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PubMedDate not supplied

Laser Doppler flowmetry evaluation of burn wound depth.

Hypothesizing that reduced blood flow to various levels in thermally damaged dermis is related to the depth of burn, we studied 59 burns in 41 patients, with an age range of 18 months to 67 years, with improved laser Doppler blood flow technology to determine burn depth on admission. Two hundred and sixty-eight laser Doppler measurements were made in 59 burn wounds in 41 patients. Of the 129 burn wounds with laser Doppler readings of less than 1.4 on admission, 127 were classified ultimately through clinical observation as either deep second- or third-degree burns and required excision and closure. Therefore predictive value of a positive result (i.e., laser Doppler value less than 1.4) on admission was 98.4% using laser Doppler measurements. Clinical estimation did not correlate as well with the depth of injury.

Adolescent↗

PubMed1997

Picture naming deficits in developmental dyslexia: the phonological representations hypothesis.

The picture and word naming performance of developmental dyslexics was compared to the picture and word naming performance of non-dyslexic ("garden variety") poor readers, reading age, and chronological age-matched controls. The stimulus list used for both tasks was systematically manipulated for word length and word frequency. In order to examine picture naming errors in more depth, an object name recognition test assessed each subject's vocabulary knowledge of those names which they were unable to spontaneously label in the picture naming task. Findings indicated that the dyslexic and the garden variety poor readers exhibited a picture naming deficit relative to both chronological and reading age-matched controls. Findings also indicated that both groups of impaired readers obtained superior scores in the word naming task than in the picture naming task, while both groups of controls showed no difference in performance across tasks. The dyslexics' picture naming errors, but not those of the garden variety poor readers, were particularly marked on polysyllabic and/or low frequency words, indicating a possible phonological basis to the picture naming deficit of the dyslexic children. These children also recognized significantly more unnamed target words than all comparison groups, suggesting a particular difficulty in retrieving the phonological codes of known picture names rather than a vocabulary deficit. Results are discussed in terms of dyslexics' difficulty in encoding full segmental phonological representations of names in long-term memory and/or in processing these representations in order to generate required names on demand.

Adolescent↗

PubMed2004

M error patterns in word reading among primary school children: a cross-orthographic study.

A comparative investigation of word reading efficiency indicates that different strategies may be used by English and Swedish early readers. In a first study, 328 native English speakers from UK Years 3 and 6 completed a pen-and-paper word recognition task (the Wordchains test). Results were analysed for frequency and type of errors committed. A sample of 123 chronological-age-matched Swedish children carried out the same task on a matched Swedish test. For a sub-sample of 68 English/Swedish pairs matched on word recognition score and sex, significant differences were observed in a comparison of average and low scorers from the two language groups. The English children attempted more task items and committed more errors, while the Swedish group corrected their errors more, suggesting a difference in approach to the task. A second study of a larger Swedish sample (241 participants) found the same pattern of errors as Study 1. The implications of these findings are discussed in relation to the effects of orthographic depth and morphemic complexity.

Child↗

PubMed2007

Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes.

Because paired-end genomic signature tags are sequenced-based, they have the potential to become an alternate tool to tiled microarray hybridization as a method for genome-wide localization of transcription factors and other sequence-specific DNA binding proteins. As outlined here the method also can be used for global analysis of DNA methylation. One advantage of this approach is the ability to easily switch between different genome types without having to fabricate a new microarray for each and every DNA type. However, the method does have some disadvantages. Among the most rate-limiting steps of our PE-GST protocol are the need to concatemerize the diTAGs, size fractionate them and then clone them prior to sequencing. This is usually followed by additional steps to amplify and size select for long (> or = 500) concatemer inserts prior to sequencing. These time-consuming steps are important for standard DNA sequencing as they increase efficiency approximately 20-30-fold since each amplified concatemer can now provide information on multiple tags; the limitation on data acqui- sition is read length during sequencing. However, the development of new sequencing methods such as Life Sciences' 454 new nanotechnology-based sequencing instrument (41) could increase tag sequencing efficiency by several orders of magnitude (> or = 100,000 diTAG reads/run), which is sufficient to provide in-depth global analysis of all ChIP PE-GSTs in a single run. This is because the lengths of our paired-end diTAGs (approximately 60 bp) fall well within the region of high accuracy for read lengths on this instrument. In principle, sequence analysis of diTAGs could begin as soon as they are generated, thereby completely bypassing the need for the concatemerization, sizing, downstream cloning steps and sequencing template purification. In addition, our protocol places any one of several unique four-base long nucleotide sequences, such as GATC, between each and every diTAG pair, which could be used to help the instrument's software keep base register and also provide a well-located peak height indicator in the middle of every sequence run. This additional feature could permit multiplexing of the data by simultaneous sequencing of several pooled libraries if each used a different linker sequence during diTAG formation (Figure 4).

