Miracle-dz/UniFAR-FTUs huggingface dataset:
Reliability of a Computer-Aided Manual Procedure for Segmenting Optical Coherence Tomography Scans

Purpose. To assess the within- and between-operator agreement of a computer-aided manual segmentation procedure for frequency-domain optical coherence tomography scans. Methods. Four individuals (segmenters) used a computer-aided manual procedure to mark the borders defining the layers analyzed in glaucoma studies. After training, they segmented two sets of scans, an Assessment Set and a Test Set. Each set had scans from 10 patients with glaucoma and 10 healthy controls. Based on an analysis of the Assessment Set, a set of guidelines was written. The Test Set was segmented twice with a ≥1 month separation. Various measures were used to compare test and retest (within-segmenter) variability and between-segmenter variability including concordance correlations between layer borders and the mean across scans (n = 20) of the mean of absolute differences between local border locations of individual scans, MEAN{mean( &Dgr;LBL )}. Results. Within-segmenter reliability was good. The mean concordance correlations values for an individual segmenter and a particular border ranged from 0.999 ± 0.000 to 0.978 ± 0.084. The MEAN{mean( &Dgr;LBL )} values ranged from 1.6 to 4.7 &mgr;m depending on border and segmenter. Similarly, between-segmenter agreement was good. The mean concordance correlations values for an individual segmenter and a particular border ranged from 0.999 ± 0.001 to 0.992 ± 0.023. The MEAN{mean( &Dgr;LBL )} values ranged from 1.9 to 4.0 &mgr;m depending on border and segmenter. The signed and unsigned average positions were considerably smaller than the MEAN{mean( &Dgr;LBL )} values for both within- and between-segmenter comparisons. Measures of within-segmenter variability were only slightly larger than those of between-segmenter variability. Conclusions. When human segmenters are trained, the within-and between-segmenter reliability of manual border segmentation is quite good. When expressed as a percentage of retinal layer thickness, the results suggest that manual segmentation provides a reliable measure of the thickness of layers typically measured in studies of glaucoma.
A phase matching and region segmentation stereo depth mixed extraction algorithm

This paper presents a novel dense disparity estimation method using phase matching and color segmentation. In the proposed method, the initial disparity map is firstly obtained by an improved phase-based stereo matching solution. The solution effectively restrains two tough problems of phase singularities and phase wrap, in a coarse-to-fine approach, by using Dual-Tree Complex Wavelet Transform (DT CWT) to extract the phase of the stereo images. The initial disparity is then refined by color segmentation and disparity plane fitting. Segmentation-based methods have an advantage of well representation of disparities on discontinuous region. Experimental results indicate that the proposed method is superior in generating disparity maps with high accuracy and clean edges.
Neurodegeneration in the Spinal Ventral Horn Prior to Motor Impairment in Cervical Spondylotic Myelopathy.

Remote gray matter pathology has been suggested rostral to the compression site in cervical spondylotic myelopathy (CSM). We therefore assessed neurodegeneration in the gray matter ventral and dorsal horns. Twenty patients with CSM and 18 healthy subjects underwent a high-resolution structural and diffusion magnetic resonance imaging protocol at vertebra C2/C3. Patients received comprehensive clinical assessments. T2*-weighted data provided cross-sectional area measurements of gray matter ventral and dorsal horns to identify atrophy. At the identical location, mean diffusivity (MD) and fractional anisotropy (FA) determined the microstructural integrity. Finally, the relationships between neurodegeneration occurring in the gray and white matter and clinical impairment were investigated. Patients suffered from mild-to-moderate CSM with mainly sensory impairment. In the ventral horns, cross-sectional area was not reduced (p = 0.863) but MD was increased (p = 0.045). The magnitude of MD changes within the ventral horn was associated with white matter diffusivity changes (MD: p = 0.013; FA: p = 0.028) within the lateral corticospinal tract. In contrast, dorsal horn cross-sectional area was reduced by 16.0% (p < 0.001) without alterations in diffusivity indices, compared with controls. No associations between the magnitude of ventral and dorsal horn neurodegeneration and clinical impairment were evident. Focal cord gray matter pathology is evident remote to the compression site in vivo in CSM patients. Microstructural changes in the ventral horns (i.e., motoneurons) related to corticospinal tract integrity in the absence of atrophy and marked motor impairment. Dorsal horn atrophy corresponded to main clinical representation of sensory impairment. Thus, neuroimaging biomarkers of cord gray matter integrity reveal focal neurodegeneration prior to marked clinical impairment and thus could serve as predictors of ensuing impairment in CSM patients.
Feasibility study of a membrane-type magnetostrictive acoustic transducer for ultrasonic thrombolysis

