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PubMed2005

[Psychodiagnostic instruments for the assessment of autism spectrum disorders].

OBJECTIVES: Established scales for the early detection and general diagnostics of autism will be reviewed with a focus on the instruments available in German. METHODS: All questionnaires, observation scales and interviews for the assessment of autism and associated conditions found in a search of Medline, PsychInfo, Psyndex and Google up to May 2004 are quoted. Instruments adapted and developed for the German-speaking countries are presented in more depth. RESULTS: An increasing number of reliable national and international scales for the assessment of disorders of the autism spectrum are available. Currently a combination of the Social Communication Questionnaire (SCQ), the Autism Diagnostic Observation Schedule (ADOS) and the Autism Diagnostic Interview-Revised (ADI-R) is regarded as the standard for a psychometrically based diagnosis of autism. CONCLUSIONS: For certain diagnostic groups and issues there continues to be a need for German-language instruments. Particularly scales for the assessment of the broader phenotype of autism, as well as instruments that are more sensitive to change would be desirable for outcome measurement and intervention evaluation.

Autistic Disorder↗

PubMed2025

The chromosome-level genome assembly and annotation of the silver-lipped pearl oyster, Pinctada maxima.

The silver-lipped pearl oyster (Pinctada maxima) is a valuable tropical aquaculture species, playing a crucial economic role in the global pearl industry. However, the lack of genomic reference limits our in-depth understanding of this species in genome-based breeding, conservation, evolution and adaptation. Here, annotated chromosome-level reference genome for P. maxima was generated by integrating PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing data. The total genome size is 1,264.93 Mb, with contig N50 and scaffold N50 of 649 kb and 89.19 Mb, respectively. The majority (97.94%) of the assembled genome was anchored to the 14 chromosomes by Hi-C analysis. The relatively high genome completeness was observed, with 97.38% (metazoa_odb10 database) and 95.26% (mollusca_odb10 database) in BUSCO analysis. Genome annotation revealed approximately 65.46% of the repeat sequences and 26,315 protein-coding genes. Comparative genome analysis revealed 28 expanded and 48 contracted families (p < 0.05) in P. maxima, with 3.2% of genes (894) being species-specific. This chromosome-level genome serves as an essential resource for research in evolutionary genomics, phylogenetics, and biomineralization.

Animals↗

PubMed2025

UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.

MOTIVATION: One of the key applications of Unique Molecular Identifiers (UMIs) in high-throughput sequencing is to correct for PCR amplification bias and removal of PCR duplicates, thereby improving quantification in DNA-seq and RNA-seq applications. Accurately grouping error-bearing UMIs that originate from the same input molecule through a UMI deduplication method is a critical step in this process. However, many existing UMI deduplication tools rely on simple Hamming distance comparisons or suboptimal clustering algorithms, often resulting in erroneous UMI groupings, particularly in error-prone long-read sequencing or ultra-high-depth short-read sequencing. RESULTS: We introduce UMI-nea, a tool that utilizes Levenshtein distance comparisons and a novel clustering approach to optimize multithreading workflows. Compared against three other indel-aware UMI deduplication tools, UMI-nea achieves more accurate UMI groupings with efficient run time. It demonstrates robust performance across diverse sequencing platforms, depths, and UMI lengths. Additionally, UMI-nea incorporates a data-guided adaptive UMI filter, further enhancing quantification accuracy. AVAILABILITY AND IMPLEMENTATION: UMI-nea is available on github https://github.com/Qiaseq-research/UMI-nea.git or Zenodo https://doi.org/10.5281/zenodo.16745758. Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.

High-Throughput Nucleotide Sequencing↗

PubMed2000

Optical coherence tomography: a new imaging technology for dentistry.

BACKGROUND: Optical coherence tomography, or OCT, is a new diagnostic imaging technique that has many potential dental applications. The authors present the first intraoral dental images made using this technology. METHODS: The authors constructed a prototype dental OCT system. This system creates cross-sectional images by quantifying the reflections of infrared light from dental structures interferometrically. RESULTS: We used our prototype system to make dental OTC images of healthy adults in a clinical setting. These OCT images depicted both hard and soft oral tissues at high resolution. CONCLUSIONS: OCT images exhibit microstructural detail that cannot be obtained with current imaging modalities. Using this new technology, visual recordings of periodontal tissue contour, secular depth and connective tissue attachment now are possible. The internal aspects and marginal adaptation of porcelain and composite restorations can be visualized. CLINICAL IMPLICATIONS: There are several advantages of OCT compared with conventional dental imaging. This new imaging technology is safe, versatile, inexpensive and readily adapted to a clinical dental environment.

