Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of HIV receptor expression in cervical epithelial cells by Gram-negative bacterial lipopolysaccharide

Background . Sexually transmitted infections (STIs) caused by the Gram-negative bacteria Chlamydia trachomatis and Neisseria gonorrhoeae are associated with an increased risk of HIV acquisition in South African women. HIV infection involves binding of the virus to CD4 + receptors on host cells and subsequent binding to a chemokine co-receptor that mediates fusion with the host target cell membrane. Objective . To investigate the potential impact of STIs on HIV receptor expression in cervical epithelial cells, and the molecular pathways mediating this effect. Methods . Expression of Toll-like receptor 4 (TLR4), CD4 + and CCR5 was investigated in HPV type 18-positive (HeLa) and HPV-negative (C33A) cervical epithelial cells, uterine adenocarcinoma cells (Ishikawa), cervical squamous cell carcinoma tissue and normal cervical tissue by real-time polymerase chain reaction (RT-PCR) analysis. HIV receptor expression in HeLa cells was investigated in the presence/absence of 10 μg/mL bacterial lipopolysaccharide (LPS) and chemical inhibitors of epidermal growth factor receptor (EGFR), extracellular signal regulated kinase (ERK1/2) or cyclo-oxygenase-2 (COX-2) by RT-PCR analysis. Results . TLR4, CD4 + and CCR5 expression was elevated in HeLa, C33A and Ishikawa cell lines and carcinoma tissue, compared with normal cervical tissue. Treatment of HeLa cells with LPS increased expression of the primary HIV chemokine co-receptor CCR5 ( p <0.01) and several alternative HIV receptors including CCR2b (p<0.01), CXCR6 ( p <0.05) and GPR1 ( p <0.05), but not CD4 + . We found that LPSmediated CCR5 expression occurred via induction of the EGFR, ERK1/2 and COX-2 signalling pathways. Conclusion . Our findings suggest that STIs have the potential to enhance susceptibility to HIV infection in women by regulating expression of HIV receptors in cervical epithelial cells.
Assembly of transfected DNA into chromatin: structural changes in the origin‐promoter‐enhancer region upon replication.

Chimeric SV40 DNA containing only the early region, or plasmid DNA harboring the origin‐promoter‐enhancer region of SV40, when introduced into CV‐1 or Cos‐1 monkey cells by DEAE‐dextran mediated transfer are rapidly assembled in a typical chromatin structure revealed by the generation of a regular 190 bp repeat ladder after micrococcal nuclease digestion. DNA replication is not required for this assembly process. Chromatin‐specific DNase I hypersensitive sites are observed in the enhancer region of these minichromosomes. The pattern of the sites differs between non‐replicating and post‐replicated chromatin. The latter is identical to that observed in the lytic cycle. The presence of large T antigen is not sufficient for the shift in the structure of the chromatin. These experiments suggest that replication can modulate protein‐DNA interactions during viral infection or upon cell differentiation.
Stochastic resonance without external periodic force.

A model or -a two-dimensional autonomous system subject to external noise is investigated. Without noise the system has a stable limit cycle in a certain region or control parameter. Various noise-induced effects have been round numerically, such as a noise-induced frequency shirt in the presence or the deterministic limit cycle, and noise-induced coherent oscillations in the absence or the deterministic limit cycle. An interesting result is that the stochastic resonance phenomenon -appears in a system without an external signal and when the asymptotic state or the deterministic system is stationary
A physically-based muscle and skin model for facial animation

Facial animation is a popular area of research which has been around for over thirty years, but even with this long time scale, automatically creating realistic facial expressions is still an unsolved goal. This work furthers the state of the art in computer facial animation by introducing a new muscle and skin model and a method of easily transferring a full muscle and bone animation setup from one head mesh to another with very little user input. The developed muscle model allows muscles of any shape to be accurately simulated, preserving volume during contraction and interacting with surrounding muscles and skin in a lifelike manner. The muscles can drive a rigid body model of a jaw, giving realistic physically-based movement to all areas of the face. The skin model has multiple layers, mimicking the natural structure of skin and it connects onto the muscle model and is deformed realistically by the movements of the muscles and underlying bones. The skin smoothly transfers underlying movements into skin surface movements and propagates forces smoothly across the face. Once a head model has been set up with muscles and bones, moving this muscle and bone set to another head is a simple matter using the developed techniques. The developed software employs principles from forensic reconstruction, using specific landmarks on the head to map the bone and muscles to the new head model and once the muscles and skull have been quickly transferred, they provide animation capabilities on the new mesh within minutes.
PAC Algorithms for Detecting Nash Equilibrium Play in Social Networks: From Twitter to Energy Markets

