Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementation of an LED-based clinical spatial frequency domain imaging system

Spatial Frequency Domain Imaging (SFDI) is a non-contact imaging method that uses multiple frequency spatial illumination to generate two dimensional maps of tissue optical properties (absorption and reduced scattering) and chromophore concentrations. We present phantom validation and pilot clinical data of a deployed light-emitting diode (LED) based system. The system employs four LED wavelengths (658 nm, 730 nm, 850 nm, 970 nm) to quantitatively assess tissue health by measurement of common tissue constituents. Phantom validation results and maps of oxyhemoglobin, deoxy-hemoglobin, water content, reduced scattering, and surface topography will be presented for pilot studies assessing burn severity and efficacy of port wine stain treatment.
Studies on structural changes of the carotid arteries and the heart in asymptomatic renal transplant recipients.

BACKGROUND The present study was designed to characterize early structural changes of large arteries in renal transplant recipients with no clinical evidence of cardiovascular disease and normal blood pressure values, and to analyse the relationship between arterial alterations and those of the heart. METHODS Intima media thickness and atherosclerotic plaques of the carotid arteries as well as left ventricular geometry and function were examined in 35 asymtomatic renal transplant recipients and 29 age- and sex-matched healthy controls by high resolution B-mode ultrasound and by echocardiography. RESULTS Intima-media thickness of the carotid arteries was significantly higher in renal transplant recipients (1.21+/-0.08 mm) than in healthy controls (0.74+/-0.04 mm) (P<0.001). Atherosclerotic plaques were found in the majority of renal transplant recipients (71% vs 14% in healthy controls, P<0.001). Left ventricular mass index was significantly increased in the group of renal transplant recipients (264+/-13 g, 146+/-7 g/m2) when compared with healthy controls (155+/-8 g, 83+/-4 g/m2) (P<0.001). Multiple regression analysis in renal transplant recipients showed that intima media thickness of the carotid arteries was significantly related to left ventricular mass index (P<0.02), but not to age, blood pressure, body mass index, serum creatinine, cholesterol and lipoprotein (a) levels. In the group of healthy controls, intima-media thickness of the carotid artery was related to age (P<0.002), but not to left ventricular mass index or the other independent variables. CONCLUSIONS The present study documents pronounced intima-media thickening in asymptomatic renal transplant recipients. Atherosclerotic lesions are present in most renal transplant recipients with no clinical evidence of cardiovascular disease. We observed a parallelism between arterial wall thickening and left ventricular hypertrophy, although blood pressure levels were normal during haemodialysis therapy and after renal transplantation.
Interactive Image Segmentation using Color and Texture Features

Image segmentation is the process of selecting objects of interest in background images. Since the fully automatic segmentation is difficult for natural images due to the complex color and texture features. This paper presents the idea of image segmentation using maximum similarity based region merging with minimum user inputs using simple brush strokes called markers(object and background markers). Therefore, the proposed system presents a new region merging method that grow regions from foreground/background seeds based on the color and texture features for interactive image segmentation. An initial segmentation is required to partition the image into homogeneous regions for merging. After the completion of the initial segmentation, initial segmented regions are represented by means of some descriptors such as color and texture to guide the region merging process. Therefore, the proposed method is very effective and it can quickly and accurately segment a wide variety of natural images with ease.
Clinical validation of three short forms of the Dutch Wechsler Memory Scale–Fourth Edition (WMS-IV-NL) in a mixed clinical sample

The reliability and validity of three short forms of the Dutch version of the Wechsler Memory Scale–Fourth Edition (WMS-IV-NL) were evaluated in a mixed clinical sample of 235 patients. The short forms were based on the WMS-IV Flexible Approach, that is, a 3-subtest combination (Older Adult Battery for Adults) and two 2-subtest combinations (Logical Memory and Visual Reproduction and Logical Memory and Designs), which can be used to estimate the Immediate, Delayed, Auditory and Visual Memory Indices. All short forms showed good reliability coefficients. As expected, for adults (16-69 years old) the 3-subtest short form was consistently more accurate (predictive accuracy ranged from 73% to 100%) than both 2-subtest short forms (range = 61%-80%). Furthermore, for older adults (65-90 years old), the predictive accuracy of the 2-subtest short form ranged from 75% to 100%. These results suggest that caution is warranted when using the WMS-IV-NL Flexible Approach short forms to estimate all four indices.
Depressive Symptom Trajectories, Aging-Related Stress, and Sexual Minority Stress Among Midlife and Older Gay Men

