bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospects for Clinical Application of Electronic-Nose Technology to Early Detection ofMycobacterium tuberculosisin Culture and Sputum
Authors: Fend Reinhard , Kolk Arend H. J. , Bessant Conrad , Buijtels Patricia , Klatser Paul R. , Woodman Anthony C. 
Published: June 2006

ABSTRACTZiehl-Neelsen (ZN) staining for the diagnosis of tuberculosis (TB) is time-consuming and operator dependent and lacks sensitivity. A new method is urgently needed. We investigated the potential of an electronic nose (EN) (gas sensor array) comprising 14 conducting polymers to detect differentMycobacteriumspp. andPseudomonas aeruginosain the headspaces of cultures, spiked sputa, and sputum samples from 330 culture-proven and human immunodeficiency virus-tested TB and non-TB patients. The data were analyzed using principal-component analysis, discriminant function analysis, and artificial neural networks. The EN differentiated between differentMycobacteriumspp. and between mycobacteria and other lung pathogens both in culture and in spiked sputum samples. The detection limit in culture and spiked sputa was found to be 1 × 104mycobacteria ml−1. After training of the neural network with 196 sputum samples, 134 samples (55M. tuberculosisculture-positive samples and 79 culture-negative samples) were used to challenge the model. The EN correctly predicted 89% of culture-positive patients; the six false negatives were the four ZN-negative and two ZN-positive patients. The specificity and sensitivity of the described method were 91% and 89%, respectively, compared to culture. At present, the reasons for the false negatives and false positives are unknown, but they could well be due to the nonoptimized system used here. This study has shown the ability of an electronic nose to detectM. tuberculosisin clinical specimens and opens the way to making this method a rapid and automated system for the early diagnosis of respiratory infections.
Detection of Carcinogenic Human Papillomavirus in Specimens Collected with a Novel Self-Sampling Device
Authors: Castle Philip E. , Aftab Asma , Saint-Jean Gilbert , Mendez Luis 
Published: June 2006

ABSTRACT
We compared the detection of carcinogenic human papillomavirus DNA in cervicovaginal specimens self-collected using a novel device to the detection in physician-collected cervical specimens from 137 women. The kappa value was 0.66 (95% confidence interval, 0.53 to 0.78), with an 83% overall test agreement and a 68% positive test agreement.
Molecular Mimicry Revisited: Gut Bacteria and Multiple Sclerosis
Authors: Westall Fred C. 
Published: June 2006

ABSTRACTMolecular mimicry is a possible explanation for autoimmune side effects of microorganism infections. Protein sequences from a particular microorganism are compared to known autoimmune immunogens. For diseases such as multiple sclerosis (MS), where the infectious agent is unknown, guesses to its identity are made. Mimics are assumed to be rare. This study takes a radically different approach. Reported sequences from all known human bacterial and viral agents were searched for autoimmune immunogen mimics. Three encephalitogenic peptides, whose autoimmune requirements have been studied extensively, were selected for comparison. Mimics were seen in a wide variety of organisms. For each immunogen, the mimics were found predominantly in nonpathogenic gut bacteria. Since the three immunogens used in this study are related to MS, it is suggested that a microorganism responsible for autoimmune activity in MS could be a normally occurring gut bacterium. This would explain many of the peculiar MS epidemiological data and why no infective agent has been identified for MS and supports recently found MS gut metabolism abnormalities.
Incidence and Pathogenic Effect of
Streptococcus pseudopneumoniae
Authors: Harf-Monteil Colette , Granello Carole , Le Brun Cécile , Monteil Henri , Riegel Philippe 
Published: June 2006

ABSTRACT

We evaluated the incidence of
Streptococcus pseudopneumoniae
in clinical isolates by phenotypic methods and DNA-DNA hybridization. The pathogenic role of this organism was investigated with the mouse peritonitis/sepsis model. Our results show a low incidence (1/120 pneumococcal isolates) and a potential pathogenic effect for
S. pseudopneumoniae
.
Attribution and Impacts of Upper-Ocean Biases in CCSM3
Authors: Large W. G. , Danabasoglu G. 
Published: June 2006

