Miracle-dz/UniFAR-FTUs huggingface dataset:
ptoelectronic holographic otoscope for measurement f nano-displacements in tympanic membranes

Current methodologies for characterizing tympanic membrane TM motion are usually limited to either average acoustic estimates admittance or reflectance or single-point mobility measurements, neither of which suffices to characterize the detailed mechanical response of the TM to sound. Furthermore, while acoustic and singlepoint measurements may aid in diagnosing some middleear disorders, they are not always useful. Measurements of the motion of the entire TM surface can provide more information than these other techniques and may be superior for diagnosing pathology. We present advances in our development of a new compact optoelectronic holographic otoscope OEHO system for full field-of-view characterization of nanometer-scale sound-induced displacements of the TM surface at video rates. The OEHO system consists of a fiber optic subsystem, a compact otoscope head, and a high-speed image processing computer with advanced software for recording and processing holographic images coupled to a computer-controlled sound-stimulation and recording system. A prototype OEHO system is in use in a medical research environment to address basic science questions regarding TM function. The prototype provides real-time observation of soundinduced TM displacement patterns over a broad frequency range. Representative time-averaged and stroboscopic holographic interferometry results in animals and human cadaver samples are shown, and their potential utility is discussed. © 2009 Society of Photo-Optical Instrumentation Engineers. DOI: 10.1117/1.3153898
Studies on schistosomiasis. 5. Sampling methods for estimating the numbers of cercariae in suspension with special reference to the infestation of experimental animals.

VANWYK, J. A. & GROENEVELD, H. T. , 1973. Studies on schistosomiasis. 5. Sampling methods for estimating the numbers of cercariae in suspension with special reference to the infestation of experimental animals. Onderstepoort J. vet. Res. 40(4) 157-174 (1973). Various sampling methods for Schistosoma mattheei cercariae, including sampling from different concentrations, were tested. The most satisfactory method consisted of mixing the cercaria! suspension b~ pouring it to and fro between two cylinders and then sampling it by oral suction on a bulb pipette with a large aperture. The aliquots withdrawn were stored in bottles containing formol-saline for later microscopic examination. This method of sampling was tested extensively. The results showed that the variation between ahquots was larger than that expected for either a binomial or a Poisson distribution, indicating that the cercariae were not randomly distributed in the suspension. Moreover, significant variations oc.c':lrred between the totals of series of aliquots, possibly indicating uncontrolled factors, e.g. in mixmg. From these results, methods of making up doses of carcariae for infesting sheep and cattle were developed: The Sheep Method is used for doses of up to 15 000 cercariae and is therefore applicable to infestation of primates as well as sheep. Several series of aliquots are made up, some of which (one or more series per animal) are used for infesting the animals concerned (Infestation Series), while others are retained for estimating the infestation doses (Estimation and Additional Estimation Series). ~ne Estii? ation and one Additional Estimation Series suffice for estimating the numbers of cercariae m up to eight Infestation Series drawn from the same cercaria! suspension, which is mixed immediately before each series of aliquots is withdrawn. In the Bovine Method, which is used for doses of over IS 000 cercariae, an Estimation Series and ~n A~ditional ~stimation Series of aliquots are withdrawn from every dose of cercariae to be used for mfestmg an ammal. Thus the number of cercariae is estimated separately for each animal. Fo:J? ulae were compiled for these methods to determine the upper levels (with a specified probability) of the percentage errors in the estimated doses. These formulae were applied to the results and some expected percentage errors in the numbers of cercariae estimated by the two methods, calculated. A result for the probability distribution of aliquot counts under the assumption of randomness is proved for the first time. * See Appendix C for particulars of the other papers in this series (') Section of Helminthology, Veterinary Research Institute, Onderstepoort (2) Dep.ar! ment of Agronomy and Biometry, University of Pretoria, Pretoria and responsible for the statistical aspects of the paper Received 22 October 1973-Editor
Children's physical activity: using accelerometers to validate a parent proxy record.