The detection of agents whose responses satisfy equilibrium play is useful for predicting the dynamics of information propagation in social networks. Using Afriat's theorem of revealed preferences, we construct a non-parametric detection test to detect if the responses of a group of agents is consistent with play from the Nash equilibrium of a concave potential game. For agents that satisfy the detection test, it is useful to learn the associated concave potential function of the game. In this paper, a non-parametric learning algorithm is provided to estimate the concave potential function of agents with necessary and sufficient conditions on the response class for the algorithm to be a probably approximately correct learning algorithm. In the case of response signals measured in noise, a statistical test to detect agents playing a concave potential game that has a pre-specified Type-I error probability is provided. The detection tests and learning algorithm are applied to real-world data sets from the Twitter social network and the Ontario power grid.
Extraction of Adverse Drug Effects from Clinical Records

With the rapidly growing use of electronic health records, the possibility of large-scale clinical information extraction has drawn much attention. We aim to extract adverse drug events and effects from records. As the first step of this challenge, this study assessed (1) how much adverse-effect information is contained in records, and (2) automatic extracting accuracy of the current standard Natural Language Processing (NLP) system. Results revealed that 7.7% of records include adverse event information, and that 59% of them (4.5% in total) can be extracted automatically. This result is particularly encouraging, considering the massive amounts of records, which are increasing daily.
Watermarking-based Color Image Authentication with Detection and Recovery Capability

In this paper a watermarking-based color image authentication with detection and recovery capability is proposed, in which a Halftone image is used as an approximated version of the luminance channel (Y) and a coded version of the coefficients of the Two Dimensional Discrete Cosine Transform of the chrominance channels (Cb, Cr) of the YCbCr color space are used as watermark signal. The luminance and chrominance information is embedded into the sub-bands of lowest frequency of the Integer Wavelet Transform of the original luminance channel using Quantization Index Modulation Dither Modulation. The luminance information in embedded into the LL sub-band meanwhile the chrominance information is embedded into the LH and HL sub-bands. Besides, a Multilayer Perceptron Neural Network is used as inverse halftoning to increase the quality of the recovered image. The experimental results show the effectiveness of the proposed method compared with some published before.
Neointimal hyperplasia rapidly reaches steady state in a novel murine vein graft model.

OBJECTIVE Neointimal hyperplasia remains a principal cause of vein graft failure. Genetic contributions to vein graft neointimal hyperplasia could be well studied in the mouse; however, surgical approaches to vein bypass surgery in the mouse have yet to replicate approaches commonly employed in human patients. Consequently, the goal of this study was to develop a murine interposition vein graft model that reproduces characteristics of human vein graft disease. METHOD Using C57BL/6J mice, we excised inferior venae cavae (IVCs) from donor mice and grafted them, with end-to-side anastomosis, into the carotid circulation of recipients. IVC grafts were harvested from 3 to 56 days postoperatively, and analyzed for the development of neointima and media. RESULTS Thickening of both the vein graft neointima and media progressed rapidly between postoperative weeks 1 and 4, and reached steady state levels by approximately week four, with a graft-wall thickness of 91 +/- 4 microm (14 cell layers), a lumen area of 0.56 mm(2), an average neointima-media ratio of 0.4 to 0.6, and a predominance of alpha-smooth muscle actin-staining cells. Comprising predominately smooth muscle actin-expressing cells, the neointima was 50% thicker in the proximal than in the distal third of the grafts (P <.001), but proximal and distal vein graft anastomoses were widely patent. CONCLUSIONS In syngeneic murine carotid interposition IVC grafts implanted with end-to-side anastomoses, moderate, nonocclusive neointimal hyperplasia reaches steady state after the fourth postoperative week. This neointimal hyperplasia, like that of human grafts, predominates near vein graft anastomoses. This vein graft model should facilitate genetic analyses of the pathogenesis of neointimal hyperplasia.
Brief review of equine genomics: prospects toward exercise and sports science

