Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete mitochondrial genome of Gekko swinhonis (Squamata, Gekkonidae)

The complete mitochondrial genome sequence of Gekko swinhonis was determined in this paper. The genome was 16,818 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (CR). The gene composition and order of G. swinhonis were similar to most other squamate reptiles. The overall base composition of the genome in descending order was 31.35% A, 27. 71% C, 26.28% T, and 14.67% G, with a slight AT bias of 57.62%. CR is located between the tRNA-Pro and tRNA-Phe genes and is 1456 bp in length; some tandem repeat sequences and conserved elements (TAS, CSB1–3) were found in the CR.
Sublinear summation of afferent inputs to the nucleus accumbens in the awake rat

The mechanisms by which the nucleus accumbens integrates afferent input from limbic and cortical structures have been influential in the development of models of psychiatric disorders such as schizophrenia. Previous studies of the response of nucleus accumbens (Nacb) cells to the stimulation of afferent inputs from hippocampus (HC) and prefrontal cortex (PFC) have demonstrated that PFC throughput can be modulated by preceding HC input. Examination of the post‐synaptic potential size has suggested, however, that summation of these inputs is sublinear. All studies to date examining Nacb integration of inputs via stimulation of afferents have been performed in the anaesthetized rat. The present experiments compare the response of Nacb cells to different combinations of PFC and HC stimulation in awake and isoflurane‐anaesthetized rats that were chronically implanted with both stimulating and recording electrodes. The results of these experiments suggest that summation of afferent input in the Nacb of the awake rat is predominantly sublinear, with only a minority of neurons demonstrating modulation of PFC inputs by the HC in the awake or the anaesthetized animal. The response profile of many cells changed during anaesthesia when compared to the awake condition, and on average showed suppression to PFC input 50 and 150 ms following HC stimulation while under deep isoflurane anaesthesia. These results suggest that sublinear integration of afferent input from the PFC and HC is the dominant mode of integration of Nacb cells in the awake animal, which has implications for corticostriatal models of psychiatric dysfunction.
Leveraging Multiple Features for Image Retrieval and Matching

Research Scientist at eBay Inc., San Jose, CA 04/2016 – 12/2018 • Key contributor of visual search deployed in eBay Shopbot and Close5 that increased CTR by 100% • Led research on fine-grained image recognition and object detection using deep neural networks • Implemented and deployed production services on Google Cloud to support billions of listings on eBay • Mentored interns to work on real-time visual saliency detection and generative adversarial networks
Design of a Fuzzy Compensator for Balancing Control of a One-wheel Robot

For the balancing control of a one-wheel mobile robot, CMG (Control Moment Gyro) can be used as a gyroscopic actuator. Balancing control has to be done in the roll angle direction by an induced gyroscopic motion. Since the dedicated CMG cannot produce the rolling motion of the body directly, the yawing motion with the help of the frictional reaction can be used. The dynamic uncertainties including the chattering of the control input, disturbances, and vibration during the flipping control of the high rotating flywheel, however, cause ill effect on the balancing performance and even lead to the instability of the system. Fuzzy compensation is introduced as an auxiliary control method to prevent the robot from the failure due to leaning aside of the flywheel. Simulation studies are conducted to see the feasibility of the proposed control method. In addition, experimental studies are conducted for the verification of the proposed control.
Feasibility of MRI-guided hyperthermia treatment of head and neck cancer

Clinical studies have established a strong benefit from adjuvant mild hyperthermia to radio- and chemotherapy for many tumor sites, including the head and neck. The recently developed HYPERcollar allows applying local radiofrequency hyperthermia to tumors in the entire head and neck. Treatment quality is optimized using a combination of electromagnetic and temperature simulators and assessed using invasively placed thermometers. To replace the current invasive thermometry, we are investigating if magnetic resonance (MR) measurements can be exploited for continuous and 3D thermal dose assessment during treatment. In this study, we designed an MR compatible laboratory prototype applicator. We showed that the laboratory prototype applicator, based on re-designed patch antennas, enables MR guided focused heating and allows effective mitigating of image distortion. Hence, we conclude that hybrid MR-hyperthermia treatment in the head and neck region is feasible. The novel hybrid laboratory prototype further allows thorough investigation of patient and systems induced imaging distortions in preparation of the design of a clinical applicator.
Invariant Gender Identification

