Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of subpopulations of Pax3 and Pax7 expressing cells in developing chick somites and limb buds

Pax3 and Pax7 are closely related paired‐boxed family transcription factors that are known to play important roles in embryonic and adult myogenesis. Previous reports describing the expression of Pax3 and Pax7 transcripts reveal expression in many overlapping domains. In this manuscript, we extend these studies by examining the protein expression profiles for Pax3 and Pax7 in developing chick somites and limbs with cellular resolution. Our studies show the existence of distinct subpopulations of cells in the somite and developing limb that are defined by the relative expression levels of Pax3 and Pax7. We also show that Pax3 and Pax7 negatively regulate each other's expression in the dermomyotome, thus providing a possible mechanism for the maintenance of observed expression patterns in the dermomyotome. Further characterization of Pax3‐ and/or Pax7‐positive cells in the dermomyotome and myotome with respect to proliferation and differentiation reveals subpopulations of cells with distinct properties. Developmental Dynamics 237:1862–1874, 2008. © 2008 Wiley‐Liss, Inc.
High incidence of ankle arthropathy in mild and moderate haemophilia A

Summary A clinical study of patients with mild haemophilia A to document the frequency and severity of arthropathy has not been previously published. We studied ankle arthropathy in 34 patients with mild/moderate haemophilia A. The patients were assessed for the presence and severity of pain, and by the physical and radiological scoring systems for the evaluation of haemophilic arthropathy recommended by the World Federation of Haemophilia (WFH). Of the 34 patients, 16 (47%) had ankle pain, which was of moderate to severe degree in nine patients, and associated with limitation of physical activities in 13 patients. Of 33 patients examined by radiology 17 (52%) were positive for ankle arthropathy, and of these, 16 were also positive by the physical score. The presence and severity of ankle arthropathy was more common in patients with a one-stage factor VIII level of less than or equal to 11 IU/ dl. There was a significant relationship between the presence of ankle arthropathy and a history of bleeds into the ankle joint as a child. We conclude that arthropathy of the ankle in these patients is common, is often severe and disabling, and is due to episodes of bleeding into the ankle joint during childhood.
Immunological Evaluation and Cellular Location Analysis of the TprI Antigen of Treponema pallidum subsp. pallidum

ABSTRACT The TprI antigen of Treponema pallidum subsp. pallidum is a putative virulence factor predicted to be located in the outer membrane of the syphilis spirochete. In this study, we analyzed the immune response against TprI and its subunits in sera collected both from rabbits experimentally infected with the Nichols strain and from patients with syphilis, showing a different pattern of reactivity toward the antigen in these two groups of samples. The protective ability of recombinant TprI and its hypothetical outer membrane location were also investigated. Although no rabbit was protected after challenge, immunoelectron microscopy results, to be further investigated, were compatible with the outer membrane location of the antigen.
The RAPTOR experiment: a system for monitoring the optical sky in real time

The Rapid Telescopes for Optical Response (RAPTOR) experiment is a spatially distributed system of autonomous robotic telescopes that is designed to monitor the sky for optical transients. The core of the ystem is composed of two telescope arrays, separated by 38 kilometers, that stereoscopically view the same 1500 square-degree field with a wide-field imaging array and a central 4 square-degree field with a more sensitive narrow-field ``fovea" imager. Coupled to each telescope array is a real-time data analysis pipeline that is designed to identify interesting transients on timescales of seconds and, when a celestial transient is identified, to command the rapidly slewing robotic mounts to point the narrow-field ``fovea'' imagers at the transient. The two narrow-field telescopes then image the transient with higher spatial resolution and at a faster cadence to gather light curve information. Each ``fovea" camera also images the transient through a different filter to provide color information. This stereoscopic monitoring array is supplemented by a rapidly slewing telescope with a low resolution spectrograph for follow-up observations of transients and a sky patrol telescope that nightly monitors about 10,000 square-degrees for variations, with timescales of a day or longer, to a depth about 100 times fainter. In addition to searching for fast transients, we will use the data stream from RAPTOR as a real-time sentinel for recognizing important variations in known sources. All of the data will be publically released through a virtual observatory called SkyDOT (Sky Database for Objects in the Time Domain) that we are developing for studying variability of the optical sky. Altogether, the RAPTOR project aims to construct a new type of system for discovery in optical astronomy---one that explores the time domain by "mining the sky in real time".
Application of automated medial temporal lobe atrophy scale to Alzheimer disease.