INTRODUCTION The purpose of this study was to validate a parent proxy record of children's physical activity with CSA Model 7164 accelerometers. METHODS A parent proxy record was developed to record children's activity after school on weekdays and all day long on weekends for 7 d. Parents recorded both duration and intensity of activity (light, medium, hard and very hard). Children simultaneously wore a CSA-7164 accelerometer around their right hip, which served as the objective measurement against which the proxy record was validated. Sixty-five parent/child dyads participated in the study. RESULTS The overall activity level of the children was low (<3 METs). Spearman-rho analyses indicated that the accelerometer and proxy record showed poor to fair agreement for the entire monitoring period, with parents consistently overreporting their child's activity levels. Correlation between the two instruments was highest at midday on weekends (0.383) and immediately after school on weekdays (0.267). CONCLUSION Due to the low correlation between this proxy record and the accelerometer, the need still exists for a valid measurement of child physical activity that is both inexpensive and easy to employ in larger community-based interventions.
Vibrio cholerae O395 tcpA pilin gene sequence and comparison of predicted protein structural features to those of type 4 pilins

Vibrio cholerae O1 expresses a pilus that is coordinately regulated with cholera toxin production and hence termed TCP, for toxin-coregulated pilus. Insertion of Tn5 IS50L::phoA (TnphoA) into the major pilin subunit gene, tcpA, has previously been shown to render the strain avirulent as a result of its inability to colonize. One such insertion was isolated and used as a probe to screen for clones containing the intact tcpA gene. The DNA sequence of tcpA was determined by using the intact gene and several tcpA-phoA gene fusions. The deduced protein sequence agreed completely with that previously determined for the TcpA N terminus and with the size of the mature pilin protein. The reported homology with N-methylphenylalanine (type 4) pilins near the N terminus was extended and shown to include components of the atypical leader peptide as well as overall predicted structural similarities in other regions of the pilins. In contrast to the modified N-terminal phenylalanine residue found in all characterized type 4 pilins, the corresponding position in tcpA contains a Met codon, thus implying that the previously uncharacterized amino acid corresponding to the N-terminal position of the mature TcpA pilin is a modified form of methionine. Except for this difference, mature TcpA has the overall predicted structural motifs shared among type 4 pilins.
Cost‐effective non‐metric photogrammetry from consumer‐grade sUAS: implications for direct georeferencing of structure from motion photogrammetry

The declining costs of small Unmanned Aerial Systems (sUAS), in combination with Structure‐from‐Motion (SfM) photogrammetry have triggered renewed interest in image‐based topography reconstruction. However, the potential uptake of sUAS‐based topography is limited by the need for ground control acquired with expensive survey equipment. Direct georeferencing (DG) is a workflow that obviates ground control and uses only the camera positions to georeference the SfM results. However, the absence of ground control poses significant challenges in terms of the data quality of the final geospatial outputs. Notably, it is generally accepted that ground control is required to georeference, refine the camera calibration parameters, and remove any artefacts of optical distortion from the topographic model. Here, we present an examination of DG carried out with low‐cost consumer‐grade sUAS. We begin with a study of surface deformations resulting from systematic perturbations of the radial lens distortion parameters. We then test a number of flight patterns and develop a novel error quantification method to assess the outcomes. Our perturbation analysis shows that there exists families of predictable equifinal solutions of K1‐K2 which minimize doming in the output model. The equifinal solutions can be expressed as K2 = f (K1) and they have been observed for both the DJI Inspire 1 and Phantom 3 sUAS platforms. This equifinality relationship can be used as an external reliability check of the self‐calibration and allow a DG workflow to produce topography exempt of non‐affine deformations and with random errors of 0.1% of the flying height, linear offsets below 10 m and off‐vertical tilts below 1°. Whilst not yet of survey‐grade quality, these results demonstrate that low‐cost sUAS are capable of producing reliable topography products without recourse to expensive survey equipment and we argue that direct georeferencing and low‐cost sUAS could transform survey practices in both academic and commercial disciplines. Copyright © 2016 John Wiley & Sons, Ltd.
Minocycline safety and tolerability in Huntington disease

