bluuebunny/crossref_metadata_2025_split huggingface dataset:
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays
Authors: Rouchka Eric C , Khalyfa Abdelnaby , Cooper Nigel GF 
Published: July 2005

Abstract
Background
Enhancements in sequencing technology have recently yielded assemblies of large genomes including rat, mouse, human, fruit fly, and zebrafish. The availability of large-scale genomic and genic sequence data coupled with advances in microarray technology have made it possible to study the expression of large numbers of sequence products under several different conditions in days where traditional molecular biology techniques might have taken months, or even years. Therefore, to efficiently study a number of gene products associated with a disease, pathway, or other biological process, it is necessary to be able to design primer pairs or oligonucleotides en masse rather than using a time consuming and laborious gene-by-gene method.

Results
We have developed an integrated system, MPrime, in order to efficiently calculate primer pairs or specific oligonucleotides for multiple genic regions based on a keyword, gene name, accession number, or sequence fasta format within the rat, mouse, human, fruit fly, and zebrafish genomes. A set of products created for mouse housekeeping genes from MPrime-designed primer pairs has been validated using both PCR-amplification and DNA sequencing.

Conclusion
These results indicate MPrime accurately incorporates standard PCR primer design characteristics to produce high scoring primer pairs for genes of interest. In addition, sequence similarity for a set of oligonucleotides constructed for the same set of genes indicates high specificity in oligo design.
Correlation of same-visit HbA1c test with laboratory-based measurements: A MetroNet study
Authors: Schwartz Kendra L , Monsur Joseph C , Bartoces Monina G , West Patricia A , Neale Anne Victoria 
Published: July 2005

Abstract

Background
Glycated hemoglobin (HbA1c) results vary by analytical method. Use of same-visit HbA1c testing methodology holds the promise of more efficient patient care, and improved diabetes management. Our objective was to test the feasibility of introducing a same-visit HbA1c methodology into busy family practice centers (FPC) and to calculate the correlation between the same-visit HbA1c test and the laboratory method that the clinical site was currently using for HbA1c testing.

Methods
Consecutive diabetic patients 18 years of age and older having blood samples drawn for routine laboratory analysis of HbA1c were asked to provide a capillary blood sample for same-visit testing with the BIO-RAD Micromat II. We compared the results of the same-visit test to three different laboratory methods (one FPC used two different laboratories).

Results
147 paired samples were available for analysis (73 from one FPC; 74 from the other). The Pearson correlation of Micromat II and ion-exchange HPLC was 0.713 (p < 0.001). The Micromat II mean HbA1c was 6.91%, which was lower than the 7.23% from the ion-exchange HPLC analysis (p < 0.001). The correlation of Micromat II with boronate-affinity HPLC was 0.773 (p < 0.001); Micromat II mean HbA1c 6.44%, boronate-affinity HPLC mean 7.71% (p < 0.001). Correlation coefficient for Micromat II and immuno-turbidimetric analysis was 0.927 (p < 0.001); Micromat II mean HbA1c was 7.15% and mean HbA1c from the immuno-turbidimetric analysis was 7.99% (p = 0.002). Medical staff found the same-visit measurement difficult to perform due to the amount of dedicated time required for the test.

Conclusion
For each of the laboratory methods, the correlation coefficient was lower than the 0.96 reported by the manufacturer. This might be due to variability introduced by the multiple users of the Micromat II machine. The mean HbA1c results were also consistently lower than those obtained from laboratory analysis. Additionally, the amount of dedicated time required to perform the assay may limit its usefulness in a busy clinical practice. Before introducing a same-visit HbA1c methodology, clinicians should compare the rapid results to their current method of analysis.
Hospitalization and emergency department visits among seniors receiving homecare: a pilot study
Authors: Smith Andrew A , Carusone Soo B Chan , Willison Kathleen , Babineau Tamara J , Smith Stephanie D , Abernathy Tom , Marrie Tom , Loeb Mark 
Published: July 2005

Abstract

Background
Despite the recent growth in home health services, data on clinical outcomes and acute health care utilization among older adults receiving homecare services are sparse. Obtaining such data is particularly relevant in Ontario where an increasing number of frail seniors receiving homecare are awaiting placement in long-term care facilities. In order to determine the feasibility of a large-scale study, we conducted a pilot study to assess utilization of acute health care services among seniors receiving homecare to determine associated clinical outcomes.

Methods
This prospective cohort study followed forty-seven seniors admitted to homecare by two homecare agencies in Hamilton, Ontario over a 12-month period. Demographic information and medical history were collected at baseline, and patients were followed until either termination of homecare services, death, or end of study. The primary outcome was hospitalization. Secondary outcomes included emergency department visits that did not result in hospitalization and death. Rates of hospitalization and emergency department visits without admission were calculated, and univariate analyses were performed to test for potential risk factors. Survival curves for accumulative rates of hospitalization and emergency department visits were created.

