Miracle-dz/UniFAR-FTUs huggingface dataset:
Population HIV‐1 Dynamics In Vivo: Applicable Models and Inferential Tools for Virological Data from AIDS Clinical Trials

Summary. In this paper, we introduce a novel application of hierarchical nonlinear mixed‐effect models to HIV dynamics. We show that a simple model with a sum of exponentials can give a good fit to the observed clinical data of HIV‐1 dynamics (HIV‐1 RNA copies) after initiation of potent antiviral treatments and can also be justified by a biological compartment model for the interaction between HIV and its host cells. This kind of model enjoys both biological interpretability and mathematical simplicity after reparameterization and simplification. A model simplification procedure is proposed and illustrated through examples. We interpret and justify various simplified models based on clinical data taken during different phases of viral dynamics during antiviral treatments. We suggest the hierarchical nonlinear mixed‐effect model approach for parameter estimation and other statistical inferences. In the context of an AIDS clinical trial involving patients treated with a combination of potent antiviral agents, we show how the models may be used to draw biologically relevant interpretations from repeated HIV‐1 RNA measurements and demonstrate the potential use of the models in clinical decision‐making.
Research of particle filter tracking algorithm based on structural similarity

In this paper, we address the problem of tracking a randomly moving target in the similar background. Traditional color particle filter algorithm cannot actively judge the interference created by similar background, and cause that particle filter estimate by mistakes. So we propose and implement the tracking by using structural similarity as a standard for judging tracking states. We establish unified color scale for background to extract color histogram so that we can real-time track moving target. Further we calculate the average structural similarity between the target and background, which is weighed by particles weight, to establish tracking model. The performance of the considered algorithm which is illustrated through computer simulations shows the improved color particle filter that is more effective when both the moving target and the background are very similar.
FDEVS : A GENERAL DEVS-BASED FORMALISM FOR FAULT MODELING AND SIMULATION

A new formalism for fault modeling and simulation in discrete event systems is introduced. This formalism, called FDEVS and based on the DEVS formalism developed by Zeigler, allows to handle typical classes of fault hypotheses (like behavioral, structural, and delay faults) via the classical technique of fault injection. It also embodies the necessary features to automatically generate and propagate fault hypotheses in the system. It is shown that atomic FDEVS models can be coupled in a modular and hierarchical way, in order to represent complex systems. It is also shown that coupled FDEVS models can be easily simulated in a digital computer. Some examples are presented, in order to illustrate the features of the methodology.
Anti-melanogenic effects of black, green, and white tea extracts on immortalized melanocytes

Tea contains polyphenols and is one of the most popular beverages consumed worldwide. Because most tyrosinase inhibitors that regulate melanogenesis are phenol/catechol derivatives, this study investigated the inhibitory effects of Camellia sinensis water extracts (CSWEs), including black tea, green tea, and white tea extracts, on melanogenesis using immortalized melanocytes. CSWEs inhibited melanin accumulation and melanin synthesis along with tyrosinase activity in a concentration-dependent manner. These inhibitory effects were superior to those of arbutin, a well-known depigmenting agent. The anti-melanogenic activity of black (fermented) tea was higher than that of a predominant tea catecholamine, epigallocatechin gallate. CSWEs, especially black tea extract, decreased tyrosinase protein levels in a concentration-dependent manner. These results suggest that the anti-melanogenic effect of CSWEs is mediated by a decrease in both tyrosinase activity and protein expression, and may be augmented by fermentation. Thus, CSWEs could be useful skin-whitening agents in the cosmetic industry.
DDChord -- A Double Deck P2P System Based on Chord

Aiming at the system instability of Chord which is caused by the heterogeneity of nodes in model, this paper proposes a Double Deck P2P System based on Chord (DDChord). It considers the actual processing capacity of nodes. In every group, a super-node manages the ordinary-nodes to improve system stability. To solve the routing detour which caused by DHT technical, the system proposes search algorithm which is based on topology-aware. Experimental results show that the search algorithm can reduce the query delay and improve the efficiency of query.
MicroRNAs Show Mutually Exclusive Expression Patterns in the Brain of Adult Male Rats

