bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating linkage and radiation hybrid mapping data for bovine chromosome 15
Authors: Snelling Warren M , Gautier Mathieu , Keele John W , Smith Timothy PL , Stone Roger T , Harhay Gregory P , Bennett Gary L , Ihara Naoya , Takasuga Akiko , Takeda Haruko , Sugimoto Yoshikazu , Eggen André 
Published: October 2004

Abstract
Background
Bovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs.

Results
The integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments.

Conclusions
Combining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about genes near mapped bovine markers, but bovine gene order may be different than human. Procedures to connect genetic and physical mapping data, build integrated maps for livestock species, and connect those maps to more fully annotated sequence can be automated, facilitating the maintenance of up-to-date maps, and providing a valuable tool to further explore genetic variation in livestock.
i-Genome: A database to summarize oligonucleotide data in genomes
Authors: Lin Feng-Mao , Huang Hsien-Da , Chang Yu-Chung , Horng Jorng-Tzong 
Published: October 2004

Abstract
Background
Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming.

Results
The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes.

Conclusions
This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.
Erytrocyte membrane anionic charge in type 2 diabetic patients with retinopathy
Authors: Budak Yasemin , Demirci Hakan , Akdogan Muberra , Yavuz Dilek 
Published: October 2004

Abstract
Background
The Steno hypothesis states that changes in basement membrane anionic charge leads to diabetic microvascular complications. In diabetic nephropathy, loss of basement membrane glycosaminoglycans and the association between glomerular basement membrane heparan sulphate and proteinuria has been documented. A correlation between erythrocyte surface and the glomerular capillary wall charges has also been observed.
The aim of this study is to evaluate the relationship between retinopathy and erythrocyte anionic charge and urinary glycosaminoglycan excretion in type 2 diabetic patients.

Methods
49 subjects (58 ± 7 yrs, M/F 27/22) with type 2 diabetes with proliferative retinopathy (n = 13), nonproliferative retinopathy (n = 13) and without retinopathy (n = 23) were included in the study. 38 healthy subjects were selected as control group (57 ± 5 yrs, M/F 19/19). Erythrocyte anionic charge (EAC) was determined by the binding of the cationic dye, alcian blue. Urinary glycosaminoglycan and microalbumin excretion were measured.

Results
EAC was significantly decreased in diabetic patients with retinopathy (255 ± 30 ng alcian blue/106 RBC, 312 ± 30 ng alcian blue/106 RBC for diabetic and control groups respectively, p < 0.001). We did not observe an association between urinary GAG and microalbumin excretion and diabetic retinopathy. EAC is found to be negatively corralated with microalbuminuria in all groups.

Conclusions
We conclude that type 2 diabetic patients with low erythrocyte anionic charge are associated with diabetic retinopathy. Reduction of negative charge of basement membranes may indicate general changes in microvasculature rather than retinopathy. More prospective and large studies needs to clarify the role of glycosaminoglycans on progression of retinopathy in type 2 diabetic patients.
Long-term patterns in European brown hare population dynamics in Denmark: effects of agriculture, predation and climate
Authors: Schmidt Niels M , Asferg Tommy , Forchhammer Mads C 
Published: October 2004

Abstract
Background
In Denmark and many other European countries, harvest records suggest a marked decline in European brown hare numbers, a decline often attributed to the agricultural practice. In the present study, we analyse the association between agricultural land-use, predator abundance and winter severity on the number of European brown hares harvested in Denmark in the years 1955 through 2000.

Results
Winter cereals had a significant negative association with European brown hare numbers. In contrast to this, root crop area was positively related to their numbers. Remaining crop categories were not significantly associated with the European brown hare numbers, though grass out of rotation tended to be positively related. The areas of root crop production and of grass out of rotation have been reduced by approximately 80% and 50%, respectively, while the area of winter cereals has increased markedly (>70%). However, European brown hare numbers were primarily negatively associated with the number of red fox. Finally, we also found a positive association between mild winters and European brown hare numbers.

Conclusion
The decline of Danish European brown hare populations can mainly be attributed to predation by red fox, but the development in agricultural land-use during the last 45 years have also affected the European brown hare numbers negatively. Additionally, though mild winters were beneficial to European brown hares, the increasing frequency of mild winters during the study period was insufficient to reverse the negative population trend.
Feasibility of rapid and automated importation of 3D echocardiographic left ventricular (LV) geometry into a finite element (FEM) analysis model
Authors: Verhey Janko F , Nathan Nadia S 
Published: October 2004

Abstract
Background
Finite element method (FEM) analysis for intraoperative modeling of the left ventricle (LV) is presently not possible. Since 3D structural data of the LV is now obtainable using standard transesophageal echocardiography (TEE) devices intraoperatively, the present study describes a method to transfer this data into a commercially available FEM analysis system: ABAQUS©.