It is well known that ultrasound helps increase the efficiency of thrombolysis when used together with tissue plasminogen activators. Recently, a catheter device mounting a piezoelectric ultrasound transducer on its tip has been proposed. However, this device has some limitations because the supply of high-voltage electric power to piezoelectric elements in the transducer can be dangerous to a human. To overcome this limitation, the use of a magnetostrictive acoustic transducer instead of piezoelectric one was considered. A magnetostrictive transducer can generate ultrasound by the magnetic field not by electric field. In this work, we propose a magnetostrictive transducer and investigate its feasibility as a device for thrombolysis. Specifically, the membrane shaped element was considered instead of a cylindrical block since it is easily made of a nickel or Fe-Co alloy thin plate having strong magnetostriction. For experiments, the transducer was submerged under water and, then, the velocity of water surface was measured by a laser vibrometer to evaluate the near field acoustic wave from the membrane. The results show that the membrane vibration can be effectively transferred into acoustic waves in water. This result confirms that the proposed transducer has strong potential for ultrasonic thrombolysis without electric current flow into a body.
A Bayesian Approach for Inference from a Bridging Study with Binary Outcomes

To address concerns that ethnic differences in any clinical trial may affect the performance of a treatment, separate clinical trials may be required for different regions. If a drug is approved in one region based on a bigger clinical trial, a bridging study with smaller size may be conducted in a new region to evaluate the similarity of the earlier clinical data to the new population. This article applies a Bayesian strategy to combine a bridging study with reference studies to assess treatment effect similarity for binary endpoints. The methods have been illustrated with a numerical example using Markov-chain Monte Carlo (MCMC) techniques.
Uncovering Gene Regulatory Networks During Mouse Fetal Germ Cell Development1

The commitment of germ cells to either oogenesis or spermatogenesis occurs during fetal gonad development: germ cells enter meiosis or mitotic arrest, depending on whether they reside within an ovary or a testis, respectively. Despite the critical importance of this step for sexual reproduction, gene networks underlying germ cell development have remained only partially understood. Taking advantage of the Wv mouse model, in which gonads lack germ cells, we conducted a microarray study to identify genes expressed in fetal germ cells. In addition to distinguishing genes expressed by germ cells from those expressed by somatic cells within the developing gonads, we were able to highlight specific groups of genes expressed only in female or male germ cells. Our results provide an important resource for deciphering the molecular pathways driving proper germ cell development and sex determination and will improve our understanding of the etiology of human germ cell tumors that arise from dysregulation of germ cell differentiation.
Patterns of Progression in Metastatic Estrogen Receptor Positive Breast Cancer: An Argument for Local Therapy

Purpose Despite advances in endocrine therapy (ET), metastatic estrogen receptor positive breast cancer (BrCA) remains incurable. Though the mechanisms of resistance to ET have been studied extensively, the anatomic pattern of disease progression remains poorly characterized. The purpose of this study was to characterize the pattern of progression for patients receiving ET for metastatic BrCA. Methods The records of 108 patients with metastatic BrCA who progressed on ET were reviewed. Progression was characterized as follows: diffuse progression, progression in greater than 3 sites; oligoprogression, progression in fewer than 3 sites with prior diffuse metastases; and oligometastatic disease with progression, progression in 3 or fewer sites with prior limited metastases. Results Seventy-four patients (69%) displayed only diffuse disease progression. Conversely, 23 patients (21%) displayed oligoprogression and 11 patients (10%) displayed oligometastases with progression at least once in their disease course. Further analysis of the patients with oligoprogression suggested that in 14 patients the sites of progression would have been amenable to local therapy. Conclusion Oligoprogressive disease occurs in a significant subset of patients with metastatic BrCA treated with ET. These patients with oligoprogressive disease may be eligible for local therapy, potentially obviating the need to change of systemic therapy.
Late vascular response at the edges of sirolimus analogous‐eluting stents in diabetic patients: An intravascular ultrasound study

