Miracle-dz/UniFAR-FTUs huggingface dataset:
Nanoparticles prepared from the water extract of Gusuibu (Drynaria fortunei J. Sm.) protects osteoblasts against insults and promotes cell maturation

Our previous study showed that Gusuibu (Drynaria fortunei J. Sm.) can stimulate osteoblast maturation. This study was further designed to evaluate the effects of nanoparticles prepared from the water extract of Gusuibu (WEG) on osteoblast survival and maturation. Primary osteoblasts were exposed to 1, 10, 100, and 1000 μg/mL nanoparticles of WEG (nWEG) for 24, 48, and 72 hours did not affect morphologies, viability, or apoptosis of osteoblasts. In comparison, treatment of osteoblasts with 1000 μg/mL WEG for 72 hours decreased cell viability and induced DNA fragmentation and cell apoptosis. nWEG had better antioxidant bioactivity in protecting osteoblasts from oxidative and nitrosative stress-induced apoptosis than WEG. In addition, nWEG stimulated greater osteoblast maturation than did WEG. Therefore, this study shows that WEG nanoparticles are safer to primary osteoblasts than are normal-sized products, and may promote better bone healing by protecting osteoblasts from apoptotic insults, and by promoting osteogenic maturation.
Reliability evaluation for integrated circuit with defective interconnect under electromigration

In electromigration degradation process the existing physical defects on interconnect play a critical role by significantly accelerating the EM damage under increased current density and elevated temperature. In this work the simulation models were upgraded in the IC reliability simulator ARET to incorporate the effect of interconnect physical defects in expected lifetime prediction. Then based on the statistical approach, a probability model was developed to evaluate the system-level circuit reliability with defective interconnect under EM degradation. The probability model has been successfully implemented in ARET tool to simulate and evaluate both interconnect and circuit level reliabilities.
Chronic prostatitis and chronic pelvic pain in men: aetiology, diagnosis and management 1

Patients with chronic prostatitis/pelvic pain syndrome typically report genital or pelvic pain (in or around the penis, perineum, scrotum) lasting >3 months. Whereas true chronic bacterial prostatitis is an uncommon condition characterised by recurrent prostatic and urinary infection, chronic pelvic pain syndrome (CPPS) is a common condition in which no infection is found. Recent surveys suggest a prevalence of 2.5–3% for CPPS. The four‐glass test, traditionally used to distinguish inflammatory and inflammatory forms of CPPS, has not been adequately validated; whether the distinction is clinically meaningful is increasingly questioned. The aetiology of CPPS is not known; urodynamic studies imply a neuromuscular origin. More recent work supports a role for proinflammatory cytokines in the pathogenesis. In the management of chronic bacterial prostatitis, trials support the use of quinolone antibiotics as first‐line treatment. In contrast, the management of CPPS is generally unsatisfactory, as no reliable treatment has been identified. Treatments commonly tried include antibiotics (notably tetracyclines, quinolones and macrolides), anti‐inflammatory agents, and alpha blockers. Newer approaches include trials of finasteride, quercetin and rofecoxib. A recent systematic review demonstrated that none of the current diagnostic and treatment methods for CPPS is supported by a robust evidence base.
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution

To study the evolutionary effects of polyploidy on plant gene functions, we analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences functional categories, which indicates a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, and those involved in DNA repair have been preferentially lost. Although the two members of each gene pair must originally have had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. We identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. We also find that the rate of protein sequence evolution has been significantly asymmetric in >20% of duplicate pairs. Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids.
Integrated Power-Gating and State Assignment for Low Power FSM Synthesis

Power-gating is an effective technique for reducing standby leakage power and dynamic power. In power-gating one can shut off the power supply to sections of logic block while keeping other logic blocks active. However, careful design is required to make power-gating technique effective, otherwise, negative effect of power-gating may overwhelm the potential gain. In this paper we have presented the state partitioning and state encoding strategy targeting low power finite state machine (FSM) decomposition based on genetic algorithmic approach. All the previous works dealt only FSM partitioning but did not consider state encoding together. This is the first ever approach considering FSM partitioning and state encoding together in power-gating technique. Experimental result shows that upto 73% power saving can be done giving small amount of area penalty.
The controversial 30 nm chromatin fibre