Adult↗

PubMed1999

Prochlorococcus, a marine photosynthetic prokaryote of global significance.

The minute photosynthetic prokaryote Prochlorococcus, which was discovered about 10 years ago, has proven exceptional from several standpoints. Its tiny size (0.5 to 0.7 microm in diameter) makes it the smallest known photosynthetic organism. Its ubiquity within the 40 degrees S to 40 degrees N latitudinal band of oceans and its occurrence at high density from the surface down to depths of 200 m make it presumably the most abundant photosynthetic organism on Earth. Prochlorococcus typically divides once a day in the subsurface layer of oligotrophic areas, where it dominates the photosynthetic biomass. It also possesses a remarkable pigment complement which includes divinyl derivatives of chlorophyll a (Chl a) and Chl b, the so-called Chl a2 and Chl b2, and, in some strains, small amounts of a new type of phycoerythrin. Phylogenetically, Prochlorococcus has also proven fascinating. Recent studies suggest that it evolved from an ancestral cyanobacterium by reducing its cell and genome sizes and by recruiting a protein originally synthesized under conditions of iron depletion to build a reduced antenna system as a replacement for large phycobilisomes. Environmental constraints clearly played a predominant role in Prochlorococcus evolution. Its tiny size is an advantage for its adaptation to nutrient-deprived environments. Furthermore, genetically distinct ecotypes, with different antenna systems and ecophysiological characteristics, are present at depth and in surface waters. This vertical species variation has allowed Prochlorococcus to adapt to the natural light gradient occurring in the upper layer of oceans. The present review critically assesses the basic knowledge acquired about Prochlorococcus both in the ocean and in the laboratory.

Animals↗

PubMed2005

Heterogeneity in patellofemoral cartilage adaptation to anterior cruciate ligament transection; chondrocyte shape and deformation with compression.

OBJECTIVE: The purpose of this study was to determine if the opposing cartilages of the feline patellofemoral joint adapted differently to short-term anterior cruciate ligament transection (ACL-T) and if the magnitude of chondrocyte deformation upon tissue loading was altered under ACL-T conditions compared to contralateral controls. In situ static compression of physiological magnitude was applied to the feline patellofemoral cartilage 16 weeks post-ACL-T and cartilage and chondrocyte deformation were evaluated by histomorphometry. DESIGN: Six adult cats were euthanized 16 weeks after unilateral ACL-T. A peak surface pressure of 9 MPa was applied to the fully intact patella and femoral groove cartilages. After in situ fixation under compression, sections from the centre of the indent and from an adjacent unloaded area of the cartilages were analysed. Chondrocyte shape, size, clustering and volumetric fraction were quantified. RESULTS: Experimental patellar articular cartilage was thicker, contained larger chondrocytes that were more frequently arranged in clusters and had, on average, a larger chondrocyte volumetric fraction compared to contralateral controls. In contrast, the experimental femoral groove cartilage demonstrated little adaptation to ACL-T. CONCLUSIONS: The patellar articular cartilage adapts to short-term ACL-T to a greater extent than femoral groove cartilage. We speculate that differences in the histological parameters of control tissues, such as cartilage thickness and the magnitude and depth distribution of chondrocyte shape, size and volumetric fraction may contribute to predisposing patellar cartilage, and not femoral groove cartilage, to adaptation after ACL-T.

Adaptation, Physiological↗

PubMed2001

Intestinal adaptation: structure, function, and regulation.

After massive small bowel resection (SBR), the remnant intestine undergoes an adaptive process characterized by increases in wet weight, protein and DNA content, villus height and crypt depth, and absorptive surface area. These changes are the result of a proliferative stimulus that increases crypt cell mitosis and augments cellular progression along the villus axis. Functionally, there is upregulation of the Na(+)/glucose cotransporter, Na(+)/H(+) exchanger, and other enzymes involved in intestinal digestion and absorption. These physiologic events are a compensatory response to the sudden loss of digestive and absorptive capacity by the remnant intestine. A major consequence of inadequate intestinal adaptation is lifelong dependence on parenteral nutrition, which results ultimately in cholestatic liver dysfunction. Furthermore, adaptation may be associated with changes in intestinal permeability and an increased risk of bacterial translocation and sepsis. Several mediators thought to be integral to the postresection adaptive response have been proposed, including luminal nutrients, gastrointestinal secretions, and humoral factors. A thorough understanding of intestinal adaptation will be essential in the rational development of new and innovative therapies that amplify this complex but important process.