Abstract Tolba, A. S. , Invariant Gender Identification, Digital Signal Processing11 (2001) 222–240 In this paper, we address the problem of gender identification using different neural network classifiers: a learning vector quantization (LVQ) network and a radial basis function (RBF) network. Our results indicate that it is more favorable to use either the LVQ network or the RBF network than any feature-based methods. We present results showing identification of gender with a hit rate of 100% in the case of a LVQ network and 98.04% in the case of an RBF network. When hair information was excluded, the best LVQ classifier resulted in 95.1% correct identification. We show that while the two models are nearly accurate, the RBF model learns the task considerably faster than the LVQ model. These results are favorable compared with eigen-decomposition-based techniques. The effect of head covers (e.g., a scarf) used by both men and women on system performance is studied.
A convex multi-view low-rank sparse regression for feature selection and clustering

Many real-world problems involve multi-view high-dimension-small-sample-size data analysis, such as multi-omics data. The combination of multi-view databases is supposed to provide a better biological significance. However, the multi-view data always contain noise and outlying entries that result in inaccurate and unreliable. It has become an urgent need how to effectively analyze these data. We proposed a novel convex multi-view low-rank sparse regression (CMLSR) algorithm to do cluster and feature selection. The model was constructed by imposing L2,1-norm and trace norm constraints on the regularization functions. It can diminish the impact of noises and outliers and produce more precise results. Clustering quality was determined by both sparse constraint and low-rank constraint. Finally, we selected characteristic genes based on the projection matrix. The method was used in TCGA multi-view genes expression data sets, annotated according to Gene Ontology (GO). In this paper, we demonstrated the effectiveness of the proposed algorithm through comparing it with the existing methods.
Application of Kalman filters to the control of independent power electronic voltage sources

Power electronic independent voltage sources are used i.a. in electroacoustics and different special spheres; as systems realizing eg. the optimal control of electric drives, and also as executive blocks in active compensation systems. In the paper we discuss possibility of realization of a broadband power electronic voltage source with application of Kalman filter and basic quantities describing the working system. Selected simulation results of the independent voltage source for different reference signals are also included.
In Vitro Activity of BAY 12-8039, a New Fluoroquinolone, against Mycoplasmas

ABSTRACT The in vitro activity of the fluoroquinolone BAY 12-8039 against 66 strains of different mycoplasma species and 30 strains ofUreaplasma urealyticum was compared with those of three other antimicrobial agents. BAY 12-8039 at 0.5 μg/ml inhibited 100% of all the mycoplasmal and ureaplasmal strains tested. The minimal bactericidal concentrations of BAY 12-8039 increased only two- to eightfold compared to the MICs. Furthermore, they were comparable to those of sparfloxacin and lower than those of doxycycline and clarithromycin.
Formulating Enhancement and Restoration Strategy to Improve the Quality of Dusty Images

Analyses of images acquired in dusty environments show that the images tend to have noise, blur, a small dynamic range, low contrast, diminished blue components, and high red components. The goals of this paper are to develop a modeling of dust noise on ordinary images and formulating enhancement and restoration strategy to improve the quality of dusty images using a sequence of image processing steps. This paper proposes that the dust noise model on ordinary images consisting of the atmospheric turbulence-blurring model, adjusting image brightness, and simulating real dust images colors contrasts. In addition, an automatic color correction algorithm consisting of image restoration using the Wiener filter, luminance stretching using YCbCr color model, and enhancing the image contrast using a modified homomorphic filter. Enhancement experiments are conducted on real and simulated dusty images and it is shown that the strategy is quite effective in enhancing dusty images. Furthermore the results are superior to those obtained through, a statistical adaptive algorithm, histogram equalization, gray world, and white patch algorithms. In addition, the complexity of the proposed algorithm is very low thus making it attractive for real time-image processing.
Inhibition of influenza virus uncoating by rimantadine hydrochloride

