Miracle-dz/UniFAR-FTUs huggingface dataset:
Inhibition of Tip60 Reduces Lytic and Latent Gene Expression of Kaposi’s Sarcoma-Associated Herpes Virus (KSHV) and Proliferation of KSHV-Infected Tumor Cells

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic virus responsible for the development of Kaposi’s sarcoma, primary effusion lymphoma (PEL), and Multicentric Castleman’s disease in immunocompromised individuals. Despite the burden of these diseases there are few treatment options for afflicted individuals, due in part to our limited understanding of virus-host interactions. Tip60, a histone aceytltransferase (HAT) has been previously shown to interact with both the KSHV latency associated nuclear antigen protein (LANA), which is the main factor in maintaining the viral latent state, and ORF36, a viral kinase expressed in the lytic phase. We further investigated Tip60-virus interaction to ascertain Tip60’s role in the viral life cycle and its potential as a target for future therapeutics. Through modulation of Tip60 expression in HEK293T cells harboring a plasmid containing the KSHV viral episome, Bac36, we found that Tip60 is vital for both lytic replication as well as efficient expression of latent genes. Interestingly, Tip60 small molecule inhibitors, MG149 and NU9056, similarly inhibited latent and lytic genes, and reduced virion production in wild-type KSHV+/EBV- PEL, BCBL-1 cells. Long-term treatment with these Tip60 inhibitors selectively decreased the viability of KSHV-infected B lymphoma cells compared to uninfected cells. From this study, we conclude that Tip60 is important for KSHV infection and its associated cancer development, and Tip60 is therefore a potential target for future antiviral and anticancer therapeutics.
Face Validity of the Single Work Ability Item: Comparison with Objectively Measured Heart Rate Reserve over Several Days

Purpose: The purpose of this study was to investigate the face validity of the self-reported single item work ability with objectively measured heart rate reserve (%HRR) among blue-collar workers. Methods: We utilized data from 127 blue-collar workers (Female = 53; Male = 74) aged 18–65 years from the cross-sectional “New method for Objective Measurements of physical Activity in Daily living (NOMAD)” study. The workers reported their single item work ability and completed an aerobic capacity cycling test and objective measurements of heart rate reserve monitored with Actiheart for 3–4 days with a total of 5,810 h, including 2,640 working hours. Results: A significant moderate correlation between work ability and %HRR was observed among males (R = −0.33, P = 0.005), but not among females (R = 0.11, P = 0.431). In a gender-stratified multi-adjusted logistic regression analysis, males with high %HRR were more likely to report a reduced work ability compared to males with low %HRR [OR = 4.75, 95% confidence interval (95% CI) = 1.31 to 17.25]. However, this association was not found among females (OR = 0.26, 95% CI 0.03 to 2.16), and a significant interaction between work ability, %HRR and gender was observed (P = 0.03). Conclusions: The observed association between work ability and objectively measured %HRR over several days among male blue-collar workers supports the face validity of the single work ability item. It is a useful and valid measure of the relation between physical work demands and resources among male blue-collar workers. The contrasting association among females needs to be further investigated.
The use of biomarkers of exposure of N,N-dimethylformamide in health risk assessment and occupational hygiene in the polyacrylic fibre industry