We concatenate 28 years of historical depressive symptoms data from a longitudinal cohort study of U.S. gay men who are now midlife and older (n = 312), with newly collected survey data to analyze trajectories of depressive symptomatology over time and their impact on associations between current stress and depressive symptoms. Symptoms are high over time, on average, and follow multiple trajectories. Aging-related stress, persistent life-course sexual minority stress, and increasing sexual minority stress are positively associated with depressive symptoms, net of symptom trajectories. Men who had experienced elevated and increasing trajectories of depressive symptoms are less susceptible to the damaging effects of aging-related stress than those who experienced a decrease in symptoms over time. Intervention efforts aimed at assisting gay men as they age should take into account life-course depressive symptom histories to appropriately contextualize the health effects of current social stressors.
Speed Control of Induction Motor using Fuzzy Rule Base

induction motors are characterized by complex, highly non- linear and time-varying dynamics, and hence their speed control is a challenging engineering problem. The advent of vector control techniques has partially solved induction motor control problems, but they are sensitive to drive parameter variations and performance may deteriorate if conventional controllers are used. By exploiting the fuzzy logic structure of the controller, heuristic knowledge is incorporated into the design, resulting in a non-linear controller with improved large signal performance over linear PI controllers. This paper proposes a novel design procedure for speed control of induction motor using fuzzy logic controller (FLC). The input to the controller is error and change in error and output of the controller is torque producing component of current, applied for the speed control of an induction motor. The effectiveness of the controller is demonstrated on the 1 hp three phase induction motor using DSP 2407 for different operating conditions of the drive system.
A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

Background & Methods The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospital and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. Results The pipeline generated sequences of at least 1Kb of length (median=7.4Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n=149, 40.8%) and C (n=77, 21.1%) and the circulating recombinant form CRF02_AG (n=32, 8.8%). We found 14 different CRFs (n=66, 18.1%) and multiple URFs (n=32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. Conclusions The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
Lack of Laminin γ1 in Embryonic Stem Cell‐Derived Cardiomyocytes Causes Inhomogeneous Electrical Spreading Despite Intact Differentiation and Function

Laminins form a large family of extracellular matrix (ECM) proteins, and their expression is a prerequisite for normal embryonic development. Herein we investigated the role of the laminin γ1 chain for cardiac muscle differentiation and function using cardiomyocytes derived from embryonic stem cells deficient in the LAMC1 gene. Laminin γ1 (−/−) cardiomyocytes lacked basement membranes (BM), whereas their sarcomeric organization was unaffected. Accordingly, electrical activity and hormonal regulation were found to be intact. However, the inadequate BM formation led to an increase of ECM deposits between adjacent cardiomyocytes, and this resulted in defects of the electrical signal propagation. Furthermore, we also found an increase in the number of pacemaker areas. Thus, although laminin and intact BM are not essential for cardiomyocyte development and differentiation per se, they are required for the normal deposition of matrix molecules and critical for intact electrical signal propagation. STEM CELLS 2009;27:88–99
Ferroelectric Nanoparticles in Liquid Crystals: Recent Progress and Current Challenges

The dispersion of ferroelectric nanomaterials in liquid crystals has recently emerged as a promising way for the design of advanced and tunable electro-optical materials. The goal of this paper is a broad overview of the current technology, basic physical properties, and applications of ferroelectric nanoparticle/liquid crystal colloids. By compiling a great variety of experimental data and discussing it in the framework of existing theoretical models, both scientific and technological challenges of this rapidly developing field of liquid crystal nanoscience are identified. They can be broadly categorized into the following groups: (i) the control of the size, shape, and the ferroelectricity of nanoparticles; (ii) the production of a stable and aggregate-free dispersion of relatively small (~10 nm) ferroelectric nanoparticles in liquid crystals; (iii) the selection of liquid crystal materials the most suitable for the dispersion of nanoparticles; (iv) the choice of appropriate experimental procedures and control measurements to characterize liquid crystals doped with ferroelectric nanoparticles; and (v) the development and/or modification of theoretical and computational models to account for the complexity of the system under study. Possible ways to overcome the identified challenges along with future research directions are also discussed.
Inorganic carbon and oxygen dynamics in a marsh‐dominated estuary