AbstractThe largest and potentially most important ocean near-surface biases are examined in the Community Climate System Model coupled simulation of present-day conditions. They are attributed to problems in the component models of the ocean or atmosphere, or both. Tropical biases in sea surface salinity (SSS) are associated with precipitation errors, with the most striking being a band of excess rainfall across the South Pacific at about 8°S. Cooler-than-observed equatorial Pacific sea surface temperature (SST) is necessary to control a potentially catastrophic positive feedback, involving precipitation along the equator. The strength of the wind-driven gyres and interbasin exchange is in reasonable agreement with observations, despite the generally too strong near-surface winds. However, the winds drive far too much transport through Drake Passage [&gt;190 Sv (1 Sv ≡ 106 m3 s−1)], but with little effect on SST and SSS. Problems with the width, separation, and location of western boundary currents and their extensions create large correlated SST and SSS biases in midlatitudes. Ocean model deficiencies are suspected because similar signals are seen in uncoupled ocean solutions, but there is no evidence of serious remote impacts. The seasonal cycles of SST and winds in the equatorial Pacific are not well represented, and numerical experiments suggest that these problems are initiated by the coupling of either or both wind components. The largest mean SST biases develop along the eastern boundaries of subtropical gyres, and the overall coupled model response is found to be linear. In the South Atlantic, surface currents advect these biases across much of the tropical basin. Significant precipitation responses are found both in the northwest Indian Ocean, and locally where the net result is the loss of an identifiable Atlantic intertropical convergence zone, which can be regained by controlling the coastal temperatures and salinities. Biases off South America and Baja California are shown to significantly degrade precipitation across the Pacific, subsurface ocean properties on both sides of the equator, and the seasonal cycle of equatorial SST in the eastern Pacific. These signals extend beyond the reach of surface currents, so connections via the atmosphere and subsurface ocean are implicated. Other experimental results indicate that the local atmospheric forcing is only part of the problem along eastern boundaries, with the representation of ocean upwelling another likely contributor.
Climate Change Projections for the Twenty-First Century and Climate Change Commitment in the CCSM3
Authors: Meehl Gerald A. , Washington Warren M. , Santer Benjamin D. , Collins William D. , Arblaster Julie M. , Hu Aixue , Lawrence David M. , Teng Haiyan , Buja Lawrence E. , Strand Warren G. 
Published: June 2006

Abstract
Climate change scenario simulations with the Community Climate System Model version 3 (CCSM3), a global coupled climate model, show that if concentrations of all greenhouse gases (GHGs) could have been stabilized at the year 2000, the climate system would already be committed to 0.4°C more warming by the end of the twenty-first century. Committed sea level rise by 2100 is about an order of magnitude more, percentage-wise, compared to sea level rise simulated in the twentieth century. This increase in the model is produced only by thermal expansion of seawater, and does not take into account melt from ice sheets and glaciers, which could at least double that number. Several tenths of a degree of additional warming occurs in the model for the next 200 yr in the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emissions Scenarios (SRES) B1 and A1B scenarios after stabilization in the year 2100, but with twice as much sea level rise after 100 yr, and doubling yet again in the next 100 yr to 2300. At the end of the twenty-first century, the warming in the tropical Pacific for the A2, A1B, and B1 scenarios resembles an El Niño–like response, likely due to cloud feedbacks in the model as shown in an earlier version. Greatest warming occurs at high northern latitudes and over continents. The monsoon regimes intensify somewhat in the future warmer climate, with decreases of sea level pressure at high latitudes and increases in the subtropics and parts of the midlatitudes. There is a weak summer midlatitude soil moisture drying in this model as documented in previous models. Sea ice distributions in both hemispheres are somewhat overextensive, but with about the right ice thickness at the end of the twentieth century. Future decreases in sea ice with global warming are proportional to the temperature response from the forcing scenarios, with the high forcing scenario, A2, producing an ice-free Arctic in summer by the year 2100.
The Formulation and Atmospheric Simulation of the Community Atmosphere Model Version 3 (CAM3)
Authors: Collins William D. , Rasch Philip J. , Boville Byron A. , Hack James J. , McCaa James R. , Williamson David L. , Briegleb Bruce P. , Bitz Cecilia M. , Lin Shian-Jiann , Zhang Minghua 
Published: June 2006