Methods
In this prospective study TomTec LV Analysis TEE© Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. A newly developed software program MVCP FemCoGen©, written in Delphi, reformats the TomTec file structures in five patients for use in ABAQUS and allows visualization of regional deformation of the LV.

Results
This study demonstrates that a fully automated importation of 3D TEE data into FEM modeling is feasible and can be efficiently accomplished in the operating room.

Conclusion
For complete intraoperative 3D LV finite element analysis, three input elements are necessary: 1. time-gaited, reality-based structural information, 2. continuous LV pressure and 3. instantaneous tissue elastance. The first of these elements is now available using the methods presented herein.
Association of mitral annulus calcification, aortic valve calcification with carotid intima media thickness
Authors: Sgorbini Luca , Scuteri Angelo , Leggio Massimo , Leggio Francesco 
Published: October 2004

Abstract
Background
Mitral annular calcification (MAC) and aortic annular calcification (AVC) may represent a manifestation of generalized atherosclerosis in the elederly. Alterations in vascular structure, as indexed by the intima media thickness (IMT), are also recognized as independent predictors of adverse cardiovascular outcomes.

Aim
To examine the relationship between the degree of calcification at mitral and/or aortic valve annulus and large artery structure (thickness).

Methods
We evaluated 102 consecutive patients who underwent transthoracic echocardiography and carotid artery echoDoppler for various indications; variables measured were: systemic blood pressure (BP), pulse pressure (PP=SBP-DBP), body mass index (BMI), fasting glucose, total, HDL, LDL chlolesterol, triglycerides, cIMT. The patients were divided according to a grading of valvular/annular lesions independent scores based on acoustic densitometry: 1 = annular/valvular sclerosis/calcification absence; 2 = annular/valvular sclerosis; 3 = annular calcification; 4 = annular-valvular calcification; 5 = valvular calcification with no recognition of the leaflets.

Results
Patient score was the highest observed for either valvular/annulus. Mean cIMT increased linearly with increasing valvular calcification score, ranging from 3.9 ± 0.48 mm in controls to 12.9 ± 1.8 mm in those subjects scored 5 (p < 0.0001). In the first to fourth quartile of cIMT values the respective maximal percentual of score were: score 1: 76.1%, score 2: 70.1%, score 4: 54.3% and score 5: 69.5% (p > 0.0001).

Conclusion
MAC and AVC score can identify subgroups of patients with different cIMT values which indicate different incidence and prevalence of systemic artery diseases. This data may confirm MAC-AVC as a useful important diagnostic parameter of systemic atherosclerotic disease.
Ventilator associated pneumonia: comparison between quantitative and qualitative cultures of tracheal aspirates
Authors: Camargo Luis FernandoAranha , De Marco Fernando Vinícius , Barbas Carmen SílviaValente , Hoelz Cristiane , Bueno Marco AurélioScarpinella , Rodrigues Jr Milton , Amado Verônica Moreira , Caserta Raquel , Martino Marinês DallaValle , Pasternak Jacyr , Knobel Elias 
Published: October 2004

Abstract
Introduction
Deferred or inappropriate antibiotic treatment in ventilator-associated pneumonia (VAP) is associated with increased mortality, and clinical and radiological criteria are frequently employed to establish an early diagnosis. Culture results are used to confirm the clinical diagnosis and to adjust or sometimes withdraw antibiotic treatment. Tracheal aspirates have been shown to be useful for these purposes. Nonetheless, little is known about the usefulness of quantitative findings in tracheal secretions for diagnosing VAP.

Methods
To determine the value of quantification of bacterial colonies in tracheal aspirates for diagnosing VAP, we conducted a prospective follow-up study of 106 intensive care unit patients who were under ventilatory support. In total, the findings from 219 sequential weekly evaluations for VAP were examined. Clinical and radiological parameters were recorded and evaluated by three independent experts; a diagnosis of VAP required the agreement of at least two of the three experts. At the same time, cultures of tracheal aspirates were analyzed qualitatively and quantitatively (105 colony-forming units [cfu]/ml and 106 cfu/ml)

Results
Quantitative cultures of tracheal aspirates (105 cfu/ml and 106 cfu/ml) exhibited increased specificity (48% and 78%, respectively) over qualitative cultures (23%), but decreased sensitivity (26% and 65%, respectively) as compared with the qualitative findings (81%). Quantification did not improve the ability to predict a diagnosis of VAP.