We conducted a free‐water mass balance‐based study to address the rate of metabolism and net carbon exchange for the tidal wetland and estuarine portion of the coastal ocean and the uncertainties associated with this approach were assessed. We measured open water diurnal O2 and dissolved inorganic carbon (DIC) dynamics seasonally in a salt marsh‐estuary in Georgia, U.S.A. with a focus on the marsh‐estuary linkage associated with tidal flooding. We observed that the overall estuarine system was a net source of CO2 to the atmosphere and coastal ocean and a net sink for oceanic and atmospheric O2. Rates of metabolism were extremely high, with respiration (43 mol m−2 yr−1) greatly exceeding gross primary production (28 mol m−2 yr−1), such that the overall system was net heterotrophic. Metabolism measured with DIC were higher than with O2, which we attribute to high rates of anaerobic respiration and reduced sulfur storage in salt marsh sediments, and we assume substantial levels of anoxygenic photosynthesis. We found gas exchange from a flooded marsh is substantial, accounting for about 28% of total O2 and CO2 air–water exchange. A significant percentage of the overall estuarine aquatic metabolism is attributable to metabolism of marsh organisms during inundation. Our study suggests not rely on oceanographic stoichiometry to convert from O2 to C based measurements when constructing C balances for the coastal ocean. We also suggest eddy covariance measurements of salt marsh net ecosystem exchange underestimate net ecosystem production as they do not account for lateral DIC exchange associated with marsh tidal inundation.
Text Line Extraction from Complex Layout Documents

are numerous stylish documents which do not have the traditional text layouts where printed text regions are not parallel to each other. Such complex layouts make text line extraction challenging due to multi-orientation of paragraphs. This paper introduces a system for the text line extraction from the complex layout documents. Proposed method is based on the concept of dilation and histogram profiling. The text regions are extracted using dilation and food fill based approach, then paragraph orientation is determined and individual text lines are extracted. The accuracy of extracted text lines are evaluated using the new proposed concept that is also based on the histogram profiling. The results of proposed approach on the complex layouts are promising.
Circa 2010 Land Cover of Canada: Local Optimization Methodology and Product Development

Land cover information is necessary for a large range of environmental applications related to climate impacts and adaption, emergency response, wildlife habitat, etc. In Canada, a 2008 user survey indicated that the most practical land cover data is provided in a nationwide 30 m spatial resolution format, with an update frequency of five years. In response to this need, the Canada Centre for Remote Sensing (CCRS) has generated a 30 m land cover map of Canada for the base year 2010, as the first of a planned series of maps to be updated every five years, or more frequently. This land cover dataset is also the Canadian contribution to the 30 m spatial resolution 2010 Land Cover Map of North America, which is produced by Mexican, American and Canadian government institutions under a collaboration called the North American Land Change Monitoring System (NALCMS). This paper describes the mapping approach used for generating this land cover dataset for Canada from Thematic Mapper (TM) and Enhanced Thematic Mapper (ETM+) Landsat sensor observations. The innovative part of the mapping approach is the local optimization of the land cover classifier, which has resulted in increased spatial consistency and accuracy. Training and classifying with locally confined reference samples over a large number of partially overlapping areas (i.e., moving windows) ensures the optimization of the classifier to a local land cover distribution, and decreases the negative effect of signature extension. A weighted combination of labels, which is determined by the classifier in overlapping windows, defines the final label for each pixel. Since the approach requires extensive computation, it has been developed and deployed using the Government of Canada’s High-Performance Computing Center (HPC). An accuracy assessment based on 2811 randomly distributed samples shows that land cover data produced with this new approach has achieved 76.60% accuracy with no marked spatial disparities.
An integrated framework for both compression noise reduction and super-resolution

Even though super-resolution is a promising technique, it can cause unwanted increase of compression noises, if it is applied to an image coded with a low bit-rate. To solve this problem, we propose an integrated framework to reduce compression noises and to recover high-frequency components of a coded low-resolution image. The framework effectively combines two patch-based algorithms, a patch-matching-based 3-D filtering algorithm and an example-based super-resolution algorithm, based on the combination of 3-D transform coefficients. Experimental results demonstrate that the proposed framework successfully improves the resolution while alleviating compression noises in the images coded with low bit-rates.
Overexpression of Zwint predicts poor prognosis and promotes the proliferation of hepatocellular carcinoma by regulating cell-cycle-related proteins

