bluuebunny/crossref_metadata_2025_split huggingface dataset:
AVID: An integrative framework for discovering functional relationships among proteins
Authors: Jiang Taijiao , Keating Amy E 
Published: June 2005

Abstract
Background
Determining the functions of uncharacterized proteins is one of the most pressing problems in the post-genomic era. Large scale protein-protein interaction assays, global mRNA expression analyses and systematic protein localization studies provide experimental information that can be used for this purpose. The data from such experiments contain many false positives and false negatives, but can be processed using computational methods to provide reliable information about protein-protein relationships and protein function. An outstanding and important goal is to predict detailed functional annotation for all uncharacterized proteins that is reliable enough to effectively guide experiments.

Results
We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among proteins. We illustrate use of the networks by making predictions of detailed Gene Ontology (GO) annotations in three categories: molecular function, biological process, and cellular component. Applied to the yeast Saccharomyces cerevisiae, AVID provides 37,451 pair-wise functional linkages between 4,191 proteins. These relationships are ~65–78% accurate, as assessed by cross-validation testing. Assignments of highly detailed functional descriptors to proteins, based on the networks, are estimated to be ~67% accurate for GO categories describing molecular function and cellular component and ~52% accurate for terms describing biological process. The predictions cover 1,490 proteins with no previous annotation in GO and also assign more detailed functions to many proteins annotated only with less descriptive terms. Predictions made by AVID are largely distinct from those made by other methods. Out of 37,451 predicted pair-wise relationships, the greatest number shared in common with another method is 3,413.

Conclusion
AVID provides three networks reflecting functional associations among proteins. We use these networks to generate new, highly detailed functional predictions for roughly half of the yeast proteome that are reliable enough to drive targeted experimental investigations. The predictions suggest many specific, testable hypotheses. All of the data are available as downloadable files as well as through an interactive website at http://web.mit.edu/biology/keating/AVID. Thus, AVID will be a valuable resource for experimental biologists.
Automatic selection of representative proteins for bacterial phylogeny
Authors: Bern Marshall , Goldberg David 
Published: June 2005

Abstract
Background
Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence.

Results
We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria"), and another containing Planctomycetes and Chlamydiales.

Conclusion
Representative proteins provide an effective solution to the problem of selecting phylogenetic characters.
Preclinical evaluation of the proteasome inhibitor bortezomib in cancer therapy
Authors: Boccadoro Mario , Morgan Gareth , Cavenagh Jamie 
Published: June 2005

AbstractBortezomib is a highly selective, reversible inhibitor of the 26S proteasome that is indicated for single-agent use in the treatment of patients with multiple myeloma who have received at least 2 prior therapies and are progressing on their most recent therapy. Clinical investigations have been completed or are under way to evaluate the safety and efficacy of bortezomib alone or in combination with chemotherapy in multiple myeloma, both at relapse and presentation, as well as in other cancer types. The antiproliferative, proapoptotic, antiangiogenic, and antitumor activities of bortezomib result from proteasome inhibition and depend on the altered degradation of a host of regulatory proteins. Exposure to bortezomib has been shown to stabilize p21, p27, and p53, as well as the proapoptotic Bid and Bax proteins, caveolin-1, and inhibitor κB-α, which prevents activation of nuclear factor κB-induced cell survival pathways. Bortezomib also promoted the activation of the proapoptotic c-Jun-NH2terminal kinase, as well as the endoplasmic reticulum stress response. The anticancer effects of bortezomib as a single agent have been demonstrated in xenograft models of multiple myeloma, adult T-cell leukemia, lung, breast, prostate, pancreatic, head and neck, and colon cancer, and in melanoma. In these preclinicalin vivostudies, bortezomib treatment resulted in decreased tumor growth, angiogenesis, and metastasis, as well as increased survival and tumor apoptosis. In severalin vitroand/orin vivocancer models, bortezomib has also been shown to enhance the antitumor properties of several antineoplastic treatments. Importantly, bortezomib was generally well tolerated and did not appear to produce additive toxicities when combined with other therapies in the dosing regimens used in these preclinicalin vivoinvestigations. These findings provide a rationale for further clinical trials using bortezomib alone or in combination regimens with chemotherapy, radiation therapy, immunotherapy, or novel agents in patients with hematologic malignancies or solid tumors.
Use of plant stanol ester margarine among persons with and without cardiovascular disease: Early phases of the adoption of a functional food in Finland
Authors: Simojoki Meri , Luoto Riitta , Uutela Antti , Rita Hannu , Boice John D , McLaughlin Joseph K , Puska Pekka 
Published: June 2005

Abstract

Background
The plant stanol ester margarine Benecol® is a functional food that has been shown to lower effectively serum total and LDL-cholesterol. The purpose of this post-marketing study is to characterize users of plant stanol ester margarine with and without cardiovascular disease.

