bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Perl toolkit for LIMS development
Authors: Morris James A , Gayther Simon A , Jacobs Ian J , Jones Christopher 
Published: March 2008

Abstract

Background
High throughput laboratory techniques generate huge quantities of scientific data. Laboratory Information Management Systems (LIMS) are a necessary requirement, dealing with sample tracking, data storage and data reporting. Commercial LIMS solutions are available, but these can be both costly and overly complex for the task. The development of bespoke LIMS solutions offers a number of advantages, including the flexibility to fulfil all a laboratory's requirements at a fraction of the price of a commercial system. The programming language Perl is a perfect development solution for LIMS applications because of Perl's powerful but simple to use database and web interaction, it is also well known for enabling rapid application development and deployment, and boasts a very active and helpful developer community. The development of an in house LIMS from scratch however can take considerable time and resources, so programming tools that enable the rapid development of LIMS applications are essential but there are currently no LIMS development tools for Perl.

Results
We have developed ArrayPipeline, a Perl toolkit providing object oriented methods that facilitate the rapid development of bespoke LIMS applications. The toolkit includes Perl objects that encapsulate key components of a LIMS, providing methods for creating interactive web pages, interacting with databases, error tracking and reporting, and user and session management. The MT_Plate object provides methods for manipulation and management of microtitre plates, while a given LIMS can be encapsulated by extension of the core modules, providing system specific methods for database interaction and web page management.

Conclusion
This important addition to the Perl developer's library will make the development of in house LIMS applications quicker and easier encouraging laboratories to create bespoke LIMS applications to meet their specific data management requirements.
Takayasu's arteritis associated with Crohn's disease: a case report
Authors: Daryani Nasser E , Habibi Atoosa Nayer , Bashashati Mohammad , Keramati Mohammad Reza , Rafiee Moezedin Javad , Ajdarkosh Hossein , Azmi Mehrdad 
Published: March 2008

Abstract

Introduction
The simultaneous presence of Takayasu's arteritis and Crohn's disease in a patient seems to be rare. To our knowledge, no patient with the combination of Crohn's disease and Takayasu's arteritis has been reported from our region.

Case presentation
Herein we present the case of a 22-year-old Iranian woman previously diagnosed as Crohn's disease and who had subsequently developed Takayasu's arteritis.

Conclusion
Clinical suspicion, proper imaging, and consideration of the differential diagnosis are important for the correct diagnosis and management of patients with this coincidence.
Resting CD4+effector memory T cells are precursors of bystander-activated effectors: a surrogate model of rheumatoid arthritis synovial T-cell function
Authors: Brennan Fionula M , Smith Nicola MG , Owen Sally , Li Ching , Amjadi Parisa , Green Patricia , Andersson Anna , Palfreeman Andrew C , Hillyer Philippa , Foey Andrew , Beech Jonathan T , Feldmann Marc 
Published: March 2008

Abstract
Background
Previously we described a system whereby human peripheral blood T cells stimulated for 8 days in a cytokine cocktail acquired effector function for contact-dependent induction of proinflammatory cytokines from monocytes. We termed these cells cytokine-activated (Tck) cells and found that the signalling pathways elicited in the responding monocytes were identical whether they were placed in contact with Tck cells or with T cells isolated from rheumatoid arthritis (RA) synovial tissue.

Methods
Here, using magnetic beads and fluorescence-activated cell sorting, we extensively phenotype the Tck effector cells and conclude that effector function resides within the CD4+CD45RO+, CCR7-, CD49dhigh population, and that these cells are derived from the effector memory CD4+ T cells in resting blood.

Results
After stimulation in culture, these cells produce a wide range of T-cell cytokines, undergo proliferation and differentiate to acquire an extensively activated phenotype resembling RA synovial T cells. Blocking antibodies against CD69, CD18, or CD49d resulted in a reduction of tumour necrosis factor-α production from monocytes stimulated with CD4+CD45RO+ Tck cells in the co-culture assay. Moreover, blockade of these ligands also resulted in inhibition of spontaneous tumour necrosis factor-α production in RA synovial mononuclear cell cultures.