Results
312 seniors were eligible for the study, of which 123 (39%) agreed to participate initially. After communicating with the research nurse, of the 123 who agreed to participate initially, 47 (38%) were enrolled in the study. Eleven seniors were hospitalized during 3,660 days of follow-up for a rate of 3.0 incident hospitalizations per 1,000 homecare-days. Eleven seniors had emergency department visits that did not result in hospitalization, for a rate of 3.3 incident emergency department visits per 1,000 homecare-days. There were no factors significantly associated with hospitalization or emergency department visits when adjustment was made for multiple comparisons.

Conclusion
The incidence of hospitalization and visits to the emergency department among seniors receiving homecare services is high. Getting satisfactory levels of enrolment will be a major challenge for larger prospective studies.
A new approach to estimation of the number of central synapse(s) included in the H-reflex
Authors: Ghavanini Mohammadreza Alavian , Ashraf Alireza , Sadeghi Shahram , Emad Mohammadreza 
Published: July 2005

Abstract

Background
Among the main clinical applications of the H-reflex are the evaluation of the S1 nerve root conductivity such as radiculopathy and measurement of the excitability of the spinal motoneurons in neurological conditions. An attempt has been made to reduce the pathway over which H-reflex can be obtained in a hope to localize a lesion to the S1 nerve root, so the S1 central loop has been suggested. The main goal of this study is the estimation of the H-reflex number of synapse(s) for better understanding of the physiology of this practical reflex.

Methods
Forty healthy adult volunteers (22 males, 18 females) with the mean age of (37.7 ± 10.2) years participated in this study. They were positioned comfortably in the prone position, with their feet off the edge of the plinth. Recording electrodes were positioned at the mid point of a line connecting the mid popliteal crease to the proximal flare of the medial malleolus. Stimulation was applied at the tibial nerve in the popliteal fossa and H, F and M waves were recorded. Without any change in the location of the recording electrodes, a monopolar needle was inserted as cathode at a point 1 cm medial to the posterior superior iliac spine, perpendicular to the frontal plane. The anode electrode was placed over the anterior superior iliac spine, and then M and H waves of the central loop were recorded. After processing the data, sacral cord conduction delay was determined by this formula:

* Sacral cord conduction delay = central loop of H-reflex – (delays of the proximal motor and sensory fibers in the central loop).

Results
The central loop of H-reflex was (6.77 ± 0.28) msec and the sacral cord conduction delay was (1.09 ± 0.06) msec.

Conclusion
The sacral cord conduction time was estimated to be about 1.09 msec in this study and because at least 1 msec is required to transmit the signal across the synapse between the sensory ending and the motor cell, so this estimated time was sufficient for only one central synapse in this reflex.
Nh3D: A reference dataset of non-homologous protein structures
Authors: Thiruv B , Quon G , Saldanha SA , Steipe B 
Published: July 2005

Abstract

Background
The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfil minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here we provide a reference dataset of non-homologous protein domains, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. The dataset is based on domains at the Topology level of the CATH database which hierarchically classifies all protein structures. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted.

Results
The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. We observe that even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%.

Conclusion
Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. Regularly updated versions of Nh3D and the corresponding PDB-formatted coordinate sets are accessible from our Web site http://www.schematikon.org.
Mechanistic aspects of biosynthesis of silver nanoparticles by several Fusarium oxysporum strains
Authors: Durán Nelson , Marcato Priscyla D , Alves Oswaldo L , De Souza Gabriel IH , Esposito Elisa 
Published: July 2005

Abstract
Extracellular production of metal nanoparticles by several strains of the fungus Fusarium oxysporum was carried out. It was found that aqueous silver ions when exposed to several Fusarium oxysporum strains are reduced in solution, thereby leading to the formation of silver hydrosol. The silver nanoparticles were in the range of 20–50 nm in dimensions. The reduction of the metal ions occurs by a nitrate-dependent reductase and a shuttle quinone extracellular process. The potentialities of this nanotechnological design based in fugal biosynthesis of nanoparticles for several technical applications are important, including their high potential as antibacterial material.
Assessment of the health of Americans: the average health-related quality of life and its inequality across individuals and groups
Authors: Asada Yukiko 
Published: July 2005

Abstract

Background
The assessment of population health has traditionally relied on the population's average health measured by mortality related indicators. Researchers have increasingly recognized the importance of including information on health inequality and health-related quality of life (HRQL) in the assessment of population health. The objective of this study is to assess the health of Americans in the 1990s by describing the average HRQL and its inequality across individuals and groups.

