bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1gene with missense sequence changes and in-frame deletions, but not polymorphisms
Authors: Pettigrew Christopher , Wayte Nicola , Lovelock Paul K , Tavtigian Sean V , Chenevix-Trench Georgia , Spurdle Amanda B , Brown Melissa A 
Published: September 2005

Abstract
Introduction
Aberrant pre-mRNA splicing can be more detrimental to the function of a gene than changes in the length or nature of the encoded amino acid sequence. Although predicting the effects of changes in consensus 5' and 3' splice sites near intron:exon boundaries is relatively straightforward, predicting the possible effects of changes in exonic splicing enhancers (ESEs) remains a challenge.

Methods
As an initial step toward determining which ESEs predicted by the web-based tool ESEfinder in the breast cancer susceptibility gene BRCA1 are likely to be functional, we have determined their evolutionary conservation and compared their location with known BRCA1 sequence variants.

Results
Using the default settings of ESEfinder, we initially detected 669 potential ESEs in the coding region of the BRCA1 gene. Increasing the threshold score reduced the total number to 464, while taking into consideration the proximity to splice donor and acceptor sites reduced the number to 211. Approximately 11% of these ESEs (23/211) either are identical at the nucleotide level in human, primates, mouse, cow, dog and opossum Brca1 (conserved) or are detectable by ESEfinder in the same position in the Brca1 sequence (shared). The frequency of conserved and shared predicted ESEs between human and mouse is higher in BRCA1 exons (2.8 per 100 nucleotides) than in introns (0.6 per 100 nucleotides). Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database. Applying the filters described above increased the colocalization of predicted ESEs with missense changes, in-frame deletions and unclassified variants predicted to be deleterious to protein function, whereas they decreased the colocalization with known polymorphisms or unclassified variants predicted to be neutral.

Conclusion
In this report we show that evolutionary conservation analysis may be used to improve the specificity of an ESE prediction tool. This is the first report on the prediction of the frequency and distribution of ESEs in the BRCA1 gene, and it is the first reported attempt to predict which ESEs are most likely to be functional and therefore which sequence variants in ESEs are most likely to be pathogenic.
Quantifying bedside-derived imaging of microcirculatory abnormalities in septic patients: a prospective validation study
Authors: Boerma E Christiaan , Mathura Keshen R , van der Voort Peter HJ , Spronk Peter E , Ince Can 
Published: September 2005

Abstract
Introduction
The introduction of orthogonal polarization spectral (OPS) imaging in clinical research has elucidated new perspectives on the role of microcirculatory flow abnormalities in the pathogenesis of sepsis. Essential to the process of understanding and reproducing these abnormalities is the method of quantification of flow scores.

Methods
In a consensus meeting with collaboraters from six research centres in different fields of experience with microcirculatory OPS imaging, premeditated qualifications for a simple, translucent and reproducible way of flow scoring were defined. Consecutively, a single-centre prospective observational validation study was performed in a group of 12 patients with an abdominal sepsis and a new stoma. Flow images of the microcirculation in vascular beds of the sublingual and stoma region were obtained, processed and analysed in a standardised way. We validated intra-observer and inter-observer reproducibility with kappa cross-tables for both types of microvascular beds.

Results
Agreement and kappa coefficients were >85% and >0.75, respectively, for interrater and intrarater variability in quantification of flow abnormalities during sepsis, in different subsets of microvascular architecture.

Conclusion
Semi-quantitative analysis of microcirculatory flow, as described, provides a reproducible and transparent tool in clinical research to monitor and evaluate the microcirculation during sepsis.
Transient conduction analytical solutions for testing of building energy simulation programs
Authors: Xiao Dongyi , Spitler Jeffrey D , Rees Simon J , Dougherty Ronald L 
Published: September 2005