Submit Manuscript | http://medcraveonline.com mammals. Natural selection and more recently, artificial selection for speed and stamina provided to the modern horses unique adaptations to exercise and training. The actual phenotypes show high aerobic and anaerobic capacities (up to 200 ml/kg.min-1) [1,2] increased muscle mass to body weight ratio [2,3] and efficient locomotion [4,5], however weather these structure and functional changes are related to specific genetic variants remains unclear.
Toddler's Fracture: Presumptive Diagnosis and Treatment

The diagnosis of a toddler's fracture is frequently difficult at the initial evaluation because of negative radiographs. We propose the presumptive diagnosis of toddler's fracture, despite negative radiographs, when the history and physical examination are consistent with the diagnosis. This retrospective study was designed to evaluate how frequently the diagnosis is correct and to determine if there were any differentiating characteristics with respect to history, gait, or physical examination. Thirty-nine children were presumptively diagnosed with toddler's fracture. A total of 16 (41%) toddler's fractures was confirmed on follow-up radiographs. Comparing the children who demonstrated a toddler's fracture with those who did not, no particular characteristic was found that could predict the outcome. To avoid delay in the treatment of toddler's fracture, we recommend a long-leg cast on those children with a history of an acute injury, inability to walk or limp, no constitutional signs, and negative radiographs.
Wnt signalling: variety at the core

The Wnt/β-catenin pathway is a conserved cell-cell signalling mechanism in animals that regulates gene expression via TCF/LEF DNA-binding factors to coordinate many cellular processes. Vertebrates normally have four Tcf/Lef genes, which, through alternative splicing and alternative promoter use give rise to a variety of TCF/LEF isoforms. Recent evidence from several experimental systems suggests that this diversity of TCF/LEF factors is functionally important in vertebrates for mediating tissue- and stage-specific Wnt regulation in embryonic development, stem cell differentiation and associated diseases, such as cancer.
NeuCube for obstacle avoidance in simulated prosthetic vision

Limited by visual percepts elicited by existing visual prothesis, it’s necessary to enhance its functionality to fulfill some challenging tasks for the blind such as obstacle avoidance. This paper provides a new methodology for obstacle avoidance in simulated prosthetic vision by modelling and classifying spatiotemporal (ST) video data. The proposed methodology is based on a novel spiking neural network architecture, called NeuCube as a general framework for video data modelling in simulated prosthetic vision. As an integrated environment including spiking trains encoding, input variable mapping, unsupervised reservoir training and supervised classifier training, the NeuCube consists of a spiking neural network reservoir (SNNr) and a dynamic evolving spiking neural network classifier (deSNN). First input is captured by visual prothesis, then ST feature extraction is utilized in the low-resolution prosthetic vision generated by the prothesis. Finally such ST features are fed to the NeuCube to output classification result of obstacle analysis. Experiments on collected video data and comparison with other computational intelligence methods indicate promising results. The proposed NeuCube-based obstacle avoidance methodology provides useful guidance to the blind, thus improving the current prothesis and hopefully benefiting the future prothesis wearers.
Identification and characterization of two divergently transcribed iron regulated genes in Mycobacterium tuberculosis.