Abstract
A new version of the Community Atmosphere Model (CAM) has been developed and released to the climate community. CAM Version 3 (CAM3) is an atmospheric general circulation model that includes the Community Land Model (CLM3), an optional slab ocean model, and a thermodynamic sea ice model. The dynamics and physics in CAM3 have been changed substantially compared to implementations in previous versions. CAM3 includes options for Eulerian spectral, semi-Lagrangian, and finite-volume formulations of the dynamical equations. It supports coupled simulations using either finite-volume or Eulerian dynamics through an explicit set of adjustable parameters governing the model time step, cloud parameterizations, and condensation processes. The model includes major modifications to the parameterizations of moist processes, radiation processes, and aerosols. These changes have improved several aspects of the simulated climate, including more realistic tropical tropopause temperatures, boreal winter land surface temperatures, surface insolation, and clear-sky surface radiation in polar regions. The variation of cloud radiative forcing during ENSO events exhibits much better agreement with satellite observations. Despite these improvements, several systematic biases reduce the fidelity of the simulations. These biases include underestimation of tropical variability, errors in tropical oceanic surface fluxes, underestimation of implied ocean heat transport in the Southern Hemisphere, excessive surface stress in the storm tracks, and offsets in the 500-mb height field and the Aleutian low.
Lutein supplementation in retinitis pigmentosa: PC-based vision assessment in a randomized double-masked placebo-controlled clinical trial [NCT00029289]
Authors: Bahrami Hossein , Melia Michele , Dagnelie Gislin 
Published: June 2006

Abstract

Background
There is no generally accepted medical or surgical treatment to stop the progressive course of retinitis pigmentosa. Previous studies have suggested lutein as a potential treatment with positive effects on macular pigment density. The objective of this study was to examine the effect of lutein supplementation on preservation of visual function in patients with retinitis pigmentosa (RP)

Methods
In a double-masked randomized placebo-controlled phase I/II clinical trial with a cross-over design, 34 adult patients with RP were randomized to two groups. One group, consisted of 16 participants, received lutein supplementation (10 mg/d for 12 wks followed by 30 mg/d) for the first 24 weeks and then placebo for the following 24 weeks, while the other group included 18 participants for whom placebo (24 weeks) was administered prior to lutein. Visual acuity, contrast sensitivity, and central visual field were measured at different illumination levels at baseline and every week using a PC-based test at home.

Results
For visual acuity (VA) at normal illumination level, treatment with lutein reduced logMAR, i.e. improved VA, but this effect was not statistically significant. The changes in normal (100%), low (4%), and very low (0.1%) illumination log CS were not statistically significant (p-values: 0.34, 0.23, and 0.32, respectively). Lutein had a statistically significant effect on visual field (p-value: 0.038) and this effect increased in the model assuming a 6-week delay in effect of lutein. Comparing the development of vision measures against the natural loss expected to occur over the course of 48 weeks, most measures showed reduced decline, and these reductions were significant for normal illumination VA and CS.

Conclusion
These results suggest that lutein supplementation improves visual field and also might improve visual acuity slightly, although these results should be interpreted cautiously. As a combined phase I and II clinical trial, this study demonstrated the efficacy and safety of lutein supplementation.
ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces
Authors: Saha Rudra P , Bahadur Ranjit P , Pal Arumay , Mandal Saptarshi , Chakrabarti Pinak 
Published: June 2006

Abstract

Background
Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the interface formed by protein-protein association would allow us to better understand protein interaction networks on one hand, and to design molecules that can engage a given interface and thereby control protein function on the other hand.