Conclusion
Taken together, these data strengthen our understanding of T-cell effector function, highlight the multiple involvement of different cell surface ligands in cell-cell contact and, provide novel insights into the pathogenesis of inflammatory RA disease.
Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays
Authors: Li Lei , He Hang , Zhang Juan , Wang Xiangfeng , Bai Sulan , Stolc Viktor , Tongprasit Waraporn , Young Nevin D , Yu Oliver , Deng Xing-Wang 
Published: March 2008

Abstract
Background
Legumes are the third largest family of flowering plants and are unique among crop species in their ability to fix atmospheric nitrogen. As a result of recent genome sequencing efforts, legumes are now one of a few plant families with extensive genomic and transcriptomic data available in multiple species. The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery.

Results
We report here a transcriptional analysis in six different organ types of syntenic regions totaling approximately 1 Mb between the legume plants barrel medic (Medicago truncatula) and soybean (Glycine max) using oligonucleotide tiling microarrays. This analysis detected transcription of over 80% of the predicted genes in both species. We also identified 499 and 660 transcriptionally active regions from barrel medic and soybean, respectively, over half of which locate outside of the predicted exons. We used the tiling array data to detect differential gene expression in the six examined organ types and found several genes that are preferentially expressed in the nodule. Further investigation revealed that some collinear genes exhibit different expression patterns between the two species.

Conclusion
These results demonstrate the utility of genome tiling microarrays in generating transcriptomic data to complement computational annotation of the newly available legume genome sequences. The tiling microarray data was further used to quantify gene expression levels in multiple organ types of two related legume species. Further development of this method should provide a new approach to comparative genomics aimed at elucidating genome organization and transcriptional regulation.
Insulin-Stimulated Rates of Glucose Uptake in Muscle in Hyperthyroidism: The Importance of Blood Flow
Authors: Dimitriadis George , Mitrou Panayota , Lambadiari Vaia , Boutati Eleni , Maratou Eirini , Koukkou Eftychia , Panagiotakos Demosthenes , Tountas Nikos , Economopoulos Theofanis , Raptis Sotirios A. 
Published: March 2008

AbstractBackground: In hyperthyroidism, although hepatic insulin resistance is well established, information on the effects of insulin on glucose uptake in skeletal muscle is variable.Methods: To investigate this, a meal was given to nine hyperthyroid (HR) and seven euthyroid (EU) subjects. Blood was withdrawn for 360 min from a forearm deep vein and the radial artery for measurements of insulin and glucose. Forearm blood flow (BF) was measured with strain-gauge plethysmography. Glucose flux was calculated as arteriovenous difference multiplied by BF and fractional glucose extraction as arteriovenous difference divided by arterial glucose concentrations.Results: Both groups displayed comparable postprandial glucose levels, with the HR having higher insulin levels than the EU. In the forearm of HR vs. EU: 1) glucose flux was similar [area under the curve (AUC)0–360 673 ± 143 vs. 826 ± 157 μmol per 100 ml tissue]; 2) BF was increased (AUC0–360 3076 ± 338 vs. 1745 ± 145 ml per 100 ml tissue, P = 0.005); and 3) fractional glucose extraction was decreased (AUC0–360 14.5 ± 3 vs. 32 ± 5%min, P = 0.03).Conclusions: These results suggest that, in hyperthyroidism, insulin-stimulated glucose uptake in muscle is impaired; this defect is corrected, at least in part, by the increases in BF.
Experimental set-up and sensory glove interface for microsurgery
Authors: Amirouche F , Martin J R , Gonzalez M , Fergusson L 
Published: March 2008