Introduction Zwint, a centromere-complex component required for the mitotic spindle checkpoint, has been reported to be overexpressed in different human cancers, but it has not been studied in human hepatocellular carcinoma (HCC). Materials and methods The role of Zwint in hepatocellular carcinoma cell proliferation capacities was evaluated by using cell counting kit-8 (CCK8), flow cytometry, clone formation and tumor formation assay in nude mice. Western blot analysis and qPCR assay were performed to assess Zwint interacting with cell-cycle-related proteins. Results We report that ZWINT mRNA and protein expression were upregulated in HCC samples and cell lines. An independent set of 106 HCC-tissue pairs and corresponding noncancerous tissues was evaluated for Zwint expression using immunohistochemistry, and elevated Zwint expression in HCC tissues was significantly correlated with clinicopathological features, such as tumor size and number. Kaplan–Meier survival and Cox regression analysis revealed that high expression of Zwint was correlated with poor overall survival and a greater tendency for tumor recurrence. Ectopic expression of Zwint promoted HCC-cell proliferation, and Zwint expression affected the expression of several cell-cycle proteins, including PCNA, cyclin B1, Cdc25C and CDK1. Conclusion Our findings suggest that upregulation of Zwint may contribute to the progression of HCC and may be a prognostic biomarker and potential therapeutic target for treating HCC.
Reconfiguration of Colorable Sets in Classes of Perfect Graphs

A set of vertices in a graph is c-colorable if the subgraph induced by the set has a proper c-coloring. In this paper, we study the problem of finding a step-by-step transformation (reconfiguration) between two c-colorable sets in the same graph. This problem generalizes the well-studied Independent Set Reconfiguration problem. As the first step toward a systematic understanding of the complexity of this general problem, we study the problem on classes of perfect graphs. We first focus on interval graphs and give a combinatorial characterization of the distance between two c-colorable sets. This gives a linear-time algorithm for finding an actual shortest reconfiguration sequence for interval graphs. Since interval graphs are exactly the graphs that are simultaneously chordal and co-comparability, we then complement the positive result by showing that even deciding reachability is PSPACE-complete for chordal graphs and for co-comparability graphs. The hardness for chordal graphs holds even for split graphs. We also consider the case where c is a fixed constant and show that in such a case the reachability problem is polynomial-time solvable for split graphs but still PSPACE-complete for co-comparability graphs. The complexity of this case for chordal graphs remains unsettled. As by-products, our positive results give the first polynomial-time solvable cases (split graphs and interval graphs) for Feedback Vertex Set Reconfiguration.
Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates

ABSTRACT The whole-genome sequences are described here for three group B Streptococcus (GBS) (S. agalactiae) serotype Ib isolates obtained from tilapia (Oreochromis niloticus) farmed at sites in Honduras, Costa Rica, and the United States. The bacteria were isolated from the brains of fish displaying signs of streptococcosis.
Nano-Immobilized Biocatalysts for Biodiesel Production from Renewable and Sustainable Resources

The cost of biodiesel production relies on feedstock cost. Edible oil is unfavorable as a biodiesel feedstock because of its expensive price. Thus, non-edible crop oil, waste oil, and microalgae oil have been considered as alternative resources. Non-edible crop oil and waste cooking oil are more suitable for enzymatic transesterification because they include a large amount of free fatty acids. Recently, enzymes have been integrated with nanomaterials as immobilization carriers. Nanomaterials can increase biocatalytic efficiency. The development of a nano-immobilized enzyme is one of the key factors for cost-effective biodiesel production. This paper presents the technology development of nanomaterials, including nanoparticles (magnetic and non-magnetic), carbon nanotubes, and nanofibers, and their application to the nano-immobilization of biocatalysts. The current status of biodiesel production using a variety of nano-immobilized lipase is also discussed.
Cross-language differences in cue use for speech segmentation.

Two artificial-language learning experiments directly compared English, French, and Dutch listeners' use of suprasegmental cues for continuous-speech segmentation. In both experiments, listeners heard unbroken sequences of consonant-vowel syllables, composed of recurring three- and four-syllable "words. " These words were demarcated by (a) no cue other than transitional probabilities induced by their recurrence, (b) a consistent left-edge cue, or (c) a consistent right-edge cue. Experiment 1 examined a vowel lengthening cue. All three listener groups benefited from this cue in right-edge position; none benefited from it in left-edge position. Experiment 2 examined a pitch-movement cue. English listeners used this cue in left-edge position, French listeners used it in right-edge position, and Dutch listeners used it in both positions. These findings are interpreted as evidence of both language-universal and language-specific effects. Final lengthening is a language-universal effect expressing a more general (non-linguistic) mechanism. Pitch movement expresses prominence which has characteristically different placements across languages: typically at right edges in French, but at left edges in English and Dutch. Finally, stress realization in English versus Dutch encourages greater attention to suprasegmental variation by Dutch than by English listeners, allowing Dutch listeners to benefit from an informative pitch-movement cue even in an uncharacteristic position.