Base Sequence↗

PubMed2001

A wide dynamic range, high-spatial-resolution scanning system for radiochromic dye films.

This paper describes the evaluation of an inexpensive, commercially available 35 mm transparency slide scanner as a potential alternative scanning device for GafChromic HD-810 radiochromic dye film. Besides its low cost, the principal advantages of this type of scanner are high spatial resolution and high speed (a typical scan taking less than 1 min). With broad-band illumination the useful dose range using grey-scale imaging of GafChromic HD-810 is limited to about 50-800 Gy. By using the colour-scale imaging capability of the scanner we have been able to achieve a significant extension covering a similar range (15-2000 Gy) to that attainable using monochromatic illumination. The short-term reproducibility of the system is good, with a coefficient of variation of doses estimated from repeat scanning of uniformly exposed calibration films of less than 2%. Long-term stability is ensured by the scanning of a manufacturer-supplied test slide. The slide scanner system has been used in the determination of depth dose distributions from a model 'hot particle' source containing 106Ru/Rh. GafChromic dye film stacks irradiated by the source were read out on both the slide scanner and a conventional Joyce Loebl MDM6 scanning stage microdensitometer. The overall agreement between the dose estimates provided by the two systems was within 10%.

Beta Particles↗

PubMed2002

Excimer laser phototherapeutic keratectomy retreatment of anterior basement membrane dystrophy and Salzmann's nodular degeneration with topical mitomycin C.

PURPOSE: To report a case of excimer laser phototherapeutic keratectomy retreatment of anterior basement membrane (ABM) dystrophy and Salzmann's nodular degeneration with a single intraoperative application of topical mitomycin C (0.02%). METHODS: Case report. RESULTS: A 91-year-old woman underwent excimer laser phototherapeutic keratectomy (PTK) in the left eye for ABM dystrophy and Salzmann's nodular degeneration causing decreased visual acuity (VA), ocular irritation, and recurrent erosions. Slit-lamp examination of both eyes revealed diffuse ABM dystrophy changes with mild to moderate subepithelial and anterior stromal haze and scarring involving the visual axis. The PTK treatment was preceded by a superficial keratectomy with a blade. The excimer laser was set for a 6-mm circular ablation zone with a treatment depth of 5 microm. The cornea remained clear for several months. Six months after surgery, the patient presented with difficulty reading and VA of 20/70. Slit-lamp examination of the left eye revealed recurrent Salzmann-type nodular degeneration inferior to the visual axis. A treatment course of topical steroids was not successful. She underwent another superficial keratectomy with a blade and PTK treatment (same laser parameters as the first procedure) with a 2-minute application of 0.02% mitomycin C on a cellulose sponge. The surgery proceeded without complications. On postoperative day 7, she presented with a healed epithelium and faint anterior stromal haze. Best-corrected visual acuity was 20/50, which is her best-expected VA. Six months after the procedure, the cornea revealed no signs of recurrence. CONCLUSION: The use of topical mitomycin C in conjunction with PTK may prevent recurrence of Salzmann's nodular degeneration.

Aged↗

PubMed2001

Automated finishing with autofinish.

Currently, the genome sequencing community is producing shotgun sequence data at a very high rate, but finishing (collecting additional directed sequence data to close gaps and improve the quality of the data) is not matching that rate. One reason for the difference is that shotgun sequencing is highly automated but finishing is not: Most finishing decisions, such as which directed reads to obtain and which specialized sequencing techniques to use, are made by people. If finishing rates are to increase to match shotgun sequencing rates, most finishing decisions also must be automated. The Autofinish computer program (which is part of the computer software package) does this by automatically choosing finishing reads. Autofinish is able to suggest most finishing reads required for completion of each sequencing project, greatly reducing the amount of human attention needed. sometimes completely finishes the project, with no human decisions required. It cannot solve the most complex problems, so we recommend that Autofinish be allowed to suggest reads for the first three rounds of finishing, and if the project still is not finished completely, a human finisher complete the work. We compared this Autofinish-Hybrid method of finishing against a human finisher in five different projects with a variety of shotgun depths by finishing each project twice--once with each method. This comparison shows that the Autofinish-Hybrid method saves many hours over a human finisher alone, while using roughly the same number and type of reads and closing gaps at roughly the same rate. Autofinish currently is in production use at several large sequencing centers. It is designed to be adaptable to the finishing strategy of the lab--it can finish using some or all of the following: resequencing reads, reverses, custom primer walks on either subclone templates or whole clone templates, PCR, or minilibraries. Autofinish has been used for finishing cDNA, genomic clones, and whole bacterial genomes (see http://www.phrap.org).