DNA is packed as chromatin on several levels in the eukaryotic nucleus. Dissection of chromatin with nucleases produces three stable substructures: the nucleosome core particle, the chromatosome and the 30 nm fibre. Whilst the first two allow transcription, the 30 nm fibre is taken to be the first level of transcriptionally dormant chromatin and it has an important functional role in cell differentiation and epigenetic regulation. Its structure has been a subject of continuing discussion since native fibres cannot readily be crystallized. This problem has recently been addressed by reconstitution of fibres on repeats of DNA sequences having nucleosome‐positioning properties and two different structures were reported. 1,2
CpG Methylation Profiles of Endothelial Cell‐Specific Gene Promoter Regions in Adipose Tissue Stem Cells Suggest Limited Differentiation Potential Toward the Endothelial Cell Lineage

In vivo endothelial commitment of adipose stem cells (ASCs) has scarcely been reported, and controversy remains on the contribution of ASCs to vascularization. We address the epigenetic commitment of ASCs to the endothelial lineage. We report a bisulfite sequencing analysis of CpG methylation in the promoters of two endothelial‐cell‐specific genes, CD31 and CD144, in freshly isolated and in cultures of ASCs before and after induction of endothelial differentiation. In contrast to adipose tissue‐derived endothelial (CD31+) cells, freshly isolated ASCs display a heavily methylated CD31 promoter and a mosaically methylated CD144 promoter despite basal transcription of both genes. Methylation state of both promoters remains globally stable upon culture. Endothelial stimulation of ASCs in methylcellulose elicits phenotypic changes, marginal upregulation of CD31, and CD144 expression and restrictive induction of a CD31+CD144+ immunophenotype. These events are accompanied by discrete changes in CpG methylation in CD31 and CD144 promoters; however, no global demethylation that marks CD31+ cells and human umbilical vein endothelial cells occurs. Immunoselection of CD31+ cells after endothelial stimulation reveals consistent demethylation of one CpG immediately 3′ of the transcription start site of the CD31 promoter. Adipogenic or osteogenic differentiation maintains CD31 and CD144 methylation patterns of undifferentiated cells. Methylation profiles of CD31 and CD144 promoters suggest a limited commitment of ASCs to the endothelial lineage. This contrasts with the reported hypomethylation of adipogenic promoters, which reflects a propensity of ASCs toward adipogenic differentiation. Analysis of CpG methylation at lineage‐specific promoters provides a robust assessment of epigenetic commitment of stem cells to a specific lineage.
Analysis and prediction of affinity of TAP binding peptides using cascade SVM

The generation of cytotoxic T lymphocyte (CTL) epitopes from an antigenic sequence involves number of intracellular processes, including production of peptide fragments by proteasome and transport of peptides to endoplasmic reticulum through transporter associated with antigen processing (TAP). In this study, 409 peptides that bind to human TAP transporter with varying affinity were analyzed to explore the selectivity and specificity of TAP transporter. The abundance of each amino acid from P1 to P9 positions in high‐, intermediate‐, and low‐affinity TAP binders were examined. The rules for predicting TAP binding regions in an antigenic sequence were derived from the above analysis. The quantitative matrix was generated on the basis of contribution of each position and residue in binding affinity. The correlation of r = 0.65 was obtained between experimentally determined and predicted binding affinity by using a quantitative matrix. Further a support vector machine (SVM)‐based method has been developed to model the TAP binding affinity of peptides. The correlation (r = 0.80) was obtained between the predicted and experimental measured values by using sequence‐based SVM. The reliability of prediction was further improved by cascade SVM that uses features of amino acids along with sequence. An extremely good correlation (r = 0.88) was obtained between measured and predicted values, when the cascade SVM‐based method was evaluated through jackknife testing. A Web service, TAPPred (http://www.imtech.res.in/raghava/tappred/ or http://bioinformatics.uams.edu/mirror/tappred/), has been developed based on this approach.
A CORPUS-BASED BEHAVIOURAL PROFILE STUDY OF NEAR-SYNONYMS: IMPORTANT, ESSENTIAL, VITAL, NECESSARY AND CRUCIAL

