bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequent Multidrug-ResistantAcinetobacter baumanniiContamination of Gloves, Gowns, and Hands of Healthcare Workers
Authors: Morgan Daniel J. , Liang Stephen Y. , Smith Catherine L. , Johnson J. Kristie , Harris Anthony D. , Furuno Jon P. , Thorn Kerri A. , Snyder Graham M. , Day Hannah R. , Perencevich Eli N. 
Published: May 2010

Background.Multidrug-resistant (MDR) gram-negative bacilli are important nosocomial pathogens.Objective.To determine the incidence of transmission of MDRAcinetobacter baumanniiandPseudomonas aeruginosafrom patients to healthcare workers (HCWs) during routine patient care.Design.Prospective cohort study.Setting.Medical and surgical intensive care units.Methods.We observed HCWs who entered the rooms of patients colonized with MDRA. baumanniior colonized with both MDRA. baumanniiand MDRP. aeruginosa. We examined their hands before room entry, their disposable gloves and/or gowns upon completion of patient care, and their hands after removal of gloves and/or gowns and before hand hygiene.Results.Sixty-five interactions occurred with patients colonized with MDRA. baumanniiand 134 with patients colonized with both MDRA. baumanniiand MDRP. aeruginosa. Of 199 interactions between HCWs and patients colonized with MDRA. baumannii, 77 (38.7% [95% confidence interval {CI}, 31.9%–45.5%]) resulted in HCW contamination of gloves and/or gowns, and 9 (4.5% [95% CI, 1.6%–7.4%]) resulted in contamination of HCW hands after glove removal before hand hygiene. Of 134 interactions with patients colonized with MDRP. aeruginosa, 11 (8.2% [95% CI, 3.6%–12.9%]) resulted in HCW contamination of gloves and/or gowns, and 1 resulted in HCW contamination of hands. Independent risk factors for contamination with MDRA. baumanniiwere manipulation of wound dressing (adjusted odds ratio [aQR], 25.9 [95% CI, 3.1–208.8]), manipulation of artificial airway (aOR, 2.1 [95% CI, 1.1–4.0]), time in room longer than 5 minutes (aOR, 4.3 [95% CI, 2.0–9.1]), being a physician or nurse practitioner (aOR, 7.4 [95% CI, 1.6–35.2]), and being a nurse (aOR, 2.3 [95% CI, 1.1–4.8]).Conclusions.Gowns, gloves, and unwashed hands of HCWs were frequently contaminated with MDRA. baumannii. MDRA. baumanniiappears to be more easily transmitted than MDRP. aeruginosaand perhaps more easily transmitted than previously studied methicillin-resistantStaphylococcus aureusor vancomycin-resistantEnterococcus. This ease of transmission may help explain the emergence of MDRA. baumannii.
Automated analysis of protein subcellular location in time series images
Authors: Hu Yanhua , Osuna-Highley Elvira , Hua Juchang , Nowicki Theodore Scott , Stolz Robert , McKayle Camille , Murphy Robert F. 
Published: May 2010

Abstract
Motivation: Image analysis, machine learning and statistical modeling have become well established for the automatic recognition and comparison of the subcellular locations of proteins in microscope images. By using a comprehensive set of features describing static images, major subcellular patterns can be distinguished with near perfect accuracy. We now extend this work to time series images, which contain both spatial and temporal information. The goal is to use temporal features to improve recognition of protein patterns that are not fully distinguishable by their static features alone.
Results: We have adopted and designed five sets of features for capturing temporal behavior in 2D time series images, based on object tracking, temporal texture, normal flow, Fourier transforms and autoregression. Classification accuracy on an image collection for 12 fluorescently tagged proteins was increased when temporal features were used in addition to static features. Temporal texture, normal flow and Fourier transform features were most effective at increasing classification accuracy. We therefore extended these three feature sets to 3D time series images, but observed no significant improvement over results for 2D images. The methods for 2D and 3D temporal pattern analysis do not require segmentation of images into single cell regions, and are suitable for automated high-throughput microscopy applications.
Availability: Images, source code and results will be available upon publication at http://murphylab.web.cmu.edu/software
Contact: murphy@cmu.edu
Effects of mangrove removal on benthic communities and sediment characteristics at Mangawhai Harbour, northern New Zealand
Authors: Alfaro Andrea C. 
Published: May 2010