Conclusion
Quantitative cultures of tracheal aspirates in selected critically ill patients have decreased sensitivity when compared with qualitative results, and they should not replace the latter to confirm a clinical diagnosis of VAP or to adjust antimicrobial therapy.
Quantitative, Highly Sensitive Liquid Chromatography–Tandem Mass Spectrometry Method for Detection of Synthetic Corticosteroids
Authors: Taylor Robert L , Grebe Stefan K , Singh Ravinder J 
Published: October 2004

Abstract
Background: Measurements of serum or urine concentrations of synthetic glucocorticoids are useful for assessing suspected iatrogenic hypothalamic-pituitary-adrenal axis suppression and Cushing syndrome. We have developed a liquid chromatography–tandem mass spectrometry (LC-MS/MS) assay for the simultaneous quantitative analysis of beclomethasone dipropionate, betamethasone, budesonide, dexamethasone, fludrocortisone, flunisolide, fluorometholone, fluticasone propionate, megestrol acetate, methylprednisolone, prednisolone, prednisone, triamcinolone, and triamcinolone acetonide.
Methods: Stable isotopes of cortisol-9,11,12,12-d4 and triamcinolone-d1 acetonide-d6 were added as internal standards to calibrators, controls, and unknown samples. After acetonitrile precipitation, these samples were extracted with methylene chloride, and the extracts were washed and dried. Reconstituted extract (15 μL) was injected on a reversed-phase column and analyzed by LC-MS/MS in positive-ion mode. Assay precision, accuracy, linearity, and sample stability were determined by use of enriched samples. Clinical validation included analysis of 8 serum and 20 urine samples from patients with undetectable cortisol concentrations and analysis of different types of tablets.
Results: Functional assay sensitivity was as low as 0.6–1.6 nmol/L for all compounds except for triamcinolone (7.6 nmol/L). Interassay CVs were 3.0–20% for concentrations of 0.6–364 nmol/L for all analytes. Recoveries of all analytes (except triamcinolone in serum) were 82–138% at 19.2–693 nmol/L. All but one of the serum and urine samples from patients who were tested because of suppressed cortisol concentrations contained at least one synthetic steroid. Tablet analysis recovered 75% of the synthetic steroids in suspected drugs.
Conclusions: LC-MS/MS allows simultaneous quantitative detection of various synthetic steroids in serum, plasma, urine, and tablets. This provides a valuable tool for evaluating the clinical effects of topical and systemic synthetic corticosteroids.
Immunoassay to Measure Ataxia-Telangiectasia Mutated Protein in Cellular Lysates
Authors: Butch Anthony W , Chun Helen H , Nahas Shareef A , Gatti Richard A 
Published: October 2004

AbstractBackground: Ataxia-telangiectasia (A-T) is a neurologic disorder caused by mutations in the ataxia-telangiectasia mutated (ATM) gene. A clinical diagnosis of A-T is confirmed by radiosensitivity testing and immunoblotting for ATM protein. Because both of these tests have long turnaround times (≥3 months), we developed a rapid immunoassay to measure ATM protein and determined its sensitivity and specificity for diagnosing A-T.Methods: Recombinant ATM protein was used for standardization. Lysates of lymphoblastoid cell lines (LCLs) and peripheral blood mononuclear cells (PBMCs) from A-T patients, controls, and A-T heterozygotes were tested for ATM protein by immunoassay.Results: Between-run imprecision (CV) was ≤13%. Nuclear lysates from control LCLs and PBMCs had ATM protein concentrations of 49–610 μg/L and 48–943 μg/L, respectively. ATM protein was not detectable in LCL nuclear lysates from 18 of 21 A-T patients. The three remaining A-T patients had trace amounts of ATM protein, which was confirmed on immuoblots. ATM protein was also detectable in whole-cell lysates from 4 × 106 cells at concentrations of 64–463 μg/L and 42–444 μg/L for control LCLs and PBMCs, respectively. A-T heterozygotes had ATM protein concentrations of 52–98 μg/L. ATM protein was stable in PBMCs stored for 1 month at −70 °C, but rapidly decreased after 1 day in unprocessed blood.Conclusions: This ATM protein immunoassay can be used to confirm a diagnosis of A-T in 2 days on small numbers of PBMCs and can potentially identify A-T carriers and individuals at increased risk for cancer.
Mapping molecular landscapes inside cells
Authors: Baumeister Wolfgang 
Published: October 2004

