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PubMed2005

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.

BACKGROUND: Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. RESULTS: By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27) and Deinococcus megaplasmid (DR177). CONCLUSION: After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of horizontally transferred genes, we also show that the single megaplasmid of Thermus and the DR177 megaplasmid of Deinococcus are homologous and probably were inherited from the common ancestor of these bacteria.

Acclimatization↗

PubMed1990

Adaptation to peripheral flicker: relationship to contrast detection thresholds.

The time to disappearance of flicker of a temporally modulated uniform 1 degree field, steadily viewed with the temporal retina at an eccentricity of 12 degrees, was measured as a function of temporal frequency and depth of modulation (contrast). As found by others, for a fixed contrast, adaptation time declined as temporal frequency increased. To check whether this effect was genuinely temporal frequency-dependent, or reflected the amount above threshold of the adapting contrast, measurements were also made at contrasts which were multiples of the contrast threshold or matched across temporal frequencies. The results suggest that both temporal frequency and amount of adapting contrast above threshold are important in determining the speed of adaptation.

Adaptation, Ocular↗

PubMed1998

Two-dimensional matches from one-dimensional stimulus components in human stereopsis.

Three-dimensional visual scenes project onto the retina of the eye as two-dimensional images. The third dimension, depth, is projected as subtle differences between left and right retinal images. As early as the 1830s, stereoscopic depth perception was shown to depend on horizontal disparities between these images. To detect disparity, the visual system must match corresponding parts of the two retinal images. To identify the stimulus elements used in stereo matching, I applied a disparity-adaptation technique to visual patterns whose one-dimensional components and two-dimensional features have very different disparities. Surprisingly, the adaptors that are effective in altering depth perception appear widely separated in depth from the patterns they adapt. I conclude that stereo matching occurs in all directions of two-dimensional space and that one-dimensional components are the stimulus primitives, the fundamental elements of stereo matching. This is a reversal of the classical view of stereo correspondence as a one-dimensional (horizontal) matching of monocular two-dimensional features.

Depth Perception↗

PubMed2006

The quality of hospital-based antenatal care in Istanbul.

The aim of this study was to gather comprehensive data from three hospitals in Istanbul, Turkey, in order to gain in-depth understanding of the quality of antenatal care in this setting. The Bruce-Jain framework for quality of care was adapted for use in evaluating antenatal care. Methods included examination of hospital records, in-depth interviews, exit questionnaires, and structured observations. The study revealed deficiencies in the quality of antenatal care being delivered at the study hospitals in all six elements of the quality-of-care framework. The technical content of visits varied greatly among the hospitals, and an overuse of technology was accompanied by neglect of some essential components of antenatal care. Although at the private hospital some problems with the technical content of care were identified, client satisfaction was higher there, where the care included good interpersonal relations, information provision, and continuity. Providers at all three hospitals felt constrained by heavy patient loads and a lack of resources. Multifaceted approaches are needed to improve the quality of antenatal care in this setting.

Adult↗

PubMed2002

Lipopolysaccharide endotoxemia reduces cell proliferation and decreases enterocyte apopotosis during intestinal adaptation in a rat model of short-bowel syndrome.

Sepsis is frequently associated with or complicates short-bowel syndrome (SBS). To investigate the effects of lipopolysaccharide (LPS) endotoxemia on enterocyte proliferation and death via apoptosis in a rat model of SBS, adult male Sprague-Dawley rats were divided into three experimental groups: sham rats underwent bowel transection and reanastomosis; SBS rats underwent 75% small-bowel resection; and SBS-LPS rats underwent 75% bowel resection and were given intraperitoneal injections of LPS 10 mg/kg. Parameters of intestinal adaptation (bowel and mucosal weights, mucosal DNA and protein, villus height, and crypt depth), enterocyte proliferation, and death via apoptosis were determined on day 15 after the operation. Statistical analysis was determined by Student's and ANOVA tests with a P less than 0.05 considered significant. SBS-LPS animals demonstrated a significant decrease (vs SBS rats) in duodenal (20%), jejunal (30%), and ileal (15%) overall weight, duodenal (20%), jejunal (27%), and ileal (18%) mucosal weight, jejunal (20%) and ileal (30%) mucosal DNA, jejunal (29%) and ileal (31%) villus height, and jejunal (14%) and ileal (29%) crypt depth. LPS endotoxemia led to reduced cell proliferation and enterocyte apoptosis compared to untreated SBS animals. Thus, in a rat model of SBS, LPS endotoxemia inhibits intestinal adaptation. A possible mechanism may be decreased cell proliferation. Decreased enterocyte loss via apoptosis may reflect a reduced number of enterocytes. Other mechanisms (necrosis) may be mainly responsible for cell death following LPS injection.