OBJECTIVE To compare an automated intensity-based measure of medial temporal atrophy in Alzheimer disease (AD) with existing volumetric and visually based methods. DESIGN Longitudinal study comparing a medial temporal atrophy measure with 2 criterion standards: (1) total hippocampal (HC) volume adjusted for total intracranial volume and (2) standard visual rating scale of medial temporal atrophy. SETTING Cognitive disorders specialist clinic. PARTICIPANTS Forty-seven patients with AD and 26 age- and sex-matched controls. INTERVENTION Subjects were scanned using volumetric T1-weighted magnetic resonance imaging at baseline and 1 year later. MAIN OUTCOME MEASURE Automated Medial Temporal Lobe Atrophy Scale (ATLAS) score, derived from dividing mean intensity of a standardized perihippocampal volume by that of a standardized pontine volume. RESULTS Patients with AD had significantly reduced ATLAS scores and HC volumes and increased visual rating scores at baseline and repeat scanning. Rates of HC atrophy and decline in the ATLAS score were significantly higher in patients with AD compared with controls. The ATLAS scores were significantly correlated with HC volumes and visual rating scores. With specificity set at 85%, the sensitivities of HC volume and visual rating scale score were similar (84% and 86%, respectively), whereas ATLAS score had a lower sensitivity (73%). At repeat scanning, all 3 measures had similar sensitivities (86%-87%). Rate of decline in the ATLAS score required a similar sample size to HC atrophy rate to provide statistical power to clinical trials, but being automated, it is less labor intensive. CONCLUSIONS Like the visual rating scale, ATLAS is a simple medial temporal atrophy measure, which has the additional advantage of being able to track AD progression on serial imaging.
The Epidermis-Specific Extracellular BODYGUARD Controls Cuticle Development and Morphogenesis in Arabidopsis[W]

The outermost epidermal cell wall is specialized to withstand pathogens and natural stresses, and lipid-based cuticular polymers are the major barrier against incursions. The Arabidopsis thaliana mutant bodyguard (bdg), which exhibits defects characteristic of the loss of cuticle structure not attributable to a lack of typical cutin monomers, unexpectedly accumulates significantly more cell wall–bound lipids and epicuticular waxes than wild-type plants. Pleiotropic effects of the bdg mutation on growth, viability, and cell differentiation are also observed. BDG encodes a member of the α/β-hydrolase fold protein superfamily and is expressed exclusively in epidermal cells. Using Strep-tag epitope-tagged BDG for mutant complementation and immunolocalization, we show that BDG is a polarly localized protein that accumulates in the outermost cell wall in the epidermis. With regard to the appearance and structure of the cuticle, the phenotype conferred by bdg is reminiscent of that of transgenic Arabidopsis plants that express an extracellular fungal cutinase, suggesting that bdg may be incapable of completing the polymerization of carboxylic esters in the cuticular layer of the cell wall or the cuticle proper. We propose that BDG codes for an extracellular synthase responsible for the formation of cuticle. The alternative hypothesis proposes that BDG controls the proliferation/differentiation status of the epidermis via an unknown mechanism.
Bicycle helmet legislation for the uptake of helmet use and prevention of head injuries.