Contig Mapping↗

PubMed2000

Noise in polymer gel measurements using MRI.

With the development of conformal radiotherapy, particularly intensity modulated radiation therapy (IMRT), there is a clear need for multidimensional dosimeters. A commercial polymerizing gel, BANG-2 gel (MGS Research, Inc., Guilford, CT), has recently been developed that shows potential as a multi-dimensional dosimeter. This study investigates and characterizes the noise and magnetic resonance (MR) artifacts from imaging BANG-2 gels. Seven cylindrical vials (4 cm diam, 20 cm length) were irradiated end on in a water bath and read using MRI (B0=1.5 T, TE=20 ms/100 ms, TR=3000 ms). The gel calibration compared the measured depth-dose distributions in water against the change in solvent-proton R2 relaxivity of the gel. A larger vial (13 cm diam, 14 cm length) was also irradiated to test the calibration accuracy in a vial of sufficient volume for dose distribution measurements. The calibration curve proved accurate to within 1.3% in determining the depth dose measured by the larger vial. An investigation of the voxel-to-voxel (IXIX 3 mm3) noise and sensitivity response curve showed that the voxel-to-voxel variation dominated the dose measurement uncertainty. The voxel-to-voxel standard deviation ranged from 0.2 Gy for the unirradiated gel to 0.7 Gy at 20 Gy. Slice-to-slice R2 magnitude deviations were also observed corresponding to 0.2 Gy. These variations limited the overall accuracy of the gel dose measurements and warrant an investigation of more accurate MR readout sequences.

Calibration↗

PubMed2006

Sonographic diagnosis of gestational trophoblastic disease and comparison with retained products of conception.

OBJECTIVE: Gestational trophoblastic disease (GTD) and retained products of conception (RPC) can be difficult to distinguish sonographically. The aim of this study was to determine whether there were any sonographic criteria that could prospectively distinguish one from the other. METHODS: Institutional ethics approval was obtained, and acquisition of consent was waived by the Institutional Review Board. A retrospective review of gynecologic oncology and pathology databases identified 17 cases of GTD and 14 cases of RPC. Findings from the pre-evacuation transvaginal sonographic examinations were analyzed. The scans were independently reviewed by 2 senior radiologists with specific expertise in pelvic sonography using several predetermined sonographic features. The reviewers were blinded to the diagnosis. A consensus reading was obtained. RESULTS: The sonographic features that predicted GTD were a myometrial epicenter (P = .0002; odds ratio [OR] = 28), depth of myometrial invasion of more than one third (P = .001; OR = 20), placental venous lakes (P = .04; OR = 9), maximum mass dimensions of more than 3.45 cm (P = .009), and maximum endometrial thickness of less than 12 mm (P = .02). The remaining criteria were not statistically significant and included the characteristics of the mass, ascites, a "snowstorm" appearance, mass vascularity (including resistive index and peak systolic velocity), and the presence of ovarian cysts. CONCLUSIONS: There are specific transvaginal sonographic features that can accurately differentiate GTD and RPC.

Abortion, Incomplete↗

PubMed1987

[Theoretical formulas for the power of artificial lenses].

After having recalled the principles of lens power calculation, we analyse in detail the parameters of the (Formula: see text). Corneal power K read on keratometers has to be modified, for it is about one diopter too strong. Evaluation of the anterior chamber depth C is analysed and corrected of 0.08 mm for the 1st C and of 0.06 mm for the 2nd C. Ultrasonic axial length L should be increased by the retinal thickness; the error induced by neglecting this correction is concealed by the overestimation of K in usual formulas. The equivalent power of the lens De is slightly underestimated relative to back surface power supplied by the manufacturer. The various formulas available in the Literature are commented and compared. A new formula is proposed, which is more particularly adapted to contact ultrasound probes, such as Digiecho II, which seem to under-evaluate L and C values.

Anterior Chamber↗

PubMed2005

The effect of infection-control barriers on the light intensity of light-cure units and depth of cure of composite.