Adaptation, Physiological↗

PubMed2005

Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains.

BACKGROUND: Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4 degrees C; 16 degrees C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. RESULTS: These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. CONCLUSION: These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.

Atmospheric Pressure↗

PubMed2003

Influence of short-term antioxidant supplementation on macular function in age-related maculopathy: a pilot study including electrophysiologic assessment.

PURPOSE: To evaluate the influence of short-term antioxidant supplementation on retinal function in age-related maculopathy (ARM) patients by recording focal electroretinograms (FERGs). DESIGN: Nonrandomized, comparative clinical trial. PARTICIPANTS: Thirty patients with early ARM and visual acuity >/=20/30, divided into two groups, similar for age and disease severity: antioxidant group (ARM-A, n = 17) and no treatment group (ARM-NT, n = 13). Eight age-matched normal subjects divided into antioxidant (N-A, n = 4) or no treatment (N-NT, n = 4) groups. METHODS: ARM-A patients and N-A patients had oral supplementation of lutein, 15 mg; vitamin E, 20 mg; and nicotinamide, 18 mg, daily for 180 days, whereas ARM-NT patients and N-NT patients had no dietary supplementation during the same period. Eight of the 17 ARM-A patients took supplementation for an additional 180-day period. In all patients and normal subjects, FERG assessment was performed at the study entry (baseline) and after 180 days. Further testing was performed at 360 days for the eight ARM-A patients taking supplements and for one ARM-A patient who had discontinued supplementation after 180 days. FERGs were recorded in response to a 41-Hz sinusoidally modulated uniform field (93.5% modulation depth) presented to the macular region (18 degrees ) on a light-adapting background. In a subgroup of patients (11 ARM-A and 5 ARM-NT), whose responses had suitable signal-to-noise ratios, FERGs were also recorded at different stimulus modulation depths between 8.25% and 93.5%. MAIN OUTCOME AND MEASURES: Amplitude (in micro V) and phase (in degrees) of the FERG fundamental harmonic component. FERG modulation thresholds, estimated from the value of log modulation depth yielding a criterion response. RESULTS: At 180 days, FERGs of ARM-A patients and N-A patients were increased in amplitude (mean change, 0.11 and 0.15 log micro V, respectively, P </= 0.01) compared with baseline values, whereas no significant changes in FERG amplitudes of ARM-NT patients and N-NT patients were found (mean change, -0.004 and -0.023 log micro V, respectively). In all groups no changes in the FERG phase were found. FERG modulation thresholds decreased with respect to baseline values (mean change, -0.36 log units, P < 0.01) in ARM-A patients, whereas no significant change (mean change, 0.07 log units) in ARM-NT patients was seen. At 360 days, FERGs of ARM-A patients taking supplementation were still increased in amplitude with respect to baseline (P < 0.05) but did not differ from those recorded at 180 days. In the patient who had discontinued supplementation, FERG amplitude decreased from the 180 days value, approaching that recorded at baseline. CONCLUSIONS: Although this study provides no evidence for the long-term benefit of antioxidants in ARM, the results suggest that increasing the level of retinal antioxidants might influence macular function early in the disease process, as well as in normal aging.

Aged↗

PubMed2006

Increased apoptosis and accelerated epithelial migration following inhibition of hedgehog signaling in adaptive small bowel postresection.