BACKGROUND Evidence exists to suggest that bicycle helmets may reduce the risk of head injuries to cyclists, however helmets are not uniformly worn by all bicycle users. Legislation has been enacted in some countries to mandate helmet use by cyclists, however the issue remains controversial with opponents arguing that this may inhibit people from bicycle riding and thus from gaining the associated health benefits, or that other countermeasures may have been responsible for decline in head injuries. OBJECTIVES To assess the effects of bicycle helmet legislation on bicycle-related head injuries and helmet use, and the occurrence of unintended adverse consequences. SEARCH STRATEGY We searched CENTRAL, the Cochrane Injuries Group's specialised register, MEDLINE, EMBASE, TRANSPORT and other specialist electronic databases, up to February 2006. In addition we searched government websites, handsearched selected journals and examined the reference lists of selected publications. SELECTION CRITERIA We included studies that reported changes in either the number of head injuries, helmet use or bicycle use post- versus pre-legislation. Only studies that included a concurrent control group and which reported on the effect of legislation implemented at either the country, state or province wide level were included. DATA COLLECTION AND ANALYSIS Two authors independently extracted data and assessed methodological quality. The data were not appropriate for meta-analysis, thus the results of the included studies have been reviewed narratively. MAIN RESULTS Five studies, all from North America, met the inclusion criteria. For each of the studies, bicycle helmet legislation had been enacted for children only. Adults were used as controls in four of the studies, whilst jurisdictions with no helmet legislation were used as controls in the fifth. Three of the studies reported on changes in head injury rates and three reported on changes in helmet use. There were no included studies reporting change in bicycle use or other adverse consequences of legislation. In two studies, statistically significant decreases in head injuries were reported following the implementation of helmet legislation compared with controls, whilst one reported a non-statistically significant decline. Bicycle helmet use increased statistically significantly post-legislation in all three of the studies reporting on helmet use. AUTHORS' CONCLUSIONS Bicycle helmet legislation appears to be effective in increasing helmet use and decreasing head injury rates in the populations for which it is implemented. However, there are very few high quality evaluative studies that measure these outcomes, and none that reported data on an possible declines in bicycle use.
Can parasites synchronise the population fluctuations of sympatric tetraonids? / examining some minimum conditions

Sympatric populations of tetraonid birds tend to fluctuate in synchrony, at least on local scales. If shared parasites among sympatric populations of different tetraonid species are to operate as a local, synchronizing factor for population fluctuations at least two conditions should be met: i) the host species should share the same (or similar) parasite species, and ii) geographical location should contribute significantly more to the variation in the parasite species composition and abundance than differences among host species. We examined these conditions among subpopulations of sympatric willow ptarmigan and rock ptarmigan and found that host species shared a common pool of parasite species, and geographic location was more important than host species in determining parasite abundance across locations. There was no time lag between density oscillations in the two hosts, suggesting a symmetrical pattern of transmission and maintenance of parasites within habitats governed by the density of hosts and the environment. These findings are consistent with the idea that parasites may play a role in generating synchronous density fluctuations, but large scale experiments are needed to verify this hypothesis.
THE ACCURACY OF PHYLOGENETIC ESTIMATION USING THE NEIGHBOR‐JOINING METHOD

We studied the factors affecting the accuracy of the neighbor‐joining (NJ) method for estimating phylogenies by simulating character change under different evolutionary models applied to twenty different 8‐OTU tree topologies that varied widely with respect to tree imbalance and stemminess. The models incorporated three evolutionary rates—constant, varying among lineages, varying among characters—and three evolutionary contexts concerning patterns of character change relative to speciation events—phyletic, speciational, and punctuational. All combinations of the rate and context models were studied. In addition, three different absolute rates of change were investigated. To measure the accuracy, the strict consensus index was computed between the estimated tree and the tree topology along which the data had been generated. The results were analyzed by analysis of variance and compared to a previous study that evaluated UPGMA clustering and maximum parsimony (MP) as phylogenetic estimation techniques. We found evolutionary context and tree imbalance to be the most important factors affecting the accuracy of the NJ method. NJ was more accurate than UPGMA or MP in terms of the average strict consensus index over all treatments. However, no one method was more accurate than the other two for all combinations of treatments. Higher absolute rate of change generally resulted in higher accuracy for all three methods.
The incidence and aetiology of acute kidney injury in children in Norway between 1999 and 2008

Primary acute kidney injury (AKI) is a direct cause of hospitalisation in children, but can also result from other conditions. There is limited information on the epidemiology of this condition. Our aim was to describe the national incidence rate and aetiology of acute kidney injury in children under the age of 16 in Norway from 1999 to 2008.
Impact of Processing Method on Recovery of Bacteria from Wipes Used in Biological Surface Sampling