Abstract
Alfaro, A. C. 2010. Effects of mangrove removal on benthic communities and sediment characteristics at Mangawhai Harbour, northern New Zealand. – ICES Journal of Marine Science, 67: 1087–1104. The spread of mangroves at many locations in temperate northern New Zealand provides a stark contrast to the well-documented trend in mangrove forest decline recorded through the tropics and subtropics. To explore this difference, improved understanding is needed of New Zealand's mangrove ecosystems and how they respond to anthropogenic disturbance. The effect of mangrove removal on the community ecology of mangrove stands and adjacent habitats was investigated within Mangawhai Estuary, northern New Zealand, between March 2004 and September 2006. The vegetation, benthic macrofauna, and sediments were sampled within habitats (marshgrass, mangrove stands, pneumatophore zones, sandflats, and channels) at a treatment site (mangroves removed) and two undisturbed sites, before and after mangrove-removal activities. Mature mangrove habitats had less total abundance and fewer taxa than all the other habitats sampled and were dominated by pulmonate snails (Amphibola crenata) and mud crabs (Helice crassa). Whereas faunal composition varied seasonally as a result of life-history dynamics, temporal changes could be attributed to mangrove-removal activities. Mangrove eradication was followed by immediate changes in the sediment from a muddy to sandier environment, which favoured an overall increase in the abundance of crabs, snails, and bivalves. However, unexpected topographic catchment reconfigurations in late 2005 may have caused a subsequent increase in the delivery of silt and organic content to the study area and an overall decrease in faunal density in March and September 2006. The study provides direct evidence of the effect of mangroves on sediment and benthic faunal characteristics and the importance of catchment-derived imports to estuarine ecosystems.
Does gravity operate between galaxies? Observational evidence re-examined
Authors: Farley Francis J. M. 
Published: May 2010

The redshifts and luminosities of type 1A supernovae are conventionally fitted with the current paradigm, which holds that the galaxies are locally stationary in an expanding metric. The fit fails unless the expansion is accelerating; driven perhaps by ‘dark energy’. Is the recession of the galaxies slowed down by gravity or speeded up by some repulsive force? To shed light on this question the redshifts and apparent magnitudes of type 1A supernovae are re-analysed in a cartesian frame of reference omitting gravitational effects. The redshift is ascribed to the relativistic Doppler effect which gives the recession velocity when the light was emitted; if this has not changed, the distance reached and the luminosity follow immediately. This simple concept fits the observations surprisingly well with the Hubble constant
H
0
=62.9±0.3 km s
−1
Mpc
−1
. It appears that the galaxies recede at unchanging velocities, so on the largest scale there is no significant intergalactic force. Reasons for the apparent absence of an intergalactic force are discussed.
Long‐term increases in intrinsic water‐use efficiency do not lead to increased stem growth in a tropical monsoon forest in western Thailand
Authors: NOCK CHARLES A. , BAKER PATRICK J. , WANEK WOLFGANG , LEIS ALBRECHT , GRABNER MICHAEL , BUNYAVEJCHEWIN SARAYUDH , HIETZ PETER 
Published: May 2010

AbstractRising atmospheric carbon dioxide [CO2] can accelerate tree growth by stimulating photosynthesis and increasing intrinsic water‐use efficiency (iWUE). Little evidence exists, however, for the long‐term growth and gas‐exchange responses of mature trees in tropical forests to the combined effects of rising [CO2] and other global changes such as warming. Using tree rings and stable isotopes of carbon and oxygen, we investigated long‐term trends in the iWUE and stem growth (basal area increment, BAI) of three canopy tree species in a tropical monsoon forest in western Thailand (Chukrasia tabularis, Melia azedarach, and Toona ciliata). To do this, we modelled the contribution of ontogenetic effects (tree diameter or age) and calendar year to variation in iWUE, oxygen isotopes, and BAI using mixed‐effects models. Although iWUE increased significantly with both tree diameter and calendar year in all species, BAI at a given tree diameter was lower in more recent years. For one species, C. tabularis, differences in crown dominance significantly influence stable isotopes and growth. Tree ring Δ18O increased with calendar year in all species, suggesting that increasing iWUE may have been driven by relatively greater reductions in stomatal conductance – leading to enrichment in Δ18O – than increases in photosynthetic capacity. Plausible explanations for the observed declines in growth include water stress resulting from rising temperatures and El Niño events, increased respiration, changes in allocation, or more likely, a combination of these factors.
Modelling climate‐change‐induced nonlinear thresholds in cephalopod population dynamics
Authors: ANDRÉ JESSICA , HADDON MALCOLM , PECL GRETTA T. 
Published: May 2010