One of the most fundamental prerequisites for successful microsurgery is thoughtful and adequate training. A combination of knowledge, technical skill, and decision making directly influences the surgical outcome. This study aims to analyse microsurgical hand coordinations quantitatively and to study the utility of a sensory glove interface in identifying the hand coordination patterns during microsurgery. A sensory glove interface used to measure the angular flexion—extension movements of the major interphalangeal joints of the hand, the grasp pressure, and the relative hand movements has been developed. Experiments of two suturing techniques were conducted with five experienced microsurgeons, and microsurgery practice was examined. The custom sensory glove interface required both signal conditioning and amplification which was directly interfaced with a custom-designed LABView software code. The sensory glove interface was calibrated using regression techniques and the set-up was validated using the Bland—Altman correlation technique. The hand coordination patterns were analysed using principal-component analysis. Pareto plots showing the contribution of the principal components were analysed. The contributions of the first two sensory data components have also been compared with hand coordination studies. The temporal variations provided new insights into the underlying synergetic mechanisms and in particular the relation between different suture techniques on grasp pressure.
The internal pressure and stress environment of the scoliotic intervertebral disc — a review
Authors: Meir A , McNally D S , Fairbank J C , Jones D , Urban J P 
Published: March 2008

The aetiology, in terms of both initiation and progression, of the deformity in idiopathic scoliosis is at present unclear. Even in neuromuscular cases, the mechanisms underlying progression are not fully elucidated. It is thought, however, that asymmetrical loading is involved in the progression of the disease, with evidence mainly from animal studies and modelling. There is, however, very little direct information as to the origin or mechanism of action of these forces in the scoliotic spine. This review describes the concept of intervertebral disc pressure or stress and examines possible measurement techniques. The biological and mechanical consequences of abnormalities in these parameters are described. Future possible studies and their clinical significance are also briefly discussed. Techniques of pressure measurement have culminated in the development of ‘pressure profilometry’, which provides stress profiles across the disc in mutually perpendicular axes. A hydrated intervertebral disc exhibits mainly hydrostatic behaviour. However, in pathological states such as degeneration and scoliosis, non-hydrostatic behaviour predominates and annular peaks of stress occur. Recent studies have shown that, in scoliosis, high hydrostatic pressures are seen with asymmetrical stresses from concave to convex sides. These abnormalities could influence both disc and endplate cellular activity directly, causing asymmetrical growth and matrix changes. In addition, disc cells could be influenced via nutritional changes consequent to end-plate calcification. Evidence suggests that the stress environment of the scoliotic disc is abnormal, probably generated by high and asymmetrical loading of non-muscular origin. If present in the scoliotic spine during daily activities, this could generate a positive feedback of cellular changes, resulting in curve progression. Future advances in understanding may rely on the development of computer models owing to the difficulties of in-vivo invasive measurements.
Tibiofemoral cartilage thickness distribution and its correlation with anthropometric variables
Authors: Connolly A , FitzPatrick D , Moulton J , Lee J , Lerner A 
Published: March 2008

The objective of this study was to determine tibiofemoral cartilage thickness distribution, and to investigate the relationship between cartilage geometry and anthropometric variables. In this study, 20 magnetic resonance examinations of the knee from normal individuals were reconstructed to provide three-dimensional models of the knee joint, including bony and cartilage surfaces. Three regions were defined on the articular surface, and the cartilage thickness distribution along each of these was determined. Statistically significant differences between femoral and tibial regions were examined using the paired Student t test in Microsoft Excel. Correlations were investigated using the correlation tool in Microsoft Excel. The average tibial cartilage thickness was found to be 2.76 mm and the average femoral cartilage thickness was 2.75 mm. Significant correlations exist between the tibia cartilage thickness and body height ( R = 0.60; P<0.05) and weight ( R = 0.64; P < 0.05). Significant correlations exist between the femoral cartilage volume and the body height ( R = 0.736; P < 0.01) and weight ( R = 0.855; P < 0.01). It is suggested that the distribution and correlations of cartilage distribution indicate adaptation in response to mechanical loading. Information regarding cartilage thickness and volume distribution as found in this study may be useful in diagnosing and monitoring cartilage loss in patients with degenerative joint disease.
On the frictionless axi-symmetric contact of a thick elastic layer and the associated squeeze film problem
Authors: Jaffar M J 
Published: March 2008

