bluuebunny/crossref_metadata_2025_split huggingface dataset:
Muscle-specific creatine kinase gene polymorphism and running economy responses to an 18-week 5000-m training programme
Authors: Zhou D Q , Hu Y , Liu G , Gong L , Xi Y , Wen L 
Published: September 2006

Objective:To investigate the association between muscle-specific creatine kinase (CKMM) gene polymorphism and the effects of endurance training on running economy.Methods:102 biologically unrelated male volunteers from northern China performed a 5000-m running programme, with an intensity of 95–105% ventilatory threshold. The protocol was undertaken three times per week and lasted for 18 weeks. Running economy indexes were determined by making the participants run on a treadmill before and after the protocol, and the A/G polymorphism in the 3′ untranslated region of CKMM was detected by polymerase chain reaction-restricted fragment length polymorphism (NcoI restriction enzyme).Results:Three expected genotypes for CKMM-NcoI (AA, AG and GG) were observed in the participants. After training, all running economy indexes declined markedly. Change in steady-state consumption of oxygen, change in steady-state consumption of oxygen by mean body weight, change in steady-state consumption of oxygen by mean lean body weight and change in ventilatory volume in AG groups were larger than those in AA and GG groups.Conclusions:The findings indicate that the CKMM gene polymorphism may contribute to individual running economy responses to endurance training.
Influences of palatal side design and finishing on the wearability and retention of mouthguards
Authors: Maeda Y , Machi H , Tsugawa T 
Published: September 2006

Objectives:To examine the influences of design and finishing on mouthguard wearability and retention.Materials and methods:17 students at the Dental Technician Institute at Osaka University School of Dentistry, Osaka, Japan, participated in this study after providing informed consent. For each student, a single-layer custom-made mouthguard was fabricated from a 3.8-mm-thick ethylene-vinyl acetate sheet using a standardised procedure to obtain a precise fit. Each mouthguard was modified by changing the margin location and shape through five consecutive steps. At each step, questionnaires with a visual analogue scale regarding wearability (comfort, breathing, speaking, swallowing, lip closure, temporomandibular joint fatigue and swallowing) and retention were completed by subjects after wearing the mouthguard for 5 min. Statistical analyses were carried out among the steps using Wilcoxon’s signed-rank test with a significance level of p<0.05.Results:Significant improvements were found for comfort, breathing, speaking and swallowing by trimming the palatal margin to the cervical area, smooth finishing and occlusal adjustment of the mouthguard (p<0.01). No significant differences were found for retention throughout the procedure.Conclusions:Within the limitations of this experimental study, design and finishing at the palatal side appear to have significant influences on mouthguard wearability, but not retention.
Impacts of Localized Mixing and Topography on the Stationary Abyssal Circulation
Authors: Katsman Caroline A. 
Published: September 2006

Abstract
Stommel and coworkers calculated the stationary, geostrophic circulation in the abyssal ocean driven by prescribed sources (representing convective downwelling sites) and sinks (slow, widespread upwelling through the thermocline). The applied basin geometries were highly idealized with nearly uniform upwelling and gradual bottom slopes. In this paper, the classical Stommel–Arons theory for the abyssal circulation is extended by introducing pronounced bathymetry in the form of a midocean ridge and strongly enhanced upwelling in the vicinity of this ridge, modeled after direct observations of diapycnal mixing rates in the deep ocean. Locally enhanced upwelling over a midocean ridge drives a β-plume circulation that is modified by topographic stretching. The dynamics of this abyssal circulation pattern are explained by analyzing the combined impacts of the upwelling pattern and the bathymetry on the stationary circulation, building on their well-known separate impacts. On the western flank of the ridge, the effects of topographic stretching and upwelling oppose, and the direction of the local flow depends on their relative size. In this paper, a simple theoretical estimate is derived that can predict the direction of the flow along the ridge based on the geometry of the basin and the upwelling region. Its applicability is demonstrated for both the idealized model configurations applied in this study and for more realistic model simulations.
GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data
Authors: Sun Hongmei , Fang Hong , Chen Tao , Perkins Roger , Tong Weida 
Published: September 2006

Abstract

Background
Gene Ontology (GO) characterizes and categorizes the functions of genes and their products according to biological processes, molecular functions and cellular components, facilitating interpretation of data from high-throughput genomics and proteomics technologies. The most effective use of GO information is achieved when its rich and hierarchical complexity is retained and the information is distilled to the biological functions that are most germane to the phenomenon being investigated.