Background:N,N-dimethylformamide (DMF) was recently prioritised for field studies by the National Toxicology Program based on the potency of its reproductive toxic effects. Aims: To measure accurately exposure to DMF in occupational settings. Methods: In 35 healthy workers employed in the polyacrylic fibre industry, N-methylformamide (NMF) and N-acetyl-S-(N-methylcarbamoyl)cysteine (AMCC) in urine, and N-methylcarbamoylated haemoglobin (NMHb) in blood were measured. Workplace documentation and questionnaire information were used to categorise workers in groups exposed to low, medium, and high concentrations of DMF. Results: All three biomarkers can be used to identify occupational exposure to DMF. However, only the analysis of NMHb could accurately distinguish between workers exposed to different concentrations of DMF. The median concentrations were determined to be 55.1, 122.8, and 152.6 nmol/g globin in workers exposed to low, medium, and high concentrations of DMF, respectively. It was possible by the use of NMHb to identify all working tasks with increased exposure to DMF. While fibre crimpers were found to be least exposed to DMF, persons washing, dyeing, or towing the fibres were found to be highly exposed to DMF. In addition, NMHb measurements were capable of uncovering working tasks, which previously were not associated with increased exposure to DMF; for example, the person preparing the fibre forming solution. Conclusions: Measurement of NMHb in blood is recommended rather than measurement of NMF and AMCC in urine to accurately assess exposure to DMF in health risk assessment. However, NMF and AMCC are useful biomarkers for occupational hygiene intervention. Further investigations regarding toxicity of DMF should focus on highly exposed persons in the polyacrylic fibre industry. Additional measurements in occupational settings other than the polyacrylic fibre industry are also recommended, since the population at risk and the production volume of DMF are high.
PHOSPHODIESTERASE 4B GENETIC VARIANTS ARE NOT ASSOCIATED WITH ANTIPSYCHOTIC-INDUCED TARDIVE DYSKINESIA

Phosphodiesterase 4B (PDE4B) has been evaluated as a genetic risk factor for schizophrenia. Selective PDE4 inhibitor drugs have antipsychotic-like effects and reduce tardive dyskinesia-like movements in animal models. We investigated whether PDE4B genetic variants are associated with antipsychotic-induced tardive dyskinesia incidence and severity in schizophrenia patients. Our sample consisted of 169 Caucasian patients taking typical antipsychotic medication for at least 1 year. We found two PDE4B gene variants to be nominally associated with tardive dyskinesia (rs1338719 and rs7528545) in the overall population and two other variants nominally associated with the presence of tardive dyskinesia and severity in female patients (rs1890196 and rs783036). None of these results survived correction for multiple testing. Overall, our results do not support a genetic association between tardive dyskinesia and PDE4B.
Facial Expression Synthesis and Recognition with Intensity Alignment

This paper proposes a novel approach for facial expression synthesis that can generate arbitrary expressions for a new person with natural expression details. This approach is based on local geometry preserving between the input face image and the target expression image. In order to generate expressions with arbitrary intensity for a new person with unknown expression, this paper also develops an expression recognition scheme based on Supervised Locality Preserving Projections (SLPP), which aligns different subjects and different intensities on one generalized expression manifold. Experimental results clearly demonstrate the efficiency of the proposed algorithm.
A transprecision floating-point platform for ultra-low power computing

In modern low-power embedded platforms, the execution of floating-point (FP) operations emerges as a major contributor to the energy consumption of compute-intensive applications with large dynamic range. Experimental evidence shows that 50% of the energy consumed by a core and its data memory is related to FP computations. The adoption of FP formats requiring a lower number of bits is an interesting opportunity to reduce energy consumption, since it allows to simplify the arithmetic circuitry and to reduce the memory bandwidth required to transfer data between memory and registers by enabling vectorization. From a theoretical point of view, the adoption of multiple FP types perfectly fits with the principle of transprecision computing, allowing fine-grained control of approximation while meeting specified constraints on the precision of final results. In this paper we propose an extended FP type system with complete hardware support to enable transprecision computing on low-power embedded processors, including two standard formats (binary32 and binary16) and two new formats (binary8 and binary16alt). First, we introduce a software library that enables exploration of FP types by tuning both precision and dynamic range of program variables. Then, we present a methodology to integrate our library with an external tool for precision tuning, and experimental results that highlight the clear benefits of introducing the new formats. Finally, we present the design of a transprecision FP unit capable of handling 8-bit and 16-bit operations in addition to standard 32-bit operations. Experimental results on FP-intensive benchmarks show that up to 90% of FP operations can be safely scaled down to 8-bit or 16-bit formats. Thanks to precision tuning and vectorization, execution time is decreased by 12% and memory accesses are reduced by 27% on average, leading to a reduction of energy consumption up to 30%.
Separating the source information in repetition-dependent music and enhancing it by real-time digital audio processing