AIM: Dental curing lights are vulnerable to contamination with oral fluids during routine intra-oral use. This controlled study aimed to evaluate whether or not disposable transparent barriers placed over the light-guide tip would affect light output intensity or the subsequent depth of cure of a composite restoration. METHODS: The impact on light intensity emitted from high-, medium- and low-output light-cure units in the presence of two commercially available disposable infection-control barriers was evaluated against a no-barrier control. Power density measurements from the three intensity light-cure units were recorded with a radiometer, then converted to a digital image using an intra-oral camera and values determined using a commercial computer program. For each curing unit, the measurements were repeated on ten separate occasions with each barrier and the control. Depth of cure was evaluated using a scrape test in a natural tooth model. RESULTS: At each level of light output, the two disposable barriers produced a significant reduction in the mean power density readings compared to the no-barrier control (P<0.005). The cure sleeve inhibited light output to a greater extent than either the cling film or the control (P<0.005). Only composite restorations light-activated by the high level unit demonstrated a small but significant decrease in the depth of cure compared to the control (P<0.05). CONCLUSION: Placing disposable barriers over the light-guide tip reduced the light intensity from all three curing lights. There was no impact on depth of cure except for the high-output light, where a small decrease in cure depth was noted but this was not considered clinically significant. Disposable barriers can be recommended for use with light-cure lights.

Analysis of Variance↗

PubMed2025

Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes' tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Animals↗

PubMed2026

Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.

UNLABELLED: Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina-compatible short-read library preparation conditions in triplicate at 2 × 150 bp and 2 × 250 bp read lengths alongside PacBio HiFi long-read sequencing using a composite environmental sample of marine mangrove sediment and terrestrial palm tree soil. Longer short reads (2 × 250 bp) combined with optimal library preparation approaches improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results approaching those of long-read sequencing. TruSeq libraries at 2 × 250 bp recovered more than sevenfold more unique proteins than the same kit at 2 × 150 bp (811,701 vs 110,108) using the same number of sequencing reads, while recovering a comparable number of high-quality MAGs to PacBio HiFi long-read sequencing (11 vs 18) and surpassing it in protein discovery by almost 10-fold (811,701 vs 87,745) at less than half of the sequencing cost. Furthermore, biosynthetic gene cluster analysis identified 46 biosynthetic gene clusters in TruSeq-250PE assemblies compared to 38 in PacBio HiFi, with several showing no close match in the MIBiG database. Although long reads yield more contiguity and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating that strategic selection of library preparation chemistry and sequencing parameters can reveal more unknown microbial information in complex biomes without requiring additional sequencing depth. IMPORTANCE: Metagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2 × 150 bp and 2 × 250 bp across multiple library preparation kits, alongside PacBio HiFi long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. These findings demonstrate that short-read sequencing at 2 × 250 bp, with appropriate library preparation, can match long-read technologies in MAG recovery while substantially surpassing them in protein discovery. With less than half of the sequencing price and a 3.5-fold reduction in cost per gigabase of usable data, this method facilitates more accessible large-scale metagenomic analysis within complex environmental systems.

Metagenomics↗

PubMed2006

Radiophotoluminescence dosimetry using a small spherical glass: a preliminary phantom study.

A radiophotoluminescence dosimetry has been proposed using a spherical silver-activated phosphate glass with a diameter of 1.5 mm. A 6 MV photon dose of 2 Sv (2 Gy) was delivered to 14 spherical glass samples placed between two solid water phantoms at a depth of 10 cm. The samples were positioned within a 20 x 20 mm(2) centred at beam axis to ensure uniform dose absorption. A normalised output from a read-out system was obtained by simultaneously measuring luminescence from a non-irradiated reference and that from an irradiated reference to eliminate background contamination and time-varying fluctuation of the readout system, leading to a normalised standard deviation of 1.8%. A dose up to 3.5 Sv (3.5 Gy) was delivered to three spherical glass samples positioned between two solid water phantoms at a depth of 10 cm. The normalised output increased linearly with the applied dose.

Luminescent Measurements↗

PubMed2005

Eye growth changes in myopic children in Singapore.