Background The brain is a major site of microRNA (miRNA) gene expression, but the spatial expression patterns of miRNAs within the brain have not yet been fully covered. Methodology/Principal Findings We have characterized the regional expression profiles of miRNAs in five distinct regions of the adult rat brain: amygdala, cerebellum, hippocampus, hypothalamus and substantia nigra. Microarray profiling uncovered 48 miRNAs displaying more than three-fold enrichment between two or more brain regions. Notably, we found reciprocal expression profiles for a subset of the miRNAs predominantly found (> ten times) in either the cerebellum (miR-206 and miR-497) or the forebrain regions (miR-132, miR-212, miR-221 and miR-222). Conclusions/Significance The results indicate that some miRNAs could be important for area-specific functions in the brain. Our data, combined with previous studies in mice, provides additional guidance for future investigations of miRNA functions in the brain.
Long-term legacy of massive carbon input to the Earth system: Anthropocene versus Eocene

Over the next few centuries, with unabated emissions of anthropogenic carbon dioxide (CO2), a total of 5000 Pg C may enter the atmosphere, causing CO2 concentrations to rise to approximately 2000 ppmv, global temperature to warm by more than 8°C and surface ocean pH to decline by approximately 0.7 units. A carbon release of this magnitude is unprecedented during the past 56 million years—and the outcome accordingly difficult to predict. In this regard, the geological record may provide foresight to how the Earth system will respond in the future. Here, we discuss the long-term legacy of massive carbon release into the Earth's surface reservoirs, comparing the Anthropocene with a past analogue, the Palaeocene–Eocene Thermal Maximum (PETM, approx. 56 Ma). We examine the natural processes and time scales of CO2 neutralization that determine the atmospheric lifetime of CO2 in response to carbon release. We compare the duration of carbon release during the Anthropocene versus PETM and the ensuing effects on ocean acidification and marine calcifying organisms. We also discuss the conundrum that the observed duration of the PETM appears to be much longer than predicted by models that use first-order assumptions. Finally, we comment on past and future mass extinctions and recovery times of biotic diversity.
HOMOTOPY CLASSIFICATION OF MAPS INTO HOMOGENEOUS SPACES

We give an alternative to Postnikov’s homotopy classification of maps from 3-dimensional CW-complexes to homogeneous spaces G/H of Lie groups. It describes homotopy classes in terms of lifts to the group G and is suitable for extending the notion of homotopy to Sobolev maps. This is required in applications to variational problems of mathematical physics.
Molecular cloning, genomic structure, polymorphism and expression analysis of major histocompatibility complex class IIA gene of swamp eel Monopterus albus

Major histocompatibility complex (MHC) class II molecules play an important role in the immune response of vertebrates. In this paper, full-length MHC IIA cDNA was isolated from swamp eel (Monopterus albus) by rapid amplification of cDNA ends PCR. The genomic structure, molecular polymorphism, tissue distribution, and immune response of the MHC IIA gene to bacterial challenge were investigated. The full-length cDNA (GenBank accession No.: KC616308) is 1,509 bp in length including an 83 bp-long 5′ untranslated region (UTR) and a 709 bp-long 3′ UTR, which encoded a 238 amino acids protein. In the 2,339 bp-long MHC IIA genomic DNA, four exons and three introns were identified. Sequence comparison exhibited that the deduced amino acid sequence shared 27.1–66.3% identity with those of other species. Seven alleles were identified from five healthy individuals. Number of alleles per individual diversified from two to five. Five different 5′ UTR sequences and two different 3′ UTR sequences from one individual may infer the existence of five loci at least. Real-time quantitative PCR demonstrated that swamp eel MHC IIA transcripts were ubiquitously expressed in ten tissues, but the expression level was distinctly different. Significant changes were observed in liver, spleen, kidney and intestine after challenged with pathogenic bacteria Aeromonas hydrophilia.
Children’s Phthalate Intakes and Resultant Cumulative Exposures Estimated from Urine Compared with Estimates from Dust Ingestion, Inhalation and Dermal Absorption in Their Homes and Daycare Centers