The repetitive patterns and rhythmic components in the music signal give enough clues about its structure. Using this insight, a repetition-based source separation technique was examined in our earlier work. A set of windowing techniques were examined to optimally separate an acoustic mixture of foreground vocal signal and the repetitive background musical accompaniments, into respective constituents. In this paper, we compare two approaches and their results, for achieving the music-source separation. First, a software-based approach is implemented, by finding the repetition-period from the beat-spectrum derived using the signal processing methods short-time Fourier transform and autocorrelation. The segments having repetitive patterns are identified, and then by taking the element-wise median for these segments, a normalization-based background model is derived from the music-speech mixture. In the second hardware-based approach, the digital signal processing (DSP) capabilities of a PSoC device are explored, for achieving the same objective. Experiments conducted in the first approach using different windowing techniques, indicate better results for the foreground separation, with Blackman window. But, for the background separation, use of Hamming window gives better results. Use of Kaiser window also gives good background-separation. In the second approach using DSP of PSoC devices, the use of High-Pass Filters gives better background music separation by suppressing the foreground vocals, and thereby giving a pleasant background music output. In both the experiments, the effects of digital audio processing are taken into account by use of post-processing, in the overall source-separation problem.
The design and evaluation of a shared object system for distributed memory machines

This paper describes the design and evaluation of SAM, a shared object system for distributed memory machines. SAM is a portable run-time system that provides a global name space and automatic caching of shared data. SAM incorporates mechanisms to address the problem of high communication overheads on distributed memory machines; these mechanisms include tying synchronization to data access, chaotic access to data, prefetching of data, and pushing of data to remote processors. SAM has been implemented on the CM-5, Intel iPSC/860 and Paragon, IBM SP1, and networks of workstations running PVM. SAM applications run on all these platforms without modification. This paper provides an extensive analysis on several complex scientific algorithms written in SAM on a variety of hardware platforms. We find that the performance of these SAM applications depends fundamentally on the scalability of the underlying parallel algorithm, and whether the algorithm's communication requirements can be satisfied by the hardware. Our experience suggests that SAM is successful in allowing programmers to use distributed memory machines effectively with much less programming effort than required today.
Ocimum basilicum affects tracheal responsiveness, lung inflammatory cells and oxidant–antioxidant biomarkers in sensitized rats

Abstract The anti-inflammatory and antioxidant effects of Ocimum basilicum (O. basilicum) was shown previously. In the present study, the effect of O. basilicum on tracheal responsiveness (TR) to methacholine and ovalbumin (OVA), bronchoalveolar lavage fluid (BALF) levels of oxidant–antioxidant biomarkers as well as total and differential white blood cell (WBC) in sensitized rats was examined. Six groups of rats including control (group C), sensitized rats to OVA (group S), S groups treated with three concentrations of O. basilicum (0.75, 1.50, and 3.00 mg/ml) and one concentration of dexamethasone (1.25 μg/ml) (n = 8 for all groups) were studied. TR to methacholine and OVA, total WBC count, percentages of eosinophils, monocytes, neutrophils, and levels of oxidant biomarkers were significantly increased but other measured parameters were significantly decreased in group S compared to group C. TR to methacholine and OVA, percentages of eosinophils, monocytes, neutrophils, and levels of oxidant biomarkers were significantly decreased but lymphocytes and antioxidant biomarkers were significantly increased in S groups treated with dexamethasone and at least two higher concentrations of the extract compared to group S. Total WBC count was also decreased in treated S groups with dexamethasone and high extract concentration. The effect of extract on most measured parameters was significantly lower than dexamethasone treatment. The effects of two higher concentrations of the extract on most variables were significantly higher than the effect of low extract concentration. These results showed the concentration-dependent effect of O. basilicum on tracheal responses, lung inflammatory cells, and oxidant–antioxidant parameters in sensitized rats.
Entry of diabetogenic T cells into islets induces changes that lead to amplification of the cellular response

