Miracle-dz/UniFAR-FTUs huggingface dataset:
The stress response resolution assay. II. Quantitative assessment of environmental agent/condition effects on cellular stress resolution outcomes in epithelium

Cellular stress responses consist of a complex network of pathways and linked processes that, when perturbed, are postulated to have roles in the pathogenesis of various human diseases. To assess the impact of environmental insults upon this network, we developed a novel stress response resolution (SRR) assay for investigation of cellular stress resolution outcomes and the effects of environmental agents and conditions thereupon. SRR assay‐based criteria identified three distinct groups of surviving cell clones, including those resembling parental cells, those showing Hprt/HPRT mutations, and a third type, “Phenotype‐altered” clones, that occurred predominantly in cells pretreated with a chemical mutagen, was heterogeneous in nature, and expressed significant alterations in cell morphology and/or function compared with parental cells. Further evaluation of Phenotype‐altered clones found evidence of various alterations that resembled epithelial‐to‐mesenchymal transition, phenotype switching, checkpoint dysfunction, senescence barrier bypass, and/or epigenetic reprogramming. Phenotype‐altered clones were found to occur spontaneously in a cell line with a mutator phenotype, to represent the major surviving clone type in a variation of the SRR assay, and to be tumorigenic in nude mice. Assessment of SRR assay final results showed that pretreatment with a chemical mutagen induced significant changes in cellular stress response prosurvival capacity, in damage avoidance versus damage tolerance stress resolution outcomes, and in the damage burden in the final surviving cell populations. Taken together, these results support the conclusion that use of the SRR assay can provide novel insights into the role of environmental insults in the pathogenesis of cancer and other human diseases. Environ. Mol. Mutagen. 54:281–293, 2013. © 2013 Wiley Periodicals, Inc.
Control strategy of in-pipe robot passing through elbow

In this paper, the control strategy was proposed to take advantage of the 2-DOF(Degree of Freedom)joint module to improve the mobility of the in-pipe robot. In particular, it was described the joint module control strategy to simply pass through elbow. The angles of joint module are controlled throughout 4-step to track for the robot component on the centerline of pipe. It was confirmed that the robot pass through the proposed simple path throughout the expriments.
Successive interference cancellation in uplink cellular networks

In recent years, operators addressed the explosive growth of mobile data demand by densifying the cellular network so as to achieve a higher spectral efficiency and increase their capacity. The intense proliferation of wireless devices resulted in interference limited networks, which suggests the use of interference mitigation and coordination techniques. In this work, we study successive interference cancellation (SIC) for uplink communications and we define an analytical framework that describes the performance benefits of SIC which accounts for the computational complexity of the cancellation scheme and the relevant network related parameters such as the random position and density of the base stations and mobile users, and the characteristics of the propagation channel. In our analysis, we explicitly model the consecutive events of canceling interferers and we derive expressions of the success probability to cancel the kth strongest signal and to decode the signal of interest (SoI) after k cancellations. The analysis indicates that the performance benefit of SIC diminishes quickly with k. The framework also reveals that a substantial performance gain can only be obtained for low values of the target signal-to-interference ratio (SIR).
Parent and Stepparent Support and Psychological Control in Remarried Families and Adolescent Empathic Concern

Abstract Using a symbolic interaction perspective, this study examined the extent to which (a) perceptions of parent/stepparent support were positively related to adolescent empathic concern and (b) perceptions of parent/stepparent psychological control mediated this relationship. Participants were a convenience sample of 72 ninth and tenth grade adolescents residing in remarried family households who completed self-report questionnaires. Results showed that adolescent girls in remarried family households who perceived their residential parent as more supportive reported greater empathic concern and that the relationship was mediated by perceptions of parent psychological control.
THE EVOLUTION OF ALTERNATE MORPHOLOGIES: FITNESS AND WING MORPHOLOGY IN MALE SAND CRICKETS