Animals↗

PubMed1994

Coping with traumatic brain injury: representative case studies.

This case report compares the use of social supports and vulnerability to substance abuse for two rehabilitation clients after traumatic brain injury (TBI). Using a psychosocial assessment, the Motivational Structure Questionnaire, Adaptive Skills Battery, and Ways of Coping Checklist within a representative case method, we studied two individuals in depth to understand differences in postinjury drinking behaviors. We also examined differences in availability and use of social supports and how support was related to coping efforts. Finally, we illustrated goal-setting and the relationship between long-term planning and follow-through on goals. Social supports, adaptive problem-solving behaviors, and positive reappraisal of situations seem to be important elements in postinjury abstinence. Clinically, this research supports the need for fostering use of both social supports and substance use prevention and treatment services when working with both inpatient and outpatient TBI clients.

Adaptation, Psychological↗

PubMed2006

Effect of deep insertion of the cochlear implant electrode array on pitch estimation and speech perception.

CONCLUSION: Deeply inserted electrodes offer the possibility that apical stimulation may improve speech performances. Therefore, deep insertion is reasonable and should be performed in patients with profound or total hearing loss. OBJECTIVES: To evaluate the importance of insertion depth beyond 25 mm in a group of cochlear implant patients with deeply inserted electrodes up to 32 mm. PATIENTS AND METHODS: In the first part of the study patients were asked to perform a pitch estimation for channels across the whole length of the electrode array. We evaluated whether pitch discrimination was possible along the whole cochlea and especially in its apical part. Then, the audiological performances of 10 patients were tested in 5 conditions, in which we artificially varied the insertion depth in each patient by activating and deactivating channels. The patients were tested immediately in the new condition to avoid adaptation. RESULTS: The results showed that activating the electrodes in the uppermost region of the cochlea improves speech perception significantly. Furthermore it could be demonstrated that the pitch perceived in the cochlea with electrical stimulation decreases with increasing insertion depth along the whole length of deeply inserted electrode arrays.

Adult↗

PubMed1999

Effects of Microscale Water Level Fluctuations and Altered Ultraviolet Radiation on Periphytic Microbiota.

Abstract Microscale fluctuations in water level (1-20 mm) are common on a diurnal basis in shallow (<5-10 cm) wetlands, coupled to evapotranspiration losses during the daytime in excess of groundwater resupply. These depth variations alter the intensity of UV irradiance reaching attached periphytic algal and bacterial microbial communities. Effects of alterations of UV irradiance by micro-changes in water level on periphytic microbiota were examined experimentally. Attached microbial communities, grown on glass fiber filters in situ in a natural wetland, were exposed experimentally to near-natural levels of UV irradiance of differing spectral quality. UV intensity was altered by varying the distance of the communities from the light source, changes in UV-attenuating natural dissolved organic matter (DOM), and small changes in water level (2 or 4 mm). Algal productivity and photosynthetic oxygen production were significantly reduced by small enhancements of UV-B radiation, by decreased water levels of only 2 mm, and by reductions in concentrations of DOM. UV-B had only small short-term effects on chlorophyll a, although small increases in water depth and DOM concentration reduced pigment damage. Experimental removal of UV-B during in situ growth indicated that algae could adapt to UV radiation during growth in natural environments. Microbial oxygen consumption and bacterial productivity and biomass were also lowered significantly by UV-B exposure, and damage decreased with small (2 mm) increases in water depth or in DOM concentration. Selective inhibitors of algal photosynthesis and production of released extracellular organic substrates caused a concomitant reduction in bacterial productivity and a significant increase in magnitude of UV-B damage to bacterial biomass. These effects suggested that metabolic interactions between the periphytic autotrophs and heterotrophs altered community responses to UV-B radiation. Microscale water level reductions, common on a diurnal basis in shallow wetlands, and associated increased UV intensity can result in rapid alterations in periphytic metabolism.http://link.springer-ny.com/link/service/journals/00248/bibs/38n3p253.html</hea

Journal Article↗

PubMed2002

Neural correlates of structure-from-motion perception in macaque V1 and MT.