AIMS: To assess the longitudinal changes in biometric parameters and associated factors in young myopic children aged 7--9 years followed prospectively in Singapore. METHODS: Children aged 7--9 years from three Singapore schools were invited to participate in the SCORM (Singapore Cohort study Of the Risk factors for Myopia) study. Yearly eye examinations involving biometry measures were performed in the schools. Only myopic children (n=543) with 3 year follow up data were included in this analysis. RESULTS: The 3 year increases in axial length, anterior chamber depth, lens thickness, vitreous chamber depth, and corneal curvature were 0.89 mm, -0.02 mm, -0.01 mm, 0.92 mm, and 0.01 mm, respectively. Children who were younger, female, and who had a parental history of myopia were more likely to have greater increases in axial length. After adjustment for school, age, sex, race, parental myopia and reading in books per week, the age (p<0.001), sex (p=0.012), and parental myopia (p=0.027) remained significantly associated with the 3 year change in axial length. Reading in books per week, however, was not associated with axial length change. Children with faster rates of progression of myopia had greater increases in axial length (Pearson correlation coefficient (r)=-0.69) and vitreous chamber depth (r=-0.83). CONCLUSIONS: The 3 year change in axial length of Singapore children aged 7--9 years at baseline was high and greater in younger children, females, and children with a parental history of myopia. Myopia progression was driven largely by vitreous chamber depth increase.

Anterior Chamber↗

PubMed2026

Characterization and comparative analysis of the complete mitochondrial genome sequence of Aucklandia lappa Decne.

BACKGROUND: Aucklandia lappa Decne, a precious medicinal herb in China, utilises the dried rhizome as its medicinal part, which riches in volatile oils, sesquiterpene compounds and other active constituents. Although the mitogenome of A. lappa has been assembled, related research remains in its preliminary stages, far from achieving comprehensive and in-depth understanding. RESULTS: In this paper, the complete mitogenome of A. lappa was assembled by employing a hybrid strategy that combined Illumina short-read and Nanopore long-read sequencing. The assembled mitogenome is 436,648 bp in size with a GC content of 45.06%. The mitogenome has only one chromosomal structure, It contains 54 genes, including 31 protein-coding genes(PCG), 19 tRNA genes, and 4 rRNA genes. A total of 32 high-frequency codons exhibiting significant AT-bias, 431 RNA editing sites, and 26 homologous fragments were transferred from the chloroplast to mitochondria genes (7,337 bp, 1.68%). Furthermore, we conducted a phylogenetic analysis involving in A. lappa and 27 other taxa to clarify its evolutionary and taxonomic status. These findings provide a foundation for further understanding the evolutionary relationships within Asteraceae plant. CONCLUSION: Through the assembly and comprehensive analysis of A. lappa mitogenome, This study has for the first time fully elucidated its mitogenomic structural characteristics.These results not only provide high-quality genetic resources for research on the Asteraceae mitogenome but also lay a solid foundation for in-depth exploration of the evolution and functional genomics of medicinal plants in the Asteraceae family.

Genome, Mitochondrial↗

PubMed2000

[Stereoscopic vision before and after cataract extraction with artificial lens implantation].

BACKGROUND: Based on current insurance data patients with pseudophakia can be expected to suffer reduced stereoacuity. A prospective study was carried out to test this relationship. PATIENTS AND METHODS: Stereoacuity was measured by Titmus and Lang tests in 50 patients with cataracts who had no other ocular complaints and a minimal visual acuity of the more impaired eye of 20/50. Examinations were carried out before and for 3 days after cataract surgery (phacoemulsification, posterior chamber lens). RESULTS: Median stereoacuity improved from 60" preoperatively to 50" postoperatively in patients with bilateral phakia, from 90" to 45" in those with unilateral phakia. Results of the Lang test were difficult to interpret. CONCLUSION: Near stereoacuity is not worsened by unilateral or bilateral pseudophakia if there are no other complaints, and if the eyes are corrected for reading distance.

Adult↗

PubMed2005

Reluctant acceptance of xenotransplantation in kidney patients on the waiting list for transplantation.

Previous research has shown contradictory results regarding the acceptance of xenotransplantation (XT) by kidney patients. This variance in attitude towards XT could be explained by differences in knowledge of XT, the availability of alternative treatment options, specific beliefs and cognitions of the patient, and differences in the health status of the patients. We studied 61 patients in this contention in the Netherlands waiting for a kidney transplant. All took part in in-depth interviews and filled out questionnaires on two occasions, once before and once after an information brochure on XT had been read. We found that a better health status is correlated with a greater acceptance of XT, but only before information was given. After information had been given, the acceptance of XT decreased significantly. However, if XT is the only possibility in a life-threatening situation, almost all patients are willing to accept XT, except for a small group (approximately 10-15%) with fundamental religious and/or spiritual objections against such treatment. When alternative treatment options such as a human cadaver donor, a living related donor or commercial donor are offered, the majority of patients would prefer those to XT. The main reason for reluctance is uncertainty about the risks of XT to personal health. Because alternatives are currently available, we expect that XT will become more popular only if future results of this procedure have proved to be comparable to transplantation with a human donor kidney.

Female↗