The problem of the frictionless axi-symmetric indentation between a thick elastic layer (the contact radius does not exceed the layer thickness) and a rigid spherical indenter is investigated. The kernel of the governing integral equation was broken down into two parts. The first corresponds to the Hertzian solution and the second represents the contribution due to the finite layer thickness. The second part was approximated by an absolute and uniform convergent series. Hence, the governing elasticity equation was reduced to a set of linear equations. A set of simple formulae for the contact pressure, total load, and penetration depth are presented. The obtained formulae were compared with the existing numerical results where good agreement was found. Furthermore, the associated squeeze film problem is examined. Expressions for the variation of the film thickness with time were derived using two different pressure conditions.
Association of Pharmacist Presence on Compliance with Advanced Cardiac Life Support Guidelines During In-Hospital Cardiac Arrest
Authors: Draper Heather M , Eppert J Alex 
Published: March 2008

BACKGROUND: The pharmacist has many potential roles as part of the resuscitation team during cardiopulmonary arrest. Limited published research has evaluated the practice of advanced cardiac life support (ACLS) during in-hospital arrest. Recent reviews indicate that an audit of in-hospital resuscitation practices should be performed to guide future resuscitation training programs for hospital personnel. OBJECTIVE: To assess compliance with ACLS guidelines during in-hospital cardiopulmonary arrest in a community teaching hospital and evaluate the association of compliance with the presence of a pharmacist on the resuscitation team. METHODS: A retrospective analysis of the records of 74 consecutive in-hospital arrests occurring between January 1, 2003, and June 30, 2004, was conducted to evaluate compliance with American Heart Association ACLS guidelines. RESULTS: A total of 74 arrests were evaluated. Noncompliance was noted in 58.1% of all documented arrests; of the 650 treatment interventions identified, 10.6% were noncompliant with ACLS guidelines. The reasons cited for noncompliance included an incorrect medication dosage (20.3%), prolonged period of time between sequential interventions (26.1%), omission of an indicated treatment (17.4%), deviation from recommended treatment guidelines (26.1%), and incorrect energy for defibrillation (10.1%). A pharmacist was present at 36.5% of documented arrests. Compliance with ACLS treatment guidelines was more likely during resuscitations in which a pharmacist was present (59.3% vs 31.9%; p = 0.03). CONCLUSIONS: Noncompliance with resuscitation guidelines was common during in-hospital resuscitation. The presence of a pharmacist on the resuscitation team was associated with improved compliance with treatment guidelines. Despite institutional requirements for pharmacist participation during resuscitation efforts, participation rates remain low. Further evaluation of the role of the pharmacist on the resuscitation team and the impact of the pharmacist on resuscitation practices should be considered.
Frequency of HIV-Related Medication Errors and Associated Risk Factors in Hospitalized Patients
Authors: Pastakia Sonak D , Corbett Amanda H , Raasch Ralph H , Napravnik Sonia , Correll Todd A 
Published: March 2008

BACKGROUND: Retrospective studies of hospitalized HIV-infected patients have noted a high occurrence of drug-related errors, ranging from 5% to 30%. OBJECTIVE: To prospectively evaluate errors in antiretroviral (ARV) prescribing in the inpatient setting of a hospital tertiary care center and the association of risk factors with the occurrence of errors. METHODS: HIV-infected patients who received care and continued their ARVs for HIV infection on admission to a large academic teaching hospital between January and April 2006 were included in this study. The care and assessment of these patients was conducted on a daily basis by an infectious diseases/HIV specialized clinical pharmacist. All errors were documented and classified based on a severity scale. RESULTS: Among the 68 patients who met the study's eligibility criteria, at least one error in the initial HIV regimen occurred in 72% of patients, and in 56% of patients, the error had the potential to cause moderate-to-severe discomfort or clinical deterioration. Patients on atazanavir-based therapy had a statistically significant increased occurrence of errors throughout their hospitalization (RR = 1.69; 95% CI 1.03 to 2.78; p = 0.02). Receiving nonformulary (combination) HIV medications increased patients' risk of having more than one error occur in their ARV regimen on admission and during hospitalization (RR = 1.95; 95% CI 1.25 to 3.04; p = 0.02). The clinical pharmacist recommendations had 100% acceptance. CONCLUSIONS: The alarmingly high frequency of potentially harmful errors uncovered in this study necessitates further investigation using larger sample sizes. Interventions to reduce and prevent these errors must be sought to eliminate the unintended harm associated with hospitalization.
Safety of Glyburide for Gestational Diabetes: A Meta-Analysis of Pregnancy Outcomes
Authors: Moretti Myla E , Rezvani Massoud , Koren Gideon 
Published: March 2008