Structure-from-motion (SFM) is the perception of three-dimensional shape from motion cues. We used a bistable SFM stimulus, which can be perceived in one of two different ways, to study how neural activity in cortical areas V1 and MT is related to SFM perception. Monkeys performed a depth-order task, where they indicated in which direction the front surface of a rotating SFM cylinder display was moving. To prevent contamination of the neural data because of eye position effects, all experiments with significant effects of radius, vergence, and velocity were excluded. As expected, the activity of approximately 50% of neurons in V1 and approximately 80% of neurons in MT is affected by the stimulus. Furthermore, the activity of 20% of neurons in area V1 is modulated with the percept. This proportion is higher in MT, where the activity of >60% of neurons is modulated with the percept. In both areas, this perceptual modulation occurs only in neurons with activity that is also affected by the stimulus. The perceptual modulation is not correlated with neural tuning properties in area V1, but it is in area MT. Together, these results suggest that V1 is not directly involved in the generation of the SFM percept, whereas MT is. The perceptual modulation in V1 may be attributable to top-down feedback from MT.

Action Potentials↗

PubMed1984

The influence of rate of skin indentation on threshold and suprathreshold tactile sensations.

The effects of skin indentation depth and rate on threshold and suprathreshold tactile sensations were investigated. Indentation rates between 0.3 and 10 mm/sec had little effect on the absolute tactile thresholds measured in terms of indentation depth. Slower rates resulted in increased absolute thresholds. Estimates of the growth in intensity of tactile sensations were made as functions of indentation depth and rate. The fastest rate used (10 mm/sec), for a given depth of indentation, produced the most intense sensation; the slowest (0.1 mm/sec), the least intense sensation. The tactile sensation magnitude estimates, with rate as the parameter, could be described by power functions. At the slowest indentation rate the exponent of the function was 1.36. At faster indentation rates (0.4, 1.0, and 10 mm/sec), two functions of markedly different slopes were required to describe the estimates. The exponents of the power functions were between 0.38 and 0.49 for indentation depths up to about 0.9 mm, and between 1.07 and 1.43 for deeper indentation depths.

Adaptation, Physiological↗

PubMed2005

Adaptive imaging using an optimal receive aperture size.

Sidelobe contribution from off-axis targets degrades image quality in a coherent array imaging system. In ultrasound imaging, focusing errors resulting from sound-velocity inhomogeneities in human tissue--also known as phase aberrations reduce the coherence of the received signals and elevate the sidelobe level. This paper proposes an adaptive receive-aperture technique based on thresholding of the coherence factor (CF). The CF describes the coherence of the received array signals and can be used as an index of focusing quality. This paper demonstrates that thresholding of the CF allows the mainlobe-dominated signals to be distinguished from the sidelobe-dominated signals, after which the receive-aperture size at each imaging position can be optimally determined so as to enhance the mainlobe-dominated signals and suppress the sidelobe-dominated signals. Thus, image quality degradation resulting from sound-velocity inhomogeneities can be reduced. Simulations and measured ultrasound data are used to evaluate the efficacy of the proposed technique. The characteristics of the proposed technique including the effects of the signal-to-noise ratio (SNR) and the transmit focal depth, and speckle reduction are discussed. The proposed technique is also compared with the parallel adaptive receive compensation algorithm and shown to produce a better improvement in image quality.

Algorithms↗

PubMed2000

Light and adaptive responses in red macroalgae: an overview.

The most recent research shows an increased interest in algal photobiology following the modifications of light spectral composition induced by the 'ozone depletion' in the atmosphere. The consequences of this change on the macrophytic red algae, which possess accessory light-harvesting complexes, are currently uncertain. Moreover the underwater light field of coastal waters, where most macroalgae are living, has been well characterized only in the last few years. The presence and the variability of light components, such as red, far-red, green, blue and ultraviolet radiation, in these environments, at different depths, have raised the question of whether red macroalgae are 'light-intensity or/and light-quality adapters'. In this paper various adaptive responses of red algae, both in the field and under culture, are discussed in order to compare the physiological and ecological results. All these studies seem to suggest that red algae are both 'light-intensity and light-quality adapters'. In particular, the light quality and, overall, the modulation of the ratios between spectral components seem to play the role of photomorphogenic 'signals' regulating algal metabolism and growth. Short- and long-term responses, and potential strategies and mechanisms for adaptation to light at individual, cellular and molecular levels, are discussed with special reference to the photosynthetic equipment.