Results
Here we present a FDA GO tool named Gene Ontology for Functional Analysis (GOFFA). GOFFA first ranks GO terms in the order of prevalence for a list of selected genes or proteins, and then it allows the user to interactively select GO terms according to their significance and specific biological complexity within the hierarchical structure. GOFFA provides five interactive functions (Tree view, Terms View, Genes View, GO Path and GO TreePrune) to analyze the GO data. Among the five functions, GO Path and GO TreePrune are unique. The GO Path simultaneously displays the ranks that order GOFFA Tree Paths based on statistical analysis. The GO TreePrune provides a visual display of a reduced GO term set based on a user's statistical cut-offs. Therefore, the GOFFA visual display can provide an intuitive depiction of the most likely relevant biological functions.

Conclusion
With GOFFA, the user can dynamically interact with the GO data to interpret gene expression results in the context of biological plausibility, which can lead to new discoveries or identify new hypotheses.

Availability
GOFFA is available through ArrayTrack software

http://edkb.fda.gov/webstart/arraytrack/.
RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers
Authors: Thodima Venkata , Pirooznia Mehdi , Deng Youping 
Published: September 2006

Abstract

Background
Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize a broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology.

Results
The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search.

Conclusion
This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at http://mfgn.usm.edu/ebl/riboapt/.
Systemic inflammatory response syndrome in adult patients with nosocomial bloodstream infections due to enterococci
Authors: Bar Katharine , Wisplinghoff Hilmar , Wenzel Richard P , Bearman Gonzalo ML , Edmond Michael B 
Published: September 2006

AbstractBackgroundEnterococci are the third leading cause of nosocomial bloodstream infection (BSI). Vancomycin resistant enterococci are common and provide treatment challenges; however questions remain about VRE's pathogenicity and its direct clinical impact. This study analyzed the inflammatory response of Enterococcal BSI, contrasting infections from vancomycin-resistant and vancomycin-susceptible isolates.MethodsWe performed a historical cohort study on 50 adults with enterococcal BSI to evaluate the associated systemic inflammatory response syndrome (SIRS) and mortality. We examined SIRS scores 2 days prior through 14 days after the first positive blood culture. Vancomycin resistant (n = 17) and susceptible infections (n = 33) were compared. Variables significant in univariate analysis were entered into a logistic regression model to determine the affect on mortality.Results60% of BSI were caused byE. faecalisand 34% byE. faecium. 34% of the isolates were vancomycin resistant. Mean APACHE II (A2) score on the day of BSI was 16. Appropriate antimicrobials were begun within 24 hours in 52%. Septic shock occurred in 62% and severe sepsis in an additional 18%. Incidence of organ failure was as follows: respiratory 42%, renal 48%, hematologic 44%, hepatic 26%. Crude mortality was 48%. Progression to septic shock was associated with death (OR 14.9, p < .001). There was no difference in A2 scores on days -2, -1 and 0 between the VRE and VSE groups. Maximal SIR (severe sepsis, septic shock or death) was seen on day 2 for VSE BSI vs. day 8 for VRE. No significant difference was noted in the incidence of organ failure, 7-day or overall mortality between the two groups. Univariate analysis revealed that AP2>18 at BSI onset, and respiratory, cardiovascular, renal, hematologic and hepatic failure were associated with death, but time to appropriate therapy >24 hours, age, and infection due to VRE were not. Multivariate analysis revealed that hematologic (OR 8.4, p = .025) and cardiovascular failure (OR 7.5, p = 032) independently predicted death.ConclusionIn patients with enterococcal BSI, (1) the incidence of septic shock and organ failure is high, (2) patients with VRE BSI are not more acutely ill prior to infection than those with VSE BSI, and (3) the development of hematologic or cardiovascular failure independently predicts death.
Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling
Authors: Ruano Yolanda , Mollejo Manuela , Ribalta Teresa , Fiaño Concepción , Camacho Francisca I , Gómez Elena , de Lope Angel Rodríguez , Hernández-Moneo Jose-Luis , Martínez Pedro , Meléndez Bárbara 
Published: September 2006