SETTING Low iron availability in the host induces the expression of iron acquisition systems and virulence genes in many pathogens. IdeR is a mycobacterial iron dependent regulator that controls the iron starvation and oxidative stress responses in Mycobacterium smegmatis. It is important to determine the role of IdeR and its regulon in M. tuberculosis, as identification of iron regulated genes can aid in the design of new drugs and generation of attenuated strains. OBJECTIVE A potential IdeR binding site was found in the M. tuberculosis genome flanked by two divergently oriented open reading frames, irg1 and irg2. The aim of this study was to determine whether irg1 and irg2 were iron and IdeR regulated genes. DESIGN Interaction of IdeR with the putative binding sequence was examined by gel shift and footprinting assays. Transcriptional fusions of irg1 and irg2 to IacZ were used to study the effect of iron levels on the expression of these genes. RESULTS IdeR binds to the predicted binding site, which overlaps with the irg1 promoter. irg1 and irg2 expression was decreased by iron in M. tuberculosis and in wild type M. smegmatis, but not in a M. smegmatis ideR mutant. CONCLUSION Two M. tuberculosis iron/IdeR regulated genes were identified. irg1 is predicted to be the M. tuberculosis hisE gene, which is involved in histidine biosynthesis. It is directly upstream of the M. tuberculosis hisG. irg2 encodes a putative membrane protein that is a member of the PPE family.
Detection of Francisella tularensis in ulcers of patients with tularemia by PCR

The diagnosis of human cases of tularemia is usually confirmed by the demonstration of an antibody response to Francisella tularensis, which occurs about 2 weeks after the onset of disease. Due to a high risk of infection in the laboratory, cultivation of the causative agent tends to be avoided. During an outbreak in Sweden, the use of PCR for diagnosing the ulceroglandular form of tularemia was evaluated. Extraction and preparation of F. tularensis DNA from swab samples from the wounds of patients with tularemia involved the use of the nuclease inhibitor guanidine thiocyanate. The DNA was detected by multiplex PCR targeting the 16S rRNA gene and a 17-kDa lipoprotein gene of F. tularensis. In 29 of 40 (73%) patients with serologically confirmed tularemia, F. tularensis DNA was successfully amplified. Considering the limitations of current diagnostic procedures, PCR may become useful for the early diagnosis of tularemia.
A Complex Systems Perspective of Risk Mitigation and Modeling in Development and Acquisition Programs

Abstract : The current methodologies used in risk assessment are heavily subjective and inaccurate invarious life cycle phases of complex engineered systems. The increase in complexity has caused a paradigm shift from root cause analysis to the search of a set of concurrent causes for each event and the relevant complexity content of the system. Many of the systems life cycle risks are currently assessed subjectively by imprecise methodologies such as color-coded risk matrix, and subsequently they suffer from unforeseen failures as well as cost and schedule overruns. This research project proposes a novel approach to major improvement of risk assessment by creating a set of appropriate complexity measures (informed by historical case studies) as pre-indicators of emergence of risks at different stages of a systems development process, and also a framework that enables the decision-makers on assessing the actual risk level at each phase of the development based on requirements, design decisions, and alternatives. The goal of this research is to capture the complexity of the system with some innovative metrics, thus allowing for better decision-making in architecture and design selections.
Physiologic Variability at the Verge of Systemic Inflammation: Multiscale Entropy of Heart Rate Variability Is Affected by Very Low Doses of Endotoxin