Many organisms show distinct morphological types. We argue that the evolution of these alternate morphologies depends upon both fitness differences between morphs within each sex and the genetic correlation between sexes. In this paper, we examine the evolution of alternate morphologies using wing dimorphism in insects as a model system. Many insect species are wing dimorphic, one morph having wings and being capable of flight, the other lacking functional wings. While there is a well established trade‐off in females between macroptery and reproduction, there are few data on the possible costs in males. We examine trade‐offs between macroptery and life‐history traits in male sand crickets, Gryllus firmus, and estimate the genetic correlation of wing dimorphism between the sexes. Macropterous males develop faster than micropterous males and are either larger or the same size depending upon rearing conditions. There is no difference in absolute or relative testis size at eclosion or 7 d thereafter. Finally, there is no difference between macropterous and micropterous males in relative success at siring offspring. Thus, with respect to the above traits, there are no costs associated with being winged in male G. firmus. It is possible that there may be a trade‐off between calling rate and macroptery. A comparison of the relative frequency of macroptery between males and female across different orders of insects supports this hypothesis. The genetic correlation of wing dimorphism between the sexes is high (r8 = 0.86), and hence the frequency of macroptery in males may be strongly influenced by selection acting on females.
MCOV: A Covariance Descriptor for Fusion of Texture and Shape Features in 3D Point Clouds

In this paper we propose MCOV, a covariance-based descriptor for the fusion of shape and color information of 3D surfaces with associated texture aiming at a robust characterization and matching of areas in 3D point clouds. The proposed descriptor is based on the notion of covariance in order to create compact representations of the variations of texture and surface features in a radial neighbourhood, instead of using the absolute features themselves. Even if this representation is compact and low dimensional, it still offers discriminative power for complex scenes. The codification of feature variations in a close environment of a point provides invariance to rigid spatial transformations and robustness to changes in noise and scene resolution from a simple formulation perspective. Results on 3D points discrimination are validated by testing this approach performance on top of a selected database, corroborating the adequacy of our approach on the posed challenging conditions and outperforming other state-of-the-art 3D point descriptor methods. A qualitative test application on matching objects on scenes acquired with a common depth-sensor device is also provided.
Cluster-based secure communication mechanism in wireless ad hoc networks

In a multi-agent system, there are many intelligent agents distributed in the network. To connect with these agents easily and arbitrarily, wireless ad hoc network is a candidate. Wireless ad hoc network is a distinct network environment with characteristics in self-organisation, dynamical network topologies and easy construction. To provide such networks with secure communication, many researchers tried different ways to create the session key(s). However, there are some drawbacks in session key generation procedure, and the robust session key could not be created. The authors propose a cluster-based secure communication mechanism in wireless ad hoc networks. The proposal applies the Diffie–Hellman key exchange protocol for the session key creation. It helps the clusterhead to reduce the communication overload, to avoid the time synchronisation problem in nodes authentication and to preserve the complete secrecy requirements.
Verifying RTuinOS using VCC: From approach to practice

The correctness of implementation codes is important especially for safety-critical software which is usually written in C programming language. In this paper, we present a C code correctness verification framework (CVF for short) which is based on an automatic theorem proving tool-VCC, and pro-pose a specification checking method to improve the correctness of verification specification codes. We use a real-time OS, RTuinOS1.0. 2, to evaluate our CVF framework. And the result shows it is feasible and effective to apply CVF to a real system software. Besides, the experiments also show that the specification checking method is effective.
Local drug delivery of 0.5% azithromycin in the treatment of chronic periodontitis among smokers.