Methods
A cohort of plant stanol ester margarine users was established based on a compilation of 15 surveys conducted by the National Public Health Institute in Finland between 1996–2000. There were 29 772 subjects aged 35–84 years in the cohort. The users of plant stanol ester margarine were identified by the type of bread spread used.

Results
The plant stanol ester margarine was used as bread spread by 1332 (4.5%) subjects. Almost half (46%) of the users reported a history of cardiovascular disease. Persons with cardiovascular disease were more likely to use plant stanol ester margarine (8%) than persons without cardiovascular disease (3%). Users with and without cardiovascular disease seemed to share similar characteristics.
In particular, they were elderly people with otherwise healthy life-styles and diet. They were less likely smokers, more likely physically active and less likely obese than nonusers. The users reported being in good or average health in general and having used cholesterol-lowering drugs.

Conclusion
Plant stanol ester margarine seems to be used by persons for whom it was designed and in a way it was meant: as part of efforts for cardiovascular disease risk reduction.
Neighborhood size and local geographic variation of health and social determinants
Authors: Ali Mohammad , Park Jin-Kyung , Thiem Vu Dinh , Canh Do Gia , Emch Michael , Clemens John D 
Published: June 2005

Abstract

Background
Spatial filtering using a geographic information system (GIS) is often used to smooth health and ecological data. Smoothing disease data can help us understand local (neighborhood) geographic variation and ecological risk of diseases. Analyses that use small neighborhood sizes yield individualistic patterns and large sizes reveal the global structure of data where local variation is obscured. Therefore, choosing an optimal neighborhood size is important for understanding ecological associations with diseases. This paper uses Hartley's test of homogeneity of variance (Fmax) as a methodological solution for selecting optimal neighborhood sizes. The data from a study area in Vietnam are used to test the suitability of this method.

Results
The Hartley's Fmax test was applied to spatial variables for two enteric diseases and two socioeconomic determinants. Various neighbourhood sizes were tested by using a two step process to implement the Fmaxtest. First the variance of each neighborhood was compared to the highest neighborhood variance (upper, Fmax1) and then they were compared with the lowest neighborhood variance (lower, Fmax2). A significant value of Fmax1 indicates that the neighborhood does not reveal the global structure of data, and in contrast, a significant value in Fmax2 implies that the neighborhood data are not individualistic. The neighborhoods that are between the lower and the upper limits are the optimal neighbourhood sizes.

Conclusion
The results of tests provide different neighbourhood sizes for different variables suggesting that optimal neighbourhood size is data dependent. In ecology, it is well known that observation scales may influence ecological inference. Therefore, selecting optimal neigborhood size is essential for understanding disease ecologies. The optimal neighbourhood selection method that is tested in this paper can be useful in health and ecological studies.
Inflammatory fibroid polyp of the oesophagus
Authors: Godey Shashi Kanth , Diggory Robert T 
Published: May 2005

Abstract

Background
Inflammatory fibroid polyp of the oesophagus is an uncommon lesion and very rarely it grows rapidly.

Case presentation
We present the case of a patient with a rapidly growing inflammatory fibroid polyp (IFP) of the oesophagus, which showed up within five months after a normal endoscopy.

Conclusion
The treatment of IFP is by surgical excision, either open or endoscopic. Laser or other form of ablative treatment like thermo cautery can also be tried.
Cu/Zn superoxide dismutase expression in the postnatal rat brain following an excitotoxic injury
Authors: Peluffo Hugo , Acarin Laia , Faiz Maryam , Castellano Bernardo , Gonzalez Berta 
Published: June 2005

Abstract

Background
In the nervous system, as in other organs, Cu/Zn superoxide dismutase (Cu/Zn SOD) is a key antioxidant enzyme involved in superoxide detoxification in normal cellular metabolism and after cell injury. Although it has been suggested that immature brain has a different susceptibility to oxidative damage than adult brain, the distribution and cell-specific expression of this enzyme in immature brain and after postnatal brain damage has not been documented.

Methods
In this study, we used immunohistochemistry and western blot to analyze the expression of Cu/Zn SOD in intact immature rat brain and in immature rat brain after an NMDA-induced excitotoxic cortical injury performed at postnatal day 9. Double immunofluorescence labelling was used to identify Cu/Zn SOD-expressing cell populations.