ABSTRACT Introduction: Human injury or infection induces systemic inflammation with characteristic neuroendocrine responses. Fluctuations in autonomic function during inflammation are reflected by beat-to-beat variation in heart rate, termed heart rate variability (HRV). In the present study, we determine threshold doses of endotoxin needed to induce observable changes in markers of systemic inflammation, investigate whether metrics of HRV exhibit a differing threshold dose from other inflammatory markers, and investigate the size of data sets required for meaningful use of multiscale entropy (MSE) analysis of HRV. Methods: Healthy human volunteers (n = 25) were randomized to receive placebo (normal saline) or endotoxin/lipopolysaccharide (LPS): 0.1, 0.25, 0.5, 1.0, or 2.0 ng/kg administered intravenously. Vital signs were recorded every 30 min for 6 h and then at 9, 12, and 24 h after LPS. Blood samples were drawn at specific time points for cytokine measurements. Heart rate variability analysis was performed using electrocardiogram epochs of 5 min. Multiscale entropy for HRV was calculated for all dose groups to scale factor 40. Results: The lowest significant threshold dose was noted in core temperature at 0.25 ng/kg. Endogenous tumor necrosis factor &agr; and interleukin 6 were significantly responsive at the next dosage level (0.5 ng/kg) along with elevations in circulating leukocytes and heart rate. Responses were exaggerated at higher doses (1 and 2 ng/kg). Time domain and frequency domain HRV metrics similarly suggested a threshold dose, differing from placebo at 1.0 and 2.0 ng/kg, below which no clear pattern in response was evident. By applying repeated-measures analysis of variance across scale factors, a significant decrease in MSE was seen at 1.0 and 2.0 ng/kg by 2 h after exposure to LPS. Although not statistically significant below 1.0 ng/kg, MSE unexpectedly decreased across all groups in an orderly dose-response pattern not seen in the other outcomes. Conclusions: By using repeated-measures analysis of variance across scale factors, MSE can detect autonomic change after LPS challenge in a group of 25 subjects using electrocardiogram epochs of only 5 min and entropy analysis to scale factor of only 40, potentially facilitating MSE’s wider use as a research tool or bedside monitor. Traditional markers of inflammation generally exhibit threshold dose behavior. In contrast, MSE’s apparent continuous dose-response pattern, although not statistically verifiable in this study, suggests a potential subclinical harbinger of infectious or other insult. The possible derangement of autonomic complexity prior to or independent of the cytokine surge cannot be ruled out. Future investigation should focus on confirmation of overt inflammation following observed decreases in MSE in a clinical setting.
Altered oxidative stress in overtrained athletes

Abstract The purpose of the present study was to examine the relationship between oxidative stress and overtraining syndrome. Indicators of oxidative stress (plasma protein carbonyls, nitrotyrosine, and malondialdehyde) and antioxidant status (oxygen radical absorbance capacity) were measured in severely overtrained (two women, five men) and control athletes (five women, five men). Samples were collected from both groups at baseline (i.e. in the overtraining state of overtrained athletes) and after 6 months of recovery, both at rest and immediately after an exercise test to volitional exhaustion. At baseline, overtrained athletes had higher plasma protein carbonyls at rest than controls (mean difference 0.03 nmol · mg−1, 95% CI = 0.01–0.05 nmol · mg−1, P = 0.003, effect size = 0.40). Both at baseline and after recovery, exercise to exhaustion led to an increase in oxygen radical absorbance capacity and malondialdehyde (P = 0.001–0.006) in the controls but not in the overtrained athletes. Furthermore, at baseline, only overtrained athletes showed negative correlations between oxygen radical absorbance capacity at rest and protein carbonyls after exhaustive exercise (r = −0.98, P = 0.0001). These results suggest that increased oxidative stress has a role in the pathophysiology of overtraining syndrome. The attenuated responses of oxidative stress and antioxidant capacity to exercise in the overtrained state could be related to an inability to perform exercise effectively and impaired adaptation to exercise.
Reduced human platelet uptake by pig livers deficient in the asialoglycoprotein receptor 1 protein

The lethal thrombocytopenia that accompanies liver xenotransplantation is a barrier to clinical application. Human platelets are bound by the asialoglycoprotein receptor (ASGR) on pig sinusoidal endothelial cells and phagocytosed. Inactivation of the ASGR1 gene in donor pigs may prevent xenotransplantation‐induced thrombocytopenia.
Time-Resolved Fluorescence of Lanthanide Probes and Applications in Biotechnology

The relaxation of excited molecular states is often followed by the emission of light. Molecular excited states are related to the orbital, vibrational, and rotational levels of the orbital electrons. In addition, the electron spin determines the singlet and triplet states. In the singlet state the spin of an electron is paired, whereas in the triplet state the spin is not paired. When a molecule is excited to an upper singlet energy level, such as S2 (Figure 1), it can rapidly (10−10 sec) go to the lowest excited state S1 without emission of light. From S1 the molecule may go to any of the rotational and vibrational levels of the ground electronic state S0. This happens either by fluorescence emission or by nonradiative internal processes, referred to as intersystem crossing. From T1, the molecule can return to S0 by nonradiative processes or by a radiative process called phosphorescence. Under suitable conditions S1 and T1 can also transfer their excitation energy to other molecules.