Total daily intakes of diethyl phthalate (DEP), di(n-butyl) phthalate (DnBP), di(isobutyl) phthalate (DiBP), butyl benzyl phthalate (BBzP) and di(2-ethylhexyl) phthalate (DEHP) were calculated from phthalate metabolite levels measured in the urine of 431 Danish children between 3 and 6 years of age. For each child the intake attributable to exposures in the indoor environment via dust ingestion, inhalation and dermal absorption were estimated from the phthalate levels in the dust collected from the child’s home and daycare center. Based on the urine samples, DEHP had the highest total daily intake (median: 4.42 µg/d/kg-bw) and BBzP the lowest (median: 0.49 µg/d/kg-bw). For DEP, DnBP and DiBP, exposures to air and dust in the indoor environment accounted for approximately 100%, 15% and 50% of the total intake, respectively, with dermal absorption from the gas-phase being the major exposure pathway. More than 90% of the total intake of BBzP and DEHP came from sources other than indoor air and dust. Daily intake of DnBP and DiBP from all exposure pathways, based on levels of metabolites in urine samples, exceeded the Tolerable Daily Intake (TDI) for 22 and 23 children, respectively. Indoor exposures resulted in an average daily DiBP intake that exceeded the TDI for 14 children. Using the concept of relative cumulative Tolerable Daily Intake (TDIcum), which is applicable for phthalates that have established TDIs based on the same health endpoint, we examined the cumulative total exposure to DnBP, DiBP and DEHP from all pathways; it exceeded the tolerable levels for 30% of the children. From the three indoor pathways alone, several children had a cumulative intake that exceeded TDIcum. Exposures to phthalates present in the air and dust indoors meaningfully contribute to a child’s total intake of certain phthalates. Such exposures, by themselves, may lead to intakes exceeding current limit values.
Noise-robust speech recognition using a new spectral estimation method “PHASOR”

This paper proposes a new noise-robust spectral estimation method for speech recognition. The new method, called PHASOR, is characterized by inside-frame processing. The speech spectrum is estimated from a single impulse response obtained by summing multiple pitch periods in a frame with synchronizing the phase. PHASOR improves the spectral estimation accuracy and suppresses the additive noise because of the inside-frame processing. These improvement is more effective when the pitch fluctuates or changes in the frame. Speaker-dependent and speaker-independent phoneme recognition experiments demonstrate that the PHASOR greatly reduces the recognition error rate for speech data contaminated by noise. It also outperforms conventional noise reduction methods, cepstral mean normalization and spectral subtraction.
Comprehensive Analysis of the Rice RING E3 Ligase Family Reveals Their Functional Diversity in Response to Abiotic stress

A large number of really interesting new gene (RING) E3 ligases contribute to the post-translational modification of target proteins during plant responses to environmental stresses. However, the physical interactome of RING E3 ligases in rice remains largely unknown. Here, we evaluated the expression patterns of 47 Oryza sativa RING finger protein (OsRFP) genes in response to abiotic stresses via semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) and in silico analysis. Subsequently, molecular dissection of nine OsRFPs was performed by the examination of their E3 ubiquitin ligase activity, subcellular localization, and physical interaction with target proteins. Most of the OsRFPs examined possessed E3 ligase activity and showed diverse subcellular localization. Yeast two-hybrid analysis was then employed to construct a physical interaction map of seven OsRFPs with their 120 interacting proteins. The results indicated that these OsRFPs required dynamic translocation and partitioning for their cellular activation. Heterogeneous overexpression of each of the OsRFP genes in Arabidopsis suggested that they have functionally diverse responses to abiotic stresses, which may have been acquired during evolution. This comprehensive study provides insights into the biological functions of OsRFPs, which may be useful in understanding how rice plants adapt to unfavourable environmental conditions.
Association between serum level of anti-TPO titer and polymorphisms G1193/C Exon 8 and C2145/T Exon 12 of thyroid peroxidase gene in an Iranian population