As part of a recent effort to develop an analytical verification test suite for building fabric models of whole building energy simulation programs, two new transient conduction analytical tests have been developed. These new tests make it possible to use boundary conditions that are typical of real building conduction heat transfer conditions. This paper describes the corresponding analytical models and the derivation of the solutions. Some details of existing tests are given for the sake of completeness. The zone description and parameter requirements necessary to apply the tests, along with results from two test programs, are also presented. Practical application: Building energy simulation programs are being increasingly relied upon by practicing engineers for design, performance evaluation and in demonstrating regulation compliance. Accordingly there is a significant demand for simulation model and computer program quality assurance. These tests can be used by developers and users to demonstrate a program’s ability to calculate conduction heat transfer processes.
COX-2 and prostaglandins in atherosclerosis
Authors: Cipollone F 
Published: September 2005

Arachidonic acid metabolism is involved in acute ischemic syndromes affecting the coronary or cerebrovascular territory, as demonstrated by biochemical measurements of eicosanoid biosynthesis and the results of inhibitor trials in these settings. In particular, the efficacy of low-dose aspirin in reducing the complications of acute ischemic syndromes has focused attention on the cyclooxygenase (COX) pathway of arachidonic acid metabolism and its products, collectively termed prostanoids. Two cyclooxygenase (COX)-isozymes have been characterized, COX-1 and COX-2, that differ in terms of regulatory mechanisms of expression, tissue distribution, substrate specificity and preferential coupling to upstream and downstream enzymes. While the role of platelet COX-1 in acute ischemic diseases is firmly established, the role of COX-2 in atherothrombosis is still uncertain. Studies from our group suggest that variable expression of upstream and downstream enzymes in the prostanoid biosynthesis may represent important determinants of the functional consequences of COX-2 expression and inhibition in different clinical settings.
Oxidant stress, inflammation and atherogenesis
Authors: Davì G , Falco A 
Published: September 2005

Low-grade inflammation, enhanced oxidant stress and lipid peroxidation have been shown in association with increased cardiovascular risk associated with cardiovascular events. It has been hypothesized that the low-grade inflammatory state characterizing metabolic disorders such as obesity, hypercholesterolemia, type 2 diabetes mellitus and homozygous homocystinuria may be the primary trigger of thromboxane-dependent platelet activation mediated, at least in part, through enhanced lipid peroxidation. Interestingly, as the clinical course of systemic lupus erythematosus (SLE), in particular in the presence of antiphospholipid antibodies, may be complicated by vascular disease, several mechanism contributing to vascular complications have been documented also in this setting, including enhanced lipid peroxidation and thromboxane biosynthesis. Although epidemiological studies show an inverse relationship between antioxidant vitamin intake and cardiovascular disease, several clinical trials have obtained conflicting results on the effects of vitamin E on the risk of cardiovascular events. The availability of analytical tools for measuring F2-isoprostane biosynthesis in man has improved our understanding of the interplay between lipid peroxidation and low-grade inflammation. The use of F2-isoprostane as a biochemical end-point for dose-finding studies may allow reassessing the adequacy of vitamin supplementation in different clinical settings.
Pharmacological modulation of plaque instability
Authors: Mezzetti A 
Published: September 2005

Atherosclerotic plaque rupture is promoted by metalloproteinase (MMP)-2 and MMP-9, enzymes that degrade the fibrous cap leading to plaque erosion. MMP biosynthesis is mediated by prostaglandin (PG)E2, the product of cyclooxygenase (COX)-2/inducible PGE synthase (mPGES) activity. We have recently reported the overexpression of COX-2/mPGES-1 in vulnerable plaques as a basis of MMP-mediated plaque instability. Hypercholesterolemia and hypertension are two important risk factors for atherosclerosis. Recent trial showed that statins and AT1 receptor blockers significantly reduce the incidence of cardiovascular events in humans. Since anti-inflammatory effects have been reported in association to therapy with statins or AT1 receptor blockers, in two different studies we hypothesized that these drugs can stabilize atherosclerotic plaques through modulation of COX-2/mPGES-1-dependent MMP biosynthesis. Our data demonstrated the stabilizing effect of atherosclerotic plaques by simvastatin or irbesartan, that is due, at least in part, to the reduction of inflammatory burden and suppression of PGE2-dependent metalloproteinases release.
Viewing a Map Versus Reading a Description of a Map: Modality‐Specific Encoding of Spatial Information
Authors: Tlauka Michael , Keage Hannah , Clark C. Richard 
Published: September 2005