AbstractCryoelectron tomography opens a window into the inner space of cells. It combines the potential of three-dimensional imaging with a close-to-life preservation of biological samples. Tomograms with molecular resolution are essentially images of the cellular proteome and, in conjunction with advanced pattern recognition techniques, they can be used to map the molecular landscape inside organelles and cells.
Imprinted small RNA genes
Authors: Seitz Hervé , Royo Hélène , Lin Shau-Ping , Youngson Neil , Ferguson-Smith Anne C. , Cavaillé Jérôme 
Published: October 2004

AbstractGenomic imprinting is an epigenetic phenomenon that results in differential expression of both alleles, depending on their parent of origin. We have recently identified many imprinted small non-coding RNA genes belonging to the C/D RNA and microRNA gene families, both of which are usually known to play key roles in post-transcriptional metabolism of specific genes (e.g. C/D RNAs guide ribose methylation of target RNAs while microRNAs elicit either translational repression or RNA interference). Although the functional and evolutionary significance of this association between C/D RNA genes, microRNA genes and genomic imprinting is still highly elusive, these observations provide a framework for further analysis of the potential role of small non-coding RNAs in epigenetic control.
How do ABC transporters drive transport?
Authors: Van Der Does Chris , Tampé Robert 
Published: October 2004

Abstract
Members of the ATP-binding cassette (ABC) superfamily are integral membrane proteins that hydrolyze ATP to drive transport. In the last two decades these proteins have been extensively characterized on a genetic and biochemical level, and in recent years high-resolution crystal structures of several nucleotide-binding domains and full-length transporters have extended our knowledge. Here we discuss the possible mechanisms of transport that have been derived from these crystal structures and the extensive available biochemical data.
Automation of Urine Sediment Examination: a Comparison of the Sysmex UF-100 Automated Flow Cytometer with Routine Manual Diagnosis (Microscopy, Test Strips, and Bacterial Culture)
Authors: Hannemann-Pohl Kurt , Kampf Sieghard Carsten 
Published: October 2004

Abstract
Urine specimens from 438 patients were examined with the UF-100 flow cytometer (Sysmex TOA Medical Electronics (Europe) GmbH, Hamburg, Germany) and by manual microscopy and test strips. One hundred and forty-two of these were also examined bacteriologically. The measurements with the UF-100 were performed on native urine without prior centrifugation. Intraassay imprecision, CV of 1.3 % (547/μl) to 8.5 % (24/μl) for erythrocytes and CV of 2.4 % ( 218/μl) to 5.6 % (10/μl) for leukocytes, are similar to those usual in clinical chemistry, and are very much better than those seen in manual microscopy of sediment. In routine use, overloading the flow cytometer by an excessive concentration of particles was observed in 9% of specimens. Such specimens should be checked visually. The UF-100 is distinctly more sensitive than manual microscopy for determining leukocytes, erythrocytes, epithelial cells and bacteria. Reference ranges were estimated from the results obtained. These enabled the UF-100 to replace routine manual diagnostic methods. Although the sensitivity is improved over manual microscopy of sediment, it is always necessary to perform parallel test strip examination when determining erythrocytes in order to detect haemolysis.
In our opinion the Sysmex UF-100 is a suitable replacement for manual microscopy of urine sediment. In addition it offers an opportunity to improve standardization of basic urinalysis.
Iron Saturation of Ferritin in the Course of Phlebotomy Treatment in Patients with Haemochromatosis
Authors: ten Kate Joop , Marell Kirstin , Huizinga Reint , Kreeftenberg Herman , van Deursen Cees 
Published: October 2004

Abstract
This paper describes the iron saturation of ferritin haemochromatosis patients during phlebotomy therapy. The iron saturation of ferritin does not change during therapy and cannot be used as a parameter follow therapy. Furthermore, the iron saturation seems to be a constant characteristic of a given person. It does not vary with the body iron stores in patients with haemochromatosis.
Recommendations of the German Working Group on Medical Laboratory Testing (AML) on the Introduction and Quality Assurance of Procedures for Point-of-Care Testing (POCT) in Hospitals
Authors: Briedigkeit L. , Müller-Plathe O. , Schlebusch H. , Ziems J. 
Published: October 2004

Abstract
The following recommendations were drawn up by the Working Group “Point-of-Care Testing” of the DGKC and DGLM which was set up in 1997. This first document from the Working Group sets out the principles which should be observed when introducing point-of-care testing.
These general recommendations are to be followed by further specific recommendations on individual procedures or groups of procedures, e.g. blood glucose, electrolytes in whole blood, blood gases, coagulation, toxicology, quality control and others, which will be drawn up by experts at the suggestion of the Working Group.