Adaptation, Physiological↗

PubMed1987

Temperature adaptation of fish hemoglobins reflected in rates of autoxidation.

Observation of rapid autoxidation of oxyhemoglobin (HbO2) from a deep-sea fish (Co-ryphaenoides acrolepis) prompted a survey of rates of autoxidation of HbO2 to methemoglobin in vitro from fishes inhabiting vastly different depths (1 to 3800 m) in order to discover any relationship between autoxidation rates and different environmental temperatures and pressures to which hemoglobins may be adapted. The rate of autoxidation was found to be sensitive to temperature in both deep- and shallow-living fishes. Hemoglobin appears to be thermally adapted since autoxidation was 10 times faster at all temperatures tested with HbO2 obtained from a cold-adapted fish (Coryphaenoides armatus variabilis) than from a comparatively warm-adapted one (Paralabrax nebulifer). High hydrostatic pressure does not affect autoxidation rates in either deep- or shallow-dwelling species. Rates of autoxidation may be intimately related to hemoglobin function thus providing a means for studying hemoglobin adaptation in poikilothermic vertebrates, especially among cold-adapted species.

Adaptation, Physiological↗

PubMed1995

Effects of flicker adaptation and temporal gain control on the flicker ERG.

The flicker electroretinogram (ERG) to stimuli varying in temporal frequency and modulation depth was recorded to investigate retinal gain control. With increasing modulation of a sinusoidal flickering stimulus, the flicker ERG shows an amplitude compression and a phase retardation (of the fundamental component) at 16 Hz, an amplitude expansion and a phase advance around 40-48 Hz, and an approximately linear response at 72 Hz. With sum-of-two-sinusoids stimuli, the second stimulus enhances the fundamental response to a 40 or 48 Hz test stimulus at low modulations, and reduces the variation in phase with modulation. This interaction depends primarily on the amplitude of the response to the second stimulus, but not its frequency. With temporally alternating stimuli, a similar but smaller interaction effect is measured. The results suggest that there is an active nonlinear gain control mechanism in the outer retina and this gain control works by adjusting the phase delay of the retinal response. The phase control mechanism is set by the amplitude of the outer retinal response integrated over time.

Adaptation, Ocular↗

PubMed1996

The story of Maricela and Miguel: a narrative analysis of dimensions of adaptation.

OBJECTIVES: A mother-child life history was analyzed to examine the multiple dimensions of adaptation in a family grouping, including temporality, maternal values, and life contexts. METHOD: In-depth interviews, participant observation, and documents (e.g., therapy notes, medical records) produced the data for this study. A multiple step narrative analysis included narrative shaping, analysis of major life turnings, and macrostructural analysis of the progress toward life goals. RESULTS: This mother-child life history portrays the challenging life events of a Mexican-origin mother, Maricela, seeking care and assistance to further the development of her son with disabilities, Miguel. Major turnings in her life had both costs and benefits for her in the present and future. Analysis of her multiple roles of mother, professional, daughter, lover-wife, and spiritual devotee revealed that Maricela's life choices, driven by maternal values, diminished the achievement of her personal goals, except those related to her maternal and spiritual roles. Maricela chose actions to realign current and future happenings with her desired life trajectory for her son, which instead of enhancing life conditions for the family often involved short-term and long-term costs. CONCLUSIONS: This mother-child life history demonstrates that a series of moral, relational, and circumstantial factors influence a mother's projected life courses for herself and her child. Adaptation appears to be a dynamic process of realigning life paths to desired life courses, with success evaluated not in a microcosm of time, but from a larger view as these actions contribute to the achievement of desired life goals within a constellation of the person's life goals.

Adaptation, Psychological↗

PubMed1987

Effects of hydrostatic pressure on the motor activity of fish from shallow water and 900 m depths; some results of Challenger cruise 6B/85.

1. Two species of benthic fish from 900 m depths (90 atm pressure), Trachyscorpia cristulata echinata and Synaphobranchus kaupi, are shown to be adapted to their normal, high ambient pressure. 2. Their condition improves when they are restored to their normal pressure after experiencing decompression in a trawl and they undergo convulsions at 150 atm. 3. This contrasts with the response of shallow water species (Salmo salar, Pleuronectes platessa, Anguilla anguilla and Gadus morhua) which convulse at 93-114 atm and become immobilized and rigid at 150 atm.

Animals↗