AbstractThis study investigated whether brain neural activity that accompanied the processing of previously learned map information was influenced by the modality in which the spatial parameters of the maps were originally learned. Participants learned a map by either viewing it directly or by reading an equivalent verbal description. Following learning, the participants' ability to use their spatial knowledge was tested in a spatial orientation task. Electrophysiological recordings identified significant effects of prior learning modality on event‐related brain activity within 300 ms following the presentation of map orientation instructions. The results indicate that modality‐specificity in spatial memory is present at a very early stage of processing.
Efficacy of Cognitive—Behavioural Therapy for Children and Adolescents With Anxiety Disorders
Authors: Hudson Jennifer L. 
Published: September 2005

AbstractSupport for the efficacy of cognitive—behavioural therapy (CBT) for anxious youth has accumulated. Significant treatment effects are observed and maintained over the long term for the majority of children receiving individual, family or group-based treatments. Nevertheless, all children do not improve. In fact, there is evidence to suggest that a significant percentage of children continue to experience anxiety following treatment and will seek additional treatment for their anxiety. This article will review the substantial evidence for CBT, the current information available on predictors of outcome and mechanisms of change. The article will also discuss the need for adequately powered randomised clinical trials that continue to refine and evaluate treatments for anxious children in an effort to improve outcomes for those children whose needs are not being met by our current treatments.
Co-morbidity and Associated Clinical Problems in Schizophrenia: Their Nature and Implications for Comprehensive Cognitive—Behavioural Treatment
Authors: Tarrier Nicholas 
Published: September 2005

AbstractSchizophrenia is a multifaceted disorder that can affect many aspects of the sufferer's life. Recent advances in the use of cognitive—behaviour therapy as an adjunct treatment for schizophrenia have been shown to result in significant improvements in psychotic symptoms. However, to date, much less attention has been paid to other co-morbid and emotional disorders that often co-exist with psychosis and that can be a severe burden to the sufferer. This article briefly reviews clinical trials of cognitive—behavioural treatments for schizophrenia and their outcome and then goes on to describe clinically important co-morbid or associated clinical problems: social anxiety, posttraumatic stress disorder (PTSD), depression and suicide risk. Because the psychotic symptoms usually receive priority, there has been little in the cognitive—behavioural literature on the nature and treatment of these co-morbid disorders. The nature of these problems and issues relating to their treatment are discussed.
Mean fluorescence intensity rate is a useful marker in the detection of paroxysmal nocturnal hemoglobinuria clones
Authors: Hevessy Zsuzsa , Nagy Béla , Kiss Flóra , Kiss Attila , Kappelmayer János 
Published: September 2005

Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired disorder of the pluripotent stem cell resulting from the somatic mutation of the X-linked PIG-A gene, involved in the synthesis of the glycosylphosphatidyl-inositol anchor of membrane proteins such as CD55, CD59 and CD14. In the past decade, flow cytometry has become a valuable diagnostic tool in the detection of deficient expression of the GPI-anchored proteins. We report the diagnosis of PNH in four patients confirmed by flow cytometry. Red blood cells, granulocytes and monocytes were classified as PNH types I, II and III according to the mean fluorescence intensities (MFI) of membrane proteins. MFI rate is a numerical data reflecting the severity of decreased antigen expression, and it is obtained by dividing the MFI of the type II or type III cells by the MFI of the respective cells obtained for a normal sample. We found that the investigation of granulocytes and monocytes was more informative than red blood cells when percent negativity was evaluated. In addition, the lowest MFI rate (mean 0.011) was obtained for CD14 on monocytes while CD59 and CD55 gave higher values on all three investigated cell types (0.021–0.34). Thus, CD14 on monocytes seems to be the most reliable marker for establishing the PNH clone size and the severity of antigen deficiency.
Multicentre physiological reference values for some urinary component-to-creatinine (creatininium) concentration ratios
Authors: Fuentes-Arderiu Xavier , Mas-Serra Roser , de-Nó-Lengaran Carmen , Espejo-López Francisco , Filgueiras-Martínez Paula , Gassiot-Cordomí Paula , Idoate-Cervantes Isabel , Poncela-García María Victoria , Porras-Gracia Juan , Sanz-Lobo Irene , del Mar Viloria-Peñas María , Juvé-Cuxart Santiago 
Published: September 2005