BACKGROUND Along with conventional periodontal surgical therapy, local delivery of antibiotics may provide more effective treatment in smokers by targeting tissue-invasive bacteria. The aim of this randomized, placebo-controlled, double-masked clinical trial was to evaluate the adjunctive effects of subgingivally delivered 0.5% azithromycin (AZM) as an adjunct to scaling and root planing (SRP) in the treatment of chronic periodontitis in smokers. METHODS Fifty-four patients were randomized and categorized into two treatment groups: Group 1 - 26 subjects who received (SRP) plus placebo gel and Group 2 - 28 subjects who received (SRP) plus 0.5% azithromycin. Clinical parameters were recorded at baseline, 3, 6 and 9 months. They included Plaque Index (PI), modified Sulcus Bleeding Index (mSBI), probing depth (PD) and clinical attachment level (CAL). RESULTS Azithromycin resulted in significant improvements. A single application of AZM resulted in attachment gain at 9 months of 2.44 ± 0.64 mm as compared to 0.18 ± 0.68 mm for the placebo. Similarly, pocket depth and PI were significantly reduced but no change in the mSBI was noted. CONCLUSIONS When compared to the placebo, the adjunctive use of 0.5% AZM resulted in significant improvement in clinical outcome in the treatment of chronic periodontitis among smokers.
Increased Phagocytosis of Mycobacterium marinum Mutants Defective in Lipooligosaccharide Production

Background: Biosynthesis and functions of Mycobacterium marinum lipooligosaccharides (LOSs) remain elusive. Results: M. marinum mutants expressing various LOS profiles were generated and used to infect macrophages and amoebae. Conclusion: Deep LOS mutants are more efficiently phagocytosed than those lacking only LOS-IV. Significance: Three novel biosynthetic genes and the effect of the LOS content in modulating uptake by phagocytes are reported. Mycobacterium marinum is a waterborne pathogen responsible for tuberculosis-like infections in ectotherms and is an occasional opportunistic human pathogen. In the environment, M. marinum also interacts with amoebae, which may serve as a natural reservoir for this microorganism. However, the description of mycobacterial determinants in the early interaction with macrophages or amoebae remains elusive. Lipooligosaccharides (LOSs) are cell surface-exposed glycolipids capable of modulating the host immune system, suggesting that they may be involved in the early interactions of M. marinum with macrophages. Herein, we addressed whether LOS composition affects the uptake of M. marinum by professional phagocytes. Mutants with various truncated LOS variants were generated, leading to the identification of several previously uncharacterized biosynthetic genes (wbbL2, MMAR_2321, and MMAR_2331). Biochemical and structural approaches allowed resolving the structures of LOS precursors accumulating in this set of mutants. These strains with structurally defined LOS profiles were then used to infect both macrophages and Acanthamoebae. An inverse correlation between LOS completeness and uptake of mycobacteria by phagocytes was found, allowing the proposal of three mutant classes: class I (papA4), devoid of LOS and highly efficiently phagocytosed; class II, accumulating only early LOS intermediates (wbbL2 and MMAR_2331) and efficiently phagocytosed but less than class I mutants; class III, lacking LOS-IV (losA, MMAR_2319, and MMAR_2321) and phagocytosed similarly to the control strain. These results indicate that phagocytosis is conditioned by the LOS pattern and that the LOS pathway used by M. marinum in macrophages is conserved during infection of amoebae.
A Porphyromonas gingivalis tyrosine phosphatase is a multifunctional regulator of virulence attributes

Low Molecular Weight Tyrosine Phosphatases (LMWTP) are widespread in prokaryotes; however, understanding of the signalling cascades controlled by these enzymes is still emerging. Porphyromonas gingivalis, an opportunistic oral pathogen, expresses a LMWTP, Ltp1, that is differentially regulated in biofilm communities. Here we characterize the enzymatic activity of Ltp1 and, through the use of mutants that lack Ltp1 or expresses catalytically defective Ltp1, show that tyrosine phosphatase activity constrains both monospecies biofilm development and community development with the antecedent oral biofilm constituent Streptococcus gordonii. Exopolysaccharide production is downregulated by Ltp1 through transcriptional regulation of multiple genes involved in biosynthesis and transport. Furthermore, Ltp1 regulates transcriptional activity of luxS and thus impacts AI‐2‐dependent signalling in biofilm communities. In the absence of Ltp1 transcription across the hmu haemin uptake locus is reduced, and consequently uptake of haemin is impaired in the Ltp1 mutant. The gingipain proteinases Kgp and RgpA/B remain phosphorylated in the Ltp1 mutant. Phosphorylated Rgps are poorly secreted, whereas cell surface activity of phosphorylated Kgp is enhanced. By controlling the activity of several virulence‐associated properties, Ltp1 may restrain the pathogenic potential of P. gingivalis and maintain a commensal interaction with the host.
DNA polymerase delta in dna replication and genome maintenance