Results
In intact immature brain, Cu/Zn SOD enzyme was widely expressed at high levels in neurons mainly located in cortical layers II, III and V, in the sub-plate, in the pyriform cortex, in the hippocampus, and in the hypothalamus. Glial fibrillary acidic protein-positive cells only showed Cu/Zn SOD expression in the glia limitans and in scattered cells of the ventricle walls. No expression was detected in interfascicular oligodendroglia, microglia or endothelial cells. Following excitotoxic damage, neuronal Cu/Zn SOD was rapidly downregulated (over 2–4 hours) at the injection site before neurodegeneration signals and TUNEL staining were observed. Later, from 1 day post-lesion onward, an upregulation of Cu/Zn SOD was found due to increased expression in astroglia. A further increase was observed at 3, 5 and 7 days that corresponded to extensive induction of Cu/Zn SOD in highly reactive astrocytes and in the astroglial scar.

Conclusion
We show here that, in the intact immature brain, the expression of Cu/Zn SOD was mainly found in neurons. When damage occurs, a strong and very rapid downregulation of this enzyme precedes neuronal degeneration, and is followed by an upregulation of Cu/Zn SOD in astroglial cells.
Influence of a portable audio-biofeedback device on structural properties of postural sway
Authors: Dozza Marco , Chiari Lorenzo , Chan Becky , Rocchi Laura , Horak Fay B , Cappello Angelo 
Published: June 2005

Abstract

Background
Good balance depends on accurate and adequate information from the senses. One way to substitute missing sensory information for balance is with biofeedback technology. We previously reported that audio-biofeedback (ABF) has beneficial effects in subjects with profound vestibular loss, since it significantly reduces body sway in quiet standing tasks.

Methods
In this paper, we present the effects of a portable prototype of an ABF system on healthy subjects' upright stance postural stability, in conditions of limited and unreliable sensory information. Stabilogram diffusion analysis, combined with traditional center of pressure analysis and surface electromyography, were applied to the analysis of quiet standing tasks on a Temper foam surface with eyes closed.

Results
These analyses provided new evidence that ABF may be used to treat postural instability. In fact, the results of the stabilogram diffusion analysis suggest that ABF increased the amount of feedback control exerted by the brain for maintaining balance. The resulting increase in postural stability was not at the expense of leg muscular activity, which remained almost unchanged.

Conclusion
Examination of the SDA and the EMG activity supported the hypothesis that ABF does not induce an increased stiffness (and hence more co-activation) in leg muscles, but rather helps the brain to actively change to a more feedback-based control activity over standing posture.
Peptide inhibitors of dengue virus and West Nile virus infectivity
Authors: Hrobowski Yancey M , Garry Robert F , Michael Scott F 
Published: June 2005

Abstract
Viral fusion proteins mediate cell entry by undergoing a series of conformational changes that result in virion-target cell membrane fusion. Class I viral fusion proteins, such as those encoded by influenza virus and human immunodeficiency virus (HIV), contain two prominent alpha helices. Peptides that mimic portions of these alpha helices inhibit structural rearrangements of the fusion proteins and prevent viral infection. The envelope glycoprotein (E) of flaviviruses, such as West Nile virus (WNV) and dengue virus (DENV), are class II viral fusion proteins comprised predominantly of beta sheets. We used a physio-chemical algorithm, the Wimley-White interfacial hydrophobicity scale (WWIHS) [1] in combination with known structural data to identify potential peptide inhibitors of WNV and DENV infectivity that target the viral E protein. Viral inhibition assays confirm that several of these peptides specifically interfere with target virus entry with 50% inhibitory concentration (IC50) in the 10 μM range. Inhibitory peptides similar in sequence to domains with a significant WWIHS scores, including domain II (IIb), and the stem domain, were detected. DN59, a peptide corresponding to the stem domain of DENV, inhibited infection by DENV (>99% inhibition of plaque formation at a concentrations of <25 μM) and cross-inhibition of WNV fusion/infectivity (>99% inhibition at <25 μM) was also demonstrated with DN59. However, a potent WNV inhibitory peptide, WN83, which corresponds to WNV E domain IIb, did not inhibit infectivity by DENV. Additional results suggest that these inhibitory peptides are noncytotoxic and act in a sequence specific manner. The inhibitory peptides identified here can serve as lead compounds for the development of peptide drugs for flavivirus infection.
Intrapulmonary percussive ventilation in acute exacerbations of COPD patients with mild respiratory acidosis: a randomized controlled trial [ISRCTN17802078]
Authors: Vargas Frédéric , Bui Hoang Nam , Boyer Alexandre , Salmi Louis Rachid , Gbikpi-Benissan Georges , Guenard Hervé , Gruson Didier , Hilbert Gilles 
Published: June 2005

Abstract
Introduction
We hypothesized that the use of intrapulmonary percussive ventilation (IPV), a technique designed to improve mucus clearance, could prove effective in avoiding further deterioration in patients with acute exacerbations of chronic obstructive pulmonary disease (COPD) with mild respiratory acidosis.