Background: Autoimmune thyroid diseases (AITD) are common, with important epidemiological data, including family and twin studies, supporting a strong genetic background on the etiology of AITD. Objectives: The aim of this study was to assess the relationship between two polymorphisms of Thyroid Peroxidase gene (TPO) and serum level of Anti-TPO titer in an Iranian population. Patients and Methods: A sample of 184 participants from the Tehran Lipid and Glucose Study was selected as the case (No.=112) and control (No.=72) groups. Inclusion criteria for cases were Anti-TPO and Anti-Tg>100U/L with a history of hypothyroidism. Anti-TPO level in subjects was measured by the ELISA kit. Genomic DNA was extracted using Salting-out/Proteinase K method. Polymorphism detection of Exon 8 and 12 was done using the PCR-RFLP method. The PCR products were incubated with restriction enzymes SacII and BsrI, respectively. Results: The C allele frequency of C2145/T polymorphism Exon 12 (rs732608) was observed in 71.2% of patients and 28.8% of normal individuals. This allele was significant ly associated with increased levels of anti-TPO [(TT, 140±330 pmol/L; vs. CC, 436±380 pmol/L; P < 0.001), (OR: 9.2)]. The G1193/C was not polymorphic and no association between this SNP and the level of serum anti-TPO was found in this study. Conclusions: We found that the C allele polymorphism in C2145/T exon 12 is associated with the high level of serum anti-TPO and that carriers of this allele are predisposed to disease 9.2 times more than those, who have no C allele. The selected polymorphism of exon 8 has no effect on increased levels of anti-TPO. ARTICLE INFO
2D surface topography boundary conditions in seismic wave modelling

New formulations of boundary conditions at an arbitrary two‐dimensional (2D) free‐surface topography are derived. The top of a curved grid represents the free‐surface topography while the grid's interior represents the physical medium. The velocity–stress version of the viscoelastic wave equations is assumed to be valid in this grid. However, the rectangular grid version attained by grid transformation is used to model wave propagation in this work in order to achieve the numerical discretization. We show the detailed solution of the particle velocities at the free surface resulting from discretizing the boundary conditions by second‐order finite‐differences (FDs). The resulting system of equations is spatially unconditionally stable. The FD order is gradually increased with depth up to eighth order inside the medium. Staggered grids are used in both space and time, and the second‐order leap‐frog and Crank–Nicholson methods are used for time‐stepping. We simulate point sources at the surface of a homogeneous medium with a plane free surface containing a hill and a trench. Applying parameters representing exploration surveys, we present examples with a randomly realized surface topography generated by a 1D von Kármán function of order 1. Viscoelastic simulations are presented using this surface with a homogeneous medium and with a layered, randomized medium realization, all generating significant scattering.
State feedback stabilization of a class of discontinuous systems

This paper investigates the feedback stabilization problems for a class of discontinuous nonlinear systems. A set-valued time derivative is introduced for nonsmooth function along discontinuous vector fields, which enables us to perform Lyapunov-based design with non-regular Lyapunov function for the Fillipov solutions. The first result is to give a design approach to a discontinuous feedback control law for a class of nonlinear systems under a matched discontinuity. Then, it is shown that the control law, as virtual control, can be extended to recursive design problem when the control input is provided by an integrator. Numerical example is given to illustrate the design approach.
BENEFITS OF DEEP-CANAL HEARING AID FITTINGS