The eukaryotic genome is in a constant state of modification and repair. Faithful transmission of the genomic information from parent to daughter cells depends upon an extensive system of surveillance, signaling, and DNA repair, as well as accurate synthesis of DNA during replication. Often, replicative synthesis occurs over regions of DNA that have not yet been repaired, presenting further challenges to genomic stability. DNA polymerase δ (pol δ) occupies a central role in all of these processes: catalyzing the accurate replication of a majority of the genome, participating in several DNA repair synthetic pathways, and contributing structurally to the accurate bypass of problematic lesions during translesion synthesis. The concerted actions of pol δ on the lagging strand, pol ϵ on the leading strand, associated replicative factors, and the mismatch repair (MMR) proteins results in a mutation rate of less than one misincorporation per genome per replication cycle. This low mutation rate provides a high level of protection against genetic defects during development and may prevent the initiation of malignancies in somatic cells. This review explores the role of pol δ in replication fidelity and genome maintenance. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.
Hierarchical Screen Space Indirect Illumination For Video Games

Indirect lighting accounts for subtle but essential effects in virtual scenes, and plays a great role in our perception of geometry. It is especially wanted in video games, on fully dynamic scenes, where it greatly enhances the perceived realism. In this paper, we present a screen-space hierarchical algorithm for computing indirect lighting for animated scenes. Our algorithm is fully compatible with deferred-shading rendering engines for video games, and computes indirect lighting in less than 10 ms, leaving enough computation time for other gaming tasks, such as interaction and animation. Our algorithm works in two steps: first, we compute indirect illumination in screen-space at all possible scales, then we filter and combine together the illumination received at the different scales. We describe both the algorithm and its practical integration inside a commercial video-game rendering engine.
A Novel Enzyme-Linked Immunosorbent Assay for Diagnosis of Mycobacterium avium subsp. paratuberculosis Infections (Johne's Disease) in Cattle

ABSTRACT Enzyme-linked immunosorbent assays (ELISAs) for the diagnosis of Johne's disease (JD), caused by Mycobacterium avium subsp. paratuberculosis, were developed using whole bacilli treated with formaldehyde (called WELISA) or surface antigens obtained by treatment of M. avium subsp. paratuberculosis bacilli with formaldehyde and then brief sonication (called SELISA). ELISA plates were coated with either whole bacilli or sonicated antigens and tested for reactivity against serum obtained from JD-positive and JD-negative cattle or from calves experimentally inoculated with M. avium subsp. paratuberculosis, Mycobacterium avium subsp. avium, or Mycobacterium bovis. Because the initial results obtained from the WELISA and SELISA were similar, most of the subsequent experiments reported herein were performed using the SELISA method. To optimize the SELISA test, various concentrations (3.7 to 37%) of formaldehyde and intervals of sonication (2 to 300 s) were tested. With an increase in formaldehyde concentration and a decreased interval of sonication, there was a concomitant decrease in nonspecific binding by the SELISA. SELISAs prepared by treating M. avium subsp. paratuberculosis with 37% formaldehyde and then a 2-s burst of sonication produced the greatest difference (7×) between M. avium subsp. paratuberculosis-negative and M. avium subsp. paratuberculosis-positive serum samples. The diagnostic sensitivity and specificity for JD by the SELISA were greater than 95%. The SELISA showed subspecies-specific detection of M. avium subsp. paratuberculosis infections in calves experimentally inoculated with M. avium subsp. paratuberculosis or other mycobacteria. Based on diagnostic sensitivity and specificity, the SELISA appears superior to the commercial ELISAs routinely used for the diagnosis of JD.
Accounting for City Real Exchange Rate Changes in India