Abstract

Background
Conventional cytogenetic and comparative genomic hybridization (CGH) studies in brain malignancies have shown that glioblastoma multiforme (GBM) is characterized by complex structural and numerical alterations. However, the limited resolution of these techniques has precluded the precise identification of detailed specific gene copy number alterations.

Results
We performed a genome-wide survey of gene copy number changes in 20 primary GBMs by CGH on cDNA microarrays. A novel amplicon at 4p15, and previously uncharacterized amplicons at 13q32-34 and 1q32 were detected and are analyzed here. These amplicons contained amplified genes not previously reported. Other amplified regions containg well-known oncogenes in GBMs were also detected at 7p12 (EGFR), 7q21 (CDK6), 4q12 (PDGFRA), and 12q13-15 (MDM2 and CDK4). In order to identify the putative target genes of the amplifications, and to determine the changes in gene expression levels associated with copy number change events, we carried out parallel gene expression profiling analyses using the same cDNA microarrays. We detected overexpression of the novel amplified genes SLA/LP and STIM2 (4p15), and TNFSF13B and COL4A2 (13q32-34). Some of the candidate target genes of amplification (EGFR, CDK6, MDM2, CDK4, and TNFSF13B) were tested in an independent set of 111 primary GBMs by using FISH and immunohistological assays. The novel candidate 13q-amplification target TNFSF13B was amplified in 8% of the tumors, and showed protein expression in 20% of the GBMs.

Conclusion
This high-resolution analysis allowed us to propose novel candidate target genes such as STIM2 at 4p15, and TNFSF13B or COL4A2 at 13q32-34 that could potentially contribute to the pathogenesis of these tumors and which would require futher investigations. We showed that overexpression of the amplified genes could be attributable to gene dosage and speculate that deregulation of those genes could be important in the development and progression of GBM. Our findings highlight the important influence in GBM of signaling pathways such as the PI3K/AKT, consistent with the invasive features of this tumor.
Seeding of epithelial cells into circulation during surgery for breast cancer: the fate of malignant and benign mobilized cells
Authors: Camara Oumar , Kavallaris Andreas , Nöschel Helmut , Rengsberger Matthias , Jörke Cornelia , Pachmann Katharina 
Published: September 2006

Abstract

Background
Surgery of malignant tumors has long been suspected to be the reason for enhancement of growth of metastases with fatal outcome. This often prevented surgeons from touching the tumor if not absolutely necessary. We have shown in lung cancer patients that surgery, itself, leads to mobilization of tumor cells into peripheral blood. Some of the mobilized cells finding an appropriate niche might grow to form early metastases. Monitoring of tumor cell release during and the fate of such cells after surgery for breast cancer may help to reveal how metastases develop after surgery.

Method
We used the MAINTRAC® analysis, a new tool for online observation of circulating epithelial cells, to monitor the number of epithelial cells before, 30 min, 60 min, three and seven days after surgery and during subsequent variable follow up in breast cancer patients.