This study examines the internal semantic structure of a set of near-synonym adjectives: important, essential, vital, necessary and crucial. I used the British National Corpus (BNC) and 9 traditional reference materials as source data. I applied a corpus-based behavioural profile approach. The study focuses its attention on their distributional patterns especially types of nouns that each adjective modifies. Some of the findings challenge the several existing descriptions of this set of near-synonym adjectives by the traditional reference materials. For example, the traditional reference materials cite many examples of vital as modifier of abstract nouns but the corpus data indicates that it is mostly modified by concrete and dual nouns. This study justifies the theory and applicability of the BP approach for studying the semantic and usage patterns of a set of synonyms.
A decentralized control method for direct smart grid control of refrigeration systems

A decentralized control method is proposed to govern the electrical power consumption of supermarket refrigeration systems (SRS) for demand-side management in the smart grid. The control structure is designed in a supervisory level to provide desired set-points for distributed level controllers. No model information is required in this method. The temperature limits/constraints are respected. A novel adaptive saturation filter is also proposed to increase the system flexibility in storing and delivering the energy. The proposed control strategy is applied to a simulation benchmark that fairly simulate the CO2 booster system of a supermarket refrigeration.
Building Agent‐Based Walking Models by Machine‐Learning on Diverse Databases of Space‐Time Trajectory Samples

We introduce a novel scheme for automatically deriving synthetic walking (locomotion) and movement (steering and avoidance) behavior in simulation from simple trajectory samples. We use a combination of observed and recorded real‐world movement trajectory samples in conjunction with synthetic, agent‐generated, movement as inputs to a machine‐learning scheme. This scheme produces movement behavior for non‐sampled scenarios in simulation, for applications that can differ widely from the original collection settings. It does this by benchmarking a simulated pedestrian's relative behavioral geography, local physical environment, and neighboring agent‐pedestrians; using spatial analysis, spatial data access, classification, and clustering. The scheme then weights, trains, and tunes likely synthetic movement behavior, per‐agent, per‐location, per‐time‐step, and per‐scenario. To prove its usefulness, we demonstrate the task of generating synthetic, non‐sampled, agent‐based pedestrian movement in simulated urban environments, where the scheme proves to be a useful substitute for traditional transition‐driven methods for determining agent behavior. The potential broader applications of the scheme are numerous and include the design and delivery of location‐based services, evaluation of architectures for mobile communications technologies, what‐if experimentation in agent‐based models with hypotheses that are informed or translated from data, and the construction of algorithms for extracting and annotating space‐time paths in massive data‐sets.
TDMA scheduling design of multihop packet radio networks based on latin squares

Many transmission scheduling algorithms have been proposed to maximize the spatial reuse and minimize the time division multiple access (TDMA) frame length in multihop packet radio networks. Almost all existing algorithms assume exact network topology information and require recomputations when the network topology changes. In addition, existing work focuses on single channel TDMA systems. In this paper, we propose a multichannel topology-transparent algorithm based on latin squares. This algorithm has the flexibility to allow the growth of the network, i.e., the network can add more mobile nodes without recomputation of transmission schedules for existing nodes. At the same time, a minimum throughput is guaranteed. We analyze the efficiency of our algorithm, and examine the topology-transparent characteristics and the sensitivity on design parameters by simulation.
GPU assisted Mutual Information Analysis Attacks on AES