Minocycline is an antibiotic with anti-inflammatory and antiapoptotic properties that prolongs survival in a transgenic Huntington disease (HD) mouse model. In a double-blind, randomized, placebo-controlled study of minocycline in 60 HD patients, the authors determined that over 8 weeks, minocycline at 100 and 200 mg/day was well tolerated and safe in HD patients. Tolerability and adverse event frequency were similar between treatment and placebo groups.
CFD code comparison for 2D airfoil flows

The current paper presents the effort, in the EU AVATAR project, to establish the necessary requirements to obtain consistent lift over drag ratios among seven CFD codes. The flow around a 2D airfoil case is studied, for both transitional and fully turbulent conditions at Reynolds numbers of 3 × 106 and 15 × 106. The necessary grid resolution, domain size, and iterative convergence criteria to have consistent results are discussed, and suggestions are given for best practice. For the fully turbulent results four out of seven codes provide consistent results. For the laminar-turbulent transitional results only three out of seven provided results, and the agreement is generally lower than for the fully turbulent case.
A Survey of Current, Stand-alone OWL Reasoners

We present a survey of the current OWL reasoner landscape. Through literature and web search we have identified 35 OWL reasoners that are, at least to some degree, actively maintained. We conducted a survey directly addressing the respective developers, and collected 33 responses. We present an analysis of the survey, characterising all reasoners across a wide range of categories such as supported expressiveness and reasoning services. We will also provide some insight about ongoing research efforts and a rough categorisation of reasoner calculi.
Transgenic basmati rice transformed with the Xa21 gene shows resistance against bacterial leaf blight

Rice (Oryza sativa L.) cultivar Super Basmati was transformed with a cloned gene, Xa21, through particle bombardment method. Twenty-two plants were recovered from the selected calli. Initial screening through PCR confirmed the presence of the transgene in 21 plants. Southern analysis further confirmed the integration of the Xa21 gene into the genome of these transgenic plants. Analysis of the T1 generation revealed that both the hpt and Xa21 genes were successfully transmitted from the primary transformants to the progeny. Bioassays with two local isolates of bacterial leaf blight pathogen, Xanthomonas oryzae pv. oryzae (Xoo), showed that 14 transgenic lines were resistant to both Xoo isolates. No significant differences were observed in yield and grain characteristics between transgenic lines and the control; however, the transgenic lines took 8-12 days longer to flower and showed reduced plant height compared to the control plants. In conclusion, we have developed bacterial blight-resistant transgenic lines that can be further exploited by breeders for rice improvement.
A role for amyloid precursor-like protein 2 in corneal epithelial wound healing.

PURPOSE The authors previously showed that the mRNA encoding the amyloid precursor-like protein 2 (APLP2) was one of several genes with upregulated expression in healing corneal epithelium. To elucidate the physiological role of APLP2 in corneal epithelial cells, the expression, distribution, and posttranslational modification of APLP2 were investigated. METHODS Alternative splicing was assessed by reverse transcription-polymerase chain reaction; translational expression and posttranslational modification were assessed by chondroitinase digestion and Western blotting. The differential distribution of APLP2 in corneal epithelium was examined by in situ hybridization and immunohistochemical analyses. RESULTS In rat corneal epithelium, the majority of APLP2 mRNA generated from two alternative splicing sites was found to contain the exon encoding a Kunitz protease inhibitor domain in the first site but to lack the exon encoding a 12-amino acid insert in the second site. The absence of the 12-amino acid insert indicated that APLP2 could be modified by the addition of a chondroitin sulfate (CS) glycosaminoglycan chain. The CS proteoglycan nature of APLP2 was verified by chondroitinase digestion. After wounding, APLP2 mRNA and polypeptides were increased markedly in the basal epithelial cells that were actively migrating. Furthermore, APLP2 was observed in the denuded wound bed immediately adjacent to the leading edge of migratory cells and under the epithelial sheet after wound closure. CONCLUSIONS The wound-induced, basal-cell-specific APLP2 expression correlates with epithelial cell migration. The spatial and temporal expression of Kunitz protease inhibitor-containing, CS-modified APLP2 in healing corneal epithelium is consistent with its hypothesized role(s) in mediating reorganization of the extracellular matrix and dynamic cell-matrix adhesion during reepithelialization.
A new multimarker test for family‐based association studies