Methods
This study uses the 1990 and 1995 National Health Interview Survey from the United States. The measure of HRQL is the Health and Activity Limitation Index (HALex). The measure of health inequality across individuals is the Gini coefficient. This study provides confidence intervals (CI) for the Gini coefficient by a bootstrap method. To describe health inequality by group, this study decomposes the overall Gini coefficient into the between-group, within-group, and overlap Gini coefficient using race (White, Black, and other) as an example. This study looks at how much contribution the overlap Gini coefficient makes to the overall Gini coefficient, in addition to the absolute mean differences between groups.

Results
The average HALex was the same in 1990 (0.87, 95% CI: 0.87, 0.88) and 1995 (0.87, 95% CI: 0.86, 0.87). The Gini coefficient for the HALex distribution across individuals was greater in 1995 (0.097, 95% CI: 0.096, 0.099) than 1990 (0.092, 95% CI: 0.091, 0.094). Differences in the average HALex between all racial groups were the same in 1995 as 1990. The contribution of the overlap to the overall Gini coefficient was greater in 1995 than in 1990 by 2.4%. In both years, inequality between racial groups accounted only for 4–5% of overall inequality.

Conclusion
The average HRQL of Americans was the same in 1990 and 1995, but inequality in HRQL across individuals was greater in 1995 than 1990. Inequality in HRQL by race was smaller in 1995 than 1990 because race had smaller effect on the way health was distributed in 1995 than 1990. Analysis of the average HRQL and its inequality provides information on the health of a population invisible in the traditional analysis of population health.
Use of a novel cell-based fusion reporter assay to explore the host range of human respiratory syncytial virus F protein
Authors: Branigan Patrick J , Liu Changbao , Day Nicole D , Gutshall Lester L , Sarisky Robert T , Del Vecchio Alfred M 
Published: July 2005

Abstract
Human respiratory syncytial virus (HRSV) is an important respiratory pathogen primarily affecting infants, young children, transplant recipients and the elderly. The F protein is the only virion envelope protein necessary and sufficient for virus replication and fusion of the viral envelope membrane with the target host cell. During natural infection, HRSV replication is limited to respiratory epithelial cells with disseminated infection rarely, if ever, occurring even in immunocompromised patients. However, in vitro infection of multiple human and non-human cell types other than those of pulmonary tract origin has been reported. To better define host cell surface molecules that mediate viral entry and dissect the factors controlling permissivity for HRSV, we explored the host range of HRSV F protein mediated fusion. Using a novel recombinant reporter gene based fusion assay, HRSV F protein was shown to mediate fusion with cells derived from a wide range of vertebrate species including human, feline, equine, canine, bat, rodent, avian, porcine and even amphibian (Xenopus). That finding was extended using a recombinant HRSV engineered to express green fluorescent protein (GFP), to confirm that viral mRNA expression is limited in several cell types. These findings suggest that HRSV F protein interacts with either highly conserved host cell surface molecules or can use multiple mechanisms to enter cells, and that the primary determinants of HRSV host range are at steps post-entry.
Microsurgical Anatomic Features of the Olfactory Nerve: Relevance to Olfaction Preservation in the Pterional Approach
Authors: Cardali Salvatore , Romano Alberto , Angileri Filippo Flavio , Conti Alfredo , La Torre Domenico , de Divitiis Oreste , d'Avella Domenico , Tschabitscher Manfred , Tomasello Francesco 
Published: July 2005

Abstract

OBJECTIVE:
The pterional approach represents the standard approach for most lesions of the anterior and middle cranial fossa. It requires some degree of frontal lobe retraction, which may result in temporary or permanent damage of olfaction because of nerve avulsion or mechanical compression. The purpose of this study, based on microanatomic dissection of human cadaveric specimens, was to review the microsurgical anatomic features of the nerve and suggest operative nuances that may contribute to reducing the rate of postoperative olfactory dysfunction.

METHODS:
Twenty olfactory nerves and tracts were examined in 10 human cadaveric heads obtained from three fresh and seven formalin-fixed adult cadavers. A standard pterional craniotomy was performed. The olfactory nerve was dissected from its arachnoidal envelopes and then mobilized for an average length of 30 mm (range, 25–35 mm).

RESULTS:
The possible retraction of the frontal lobe was 10 to 15 mm. More retraction invariably resulted in nerve disruption.

CONCLUSION:
The standard sylvian and basal cistern opening may be insufficient to guarantee preservation of olfactory function. Early identification and arachnoidal dissection of the nerve may reduce the rate of olfaction compromise. The opening of the subarachnoidal space should be performed in a proximal-to-distal manner to allow early visualization of the olfactory bulb and its dissection. The arachnoidal dissection should be performed with sharp instruments, avoiding any traction on the posterior portion of the olfactory tract. Any direct retractor compression should also be avoided to spare the microvasculature lying on the dorsal surface of the nerve.
Vascular Anatomy of the Anteriorly Based Pericranial Flap
Authors: Yoshioka Nobutaka , Rhoton Albert L. 
Published: July 2005

Abstract

OBJECTIVE:
The purpose of this study was to examine the vascular supply of the anteriorly based frontal pericranial flap to determine whether separating the pericranium from the galea above the orbital rim would devascularize the pericranial flap.