The intestinal epithelium undergoes a marked adaptive response following loss of functional small bowel surface area characterized by increased crypt cell proliferation and increased enterocyte migration from crypt to villus tip, resulting in villus hyperplasia and enhanced nutrient absorption. Hedgehog (Hh) signaling plays a critical role in regulating epithelial-mesenchymal interactions during morphogenesis of the embryonic intestine. Our previous studies showed that blocking Hh signaling in neonatal mice results in increased small intestinal epithelial crypt cell proliferation and altered enterocyte fat absorption and morphology. Hh family members are also expressed in the adult intestine, but their role in the mature small bowel is unclear. With the use of a model of intestinal adaptation following partial small bowel resection, the role of Hh signaling in the adult gut was examined by determining the effects of blocking Hh signaling on the regenerative response following loss of functional surface area. Hh-inactivating monoclonal antibodies or control antibodies were administered to mice that sustained a 50% intestinal resection. mRNA analyses of the preoperative ileum by quantitative real-time PCR revealed that Indian hedgehog was the most abundant Hh family member. The Hh receptor Patched was more abundant than Patched 2. Analyses of downstream targets of Hh signaling demonstrated that Gli3 was twofold more abundant than Gli1 and Gli2 and that bone morphogenetic protein (BMP)2 was most highly expressed compared with BMP1, -4, and -7. Following intestinal resection, the expression of Hh, Patched, Gli, and most BMP genes was markedly downregulated in the remnant ileum, and, in anti-Hh antibody-treated mice, expression of Patched 2 and Gli 1 was further suppressed. In Hh antibody-treated mice following resection, the enterocyte migration rate from crypt to villus tip was increased, and by 2 wk postoperation, apoptosis was increased in the adaptive gut. However, crypt cell proliferation, villus height, and crypt depth were not augmented. These data indicate that Hh signaling plays a role in adult gut epithelial homeostasis by regulating epithelial cell migration from crypt to villus tip and by enhancing apoptosis.

Adaptation, Physiological↗

PubMedDate not supplied

Experimental imaging of intracorneal ring segments with optical coherence tomography.

PURPOSE: To investigate the imaging of corneal structures with optical coherence tomography (OCT) after implantation of intracorneal ring segments (ICRS). METHODS: In an experimental study with six porcine eyes, qualitative and quantitative imaging with corneal OCT using a wavelength of 1310 nm after implantation of ICRS was performed. The optical results were compared with light microscopy of the histological sections. RESULTS: In corneal OCT, the ICRS revealed marked hyporeflective intrastromal areas, which correlated well with macroscopic and microscopic findings. Corneal OCT enabled precise images of the incision depth for the implantation of ICRS, and the exact intrastromal segment position. CONCLUSIONS: Noncontact slit lamp-adapted corneal optical coherence tomography could be employed to clinically monitor corneal changes after implantation of ICRS, evaluate the depth of the segments to correlate refractive changes, and quantify the stromal wound healing response.

Animals↗

PubMed1991

A neural network model of kinetic depth.

We propose a network model that accounts for the kinetic depth in structure from motion phenomena. Using plausible neural mechanisms, the model accounts for (1) fluctuations in perception when viewing a simple kinetic depth stimulus, (2) disambiguation of this stimulus with stereoscopic information, and (3) subsequent bias of the percept of this stimulus following stereoscopic adaptation. The model comprises two levels: a layer of monocular directionally selective motion detectors that provide input to a second layer of disparity-selective and direction-selective binocular mechanisms. The network of facilitatory and inhibitory connections between binocular mechanisms gives rise to fluctuations in network activity that mimic the fluctuations in perception of kinetic depth in the absence of disparity information. The results of a psychophysical experiment are consistent with the nature of the proposed interactions.

Adaptation, Ocular↗

PubMed1988

The relative distribution of fluoride in erupted and unerupted enamel of human third molars from a low fluoride area.

Acid-etch biopsies were taken from the centre of the mesio-lingual, disto-lingual, disto-buccal and mesio-buccal cusps of non-carious erupted (n = 16, aged 18-28 years) and unerupted (n = 21, aged 18-28 years) teeth. The donor subjects had lived continuously in a low fluoride area (F water less than 0.1 parts/10(6] from birth, and had had no systemic fluoride supplementation. Tooth brushing, mouth rinsing and the application of sealers were the only fluoride-containing anti-caries programmes practised singly or in combination. Six successive acid-etchings were taken from each of the four cusps, and the fluoride levels in the etching solution were measured with an adapted, fluoride ion-selective electrode. Up to a depth of about 10 microns, unerupted enamel was etched significantly (p less than 0.05) more deeply than erupted enamel, which might be explained by changes in its composition. Up to a depth of approximately 10 microns, significantly more fluoride was found in erupted than in unerupted enamel. This difference may mainly be attributed to the effect of fluoride from the oral environment on erupted enamel. Fluoride concentrations, up to a depth of approximately 3 microns, were (p = 0.07) higher in the buccal cusps than in the lingual cusps of erupted molars, but not at the other etch depths. There were no significant differences (p greater than 0.10) between the buccal and lingual cusps of the unerupted molars at any depth. No significant correlations between enamel fluoride concentrations and age could be found either for erupted or unerupted third molars.