BACKGROUND: Gestational diabetes mellitus affects approximately 4% of all pregnancies. As with other oral hypoglycemics, the use of glyburide in pregnancy has been limited by fears of neonatal hypoglycemia following fetal exposure. Recent experimental and clinical studies have suggested, however, that the drug is not detectable in umbilical blood. OBJECTIVE: To determine the safety of glyburide use in pregnancy in the treatment of gestational diabetes compared with insulin therapy by analyzing all available human studies. METHODS: We conducted a systematic review and meta-analysis of all randomized and cohort studies that reported on the perinatal complications among women with gestational diabetes who received glyburide versus insulin. MEDLINE, EMBASE, and biological abstracts using BIOSIS previews were searched from inception of these databases through October 2006. The following outcomes were included: macrosomia, birthweight, gestational age, neonatal hypoglycemia, and intensive care unit (ICU) admissions. Odds ratios were calculated by the random effects method using Cochrane's Review Manager version 4.3. RESULTS: Nine studies met the inclusion criteria, including a total of 745 glyburide-exposed pregnancies and 637 insulin-exposed pregnancies, with each adverse perinatal outcome reported by 4–7 studies. The use of glyburide was not associated with risk of macrosomia (OR 1.07; 95% CI 0.78 to 1.47), differences in birth weight (weighted mean difference [WMD] OR 20.46 g; 95% CI −34.90 to 75.82), rate of large for gestational age (OR 1.04; 95% CI 0.75 to 1.43), differences in gestational age at birth (WMD 0.02 wk; 95% CI −0.23 to 0.26), ICU admission (OR 0.95; 95% CI 0.43 to 2.09), or increased risk of neonatal hypoglycemia (OR 1.24; 95% CI 0.91 to 1.69). CONCLUSIONS: The data shown here do not suggest increased perinatal risks with glyburide. The effectiveness and safety of glyburide require further evaluation, as most studies to date were not randomized.
Anti-Xa Stability of Diluted Dalteparin for Pediatric Use
Authors: Goldenberg Neil A , Jacobson Linda , Hathaway Hannah , Tripputi Mark , Primeaux Judy , Child Jason 
Published: March 2008

BACKGROUND: The low-molecular-weight heparin (LMWH) dalteparin is approved by the Food and Drug Administration for prophylaxis of venous thromboembolism (VTE) in adults and has recently received an indication for acute VTE therapy in adults with cancer. Published reports of experience with dalteparin use in European children suggest that this LMWH agent is safe and effective in the prophylaxis and treatment of VTE in the pediatric population. However, dalteparin is commonly available in the US in a concentrated form that requires dilution for accurate administration in infants and young children. OBJECTIVE: To investigate the in vitro stability of diluted dalteparin for pediatric use, as measured by serial anti-Xa activity assays over the course of 4 weeks. METHODS: At 2 clinical research pharmacies, dalteparin multidose vials (anti-Xa concentration 25,000 U/mL) of the 2 distinct lots presently available for clinical use were diluted 1:10 with preservative-free NaCl 0.9% and maintained in tuberculin syringes at 4 °C. Syringes were then sampled for anti-Xa activity by chromogenic assay at baseline and weekly over the course of 4 weeks. RESULTS: For each lot of dalteparin, there was strong agreement in anti-Xa activity between corresponding diluted syringes prepared at the 2 pharmacy sites. No statistically significant difference in anti-Xa activity was detected from baseline to any time point, nor was a trend of change detected in anti-Xa activity with time for either lot of dalteparin. CONCLUSIONS: These data indicate that the anti-Xa activity of diluted dalteparin for pediatric use is stable over the course of 4 weeks.