We propose a new multimarker test for family‐based studies in candidate genes. We use simulations under different genetic models to assess the performance of competing testing strategies, characterized in this study as combinations of the following important factors: genes, statistical tests, tag single nucleotide polymorphisms (SNP) methods, number of tag SNPs and family designs. An ANOVA model is employed to provide descriptive summaries of the effects on power of the above‐mentioned factors. We find that tag SNP methods, gene characteristics and family designs have minimal impact on the best testing strategy. The familywise error rate (FWER) controlling multiple comparison procedure and the new multimarker test offer the highest power followed by the asymptotic global haplotype test.Both the FWER and the multimarker test are invariant to family designs and gain power as we increase the number of tag SNPs. However, the performance of the global haplotype test is slightly degraded when analyzing larger numbers of tag SNPs. Within the framework of our study, the best strategy for family‐based studies in candidate genes that emerged from our analysis is to use the FWER or the multimarker test and select 6–10 tag SNPs using any of the tag SNP methods considered. We confirm the conclusions of our study with an application to Alzheimer's disease data. Genet. Epidemiol. © 2006 Wiley‐Liss, Inc.
Pathology of breast carcinomas after neoadjuvant chemotherapy: an overview with recommendations on specimen processing and reporting.

CONTEXT Currently, more women are being treated with chemotherapy or hormonal agents before surgery (neoadjuvant chemoendocrine therapy) for earlier-stage operable breast carcinoma. The pathologic examination of these specimens can be quite challenging. OBJECTIVE To give an overview of (1) pathologic changes that occur during treatment, (2) systems for evaluating response to treatment, and (3) recommendations for pathologic examination and reporting of such cases. DATA SOURCES The recommendations are based on the review of selected literature on breast carcinoma after neoadjuvant therapy and the authors' personal experience with the clinical and pathologic characteristics of cases from each of the authors' own institutions. CONCLUSIONS Pathologists play a key role in the evaluation of pathologic response, which is extremely important as a prognostic factor for individual patients, as a short-term endpoint for clinical trials, and as an adjunct for research studies. Therefore, surgical pathologists must be familiar with the gross examination, sampling, and reporting of breast carcinomas after neoadjuvant therapy.
Design of high speed FFT algorithm For OFDM technique

This paper presents a high speed FFT algorithms for high data rate wireless personal area network applications. In wireless personal area network the FFT/IFFT block leads the major role. Computational requirements of FFT/IFFT processes are a heavy burden in most applications. The FFT/IFFT block can be implemented in various methods. From this work, we can recognize that most of the FFT structures follow the divide and conquer algorithms, which improve the computational efficiency. In this work two distinct complex multiplication approaches are discussed, and the corresponding results produced by these approaches are compared with MATLAB. The pipelined architecture of Radix-2 SDF has been implemented with 16 point module.
A Business use Case Driven Methodology - A Step Forward

The present contribution reshapes a recently proposed software methodology by giving up the top-down philosophy being part of it, to follow a strictly model-driven engineering approach. The ultimate goal of our research is to define a methodological proposal ensuring the continuity between business modeling, system modeling, design, and implementation. This lays the foundations for the automatic transformation process of the behavioral business model into a software model capable of meeting user needs.
Statistical Characterization of Electromagnetic Wave Propagation in Mine Environments