Adult↗

PubMed2005

Visualizing human brain surface from T1-weighted MR images using texture-mapped triangle meshes.

We describe a novel method for visualizing brain surface from anatomical magnetic resonance images (MRIs). The method utilizes standard 2D texture mapping capabilities of OpenGL graphics language. It combines the benefits of volume rendering and triangle-mesh rendering, allowing fast and realistic-looking brain surface visualizations. Consequently, relatively low-resolution triangle meshes can be used while the texture images provide the necessary details. The mapping is optimized to provide good texture-image resolution for the triangles with respect to their original sizes in the 3D MRI volume. The actual 2D texture images are generated by depth integration from the original MRI data. Our method adapts to anisotropic voxel sizes without any need to interpolate the volume data into cubic voxels, and it is very well suited for visualizing brain anatomy from standard T(1)-weighted MR images. Furthermore, other OpenGL objects and techniques can be easily combined, for example, to use cut planes, to show other surfaces and objects, and to visualize functional data in addition to the anatomical information.

Algorithms↗

PubMed1999

Comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil.

Strains of hydrocarbon-degrading microorganisms (bacteria and fungi) were isolated from an agricultural soil in France. In a field, a portion was treated with oily cuttings resulting from the drilling of an onshore well. The cuttings which were spread at the rate of 600 g HC m-2 contained 10% of fuel oil hydrocarbons (HC). Another part of the field was left untreated. Three months after HC spreading, HC adapted bacteria and fungi were isolated at different soil depths in the two plots and identified. The biodegradation potential of the isolated strains was monitored by measuring the degradation rate of total HC, saturated hydrocarbons, aromatic hydrocarbons and resins of the fuel. Bacteria of the genera Pseudomonas, Brevundimonas Sphingomonas, Acinetobacter, Rhodococcus, Arthrobacter, Corynebacterium and fungi belonging to Aspergillus, Penicillium, Beauveria, Acremonium, Cladosporium, Fusarium, and Trichoderma were identified. The most active strains in the assimilation of saturates and aromatics were Arthrobacter sp., Sphingomonas spiritivorum, Acinetobacter baumanii, Beauveria alba and Penicillum simplicissimum. The biodegradation potential of the hydrocarbon utilizing microorganisms isolated from polluted or unpolluted soils were similar. In laboratory pure cultures, saturated HC were more degraded than aromatic HC, whereas resins were resistant to microbial attack. On an average, individual bacterial strains were more active than fungi in HC biodegradation.

Bacteria↗

PubMedDate not supplied

An adaptive microwave phased array for targeted heating of deep tumours in intact breast: animal study results.

It has previously been reported in phantoms, that an adaptive radiofrequency phased array can generate deep focused heating distributions without overheating the skin and superficial healthy tissues. The present study involves adaptive microwave phased array hyperthermia tests in animals (rabbits) with and without tumours. The design of the adaptive phased array as applied to the treatment of tumours in intact breast, is described. The adaptive phased array concept uses breast compression and dual-opposing 915 MHz air-cooled waveguide applicators with electronic phase shifters and electric-field feedback, to focus automatically by computer control the microwave radiation in deep tissue. Temperature measurements for a clinical adaptive phased array hyperthermia system demonstrate tissue heating at depth with reduced skin heating.

Animals↗

PubMed2001

Evaluating satisfaction with maternity care in women from minority ethnic communities: development and validation of a Sylheti questionnaire.