Introduction: Vascular response at edges of drug‐eluting stents is still not well established, particularly in diabetic patients who are prone to aggressive atherosclerosis progression. Recently, Biolimus and Zotarolimus have demonstrated potent antiproliferative effects. Objective: To compare the vascular responses at edges of sirolimus analogous‐eluting stents in patients with and without diabetes, using intravascular ultrasound (IVUS). Methods: 306 edges were analyzed in 153 patients treated with drug‐eluting stents and divided in: diabetics (122 edges) and nondiabetics (166 edges). IVUS was performed postintervention and at 6‐month follow‐up and included 5 mm distal and proximal to the stented segment. Vessel, lumen, and plaque volumes were calculated. Volume variation (follow‐up minus basal) was also calculated. Edge restenosis was defined as obstruction >50%. Results: Baseline characteristics were similar between groups. In both groups the entire lesion length was covered (stent length/lesion length ratio was 1.5 for both groups). There were no differences in edge volumes and restenosis rate between the groups. Among diabetics, there was no significant volume variation. However, in nondiabetic patients there was significant increase in vessel volume in proximal (from 67.1 ± 22 mm3 to 72.2 ± 25 mm3: P = 0.02) and distal (from 54.4 ± 22 mm3 to 59.8 ± 22 mm3: P = 0.001) edges. Conclusion: Nondiabetic patients showed a significant positive vascular remodeling in proximal and distal edges of sirolimus analogous‐eluting stent. This vascular mechanism was not observed in diabetic patients. Although different vascular responses were observed, restenosis rates were equivalent between the 2 groups at 6‐month follow‐up. © 2007 Wiley‐Liss, Inc.
Isometric knee-extensor torque development and jump height in volleyball players.

PURPOSE The goal of the present study was to determine the contribution of the intrinsic muscle properties and muscle activation of the knee extensors to the maximal rate of unilateral isometric torque development and to relate both factors to maximal bilateral jumping performance in experienced jumpers. On the basis of previous studies, we hypothesized that maximal rate of torque development during maximal effort isometric contractions and jump height would depend on the subjects' ability for maximal muscle activation rather than on the muscle's contractile properties. METHODS Eleven male elite volleyball players (20 +/- 2 yr, means +/- SD) performed squat jumps starting from a 120 degrees knee angle (SJ120; full extension = 180 degrees ) and countermovement jumps. In addition, maximal voluntary and electrically evoked unilateral isometric knee-extension torque development (120 degrees angle) was obtained. Torque time integral for the first 40 ms after torque onset (TTI40) and (time to) maximal rate of torque development (MRTD) were calculated. Muscle activation was quantified using surface EMG. RESULTS Voluntary TTI40 was significantly related to the preceding EMG (r2 = 0.83) and negatively related to the time to MRTD (r2 = 0.64). Voluntary MRTD and TTI40 were not related to their respective values obtained during electrical stimulation (r2 < 0.04). Only electrically evoked MRTD was significantly related to jump height (e.g., r2 = 0.70 for SJ120). CONCLUSIONS As expected initial maximal voluntary isometric torque development correlated with muscle activation and not with muscle contractile speed. However, unexpectedly, only the latter could predict jump performance in skilled jumpers.
Assessing CIAN as modeling language of collaborative learning activities