In 2008 the Mutual Information Analysis (MIA) has been introduced as a generic sidechannel key distinguisher suitable for detecting non-linear relations between measurements and hypothetical leakage. It is considered a convenient technique for higher-order scenarios as well as for attacks by an adversary not capable of obtaining an accurate leakage model. This thesis uses CUDA, Nvidia’s framework for General Purpose Computations on Graphics Processing Units (GPU), for a fast parallel implementation of MIA that achieved a performance boost of a factor of 4 to 12 compared to a sequential reference implementation. We evaluate different optimization strategies and analyze the constraints to the possible profit that MIA can draw from stream processing parallelizations. More generally our results suggest that GPUs can significantly speed up the computation time of side channel attacks. While the performance gain for our approach is decreased by hitting the memory bandwidth limits without exhausting the computational power of the GPU, attacks having a higher arithmetic intensity, e.g. in higher-order scenarios, are likely to achieve an even higher performance gain.
Discrimination reversal learning reveals greater female behavioural flexibility in guppies

Behavioural flexibility allows an animal to adapt its behaviour in response to changes in the environment. Research conducted in primates, rodents and domestic fowl suggests greater behavioural persistence and reduced behavioural flexibility in males. We investigated sex differences in behavioural flexibility in fish by comparing male and female guppies (Poecilia reticulata) in a reversal learning task. Fish were first trained on a colour discrimination, which was learned equally rapidly by males and females. However, once the reward contingency was reversed, females were better at inhibiting the previous response and reached criterion twice as fast as males. When reward reversing was repeated, males gradually reduced the number of errors, and the two sexes had a comparable performance after four reversals. We suggest that sex differences in behavioural flexibility in guppies can be explained in terms of the different roles that males and females play in reproduction.
Transferable imipenem resistance in Pseudomonas aeruginosa

We isolated an imipenem-resistant strain, GN17203, of Pseudomonas aeruginosa. The strain produced a beta-lactamase that hydrolyzed imipenem. The beta-lactamase was encoded by a 31-MDa plasmid, pMS350, which belongs to incompatibility group P-9. The plasmic conferred resistance to beta-lactams, gentamicin, and sulfonamide and was transferable by conjugation to P. aeruginosa but not to Escherichia coli. The molecular weight of the purified enzyme was estimated to be 28,000, and the isoelectric point was 9.0. The enzyme showed a broad substrate profile, hydrolyzing imipenem, oxyiminocephalosporins, 7-methoxycephalosporins, and penicillins. The enzyme activity was inhibited by EDTA, iodine, p-chloromercuribenzoate, CuSO4, and HgCl2 but not by clavulanic acid or sulbactam.
Pattern of gene alterations in intraductal breast neoplasms associated with histological type and grade.

To reveal any association between the histological type and grade of intraductal breast neoplasms and the manner of accumulation of gene alterations, eight types of gene alterations, i.e., loss of heterozygosity (LOH) on chromosomal arms 16p, 16q, 17p, 17q, and 18q, amplification of the c-erbB-2 and hst-1/int-2 genes, and mutation of the p53 gene, were examined by Southern blot analysis or single-strand conformation polymorphism analysis in a total of 60 cases of intraductal breast cancer and 18 nonmalignant proliferative lesions. Among the histological types and three histological grade groups of intraductal carcinomas, the gene alterations which occurred most frequently were LOH on 16q alone in non-comedo type and Grade 1, alterations of c-erbB-2, 17p, and 16q in comedo type and Grade 2, and alterations of 17q and p53 as well as those of 16q, 17p, and c-erbB-2 in Grade 3. LOH on 16q and 18q was frequent in intraductal carcinoma of the intracystic papillary type, whereas LOH on 18q alone was detected in 27% of papillomas. Among intraductal carcinomas, the mean number of gene alterations was largest in comedo type and Grade 3, whereas it was smallest in non-comedo type and Grade 1. It was possible that LOH on 18q and 16q was involved frequently in papillary tumori-genesis and acquisition of malignant phenotype, respectively, whereas most of the other gene alterations were involved in acquisition of aggressive biological properties by intraductal carcinoma cells. It was also possible that the phenotype of breast neoplasms was determined by the combination of gene alterations at a relatively early developmental stage.
Perception of silent and motionless prey on vegetation by echolocation in the gleaning bat Micronycteris microtis