Results
Circulating epithelial cells were already present before surgery in all patients. During the first 30–60 min after surgery values did not change immediately. They started increasing during the following 3 to 4 days up to thousand fold in 85% of treated patients in spite of complete resection of the tumor with tumor free margins in all patients. There was a subsequent re-decrease, with cell numbers remaining above pre-surgery values in 58% of cases until onset of chemotherapy. In a few cases, where no further therapy or only hormone treatment was given due to low risk stage, cell numbers were monitored for up to three years. They remained elevated with no or a slow decrease over time. This was in contrast to the observation in a patient where surgery was performed for benign condition. She was monitored before surgery with no cells detectable. Epithelial cells increased up to more than 50 000 after surgery but followed by a complete reduction to below the threshold of detection.

Conclusion
Frequently before but regularly during surgery of breast cancer, epithelial cells are mobilized into circulation. Part of these cells, most probably normal or apoptotic cells, are cleared from the circulation as also shown to occur in benign conditions. After resection even if complete and of small tumors, cells can remain in the circulation over long times. Such cells may remain "dormant" but might settle and grow into metastases, if they find appropriate conditions, even after years.
Fast calculation of the quartet distance between trees of arbitrary degrees
Authors: Christiansen Chris , Mailund Thomas , Pedersen Christian NS , Randers Martin , Stissing Martin Stig 
Published: September 2006

Abstract

Background
A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets – sub-trees induced by four leaves – that differs between the trees. Mostly, these algorithms are restricted to work on binary trees, but recently we have developed algorithms that work on trees of arbitrary degree.

Results
We present a fast algorithm for computing the quartet distance between trees of arbitrary degree. Given input trees T and T', the algorithm runs in time O(n + |V|·|V'| min{id, id'}) and space O(n + |V|·|V'|), where n is the number of leaves in the two trees, V and V are the non-leaf nodes in T and T', respectively, and id and id' are the maximal number of non-leaf nodes adjacent to a non-leaf node in T and T', respectively. The fastest algorithms previously published for arbitrary degree trees run in O(n
3) (independent of the degree of the tree) and O(|V|·|V'|·id·id'), respectively. We experimentally compare the algorithm with existing algorithms for computing the quartet distance for general trees.

Conclusion
We present a new algorithm for computing the quartet distance between two trees of arbitrary degree. The new algorithm improves the asymptotic running time for computing the quartet distance, compared to previous methods, and experimental results indicate that the new method also performs significantly better in practice.
Anemia, transfusion, and phlebotomy practices in critically ill patients with prolonged ICU length of stay: a cohort study
Authors: Chant Clarence , Wilson Gail , Friedrich Jan O 
Published: September 2006

Abstract
Introduction
Anemia among the critically ill has been described in patients with short to medium length of stay (LOS) in the intensive care unit (ICU), but it has not been described in long-stay ICU patients. This study was performed to characterize anemia, transfusion, and phlebotomy practices in patients with prolonged ICU LOS.

Methods
We conducted a retrospective chart review of consecutive patients admitted to a medical-surgical ICU in a tertiary care university hospital over three years; patients included had a continuous LOS in the ICU of 30 days or longer. Information on transfusion, phlebotomy, and outcomes were collected daily from days 22 to 112 of the ICU stay.

Results
A total of 155 patients were enrolled. The mean age, admission Acute Physiology and Chronic Health Evaluation II score, and median ICU LOS were 62.3 ± 16.3 years, 23 ± 8, and 49 days (interquartile range 36–70 days), respectively. Mean hemoglobin remained stable at 9.4 ± 1.4 g/dl from day 7 onward. Mean daily phlebotomy volume was 13.3 ± 7.3 ml, and 62% of patients received a mean of 3.4 ± 5.3 units of packed red blood cells at a mean hemoglobin trigger of 7.7 ± 0.9 g/dl after day 21. Transfused patients had significantly greater acuity of illness, phlebotomy volumes, ICU LOS and mortality, and had a lower hemoglobin than did those who were not transfused. Multivariate logistic regression analysis identified the following as independently associated with the likelihood of requiring transfusion in nonbleeding patients: baseline hemoglobin, daily phlebotomy volume, ICU LOS, and erythropoietin therapy (used almost exclusively in dialysis dependent renal failure in this cohort of patients). Small increases in average phlebotomy (3.5 ml/day, 95% confidence interval 2.4–6.8 ml/day) were associated with a doubling in the odds of being transfused after day 21.