METHODS:
The arteries supplying and the veins draining the frontal pericranial flap were examined in 17 adult cadavers using ×3 to ×30 magnification. The arteries were examined on 25 sides and the veins on 16 sides.

RESULTS:
The main trunk and superficial branches of the supraorbital and supratrochlear arteries, which course in the galea-frontalis muscle layer, give rise to the deep branches that supply the pericranium. These pericranial branches may arise in the orbit or at the level of or above the orbital rim. Pericranial arteries that arose above the level of the orbital rim and would be divided in separating the galea and pericranium were found in 28% of the sides examined. Pericranial veins that coursed above the orbital rim and would be divided in separating the galea-frontalis muscle layer from the pericranial layer were found in 43.8% of the sides examined.

CONCLUSION:
In preparing a pericranial flap based anteriorly on the supraorbital rim, the separation of the galea-frontalis muscle layer from the pericranium layer should not extend into the 10 mm above the supraorbital rim if the arterial and venous pedicle of the pericranial flap is to be preserved.
Cerebral Cavernous Malformations Associated with Venous Anomalies: Surgical Considerations
Authors: Wurm Gabriele , Schnizer Mathilde , Fellner Franz A. 
Published: July 2005

Abstract

OBJECTIVE:
Once thought to be rare entities, mixed cerebrovascular malformations with pathological features of more than one type of malformation within the same lesion are now being recognized with increasing frequency. Their identification generates several hypotheses about common pathogenesis or causation-evolution among different types of lesions and leads to controversial discussion on therapeutic strategies.

METHODS:
Fifteen patients drawn from a consecutive series of 58 patients harboring cavernous malformations (25.9%) were found to have an associated venous malformation (VM). Three (33.3%) of the first 9 patients, in whom the large draining vein of the VM had been left untouched at previous interventions, developed recurrent and/or de novo lesions.

RESULTS:
Histopathological analysis, interestingly, revealed that the new lesions were different in nature (three arteriovenous angiomas in two patients, a capillary telangiectasia in one patient). During extirpation of the new malformation, the draining vein of the VM in these three patients could be coagulated without any adverse events. Coagulation and dissection of the draining vein of the associated VM was performed in six more patients of our series, and this has prevented development of new lesions up to now.

CONCLUSION:
Our results are in favor of the hypothesis that the draining vein of a VM is the actual underlying abnormality of mixed vascular malformations. Causing flow disturbances and having the potential for hemorrhages, the VM seems to promote the development of new adjacent malformations. Thus, permanent cure of associated malformations might depend on the surgical treatment of the VM. We present a preliminary personal series and a thorough review of the literature.
Functional Monitoring for Visual Pathway Using Real-time Visual Evoked Potentials and Optic-radiation Tractography
Authors: Kamada Kyousuke , Todo Tomoki , Morita Akio , Masutani Yoshitaka , Aoki Shigeki , Ino Kenji , Kawai Kensuke , Kirino Takaaki 
Published: July 2005

Abstract

OBJECTIVE:
It has been difficult to obtain anatomic and functional information about the visual pathway during neurosurgical operations. The aim of this study was to combine the information of the visual evoked potentials (VEPs) and the anatomic navigation of the optic radiation by diffusion tensor imaging-based tractography for functional monitoring of the visual pathway.

METHODS:
The subjects were two patients with brain lesions adjacent to the visual pathway. Diffusion tensor imaging-based tractography of the optic radiation was performed by selecting appropriate regions of interest and by fractional anisotropy. During surgery, cortical VEPs were recorded continuously under general anesthesia with sevoflurane. In Patient 2, the results of optic radiation tractography were imported to a neuronavigation system to better understand the spatial relationships between the lesions and the visual pathway (functional neuronavigation).

RESULTS:
In Patient 1, the lesion did not seem to be attached to the optic radiation, and VEP profiles remained stable during resection. In Patient 2, who had a lesion adjacent to the posterior horn of the lateral ventricle, VEPs suddenly diminished when resection reached the optic radiation as illustrated on the neuronavigation system. As a result, complete left hemianopia developed after surgery in Patient 2.

CONCLUSION:
We confirmed functional correlations of the results of diffusion tensor imaging-based tractography by monitoring intraoperative VEPs. The combination of continuous VEP and optic-radiation tractography is reliable to monitor the visual function and is helpful in performing neurosurgical planning near the visual pathway.