AbstractNine clinical laboratories in different regions of Spain have shared the search for reference individuals and the production of reference values for urinary component-to-creatininium concentration ratios measured in first morning urine samples using RD/Hitachi<MODULAR ANALYTICS> analysers. These urinary quantities include albumin, calcium(II), chloride, magnesium(II), phosphate, potassium ion, protein, sodium ion, urate and urea. All the logistic work was done in co-operation with the reagents' and analysers' supplier (Roche Diagnostics España, S.L., Sant Cugat del Vallès, Catalonia, Spain). From the blend of reference values obtained by each laboratory, the multicentre reference limits were estimated parametrically after mathematical transformation of original data.
Fabrication and Electrical and Mechanical Properties of Carbon Nanotube Interconnections
Authors: Wang M. S. , Wang J. Y. , Chen Q. , Peng L.‐M. 
Published: September 2005

AbstractIndividual carbon nanotubes (CNTs) have been cut, manipulated, and soldered via electron‐beam‐induced deposition of amorphous carbon (a‐C) and using a scanning tunneling microscope inside a transmission electron microscope. All CNT structures, including simple tube–tube connections, crossed junctions, T‐junctions, zigzag structures, and even nanotube networks, have been successfully constructed with a high degree of control, and their electrical and mechanical properties have been measured in situ inside the transmission electron microscope. It is found that multiple CNTs may be readily soldered together with moderate junction resistance and excellent mechanical resilience and strength, and the junction resistance may be further reduced by current‐induced graphitization of the deposited a‐C on the junction.
Systematic review of endovenous laser treatment for varicose veins
Authors: Mundy L , Merlin T L , Fitridge R A , Hiller J E 
Published: September 2005

Abstract

Background
The safety and effectiveness of endovenous laser treatment (EVLT) for varicose veins are not yet fully evaluated.

Methods
Medical bibliographic databases, the internet and reference lists were searched from January 1966 to September 2004. Only case series were available for inclusion in the review.

Results
Thirteen studies met the inclusion criteria. Self-limiting features, such as pain, ecchymosis, induration and phlebitis, were commonly encountered after treatment. Deep vein thrombosis and incorrect placement of the laser in vessels were uncommon adverse events. No study has yet assessed the effectiveness of laser therapy in comparison to saphenofemoral junction ligation with saphenous vein stripping. Occlusion of the saphenous vein and abolition of venous reflux occurred in 87·9–100 per cent of limbs, with low rates of re-treatment and recanalization.

Conclusion
From the low-level evidence available it seems that EVLT benefits most patients in the short term, but rates of recanalization, re-treatment, occlusion and reflux may alter with longer follow-up. The lack of such data, in addition to the small numbers of patients in the available studies, demonstrates the need for a randomized clinical trial of EVLT versus conventional surgery.
Systematic review comparing laparoscopic and open repair for perforated peptic ulcer
Authors: Lunevicius R , Morkevicius M 
Published: September 2005