Methods
The study was performed in a medical intensive care unit of a university hospital. Thirty-three patients with exacerbations of COPD with a respiratory frequency ≥ 25/min, a PaCO2 > 45 Torr and 7.35 ≤ pH ≤ 7.38 were included in the study. Patients were randomly assigned to receive either standard treatment (control group) or standard treatment plus IPV (IPV group). The IPV group underwent two daily sessions of 30 minutes performed by a chest physiotherapist through a full face mask. The therapy was considered successful when both worsening of the exacerbation and a decrease in pH to under 7.35, which would have required non-invasive ventilation, were avoided.

Results
Thirty minutes of IPV led to a significant decrease in respiratory rate, an increase in PaO2 and a decrease in PaCO2 (p < 0.05). Exacerbation worsened in 6 out of 17 patients in the control group versus 0 out of 16 in the IPV group (p < 0.05). The hospital stay was significantly shorter in the IPV group than in the control group (6.8 ± 1.0 vs. 7.9 ± 1.3 days, p < 0.05).

Conclusion
IPV is a safe technique and may prevent further deterioration in patients with acute exacerbations of COPD with mild respiratory acidosis.
Intensive care unit delirium is an independent predictor of longer hospital stay: a prospective analysis of 261 non-ventilated patients
Authors: Thomason Jason WW , Shintani Ayumi , Peterson Josh F , Pun Brenda T , Jackson James C , Ely E Wesley 
Published: June 2005

Abstract
Introduction
Delirium occurs in most ventilated patients and is independently associated with more deaths, longer stay, and higher cost. Guidelines recommend monitoring of delirium in all intensive care unit (ICU) patients, though few data exist in non-ventilated patients. The study objective was to determine the relationship between delirium and outcomes among non-ventilated ICU patients.

Method
A prospective cohort investigation of 261 consecutively admitted medical ICU patients not requiring invasive mechanical ventilation during hospitalization at a tertiary-care, university-based hospital between February 2002 and January 2003. ICU nursing staff assessed delirium and level of consciousness at least twice per day using the Confusion Assessment Method for the ICU (CAM-ICU) and Richmond Agitation-Sedation Scale (RASS). Cox regression with time-varying covariates was used to determine the independent relationship between delirium and clinical outcomes.

Results
Of 261 patients, 125 (48%) experienced at least one episode of delirium. Patients who experienced delirium were older (mean ± SD: 56 ± 18 versus 49 ± 17 years; p = 0.002) and more severely ill as measured by Acute Physiology and Chronic Health Evaluation II (APACHE II) scores (median 15, interquartile range (IQR) 10–21 versus 11, IQR 6–16; p < 0.001) compared to their non-delirious counterparts. Patients who experienced delirium had a 29% greater risk of remaining in the ICU on any given day (compared to patients who never developed delirium) even after adjusting for age, gender, race, Charlson co-morbidity score, APACHE II score, and coma (hazard ratio (HR) 1.29; 95% confidence interval (CI) 0.98–1.69, p = 0.07). Similarly, patients who experienced delirium had a 41% greater risk of remaining in the hospital after adjusting for the same covariates (HR 1.41; 95% CI 1.05–1.89, p = 0.023). Hospital mortality was higher among patients who developed delirium (24/125, 19%) versus patients who never developed delirium (8/135, 6%), p = 0.002; however, time to in-hospital death was not significant the adjusted (HR 1.27; 95% CI 0.55–2.98, p = 0.58).

Conclusion
Delirium occurred in nearly half of the non-ventilated ICU patients in this cohort. Even after adjustment for relevant covariates, delirium was found to be an independent predictor of longer hospital stay.
Mechanisms of aging in senescence-accelerated mice
Authors: Carter Todd A , Greenhall Jennifer A , Yoshida Shigeo , Fuchs Sebastian , Helton Robert , Swaroop Anand , Lockhart David J , Barlow Carrolee 
Published: June 2005

Abstract
Background
Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to obtain and study. We have used gene-expression analysis and polymorphism screening to study molecular senescence of the retina and hippocampus in two rare inbred mouse models of accelerated neurological senescence (SAMP8 and SAMP10) that closely mimic human neurological aging, and in a related normal strain (SAMR1) and an unrelated normal strain (C57BL/6J).

Results
The majority of age-related gene expression changes were strain-specific, with only a few common pathways found for normal and accelerated neurological aging. Polymorphism screening led to the identification of mutations that could have a direct impact on important disease processes, including a mutation in a fibroblast growth factor gene, Fgf1, and a mutation in and ectopic expression of the gene for the chemokine CCL19, which is involved in the inflammatory response.

Conclusion
We show that combining the study of inbred mouse strains with interesting traits and gene-expression profiling can lead to the discovery of genes important for complex phenotypes. Furthermore, full-genome polymorphism detection, sequencing and gene-expression profiling of inbred mouse strains with interesting phenotypic differences may provide unique insights into the molecular genetics of late-manifesting complex diseases.