Results
ProFace is a suite of programs that uses a file, containing atomic coordinates of a multi-chain molecule, as input and analyzes the interface between any two or more subunits. The interface residues are shown segregated into spatial patches (if such a clustering is possible based on an input threshold distance) and/or core and rim regions. A number of physicochemical parameters defining the interface is tabulated. Among the different output files, one contains the list of interacting residues across the interface. Results can be used to infer if a particular interface belongs to a homodimeric molecule.

Conclusion
A web-server, ProFace (available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html) has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters.
Longitudinal residual strain and stress-strain relationship in rat small intestine
Authors: Dou Yanling , Fan Yanhua , Zhao Jingbo , Gregersen Hans 
Published: June 2006

Abstract

Background
To obtain a more detailed description of the stress-free state of the intestinal wall, longitudinal residual strain measurements are needed. Furthermore, data on longitudinal stress-strain relations in visceral organs are scarce. The present study aims to investigate the longitudinal residual strain and the longitudinal stress-strain relationship in the rat small intestine.

Methods
The longitudinal zero-stress state was obtained by cutting tissue strips parallel to the longitudinal axis of the intestine. The longitudinal residual stress was characterized by a bending angle (unit: degrees per unit length and positive when bending outwards). Residual strain was computed from the change in dimensions between the zero-stress state and the no-load state. Longitudinal stresses and strains were computed from stretch experiments in the distal ileum at luminal pressures ranging from 0–4 cmH2O.

Results
Large morphometric variations were found between the duodenum and ileum with the largest wall thickness and wall area in the duodenum and the largest inner circumference and luminal area in the distal ileum (p < 0.001). The bending angle did not differ between the duodenum and ileum (p > 0.5). The longitudinal residual strain was tensile at the serosal surface and compressive at the mucosal surface. Hence, the neutral axis was approximately in the mid-wall. The longitudinal residual strain and the bending angle was not uniform around the intestinal circumference and had the highest values on the mesenteric sides (p < 0.001). The stress-strain curves fitted well to the mono-exponential function with determination coefficients above 0.96. The α constant increased with the pressure, indicating the intestinal wall became stiffer in longitudinal direction when pressurized.

Conclusion
Large longitudinal residual strains reside in the small intestine and showed circumferential variation. This indicates that the tissue is not uniform and cannot be treated as a homogenous material. The longitudinal stiffness of the intestinal wall increased with luminal pressure. Longitudinal residual strains must be taken into account in studies of gastrointestinal biomechanical properties.
Impaired β-Cell Function in Human Aging: Response to Nicotinic Acid-Induced Insulin Resistance
Authors: Chang Annette M. , Smith Marla J. , Galecki Andrzej T. , Bloem Cathie J. , Halter Jeffrey B. 
Published: June 2006

Abstract
Context: Glucose tolerance declines with age and may involve impaired β-cell sensitivity to glucose and β-cell compensation for insulin resistance.
Objective: We investigated β-cell sensitivity to glucose and β-cell compensation for nicotinic acid-induced insulin resistance in young (age &lt;35 yr) people with normal glucose tolerance (NGT) and old (age &gt;60 yr) people with NGT and impaired glucose tolerance (IGT).
Design/Patients/Setting/Intervention: Fifteen young NGT, 16 old NGT, and 14 old IGT were randomized to 2-wk treatment with nicotinic acid or placebo in a double-blind, crossover study in a university medical setting. At the end of each treatment period, participants had a frequently sampled iv glucose tolerance test and ramp clamp, in which insulin secretion rates (ISR) were determined in response to a matched 5–10 mm glucose stimulus.
Main Outcome Measures: Insulin sensitivity (SI), acute insulin response to iv glucose (AIRg), and disposition index (AIRg × SI, or β-cell compensation for insulin resistance) from frequently sampled iv glucose tolerance testing, and ISR area under the curve (or β-cell sensitivity to glucose) from ramp clamp were determined.
Results: Progressive impairments in insulin secretion as assessed by AIRg, disposition index, and ISR area under the curve were identified in older people with NGT, with more marked defects in older people with IGT. Nicotinic acid treatment significantly reduced SI in all groups. β-Cell compensation for nicotinic acid-induced insulin resistance was incomplete in all three groups, with greater defects in the two older groups.
Conclusions: Human aging is associated with impaired β-cell sensitivity to glucose and impaired β-cell compensation to insulin resistance.
Fosamprenavir: Drug Development for Adherence
Authors: Hester E Kelly , Chandler Haley V , Sims Kelli M 
Published: June 2006