Some of these advantages include decreased occlusion (Mueller, 1994), increased patient satisfaction (Ebinger et al., 1994), decreased amplification of wind noise (Fortune & Preves, 1994), and improved localization ability (Best et al., 2010). If canal fitting of a hearing aid provides significant benefits over a BTE form factor, then it might be assumed that deep-canal hearing aid fitting could enhance those benefits. The premier option for deep-canal fitting is the Starkey SoundLensTM, the industry’s first invisible-in-the-canal (IIC) custom hearing aid. Traditionally, a CIC is fit one to two millimeters inside the aperture of the ear canal, whereas the IIC is fit to the second bend of the ear canal, positioning the faceplate well past the aperture. For additional background information on the IIC, please refer to Van Vliet and Galster (2010). A research project was developed to investigate the benefits provided by the IIC as compared to CIC and BTE hearing aids; four experimental questions were asked:
Obstructive Sleep Apnea and Metabolic Syndrome in Spanish Population

Obstructive sleep apnea (OSA) is a clinical picture characterized by repeated episodes of obstruction of the upper airway. OSA is associated with cardiovascular risk factors, some of which are components of metabolic syndrome (MS). Objectives: First, determine the prevalence of MS in patients with OSA visited in sleep clinic. Second, evaluate whether there is an independent association between MS components and the severity of OSA. Methods: Patients with clinical suspicion of OSA were evaluated by polysomnography. Three groups were defined according to apnea hypoapnea index (AHI): no OSA (AHI <5), mild-moderate (AHI≥ 5 ≤30), and severe (AHI> 30). All patients were determined in fasting blood glucose, total cholesterol, HDL cholesterol, triglycerides and insulin. MS was defined according to criteria of National Cholesterol Education Program (NCEP). Results: A total of 141 patients (mean age 54 ± 11 years) were evaluated. According to AIH, 25 subjects had no OSA and 116 had OSA (41mild-moderate and 75 severe). MS prevalence ranged from 43-81% in OSA group. Also, a significant increase in waist circumference, triglycerides, glucose, blood pressure levels, and a decrease in HDL cholesterol levels was observed in more severe OSA patients. All polysomnographic parameters correlated significantly with metabolic abnormalities. After a multiple regression analysis, abdominal obesity (p <0.02), glucose (p <0.01) and HDL cholesterol (p <0.001) were independently associated with OSA. Conclusions: Our findings show high prevalence of MS in OSA, especially in severe group. A significant association between OSA and some of the components of MS was found in Spanish population.
Defect categorization: making use of a decade of widely varying historical data

This paper describes our experience in aggregating a number of historical datasets containing inspection defect data using different categorization schemes. Our goal was to make use of the historical data by creating models to guide future development projects. We describe our approach to reconciling the different choices used in the historical datasets to categorize defects, and the challenges we faced. We also present a set of recommendations for others involved in classifying defects.
Further evaluation of a hearing loss simulator

A real-time, level-expansion system to simulate hearing loss for normal hearing persons was studied. The simulator's effect on the performance of normal hearing subjects in basic psychoacoustic tasks was investigated through experimentation. The experiments performed included measurements of intensity discrimination, critical ratio, and two-tone suppression. The results of these experiments were predicted by analyzing a model of the simulator system. The results of a psychophysical tuning curve (PTC) experiment were also predicted and compared with previous data. In addition to the expansion simulation, an additive noise based simulation of hearing loss (equivalent threshold masking) was investigated in each experiment. Results show that the noise and expansion simulations produce comparable effects that are similar to the effects of a real impairment in the PTC and critical ratio experiments. In the intensity discrimination experiment, the expansion simulation gave subjects abnormally good sensitivity, which is not associated with real impairment. Software meant to increase the precision and ease of use of the expansion simulator and stimulus generation equipment was written and documented. Thesis Supervisor: Louis D. B. Braida Title: Henry Ellis Warren Professor of Electrical Engineering
Big data: a research agenda

Recently, a great deal of interest for Big Data has risen, mainly driven from a widespread number of research problems strongly related to real-life applications and systems, such as representing, modeling, processing, querying and mining massive, distributed, large-scale repositories (mostly being of unstructured nature). Inspired by this main trend, in this paper we discuss three important aspects of Big Data research, namely OLAP over Big Data, Big Data Posting, and Privacy of Big Data. We also depict future research directions, hence implicitly defining a research agenda aiming at leading future challenges in this research field.