Learning Design (LD) involves the specification of learning/teaching activities. Therefore there are several standards and modeling languages and highlighted between them is the IMS Learning Design (IMS-LD) standard. However, the use of higher level abstraction notations can significantly facilitate the creation of these designs. In particular, our interest is centered around the modeling of group learning activities, for which the current standards present some limitations. In this paper we will identify the main features to consider for modeling collaborative tasks, and we propose the use of the CIAN notation for this purpose. Finally, we will give detailed explanations of experiments to assess the quality/validity of that notation, and its acceptance by the designers of CSCL systems.
Morphological and molecular characterization of selected species of Hysterothylacium (Nematoda: Raphidascarididae) from marine fish in Iraqi waters

Abstract Hysterothylacium species are perhaps the most abundant and diverse group of marine ascaridoids; however, their life cycle and specific identification in larval stages in many parts of the world, particularly in Iraqi marine waters, have not been completely understood. In this study three members of the genus Hysterothylacium collected from Khor Abdulla in Iraq are morphologically described, genetically characterized and their relationship with other closely related taxa are compared and discussed. A new Hysterothylacium larval type in the fourth stage of development is described, and morphological and molecular evidence (based on the sequences of internal transcribed spacers) are provided for its distinction from previously known fourth-stage Hysterothylacium larval types. Based on the sequence data it is suggested that the new larval type, which herein was assigned as Hysterothylacium larval type XVI, is H. persicum which was previously reported from the close proximity in Bandar Abbas, Iran. In addition, two other taxa, including Hysterothylacium larval type XV and H. reliquens, have been found in the present study, for which new hosts are reported. This study provides some insights into the taxonomy and systematics of these parasites, not only in this region but also for similar studies elsewhere.
Extracellular fibrils and contact-mediated cell interactions in Myxococcus xanthus

Contact-mediated cell-cell interactions play an important role in the social life-style of Myxococcus xanthus. Previous investigations have demonstrated that fimbriae (also referred to as pili) and extracellular fibrils are involved in these social interactions (L. J. Shimkets, Microbiol. Rev. 54:473-501, 1990). We have used the relatively new technique of low-voltage scanning electron microscopy (an ultra-high-resolution scanning technique that allows for the nanometer resolution of biological materials) to observe the topological details of cell-cell interactions in M. xanthus. Our observations indicated that the fibrils (which measure approximately 30 nm in diameter) are produced most extensively by cells that are in close contact with each other and are aberrantly produced by the cohesion-deficient dsp mutants. Immunogold analysis identified an antigen which is located exclusively on the extracellular fibrils. Western blots (immunoblots) of this antigen (designated FA-1 for fibrillar antigen 1) indicated that it is composed of several immunoreactive bands (molecular size range, 90 to 14 kDa), all of which are sensitive to protease digestion. A technique for fibril isolation was developed by using FA-1 as a fibril-specific marker. Low-voltage scanning electron microscope observations of swarming cells demonstrated that the expression of fibrils is differentially regulated between adventurous (individual) and socially (group) motile cells. The differential expression of fibrils suggests the existence of a mechanism for the regulation of fibril biosynthesis that functions within the overall system governing social interactions in M. xanthus.
Five common gene variants identify elevated genetic risk for coronary heart disease

Purpose: Because multiple genetic variants influence risk for coronary heart disease, we combined multiple variants that had been associated with coronary heart disease in several studies into a genetic risk score and asked whether a high genetic risk score would be significantly associated with coronary heart disease after accounting for traditional risk factors.Methods: We considered five variants that were associated with coronary heart disease in two studies and confirmed in the Atherosclerosis Risk in Communities study: rs20455 (KIF6), rs3900940 (MYH15), rs7439293 (PALLD), rs2298566 (SNX19), and rs1010 (VAMP8). We calculated a genetic risk score for each Atherosclerosis Risk in Communities study participant and estimated the hazard ratio for incident coronary heart disease of a high genetic risk score (compared with not-high) in Cox models that adjusted for traditional risk factors during a median of 13 years of follow-up.Results: For white participants with a high genetic risk score (4% of the 9129 whites), compared with those without a high genetic risk score, the hazard ratio for incident coronary heart disease was 1.57 (95% confidence interval 1.21–2.04; P = 0.001). Internal validation using bootstrap samples estimated that a hazard ratio of 1.43 could be expected in external populations.Conclusions: After adjusting for traditional risk factors, those with a high genetic risk score had a 57% increased risk of incident coronary heart disease in the Atherosclerosis Risk in Communities study.
Forecasting Unemployment with Google Searches