ABSTRACT Environmental sampling for microbiological contaminants is a key component of hygiene monitoring and risk characterization practices utilized across diverse fields of application. However, confidence in surface sampling results, both in the field and in controlled laboratory studies, has been undermined by large variation in sampling performance results. Sources of variation include controlled parameters, such as sampling materials and processing methods, which often differ among studies, as well as random and systematic errors; however, the relative contributions of these factors remain unclear. The objective of this study was to determine the relative impacts of sample processing methods, including extraction solution and physical dissociation method (vortexing and sonication), on recovery of Gram-positive (Bacillus cereus) and Gram-negative (Burkholderia thailandensis and Escherichia coli) bacteria from directly inoculated wipes. This work showed that target organism had the largest impact on extraction efficiency and recovery precision, as measured by traditional colony counts. The physical dissociation method (PDM) had negligible impact, while the effect of the extraction solution was organism dependent. Overall, however, extraction of organisms from wipes using phosphate-buffered saline with 0.04% Tween 80 (PBST) resulted in the highest mean recovery across all three organisms. The results from this study contribute to a better understanding of the factors that influence sampling performance, which is critical to the development of efficient and reliable sampling methodologies relevant to public health and biodefense.
In situ scanning electron microscopy indentation studies on multilayer nitride films: Methodology and deformation mechanisms

Systematic studies of the deformation mechanisms of multilayer transition metal nitride coatings TiN/CrN, TiN/NbN, and NbN/CrN, and corresponding reference coatings of TiN, NbN, and CrN deposited by a direct current (dc) magnetron sputtering process onto silicon 〈100〉 have been performed. Mechanical characterization was conducted using a combination of microindentation and nanoindentation in the load range 30 to 150 mN and 0.5 to 3.5 mN, respectively. For both load ranges, scanning electron microscopy (SEM) in situ indentation was used to observe the indentation process including any pileup, sink-in, and fracture mechanisms specific to each coating. The coatings’ microstructure, both before and after indentation, was analyzed using transmission electron microscopy (TEM). It was possible to both correlate the indentation load–displacement response to surface roughness effects and fracture modes (substrate and film cracking) and observe deformation mechanisms within the coatings.
Evaluation of Different Mycotoxin Binders on Broiler Breeders Induced with Aflatoxin B : Effects on Egg Quality Parameters

4 Abstract: A study was conducted with an objective to compare the efficacy of bentonite (BT), Spirulina platensis (SP) and glucomannan mycotoxin binders (GMA) on aflatoxicosis in broiler breeders. Three levels of AF, three binders and combination of different levels of AF with binders were evaluated. The Aflatoxin B1 (AF) fed at the levels of 300, 400 and 500ppb for three periods, each with duration of three weeks in broiler breeders from 28 to 36 weeks of age. Inclusion of 500 AF in the diet significantly (P 0.05) affected egg weight when compared to that of control. The results indicated no significant (P 0.05) effect of AF on egg weight, shell thickness and Haugh unit when compared to that of control. The results showed dose dependent cumulative effects of AF on all the affected parameters. Among the binders, GMA showed better counteracting effect.
Treatment of tenosynovial giant cell tumor and pigmented villonodular synovitis

Purpose of review To review recent developments in the molecular pathogenesis of tenosynovial giant cell tumor (TGCT) or pigmented villonodular synovitis (PVNS) and its therapeutic implications. Recent findings TGCT or PVNS is a benign clonal neoplastic proliferation arising from the synovium characterized by a minor population of intratumoral cells that harbor a recurrent translocation. These cells overexpress CSF1, resulting in recruitment of CSF1R-bearing macrophages that are polyclonal and make up the bulk of the tumor. Inhibition of CSF1R using small molecule inhibitors such as imatinib, nilotinib or sunitinib can result in clinical, radiological and functional improvement in the affected joint. Summary Currently, surgery remains the treatment of choice for patients with TGCT/PVNS. Localized TGCT/PVNS is managed by marginal excision. Recurrences occur in 8–20% of patients and are easily managed by re-excision. Diffuse TGCT/PVNS tends to recur more often (33–50%) and has a much more aggressive clinical course. Patients are often symptomatic and require multiple surgical procedures during their lifetime. For patients with unresectable disease or multiple recurrences, systemic therapy using CSF1R inhibitors may help delay or avoid surgical procedures and improve functional outcomes.
Thin films characterizations to design high-reflective coatings for ultrafast high power laser systems