Gleaning insectivorous bats that forage by using echolocation within dense forest vegetation face the sensorial challenge of acoustic masking effects. Active perception of silent and motionless prey in acoustically cluttered environments by echolocation alone has thus been regarded impossible. The gleaning insectivorous bat Micronycteris microtis however, forages in dense understory vegetation and preys on insects, including dragonflies, which rest silent and motionless on vegetation. From behavioural experiments, we show that M. microtis uses echolocation as the sole sensorial modality for successful prey perception within a complex acoustic environment. All individuals performed a stereotypical three-dimensional hovering flight in front of prey items, while continuously emitting short, multi-harmonic, broadband echolocation calls. We observed a high precision in target localization which suggests that M. microtis perceives a detailed acoustic image of the prey based on shape, surface structure and material. Our experiments provide, to our knowledge, the first evidence that a gleaning bat uses echolocation alone for successful detection, classification and precise localization of silent and motionless prey in acoustic clutter. Overall, we conclude that the three-dimensional hovering flight of M. microtis in combination with a frequent emission of short, high-frequency echolocation calls is the key for active prey perception in acoustically highly cluttered environments.
Cold Atmospheric Pressure Plasmas (CAPs) for Skin Wound Healing

In the past 20 years, cold atmospheric pressure plasmas (CAPs) have become a new promising way for many biomedical applications, such as disinfection, cancer treatment, root canal treatment, wound healing, and other medical applications. Among these applications, investigations of plasma for skin wound healing has gained huge success both in vitro and in vivo experiments, and also the mechanism behind it has been studied by many groups. In this chapter, we summarize the state-of-the-art progress in wound healing by CAPs. The plasma devices developed for wound healing, the interactions between plasmas and microorganisms/cells/tissues, the in vitro and in vivo treatments, the clinical trials, and biosafety issues are all included.
Prevalence and factors associated with HCV infection among elderly individuals in a southern Brazilian city.

INTRODUCTION Few Latin American studies have assessed the prevalence of hepatitis C virus (HCV) infection in elderly individuals, in whom the highest rates are expected. We aimed to investigate the prevalence of and factors associated with HCV infection in elderly residents in the municipality of Tubarão, Santa Catarina. METHODS This cross-sectional study included 820 individuals (aged ≥ 60 years) who were selected by simple random sampling. The presence of anti-HCV antibodies was tested by chemiluminescence, and HCV RNA detection was performed for the anti-HCV-reactive subjects. Those individuals who were anti-HCV reactive but had undetectable HCV RNA levels were tested using a third-generation recombinant immunoblot assay. The variables were compared using the chi-squared test or Fisher's exact test, and those variables with p < 0.05 were included in the logistic regression model. RESULTS The mean patient age was 68.6 years (SD 7.0 years); 39% were men, and 92% were Caucasian. Eighteen subjects were anti-HCV positive. Among these individuals, 4 were characterized as false-positives, leaving 14 (1.7%) individuals with confirmed infections for analysis. HCV infection was associated with an age older than 65 years, households with 3 or more residents and the previous transfusion of blood products. In the logistic regression analysis, the following variables were independently associated with HCV infection: households with 3 or more residents (OR 7.9, 95% CI 1.7-35.9, p = 0.008) and previous blood transfusion (OR 6.2, 95% CI 2.1-18.6, p = 0.001). CONCLUSIONS The HCV prevalence in the elderly population in the municipality of Tubarão was higher than that found in previous studies of blood donors in the same region. Although exposure to contaminated blood products remained important, other transmission routes, such as household transmission, could play a role in HCV infection.