We examine the role of nontraded goods in the city real exchange rate changes in India. Using the Mean Squared Error (MSE) decomposition we nd that nontraded goods explain about 30% of the variation of the Indian city real exchange rate changes, rather than the small amount found in other cross-country studies. We also analyze the role of consumption elasticity of substitution between traded and nontraded goods. JEL Classi cation: F3, F4
Exploiting bit-level parallelism in GPGPUs: A case study on KeeLoq exhaustive key search attack

Graphic Processing Units (GPU) are increasingly popular in the field of high-performance computing for their ability to provide computational power for massively parallel problems at a reduced cost. However, the programming model exposed by the GPGPU software development tools is often insufficient to achieve full performance, and a major rethinking of algorithmic choices is needed. In this paper, we showcase such an effect on a case study drawn from the cryptography application domain. The pervasive use of cryptographic primitives in modern embedded systems is a growing trend. Small, efficient cryptosystems have been effectively employed to design and implement keyless password-based access control systems in various wireless authentication applications. The security margin provided by these lightweight ciphers should be accurately examined in light of the speed and area constraints imposed by the target environment. We present a re-design of the ASIC-oriented KEELOQ implementation to perform efficient exhaustive key search attacks while fitting tightly the parallel programming model exposed by modern GPUs. Indeed, the bitslicing technique allows the intrinsic parallelism offered by word-oriented SIMD computations to be effectively exploited. Through proper adaptation of the algorithm implementation to a platform radically different from the one it was designed for, we achieved a ×40 speedup in the computation time with respect to a single-core CPU bruteforce attack, employing only consumer grade hardware. The outstanding speedup obtainable points to a significant weakening of the cipher security margin, since it proves that anyone with off-the-shelf hardware is able to circumvent the security measures in place.
The Vicious Cycle of Parental Caregiving and Financial Well-being: A Longitudinal Study of Women.

OBJECTIVES This study examines the relationship between caring for older parents and the financial well-being of caregivers by investigating whether a reciprocal association, or vicious cycle, exists between female caregiver's lower household incomes and caring for elderly parents. METHOD Data for women aged 51 or older with at least 1 living parent or parent-in-law were drawn from the Health and Retirement Survey 2006, 2008, and 2010 (N = 2,093). A cross-lagged panel design was applied with structural equation modeling. RESULTS We found support for the reciprocal relationship between parental caregiving and lower household income. Female caregivers were more likely than noncaregivers to be in lower household income at later observation points. Also, women with lower household income were more likely than women with higher household income to assume caregiving at later observation points. DISCUSSION This study suggests that there exists a vicious cycle of parental care and lower household income among women. A key concern for policy is female caregivers' financial status when care of older parents is assumed and care burden when women's financial status declines.
Development of a Multi-Disciplinary Intervention for the Treatment of Childhood Obesity Based on Cognitive Behavioral Therapy

Along the lines of the evidence-based recommendations, we developed a multi-disciplinary intervention for overweight children 7- to 12-years-old, primarily aiming at helping children to adopt healthier eating habits and a physically active lifestyle. The program combined nutrition intervention, based on a non-dieting approach, with physical activity intervention, implemented through the basic principles of Cognitive Behavioral Therapy (CBT), along with parental support. The program was conducted by dieticians with the collaboration of child psychiatrists and pediatricians. Training and regular supervision upon CBT priniciples application was intended to enhance dieticians' efficiency. The intervention is currently being evaluated to determine its effectiveness in treating childhood obesity.