Objective: To review the pharmacology, pharmacokinetics, virology, safety, efficacy, and clinical use of fosamprenavir. Data Sources: A MEDLINE (1966–July 2005) search was conducted using fosamprenavir, Lexiva, amprenavir, and GW433908 as key words. Abstracts from infectious diseases and HIV scientific meetings were identified. Bibliographies of cited articles were reviewed. Study Selection and Data Extraction: All publications, meeting abstracts, and unpublished information were reviewed and relevant items included. Information from in vitro, preclinical, and Phase II and III clinical trials was included. Data Synthesis: Fosamprenavir is a protease inhibitor (PI) prodrug used for the treatment of HIV-1 infection. The active moiety, amprenavir, is extensively metabolized by CYP3A4. In clinical trials, fosamprenavir was at least as effective as amprenavir, with a reduced pill burden. Fosamprenavir was developed with the intention of reducing the pill burden associated with amprenavir. It has demonstrated comparable safety and efficacy with comparator Pls and is associated with limited cross-resistance to other Pls. Conclusions: Fosamprenavir is a promising antiretroviral agent with favorable efficacy and tolerability. At this time, data indicate the utility of fosamprenavir in treatment-naïve and PI-experienced HIV-infected patients.
Genitopatellar syndrome: Expanding the phenotype and excluding mutations in LMX1B and TBX4
Authors: Abdul‐Rahman Omar A. , La Trang H. , Kwan Andrea , Schlaubitz Silke , Barsh Greg S. , Enns Gregory M. , Hudgins Louanne 
Published: June 2006

AbstractGenitopatellar syndrome is a newly described disorder characterized by absent/hypoplastic patellae, lower extremity contractures, urogenital anomalies, dysmorphic features, skeletal anomalies, and agenesis of the corpus callosum. More recently, cardiac anomalies and ectodermal dysplasia have been suggested as additional features of this syndrome. We report on two additional patients with genitopatellar syndrome and expand the spectrum of anomalies to include radio‐ulnar synostosis. Since there exists significant overlap in the skeletal phenotype between genitopatellar syndrome and both the nail‐patella and short patella syndromes, mutation screening of their causative genes, LMX1B and TBX4, was performed. Although there still does not appear to be an identifiable molecular etiology in genitopatellar syndrome, mutations in these two candidate genes have been excluded in our patients. Since both LMX1B and TBX4 are involved in a common molecular pathway, it is likely that the causative gene of genitopatellar syndrome functions within the same developmental process. © 2006 Wiley‐Liss, Inc.
An autosomal recessive form of spastic cerebral palsy (CP) with microcephaly and mental retardation
Authors: Rajab Anna , Yoo Seung‐Yun , Abdulgalil Aiman , Kathiri Salem , Ahmed Riaz , Mochida Ganeshwaran H. , Bodell Adria , Barkovich A. James , Walsh Christopher A. 
Published: June 2006

AbstractCerebral palsy (CP) is defined as any nonprogressive motor deficits resulting from cerebral abnormalities that occur in the prenatal or perinatal period. Symptoms become apparent during the first year of life. Genetic forms of CP account for about 2% in European populations but are thought to cause a substantial proportion in consanguineous families. We have identified a large consanguineous family from Oman with spastic diplegia, microcephaly, and mental retardation. Additional manifestations include hyperreflexia, clumsiness, unstable gait, drooling, and dysarthria. There was phenotypic variability among different individuals, but spastic diplegia, microcephaly, and mental retardation were three constant traits present in all affected individuals. © 2006 Wiley‐Liss, Inc.