Conclusion
Anemia, phlebotomy, and transfusions, despite low hemoglobin triggers, are common in ICU patients long after admission. Small decreases in phlebotomy volume are associated with significantly reduced transfusion requirements in patients with prolonged ICU LOS.
Case-Control Comparison of At-Home to Total Hospital Care for Autologous Stem-Cell Transplantation for Hematologic Malignancies
Authors: Fernández-Avilés Francesc , Carreras Enric , Urbano-Ispizua Alvaro , Rovira Montserrat , Martínez Carmen , Gaya Anna , Granell Miquel , Ramiro Laia , Gallego Cristina , Hernando Adela , Segura Susana , García Lourdes , González Manel , Valverde Montserrat , Montserrat Emili 
Published: September 2006

Purpose One of the most significant limitations of at-home autologous stem-cell transplantation (ASCT) is the necessity for hospital readmission. We developed an at-home ASCT program in which prophylactic ceftriaxone and treatment of febrile neutropenia with piperacillin and tazobactam was introduced to minimize the readmission rate. Patients and Methods Between November 2000 and February 2005, 178 consecutive patients underwent ASCT for a hematologic malignancy. Of these, 50 patients fulfilled the requirements for at-home ASCT. Results were compared with those observed in a control group of 50 patients individually matched to the group of patients treated at home for age, sex, diagnosis, stage of disease, conditioning, and source of stem cells. Results Febrile neutropenia occurred in fewer patients in the at-home group as compared with the hospitalized group (76% v 96%: P = .008), and duration of fever was also shorter in the at-home group (median, 2 and 6 days, respectively; range, 1 to 11 and 1 to 20 days, respectively; P = .00003). Hospital readmission in the at-home group was required in only four cases (8%). This resulted in a reduction of 18.6 days of hospitalization per patient. Likewise, total median charges were approximately half in the at-home group as compared with the in-hospital group (3,345 € v 6,250 €, respectively; P < .00001). Conclusion Results of at-home ASCT with prophylactic administration of ceftriaxone and domiciliary treatment of febrile neutropenia with piperacillin and tazobactam are highly satisfactory and significantly cheaper compared with those obtained with conventional in-hospital ASCT.
Thin‐needle aspiration biopsy in the diagnosis of head and neck tumors
Authors: Frable William J. , Frable Mary Ann 
Published: September 2006

AbstractThin‐needle aspiration biopsy was performed in 84 patients with head and neck lesions for definitive diagnosis. There were 53 cases of lymph nodes, 47 in the cervical area and six in the supraclavicular area. There were 10 salivary gland lesions and 10 thyroid masses. No false positive diagnoses of malignant tumors occurred in this entire series. The false negative rate for malignant tumors was 4.0 percent. No delay in therapy occurred in any case because the aspiration biopsy technique was used. The thin‐needle technique as described is non‐traumatic and is an out‐patient office procedure. A 22‐guage narrow diameter needle is used attached to a disposable 20 ml. plastic syringe. The syringe is held in a metal syringe holder which allows the operator to hold the syringe and apply vacuum with one hand. The other hand is used to fix the mass. Small masses, 1.0 cm. or larger are easily aspirated by this technique. The material obtained is smeared on glass slides in the manner of making a blood smear. The aspirate is semi‐fluid and should not be diluted with blood. This is accomplished by stopping the aspiration when material becomes visable in the hub of the syringe. The smears are either air‐dried or fixed immediately in 95 percent ethyl or methyl alcohol. We have found the metachrome B and Papanicolaou stain to be of most value. The metachrome B stain is done on the air‐dried smears and the diagnosis can be made in many cases in a matter of a few minutes, thus providing a rapid solution to the patient's clinical problem. Review of this and other series indicates no complications with this technique and no evidence that cells are implanted in the needle tract following aspiration of malignant tumors.