Data on Google searches help predict the unemployment rate in the U.S. But the predictive power of Google searches is limited to short-term predictions, the value of Google data for forecasting purposes is episodic, and the improvements in forecasting accuracy are only modest. The results, obtained by (pseudo) out-of-sample forecast comparison, are robust to a state-level fixed effects model and to different search terms. Joint analysis by cross-correlation function and Granger non-causality tests verifies that Google searches anticipate the unemployment rate. The results illustrate both the potentials and limitations of using big data to predict economic indicators.
Index-based Online Text Classification for SMS Spam Filtering

We proposed a novel index-based online text classification method, investigated two index models, and compared the performances of various index granularities for English and Chinese SMS message. Based on the proposed method, six individual classifiers were implemented according to various text features of Chinese message, which were further combined to form an ensemble classifier. The experimental results from English corpus show that the relevant feature among words can increase the classification confidence and the trigram co-occurrence feature of words is an appropriate relevant feature. The experimental results from real Chinese corpus show that the performance of classifier applying word-level index model is better than the one applying document-level index model. The trigram segment outperforms the exact segment in indexing, so it is not necessary to segment Chinese text exactly when indexing by our proposed method. Applying parallel multi-thread ensemble learning, our proposed method has constant time complexity, which is critical to large scale data and online filtering.
Suppressed sidewall injection magnetotransistor with focused emitter injection and carrier double deflection

We present a new linear magnetic field sensor (MFS) made in standard CMOS technology with a sensitivity of 1.26 percent/mT (1 percent/T ≡ 0.01 T-1). The device is a dual-collector lateral magneto-transistor (LMT) with suppressed injection of the emitter sidewalls, confinement of the injection to the center bottom of the emitter-base junction, and double deflection of carriers. Desirable collector current levels can be set without major loss of sensitivity by choosing from a wide range of operating points.
The influence of the geometry of the porcine cornea on the biomechanical response of inflation tests

To withstand the high probability of success, the growing diffusion of laser surgery for the correction of visual defects, corneal surgeons are regarding with interest numerical tools able to provide reliable predictions of the intervention outcomes. The main obstacle to the definition of a predictive numerical instrument is the objective difficulty in evaluating the in vivo mechanical properties of the human cornea. In this study, we assess the ability of a parametrised numerical model of the cornea (Pandolfi and Manganiello 2006) to describe individual pressurisation tests on whole porcine corneas once the mechanical parameters of the model have been calibrated over average data. We also aim at estimating the sensitivity of the mechanical response with the variation of basic geometrical parameters, such as the central corneal thickness, the curvature and the in-plane diameter. We conclude that the actual geometry of a cornea has a minor role in the overall mechanical response, and therefore the material properties must be considered carefully and individually in any numerical application. This study makes use of the data obtained from a wide experimental program, where a set of 21 porcine corneas has been fully characterised in terms of mechanical and geometrical properties (Boschetti et al. 2012).
Reduction of CMP /spl mu/-scratch induced metal shorts by introduction of a post CMP tungsten plasma clean process in a high volume DRAM manufacturing environment

A common problem of tungsten CMP processes used in damascene sequences is the generation of /spl mu/-scratches. These scratches form small trenches in the oxide, which are filled with tungsten during the CMP process. These metal filled trenches can short the intended patterned circuitry. By introduction of a dry plasma clean after the tungsten CMP process, the yield impact of these scratches can be reduced or eliminated: The plasma etch process removes tungsten uniformly both from the intended metal pattern and the unintended metal residue in the scratch trench. The metal short can be eliminated by adjusting the etch depth to the actual scratch depth.