In freeze-thaw lysates of MDCK cells infected with 32P-labeled influenza virus A/WSN in the presence of added RNase, acid-precipitable radioactivity diminished to about 50% of initial values within 90 min after a 1-h virus adsorption period. A similar preparation containing rimantadine at a concentration of 50 micrograms/ml exhibited only a 10% reduction in acid-precipitable radioactivity. These findings suggest that rimantadine interferes with uncoating of influenza virus in infected cells.
Flow-Induced Dilation of Human Coronary Arterioles

Background—Flow-induced vasodilation (FID) is a physiological mechanism for regulating coronary flow and is mediated largely by nitric oxide (NO) in animals. Because hyperpolarizing mechanisms may play a greater role than NO in the microcirculation, we hypothesized that hyperpolarization contributes importantly to FID of human coronary arterioles. Methods and Results —Arterioles from atria or ventricles were cannulated for videomicroscopy. Membrane potential of vascular smooth muscle cells (VSMCs) was measured simultaneously. After constriction with endothelin-1, increases in flow induced an endothelium-dependent vasodilation. Nv-Nitro-L-arginine methyl ester 10 24 mol/L modestly impaired FID of arterioles from patients without coronary artery disease (CAD), whereas no inhibition was seen in arterioles from patients with CAD. Indomethacin 10 25 mol/L was without effect, but 40 mmol/L KCl attenuated maximal FID. Tetraethylammonium 10 23 mol/L but not glibenclamide 10 26 mol/L reduced FID. Charybdotoxin 10 28
A Nucleolar PUF RNA-binding Protein with Specificity for a Unique RNA Sequence*

PUF proteins are a conserved group of sequence specific RNA-binding proteins that bind to RNA in a modular fashion. The RNA-binding domain of PUF proteins typically consists of eight clustered Puf repeats. Plant genomes code for large families of PUF proteins that show significant variability in their predicted Puf repeat number, organization, and amino acid sequence. Here we sought to determine whether the observed variability in the RNA-binding domains of four plant PUFs results in a preference for nonclassical PUF RNA target sequences. We report the identification of a novel RNA binding sequence for a nucleolar Arabidopsis PUF protein that contains an atypical RNA-binding domain. The Arabidopsis PUM23 (APUM23) binding sequence was 10 nucleotides in length, contained a centrally located UUGA core element, and had a preferred cytosine at nucleotide position 8. These RNA sequence characteristics differ from those of other PUF proteins, because all natural PUFs studied to date bind to RNAs that contain a conserved UGU sequence at their 5′ end and lack specificity for cytosine. Gel mobility shift assays validated the identity of the APUM23 binding sequence and supported the location of 3 of the 10 predicted Puf repeats in APUM23, including the cytosine-binding repeat. The preferred 10-nucleotide sequence bound by APUM23 is present within the 18S rRNA sequence, supporting the known role of APUM23 in 18S rRNA maturation. This work also reveals that APUM23, an ortholog of yeast Nop9, could provide an advanced structural backbone for Puf repeat engineering and target-specific regulation of cellular RNAs.
Benign multiple sclerosis? Clinical course, long term follow up, and assessment of prognostic factors