AbstractA significant global challenge lies in our current inability to anticipate, and therefore prepare for, critical ecological thresholds (i.e. tipping points in ecosystems). This deficit stems largely from an inadequate understanding of the many complex interactions between species and the environment at the ecosystem level, and the paucity of mechanistic models relating environment to population dynamics at the species level. In marine ecosystems, abundant, short‐lived and fast‐growing species such as anchovies or squids, consistently function as ‘keystone’ groups whose population dynamics affect entire ecosystems. Increasing exploitation coupled with climate change impacts has the potential to affect these ecological groups and consequently, the entire marine ecosystem. There are currently very few models that predict the impact of climate change on these keystone groups. Here we use a combination of individual‐based bioenergetics and stage‐structured population models to characterize the fundamental capacity of cephalopods to respond to climate change. We demonstrate the potential for, and mechanisms behind, two unfavourable climate‐change‐induced thresholds in future population dynamics. Although one threshold was the direct consequence of a decrease in incubation time caused by ocean warming, the other threshold was linked to survivorship, implying the possibility of management through a modification of fishing mortality. Additional substantive changes in phenology were also predicted, with a possible loss in population resilience. Our results demonstrate the feasibility of predicting complex nonlinear dynamics with a reasonably simplistic mechanistic model, and highlight the necessity of developing such approaches for other species if attempts to moderate the impact of climate change on natural resources are to be effective.
Middle distal canal of the mandibular first molar: a case report and literature review
Authors: Kottoor J. , Sudha R. , Velmurugan N. 
Published: May 2010

Kottoor J, Sudha R, Velmurugan N. Middle distal canal of the mandibular first molar: a case report and literature review. International Endodontic Journal.AbstractAim  To present a clinical case report in a mandibular first molar with a middle distal canal, along with a review of the literature.Summary  With the use of magnification, either by microscopes or by loupes, there is an increasing possibility of detecting additional canals. The present case describes root canal treatment in a mandibular first molar with two roots and a Sert and Bayirli Type XVIII canal configuration in the distal root. The presence of a three canals in the distal root of mandibular first molars has been reported to have an incidence of 0.2–3%.Key learning points

Clinicians should be aware of the variable root canal anatomy in the distal root of mandibular first molars.
Use of magnification helps to identify and locate additional root canals.
Three root canals in the distal root of mandibular first molar teeth might occur.
3D visualization and quantification of rat cortical bone porosity using a desktop micro‐CT system: a case study in the tibia
Authors: BRITZ H.M. , JOKIHAARA J. , LEPPÄNEN O.V. , JÄRVINEN T. , COOPER D.M.L. 
Published: May 2010