In an accompanying paper, we find specific localization of diabetogenic T cells only to islets of Langerhans bearing the specific antigen. Instrumental in the specific localization was the presence of intraislet dendritic cells bearing the β-cell-peptide-MHC complex. Here, we report that the entry of diabetogenic CD4 T cells very rapidly triggered inflammatory gene expression changes in islets and vessels by up-regulating chemokines and adhesion molecules. Vascular cell adhesion molecule-1 (VCAM-1) expression was notable in blood vessels, as was intercellular adhesion molecule-1 (ICAM-1). ICAM-1 was also found on β-cells. These expression changes induced the entry of nonspecific T cells that otherwise did not localize to the islets. In contrast to the entry of diabetogenic CD4 T cells, the entrance of nonspecific T cells required a chemokine response and VCAM-1 expression by the islets. IFN-γ was important for the early gene expression changes in the islets. By microarray analysis, we detected up-regulation of a group of IFN-inducible genes as early as 8 h post–T-cell transfer. These studies establish that entry of diabetogenic T cells induces a state of receptivity of islets to subsequent immunological insults.
ML Approach for Early Detection of Sleep Apnea Treatment Abandonment: A Case Study

Sleep apnea is a growing problem in the country, with over 200,000 new cases being identified each year. Continuous positive airway pressure (CPAP) is the best treatment for obstructive sleep apnea (OSA), but is limited by low adherence to treatment. Fairview's Sleep program actively tracks CPAP usage and outcomes and employs tele-health coaching to improve adherence. This labor-intensive protocol is applied to those who are failing to meet early adherence targets. However, the implementation of this is based on heuristic rules which may not be matched to actual outcomes, contacting some patients too late and others unnecessarily. Machine learning can facilitate efficient contact strategies through early and accurate identification of therapy trajectories based on patient history, including EHR data, health information, questionnaires, and daily PAP metrics. Prediction models for classification of patients regarding CPAP adherence at a clinically-important time of 6 months of regular use were built. Using data from the first 30 days of CPAP usage, and a more aggressive decision scenario from the first 13 days of usage, the proposed approach results in an improvement in prediction significantly better than the current approach used by the hospital. Further, it is shown that a hospital can utilize this precise and earlier prediction by implementing appropriate actions based on the patient»s predicted risk level.
Cutting Edge: Integrin α4 Is Required for Regulatory B Cell Control of Experimental Autoimmune Encephalomyelitis

The neutralization of integrin α4 (Itga4) is currently used as treatment in multiple sclerosis. Although most studies have focused on its function on lymphocyte migration to the CNS, we have uncovered the importance of Itga4 for the generation of regulatory B cells in peripheral immune organs and their control of pathogenic T cell response and CNS pathology. Our study underscores the importance of looking at the dual role of B cells in CNS autoimmunity and provides important perspectives regarding the efficacy and side effects associated with Itga4 neutralization and other B cell–targeting therapies.
Extended-Spectrum β-Lactamases and/or Carbapenemases-Producing Enterobacteriaceae Isolated from Retail Chicken Meat in Zagazig, Egypt