OBJECTIVE: To develop a reliable and valid questionnaire to evaluate satisfaction with maternity care in Sylheti-speaking Bangladeshi women. DESIGN: Two-stage, psychometric study. Firstly, focus groups, in-depth interviews and iterative methods for translation and cultural adaptation were used to develop a Sylheti questionnaire, called the survey of Bangladeshi women's experience of maternity services from an English language questionnaire. Secondly, quantitative psychometric methods were used to field test and evaluate the acceptability, reliability and validity of this questionnaire. SETTING: Four hospitals providing maternity services in London, UK. STUDY PARTICIPANTS: Two hundred and forty-two women from the London Bangladeshi communities, who were in the antenatal (at least 4 months pregnant) or postnatal phase (up to 6 months after delivery). Women spoke Sylheti; a language with no accepted written form. Two purposive samples of 40 women in the antenatal or postnatal phase, one convenience sample of six women in the antenatal phase and three consecutve samples of 60 women in the postnatal phase participated in stage one. In stage two, 135 women (main sample) completed the questionnaire two months after delivery (82% response rate); 50 women (retest sample) from the main sample completed a second questionnaire two weeks later (96% response rate). MAIN OUTCOME MEASURES: Women's views about maternity care elicited by qualitative methods and measured quantitatively using the survey of Bangladeshi women's experience of maternity services. RESULTS: The 121-item questionnaire was acceptable to women and showed good internal consistency (Cronbach's alphas 0.76-0.91), stability (test-retest reliability 0.72-0.84) and construct validity (e.g. able to detect group differences). CONCLUSION: By combining qualitative and quantitative methods, it is possible to adapt an instrument to provide an acceptable, reliable and valid Sylheti questionnaire. The approach taken in developing this questonnaire provides a model for developing outcome measures for use with other minority ethnic communities.

Adult↗

PubMed1990

Is the quality of vision with contact lenses adequate? Not in all instances.

There are several circumstances in which contact lenses (CLs) provide vision inferior to that possible with spectacles. Over time, both soft and rigid gas-permeable (RGP) lenses accumulate deposits that can cloud vision. RGP lenses are especially prone to scratching; some varieties may even become crazed, giving a spiderweb quality to vision. Certain uncommon corneal complications associated with lens wear--infection, neovascularization, ulcers, and severe epithelial edema--may also impair vision, sometimes permanently. CLs often provide less than optimal vision for patients with presbyopia or severe astigmatism. Difficulties with axis stabilization arise with both soft and rigid toric lenses, and these can take several attempts to resolve. Monovision fitting currently offers the best option for presbyopes, but it has an effect on stereopsis, compromising depth perception. Furthermore, patients often require considerable time before adapting to monovision lens use. Finally, even under normal circumstances, certain inherent features of CLs can diminish visual acuity. The water in soft lenses diffuses light; the loss of visual crispness is particularly notable with high-water-content lenses. On the other hand, the small diameter of RGP lenses often contributes to ghosting--a phenomenon in which the edge of the lenses is visible whenever the pupils are widely dilated.

Astigmatism↗

PubMed2001

Derived fuzzy knowledge model for estimating the depth of anesthesia.

Reliable and noninvasive monitoring of the depth of anesthesia (DOA) is highly desirable. Based on adaptive network-based fuzzy inference system (ANFIS) modeling, a derived fuzzy knowledge model is proposed for quantitatively estimating the DOA and validate it by 30 experiments using 15 dogs undergoing anesthesia with three different anesthetic regimens (propofol, isoflurane, and halothane). By eliciting fuzzy if-then rules, the model provides a way to address the DOA estimation problem by using electroencephalogram-derived parameters. The parameters include two new measures (complexity and regularity) extracted by nonlinear quantitative analyses, as well as spectral entropy. The model demonstrates good performance in discriminating awake and asleep states for three common anesthetic regimens (accuracy 90.3 % for propofol, 92.7 % for isoflurane, and 89.1% for halothane), real-time feasibility, and generalization ability (accuracy 85.9% across the three regimens). The proposed fuzzy knowledge model is a promising candidate as an effective tool for continuous assessment of the DOA.

Algorithms↗

PubMed1983

Enhancing decision behavior in high school "smokers".

In the first stage of the present study, personal control beliefs of smokers and nonsmokers in several high schools were analyzed. This attitudinal information was utilized for embedding implicit suggestions into an interventional format. The cognitive-behavioral intervention in two high schools consisted of identified smokers receiving various reinforcements for coping behaviors relevant to cigarette control. Matched groups in two other high schools received popular tips on how to quit smoking. Only subjects in the cognitive-behavior condition reported a significant smoking reduction at 1-month and 3-month posttests. Subjects receiving the cognitive-behavioral program revised their ideal level of marijuana consumption downward and differed on certain other beliefs compared to the popular tips group. Motivational and self-regulative characteristics of participants were also examined through in-depth questioning.

Adaptation, Psychological↗