SummaryAlthough micro‐computed tomography (micro‐CT) has become the gold standard for assessing the 3D structure of trabecular bone, its extension to cortical bone microstructure has been relatively limited. Desktop micro‐CT has been employed to assess cortical bone porosity of humans, whereas that of smaller animals, such as mice and rats, has thus far only been imaged using synchrotron‐based micro‐CT. The goal of this study was to determine if it is possible to visualize and quantify rat cortical porosity using desktop micro‐CT. Tibiae (n = 10) from 30‐week‐old female Sprague‐Dawley rats were imaged with micro‐CT (3 μm nominal resolution) and sequential ground sections were then prepared. Bland–Altman plots were constructed to compare per cent porosity and mean canal diameter from micro‐CT (3D) versus histology (2D). The mean difference or bias (histology – micro‐CT; ±95% confidence interval) for per cent porosity was found to be −0.15% (±2.57%), which was not significantly different from zero (P= 0.720). Canal diameter had a bias (±95% confidence interval) of −5.73 μm (±4.02 μm) which was found to be significantly different from zero (P < 0.001). The results indicated that cortical porosity in rat bone can indeed be visualized by desktop micro‐CT. Quantitative assessment of per cent porosity provided unbiased results, whereas direct analysis of mean canal diameter was overestimated by micro‐CT. Thus, although higher resolution, such as that available from synchrotron micro‐CT, may ultimately be required for precise geometric measurements, desktop micro‐CT – which is far more accessible – is capable of yielding comparable measures of porosity and holds great promise for assessment of the 3D arrangement of cortical porosity in the rat.
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae
Authors: Abbott D. Wade , Higgins Melanie A. , Hyrnuik Susanne , Pluvinage Benjamin , Lammerts van Bueren Alicia , Boraston Alisdair B. 
Published: May 2010

SummaryThe genome of Streptococcus pneumoniae strains, as typified by the TIGR4 strain, contain several genes encoding proteins putatively involved in α‐glucan degradation, modification and synthesis. The extracellular components comprise an ATP binding cassette‐transporter with its solute binding protein, MalX, and the hydrolytic enzyme SpuA. We show that of the commonly occurring exogenous α‐glucans, S. pneumoniae TIGR4 is only able to grow on glycogen in a MalX‐ and SpuA‐dependent manner. SpuA is able to degrade glycogen into a ladder of α‐1,4‐glucooligosaccharides while the high‐affinity interaction (Ka ∼ 106 M−1) of MalX with maltooligosaccharides plays a key role in promoting the selective uptake of the glycogen degradation products that are produced by SpuA. The X‐ray crystallographic analyses of apo‐ and complexed MalX illuminate the protein's specificity for the degradation products of glycogen and its striking ability to recognize the helical structure of the ligand. Overall, the results of this work provide new structural and functional insight into streptococcal α‐glucan metabolism while supplying biochemical support for the hypothesis that the substrate of the S. pneumoniaeα‐glucan metabolizing machinery is glycogen, which in a human host is abundant in lung epithelial cells, a common target for invasive S. pneumoniae.
Better late than early: delayed translation of intron‐encoded endonuclease I‐TevI is required for efficient splicing of its host group I intron
Authors: Gibb Ewan A. , Edgell David R. 
Published: May 2010

SummaryThe td group I intron interrupting the thymidylate synthase (TS) gene of phage T4 is a mobile intron that encodes the homing endonuclease I‐TevI. Efficient RNA splicing of the intron is required to restore function of the TS gene, while expression of I‐TevI from within the intron is required to initiate intron mobility. Three distinct layers of regulation temporally limit I‐TevI expression to late in the T4 infective cycle, yet the biological rationale for stringent regulation has not been tested. Here, we deleted key control elements to deregulate I‐TevI expression at early and middle times post T4 infection. Strikingly, we found that deregulation of I‐TevI, or of a catalytically inactive variant, generated a thymidine‐dependent phenotype that is caused by a reduction in td intron splicing. Prematurely terminating I‐TevI translation restores td splicing, full‐length TS synthesis, and rescues the thymidine‐dependent phenotype. We suggest that stringent translational control of I‐TevI evolved to prevent the ribosome from disrupting key structural elements of the td intron that are required for splicing and TS function at early and middle times post T4 infection. Analogous translational regulatory mechanisms in unrelated intron‐open reading frame arrangements may also function to limit deleterious consequences on splicing and host gene function.
Serum lipid levels are positively associated with non‐erosive reflux disease, but not with functional heartburn
Authors: Matsuzaki J. , Suzuki H. , Iwasaki E. , Yokoyama H. , Sugino Y. , Hibi T. 
Published: May 2010