AbstractBackgroundThe advantages of laparoscopic over open repair for perforated peptic ulcer are not as obvious as they may seem. This paper summarizes the published trials comparing the two approaches.MethodsTwo randomized prospective, five non-randomized prospective and eight retrospective studies were included in the analysis. Relevant trials were identified from the Medline/Pubmed database and the reference lists of the retrieved papers were then analysed. The outcome measures used were operating time, postoperative analgesic requirements, length of hospital stay, return to normal diet and usual activities, and complication and mortality rates. Published data were tested for heterogeneity by means of a χ2 test. Meta-analysis methods were used to measure the pooled estimate of the effect size. In total, 1113 patients are represented from 15 selected studies, of whom 535 were treated by laparoscopic repair and 578 by open repair; 102 patients (19·1 per cent) underwent conversion to open repair.ResultsStatistically significant findings in favour of laparoscopic repair were less analgesic use, shorter hospital stay, less wound infection and lower mortality rate. Shorter operating time and less suture-site leakage were advantages of open repair. Three variables (hospital stay, operating time and analgesic use) were significantly heterogeneous in the papers analysed.ConclusionLaparoscopic repair seems better than open repair for low-risk patients. However, limited knowledge about its benefits and risks compared with open repair suggests that the latter, more familiar, approach may be more appropriate in high-risk patients. Further studies are needed.
Pretarget sorting of retinocollicular axons in the mouse
Authors: Plas Daniel T. , Lopez Joshua E. , Crair Michael C. 
Published: September 2005

AbstractThe map of the retina onto the optic tectum is a highly conserved feature of the vertebrate visual system; the mechanism by which this mapping is accomplished during development is a long‐standing problem of neurobiology. The early suggestion by Roger Sperry that the map is formed through interactions between retinal ganglion cell axons and target cells within the tectum has gained significant experimental support and widespread acceptance. Nonetheless, reports in a variety of species indicate that some aspects of retinotopic order exist within the optic tract, leading to the suggestion that this “preordering” of retinal axons may play a role in the formation of the mature tectal map. A satisfactory account of pretarget order must provide the mechanism by which such axon order develops. Insofar as this mechanism must ultimately be determined genetically, the mouse suggests itself as the natural species in which to pursue these studies. Quantitative and repeatable methods are required to assess the contribution of candidate genes in mouse models. For these reasons, we have undertaken a quantitative study of the degree of retinotopic order within the optic tract and nerve of wild‐type mice both before and after the development of the retinotectal map. Our methods are based on tract tracing using lipophilic dyes, and our results indicate that there is a reestablishment of dorsoventral but not nasotemporal retinal order when the axons pass through the chiasm and that this order is maintained throughout the subsequent tract. Furthermore, this dorsoventral retinotopic order is well established by the day after birth, long before the final target zone is discernible within the tectum. We conclude that pretarget sorting of axons according to origin along the dorsoventral axis of the retina is both spatially and chronologically appropriate to contribute to the formation of the retinotectal map, and we suggest that these methods be used to search for the molecular basis of such order by using available mouse genetic models. J. Comp. Neurol. 491:305–319, 2005. © 2005 Wiley‐Liss, Inc.
Spatiotemporal expression of GM1 in murine medial pallial neural progenitor cells
Authors: Liour Sean S. , Dinkins Michael B. , Su Chen‐Ying , Yu Robert K. 
Published: September 2005

AbstractThe expression of gangliosides is developmentally regulated in the central nervous system. The expression of GM1 in the neural progenitor cells of the telencephalonic ventricular zone (VZ) has been reported in several studies. However, information on the spatial and temporal regulation of GM1 expression in the VZ is still lacking. In this study, we characterized the expression of GM1 in the developing mouse telencephalon. At E13, GM1 is expressed in neuronal cells as well as in the VZ. The initial expression of GM1 in the VZ is restricted to regions close to the medial pallium. Fluorescence‐activated cell sorting (FACS) analysis and characterization of E14 GM1‐positive cells showed that they contain progenitor cells that proliferate in response to epidermal growth factor (EGF) and/or basic fibroblast growth factor (bFGF) stimulation. The results obtained from quantitative gene expression analysis of region‐specific genes (Emx1, Lhx2, Ngn1, Ngn2, Pax6, Dlx2, Gsh2, Mash1, and Nkx2.1), using real‐time polymerase chain reaction indicate that FACS of GM1‐expressing cells in the fetal forebrain enriches for the medial pallial neural progenitor cells. J. Comp. Neurol. 491:330–338, 2005. © 2005 Wiley‐Liss, Inc.