A computational framework for statistically characterizing electromagnetic (EM) wave propagation through mine tunnels and galleries is presented. The framework combines a multi-element probabilistic collocation method with a full-wave fast Fourier transform and fast multipole method accelerated surface integral equation-based EM simulator to statistically characterize fields from wireless transmitters in complex mine environments.
A Comparison of Tactile Sensors for In-Hand Object Location

This work presents an extensive analysis of the usefulness of tactile sensors for in-hand object localization. Our analysis is based on a previous work where we proposed a method for the evaluation of tactile data using two algorithms: a Particle Filter algorithm and an Iterative Closest Point algorithm. In particular, we present a comparison of six different sensors, including two pairs of sensors based on similar technology, showing how the design and distribution of tactile sensors can affect the performance. Also, together with previous results where we demonstrated the importance of the synergy between tactile data and hand geometry, we corroborate that it is possible to obtain more similar performance with a simple fingertip sensor, than with more complex and expensive tactile sensors.
Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory

Using energy minimization and cluster analysis, we have analyzed a 1020 ps molecular dynamics trajectory of solvated bovine pancreatic trypsin inhibitor. Elucidation of conformational sub states in this way both illustrates the degree of conformational convergence in the simulation and reduces the structural data to a tractable subset. The relative movement of structures upon energy minimization was used to estimate the sizes of features on the protein potential energy surface. The structures were analyzed using their pairwise root‐mean‐square Cα deviations, which gave a global measure of conformational changes that would not be apparent by monitoring single degrees of freedom. At time scales of 0.1 ps, energy minimization detected sharp transitions between energy minima separated by 0.1 Å rms deviation. Larger conformational clusters containing these smaller minima and separated by 0.25 Å were seen at 1 ps time scales. Both of these small features of the conformational landscape were characterized by movements in loop regions associated with small, correlated backbone dihedral angle shifts. On a nanosecond time scale, the main features of the protein energy landscape were clusters separated by over 0.7 Å rms deviation, with only seven of these sub states visited over the 1 ns trajectory. These substates, discernible both before and after energy minimization, differ mainly in a monotonic pivot of the loop residues 11–18 over the course of the simulation. This loop contains lysine 17, which specifically binds to trypsin in the active site. The trajectory did not return to previously visited clusters, indicating that this trajectory has not been shown to have completely sampled the conformational substates available to it. Because the apparent convergence to a single region of conformation space depends on both the time scale of observation and the size of the conformational features examined, convergence must be operationally defined within the context of the simulation. © 1995 Wiley‐Liss, Inc.
Radiometric normalization of overlapping LiDAR intensity data for reduction of striping noise

ABSTRACT Airborne LiDAR data are usually collected with partially overlapping strips in order to serve a seamless and fine resolution mapping purpose. One of the factors limiting the use of intensity data is the presence of striping noise found in the overlapping region. Though recent researches have proposed physical and empirical approaches for intensity data correction, the effect of striping noise has not yet been resolved. This paper presents a radiometric normalization technique to normalize the intensity data from one data strip to another one with partial overlap. The normalization technique is built based on a second-order polynomial function fitted on the joint histogram plot, which is generated with a set of pairwise closest data points identified within the overlapping region. The proposed method was tested with two individual LiDAR datasets collected by Teledyne Optech's Gemini (1064 nm) and Orion (1550 nm) sensors. The experimental results showed that radiometric correction and normalization can significantly reduce the striping noise found in the overlapping LiDAR intensity data and improve its capability in land cover classification. The coefficient of variation of five selected land cover features was reduced by 19–65%, where a 9–18% accuracy improvement was achieved in different classification scenarios. With the proven capability of the proposed method, both radiometric correction and normalization should be applied as a pre-processing step before performing any surface classification and object recognition.