Dielectrics as single layers and broadband high-reflective stacks were deposited by electron beam deposition processes compatible with 1-meter class optics. After being physically and optically characterized, samples were irradiated with several ultrafast lasers (KYW:Yb 500fs, Ti:Sa 40fs and Ti:Sa 11fs) with single and multi-pulses. The setups of the test platforms, laser-induced damage threshold investigations of intrinsic materials, dielectric multilayers and hybrid metal/dielectric multilayers and electric field intensity distributions are described.
Comparative Study of Taste Disturbance by Losartan and Perindopril in Healthy Volunteers

The aim of this study was to compare the degree of taste disturbance by losartan, an angiotensin II receptor blocker, with that of perindopril, an angiotensin‐converting enzyme inhibitor. Perindopril erbumine (2 mg), losartan potassium (25 mg), or vehicle was given to Japanese volunteers (n = 7) for 14 days in a randomized, placebo‐controlled, 3‐way crossover design with a 14‐day washout period. Gustometry by filter‐paper test and electrogustometry were performed before and at the end of each trial. Plasma renin activity (PRA) and serum and salivary zinc concentrations were measured. One subject dropped out because of a perindopril‐induced dry cough, but no one claimed a taste disturbance. Detection thresholds of 4 basic tastes (sweet, salty, sour, and bitter) by the paper‐disc test and electrogustometry were significantly worsened, and plasma renin activity was elevated by the drugs, whereas the deteriorating effects of 2 drugs did not significantly differ. These drugs did not affect zinc concentrations in plasma and saliva. It was concluded that losartan and perindopril similarly alter taste sensitivity during repeated dosing of the drugs.
Parsing and Question Classification for Question Answering

This paper describes machine learning based parsing and question classification for question answering. We demonstrate that for this type of application, parse trees have to be semantically richer and structurally more oriented towards semantics than what most treebanks offer. We empirically show how question parsing dramatically improves when augmenting a semantically enriched Penn treebank training corpus with an additional question treebank.
Uranium doping of silver sheathed bismuth-strontium-calcium-copper-oxide superconducting tapes for increased critical current density through enhanced flux pinning

A combination of uranium doping with thermal neutron irradiation has been well demonstrated to be one of the most effective means to introduce pinning centres in (Bi,Pb) 2 Sr 2 Ca 2 Cu 3 O x /Ag tapes (Bi-2223/Ag). A substantial improvement in flux pinning and reduction of anisotropy in uranium doped Bi-2223/Ag tapes has been achieved due to thermal neutron irradiation. However, the radioactivity of the silver sheath is too high for practical application of this technique. This work aimed at minimising the detrimental effects of doping to allow for later irradiation and fission to create columnar defects for strong flux pinning. A number of uranium containing compounds, U 3 O 8 , U(Ca,Sr) 2 O 5 , and U(Ca,Sr) 3 O 6 have been identified in the U-Bi-Sr-Ca-Cu-O system. These equilibrium compounds have been synthesised and added to Bi-2223/Ag composite tapes in progressively greater amounts. The effects on the transport critical current density of Bi-2223/Ag of doping with a variety of uranium compounds up to 2 at% was determined. The compatibility and interaction between uranium compounds and the Bi-2223 matrix was systematically studied under various thermal processing conditions. Bi-2223/Ag doped with compounds using compositions closer to the equilibrium composition was shown to have superior superconducting properties to that doped with uranium oxide compounds. The effects of chemical degradation by uranium compound dopants via strontium and calcium removal from the Bi-2223 structure have been indirectly determined by critical current density (J c ) measurements. Losses in J c can be minimised by stabilising uranium into appropriate compounds.