AbstractBackground  Metabolic syndrome and obesity are known risk factors for gastro‐esophageal reflux disease (GERD), especially for erosive esophagitis. Although non‐erosive reflux disease (NERD) is probably associated with obesity or other metabolic syndrome, there is little direct evidence to support this assertion.Methods  Workers in Keio University who underwent a general health examination between September 2006 and August 2007 were enrolled. Reflux symptom questionnaires were administered and metabolic parameters were obtained. The severity of gastro‐esophageal reflux (GER) was scored using a validated scale of videoesophagography.Key Results  Two hundred and eighty‐three subjects (243 men and 40 women; mean age 49.8 ± 6.9 years) with no radiographic evidence of erosive esophagitis were enrolled. The severity of GER was worse among men than among women, whereas the severity of reflux symptoms was worse among women. The severity of GER was associated with age and serum triglyceride levels in men, and with the serum low‐density lipoprotein cholesterol levels in women. The severity of reflux symptoms, however, was not associated with metabolic parameters. There were more women than men with reflux symptoms but without GER (‘presumed’ functional heartburn group), compared with subjects with neither GER nor reflux symptoms. In men, the presence of both reflux symptoms and GER (‘presumed’ NERD group) was associated with the serum triglyceride levels.Conclusions & Inferences  While NERD is associated with serum lipid levels, functional heartburn is not. The prevalence of GER was greater among men; conversely, the prevalence of functional heartburn was greater among women.
Immunoendocrine host–parasite interactions during helminth infections: from the basic knowledge to its possible therapeutic applications
Authors: HERNÁNDEZ‐BELLO R. , ESCOBEDO G. , GUZMÁN C. , IBARRA‐CORONADO E. G. , LÓPEZ‐GRIEGO L. , MORALES‐MONTOR J. 
Published: May 2010

SummaryMost of the current research on parasitic infections that affect humans and domestic animals has been focused on vaccines, diagnostic methods, epidemiology, new drug design, and recently, with the advancement of genomics and proteomics, on the evolutionary origins of parasites. However, the basic biology of many parasites of medical and veterinary importance has not been intensively studied. Some efforts have been made to obtain information on the parasite–host relationship; however, knowledge of the intricate neuroimmunoendocrine interactions of the host–parasite network, the consequences of this interaction on the host and parasite physiology, and its possible applications needs further investigation. We review here the literature, our own studies on the host–parasite neuroimmunoendocrine network, and how this basic knowledge can be used to design new treatments, by way of using hormones, antihormones, and hormone analogues as a possible novel therapy during parasitic diseases, with special emphasis on helminth parasites. Besides the biological interest, these investigations may contribute to the future identification of alternative treatments for several parasitic diseases. This complicated neuroimmunoendocrine network management during parasitic infections, and its physiological and behavioural consequences upon the host, may be operative in other mammalian infections. Such complexity may also help to explain the often conflicting results, observed between infections with respect to the role of the host sex and age, and hints to other avenues of research and strategies for their treatment and control.
Functional adaptation of spiriferide brachiopod morphology
Authors: SHIINO Y. , KUWAZURU O. 
Published: May 2010

AbstractIt has been suggested that spiriferide morphologies have evolved to adapt to a variety of environmental conditions. Through a computational fluid dynamics approach, we examined how the spiriferide original form was optimized for a lotic condition, specifically addressing the functionalization of the Devonian spiriferide brachiopod Paraspirifer bownockeri to generate passive feeding flows. The results using four models, each of which differed in the development of the spiriferide shell depression, i.e. sulcus, showed that a deeper sulcus functions to create strong spiral flows so as to align on the feeding organ inside the shell. Among the sulcus‐developed models, only the mimic of the natural form could generate comparative slow flows with a stable inflow area. The fossil record of spiriferides shows a morphological trade‐off between the development of the sulcus and wing form. We concluded that spiriferide shells with such a morphological combination evolved to produce various feeding strategies, resulting in diversification.
Low birthweight and chronic kidney disease
Authors: XU RONG , ZUO LI 
Published: May 2010

ABSTRACTLow birthweight reflects the congenital defects of organs, which is associated with chronic kidney disease through its direct influence on nephron number and function, also through related metabolic disease‐induced kidney damage. We reviewed the current evidence regarding the role of low birthweight in the pathogenesis of chronic kidney disease.