OBJECTIVE To establish the characteristics of patients following a benign course of multiple sclerosis and evaluate the importance of potential prognostic factors. Also, an assessment of the value of the Kurtzke EDSS as a prognostic indicator has been undertaken in patients previously determined to have benign multiple sclerosis, after 10 years of follow up. METHODS A prevalence study in the Coleraine, Ballymena, Ballymoney, and Moyle districts of Northern Ireland used the Kurtzke expanded disability scale score (EDSS) in 259 patients with multiple sclerosis. Of these, 181 had had multiple sclerosis for⩾10 years, 36 having benign disease (EDSS⩽3.0) ⩾10 years after onset. Clinical and demographic details of the various patient groups, including the minimal record of disability, were compared. The 1987 study in Northern Ireland identified 33 patients with benign multiple sclerosis. Twenty eight were available for follow up in 1996 along with 42 contemporary non-benign patients. RESULTS Patients with benign multiple sclerosis were predominantly women (ratio 4.1:1 v 2.1:1) and younger at onset (25.8 v 31.2 years). Commonest symptoms at onset were sensory and optic neuritis (33.3% each). Patients with late onset (older than 40 years) were less likely to have a benign course, more likely to have a progressive course from onset, significantly more likely to have motor disturbance at presentation, and had a lesser female predominance. Optic neuritis was significantly more common in those with a younger age at onset. In the follow up study, patients with benign multiple sclerosis continued to have a more favourable course than non-benign counterparts but progression of disability and to the secondary progressive phase remained significant. CONCLUSIONS The association of female sex, early onset, and presentation with optic neuritis and sensory symptoms with a favourable course is confirmed. However, although the EDSS does provide a useful indicator of prognosis, the label “benign multiple sclerosis” is often temporary as apparently benign disease often becomes disabling.
Metasilicone: design and fabrication of composite silicone with desired mechanical properties

We present a method for designing and fabricating MetaSilicones---composite silicone rubbers that exhibit desired macroscopic mechanical properties. The underlying principle of our approach is to inject spherical inclusions of a liquid dopant material into a silicone matrix material. By varying the number, size, and locations of these inclusions as well as their material, a broad range of mechanical properties can be achieved. The technical core of our approach is formed by an optimization algorithm that, combining a simulation model based on extended finite elements (XFEM) and sensitivity analysis, computes inclusion distributions that lead to desired stiffness properties on the macroscopic level. We explore the design space of MetaSilicone on an extensive set of simulation experiments involving materials with optimized uni- and bi-directional stiffness, spatially-graded properties, as well as multi-material composites. We present validation through standard measurements on physical prototypes, which we fabricate on a modified filament-based 3D printer, thus combining the advantages of digital fabrication with the mechanical performance of silicone elastomers.
Therapeutic Hypothermia and the Risk of Infection: A Systematic Review and Meta-Analysis*

Objective:Observational studies suggest that infections are a common complication of therapeutic hypothermia. We performed a systematic review and meta-analysis of randomized trials to examine the risk of infections in patients treated with hypothermia. Data Sources:PubMed, Embase, and the Cochrane Central Register of Controlled Trials were systematically searched for eligible studies up to October 1, 2012. Study Selection:We included randomized controlled clinical trials of therapeutic hypothermia induced in adults for any indication, which reported the prevalence of infection in each treatment group. Data Extraction:For each study, we collected information about the baseline characteristics of patients, cooling strategy, and infections. Data Synthesis:Twenty-three studies were identified, which included 2,820 patients, of whom 1,398 (49.6%) were randomized to hypothermia. Data from another 31 randomized trials, involving 4,004 patients, could not be included because the occurrence of infection was not reported with sufficient detail or not at all. The risk of bias in the included studies was high because information on the method of randomization and definitions of infections lacked in most cases, and assessment of infections was not blinded. In patients treated with hypothermia, the prevalence of all infections was not increased (rate ratio, 1.21 [95% CI, 0.95–1.54]), but there was an increased risk of pneumonia and sepsis (risk ratios, 1.44 [95% CI, 1.10–1.90]; 1.80 [95% CI, 1.04–3.10], respectively). Conclusion:The available evidence, subject to its limitations, strongly suggests an association between therapeutic hypothermia and the risk of pneumonia and sepsis, whereas no increase in the overall risk of infection was observed. All future randomized trials of hypothermia should report on this important complication.
Enhanced biofilm formation and melanin synthesis by the oyster settlement-promoting Shewanella colwelliana is related to hydrophobic surface and simulated intertidal environment