Objectives The aim of the present study was to determine the prevalence and to characterize extended-spectrum β-lactamases- and/or carbapenemases-producing Enterobacteriaceae among Enterobacteriaceae isolated from retail chicken meat in Zagazig, Egypt. Methods One hundred and six Enterobacteriaceae isolates were collected from retail chicken meat samples purchased in Zagazig, Egypt in 2013. Species identification was done by MALDI-TOF MS. Screening for ESBL-E was performed by inoculation of isolates recovered from meat samples onto the EbSA (Cepheid Benelux, Apeldoorn, the Netherlands) selective screening agar. ESBL production was confirmed by combination disc diffusion test with clavulanic acid (Rosco, Taastrup, Denmark). Carbapenemases production was confirmed with double disk synergy tests. Resistance genes were characterized by PCR with specific primers for TEM, SHV, and CTX-M and carbapenemases (KPC, NDM, OXA-48, IMP and VIM). PCR products of CTX-M genes were purified and sequenced. Phylogenetic grouping of E. coli was performed by a PCR-based method. Results Of these 106 isolates 69 (65.09%) were ESBL producers. Twelve (11.32%) of these isolates were also phenotypically class B carbapenemases producer. TEM genes were detected in 61 (57.55%) isolates. 49 (46.23%) isolates harbored CTX-M genes, and 25 (23.58%) carried genes of the SHV family. All CPE belonged to the NDM group. The predominant CTX-M sequence type was CTX-M-15 (89.80%). The majority (80%) of the ESBL-EC belonged to low virulence phylogroups A and B1. Conclusions This is the first study from Egypt reporting high rates of ESBLs and carbapenemases (65.09% and 11.32%, respectively) in Enterobacteriaceae isolated from retail chicken meat. These results raise serious concerns about public health and food safety as retail meat could serve as a reservoir for these resistant bacteria which could be transferred to humans through the food chain.
The Optical Janus Effect: Asymmetric Structural Color Reflection Materials

Structurally colored materials are often used for their resistance to photobleaching and their complex viewing‐direction‐dependent optical properties. Frequently, absorption has been added to these types of materials in order to improve the color saturation by mitigating the effects of nonspecific scattering that is present in most samples due to imperfect manufacturing procedures. The combination of absorbing elements and structural coloration often yields emergent optical properties. Here, a new hybrid architecture is introduced that leads to an interesting, highly directional optical effect. By localizing absorption in a thin layer within a transparent, structurally colored multilayer material, an optical Janus effect is created, wherein the observed reflected color is different on one side of the sample than on the other. A systematic characterization of the optical properties of these structures as a function of their geometry and composition is performed. The experimental studies are coupled with a theoretical analysis that enables a precise, rational design of various optical Janus structures with highly controlled color, pattern, and fabrication approaches. These asymmetrically colored materials will open applications in art, architecture, semitransparent solar cells, and security features in anticounterfeiting materials.
Differential Private Data Collection and Analysis Based on Randomized Multiple Dummies for Untrusted Mobile Crowdsensing

Mobile crowdsensing, which collects environmental information from mobile phone users, is growing in popularity. These data can be used by companies for marketing surveys or decision making. However, collecting sensing data from other users may violate their privacy. Moreover, the data aggregator and/or the participants of crowdsensing may be untrusted entities. Recent studies have proposed randomized response schemes for anonymized data collection. This kind of data collection can analyze the sensing data of users statistically without precise information about other users’ sensing results. However, traditional randomized response schemes and their extensions require a large number of samples to achieve proper estimation. In this paper, we propose a new anonymized data-collection scheme that can estimate data distributions more accurately. Using simulations with synthetic and real datasets, we prove that our proposed method can reduce the mean squared error and the JS divergence by more than 85% as compared with other existing studies.
Cognitive Maps-Based Student Model

The main contribution of this PhD thesis is: A proposal for Student Modeling based upon Cognitive Maps (CM's). Its purpose is to anticipate the effects that a teaching-learning experience will produce on a student before its delivery. Thus, this dissertation focuses on the Student Modeling from the causal-effect perspective. Also, our approach aims at predict outcomes stemmed from teaching-learning sessions delivered by Web-based Education Systems (WBES's). Wherefore in WBES's, whose lessons have several sequence strategies and options of content, our Student Model (SM) offers a proactive and adaptive support for a student-centered education.