deficiency in women. Although either cytokine blocker reduced serum CTX by about one half, the effect of combined blockade could not be tested because of concerns about toxicity. The data do not exclude direct or indirect contributory roles for RANKL or for other cytokines.
Variation of Ultrasonic Parameters With Microstructure and Material Properties of Trabecular Bone: A 3D Model Simulation
Authors: Haïat Guillaume , Padilla Frédéric , Peyrin Françoise , Laugier Pascal 
Published: February 2007

Abstract
This study determined the influence of trabecular bone microstructure and material properties on QUS parameters using numerical simulations coupled with high-resolution synchrotron radiation μCT.
Introduction: Finite-difference time domain (FDTD) simulations coupled to 3D microstructural models of trabecular bone reconstructed from synchrotron radiation microtomography (SR-μCT) were used herein to compare and quantify the effects of bone volume fraction, microstructure, and material properties on QUS parameters.
Materials and Methods: 3D SR-μCT datasets of 30 trabecular human femoral bone specimens were used to create binary digital 3D models. We studied the sensitivity of quantitative ultrasound (QUS) to bone volume fraction by examining QUS parameters at different stages of trabecular thinning or thickening using an iterative dedicated algorithm. The sensitivity to bone material properties was also assessed by analyzing different scenarios in which density and stiffness could be varied independently. The effect of microstructure was qualitatively assessed by producing virtual bone specimens of identical bone volume fraction. Simulations of ultrasonic wave propagation through the trabecular bone volumes were performed using the FDTD simulation software SimSonic developed by our group. For each structure, both broadband ultrasonic attenuation (BUA) and speed of sound (SOS) were computed.
Results: BUA and SOS showed a strong correlation with BV/TV (r2 = 0.94, p &lt; 10−4) and varied quasi-linearly with BV/TV at an approximate rate of 2 dB/cm.MHz and 11 m/s per percent increase of BV/TV, respectively. Bone alterations caused by variation in BV/TV between 5% and 25% had a greater impact on QUS variables (variation of BUA: 40 dB/cm.MHz; variation of SOS: 200 m/s) than variations caused by alterations of material properties realized either by a 30% change of density or 40% change of stiffness (BUA: 1.7 dB/cm.MHz; SOS: 43 m/s) or than diversity in microarchitecture (BUA:7.8 dB/cm.MHz; SOS: 36 m/s). Moreover, the sensitivity of BUA and SOS to changes in BMD by a given amount realized by a pure change in bone mass (or BV/TV) was found to be predominant over a pure change of mineralization, except for low BV/TV values, where both effects are comparable.
Conclusions: Trabecular bone microstructure (i.e., trabecular thickness) and material properties were changed to quantify the impact of specific determinants on QUS variables. In this sample of unselected autopsies, specimen variability in bone volume seemed to have a somewhat larger impact on QUS variables than the variability of the other determinants assessed. Whether this is also the case for osteoporotic patients remains to be studied.