A direct relationship between biofilm formation and melanogenesis in Shewanella colwelliana with increased oyster recruitment is already established. Previously, S. colwelliana was grown in a newly patented biofilm-cultivation device, the conico-cylindrical flask (CCF), offering interchangeable hydrophobic/hydrophilic surfaces. Melanization was enhanced when S. colwelliana was cultivated in a hydrophobic vessel compared with a hydrophilic vessel. In the present study, melanogenesis in the CCF was positively correlated with increased architectural parameters of the biofilm (mean thickness and biovolume obtained by confocal laser scanning microscopy) and melanin gene (melA) expression observed by densitometry. Niche intertidal conditions were mimicked in a process operated in an ultra-low-speed rotating disk bioreactor, which demonstrated enhanced biofilm formation, melanogenesis, exopolysaccharide synthesis and melA gene expression compared with a process where 12-h periodic immersion and emersion was prevented. The wettability properties of the settling plane as well as intermittent wetting and drying, which influenced biofilm formation and melA expression, may affect oyster settlement in nature.
Yue Zhang and Qian Chen BASIS OF OLIGOMERIC ASSEMBLY Changes of Matrilin Forms during Endochondral Ossification : MOLECULAR

To understand the molecular properties of matrilin-3, a newly discovered member of the novel extracellular matrix protein family, we cloned a MAT-3 cDNA from developing chicken sterna. Real time quantitative reverse-transcription polymerase chain reaction indicates that MAT-3 mRNA is mainly expressed in the proliferation zone of a growth plate. It is also expressed in the maturation zone, overlapping with that of the mature chondrocyte-abundant matrilin-1 mRNA. This suggests that matrilin-3 may self-assemble in the proliferation zone, in addition to its co-assembly with matrilin-1 during endochondral ossification. Transfection of a MAT-3 cDNA into COS-7 cells shows that MAT-3 predominantly forms a homotetramer but also a trimer and a dimer. Co-transfection of both MAT-3 and MAT-1 cDNAs results in three major matrilins as follows: (MAT-1)3, (MAT-3)4, and (MAT-1)2(MAT-3)2. Thus matrilin-3 may assemble into both homotypic and heterotypic oligomers. Our analysis shows that the assembly of MAT-3 does not depend on the number of epidermal growth factor repeats within the molecule, but the presence of Cys and Cys within the coiled-coil domain, which form covalent disulfide linkage responsible for both homooligomerization of MAT-3 and hetero-oligomerization of MAT-3 and MAT-1. Our data suggest that the varying synthetic levels of matrilins in different zones of a growth plate may result in a change of matrilin oligomeric forms during endochondral ossification.
Nocardia puris endophthalmitis.

Emphasis must also be given on voluntary risk reductions, which will require increased awareness and change in attitude of people. Voluntary blood donations have to be made a part of a healthy lifestyle. Enlightening people about the benefits of voluntary blood donations and making it important for appraisals, admissions and employment can overcome this problem. All this, however, requires strong political commitment and multisectorial engagement.
Characterization and prevalence of Solobacterium moorei associated with oral halitosis

Previous studies suggest that Solobacterium moorei is associated with oral halitosis. In the present study, we examined the prevalence of S. moorei on the dorsal surface of the tongue in 57 adults (21 with and 36 without halitosis) by bacterial culture and direct amplification of nucleic acids. We also examined the S. moorei type strain and four clinical isolates for 16S ribosomal nucleic acid sequence, H2S and enzyme production, and antibiotic susceptibility. S. moorei was found on the dorsal surface of the tongue in 100% of the subjects with halitosis and 14% of subjects without halitosis. Infection with S. moorei was correlated with organoleptic measures of halitosis and with volatile sulfur compound levels. Nucleic acid probe detection of S. moorei as a test for halitosis exhibited 100% sensitivity and 86% specificity. The S. moorei type strain and all four clinical isolates showed >98% 16S rDNA sequence similarity, produced H2S, demonstrated acid phosphatase, beta-galactosidase, alpha-glucosidase, esterase, leucine arylamidase and naphthol phosphohydrolase enzyme activities, and were sensitive to all antibiotics tested except gentamicin, kanamycin, nalidixic acid and rifampin. This study supports the hypothesis that S. moorei is associated with halitosis.