Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibodies against Human Cytomegalovirus in the Pathogenesis of Systemic Sclerosis: A Gene Array Approach

Background Systemic sclerosis is an autoimmune disease characterized by immunological abnormalities, vascular damage, and fibroblast proliferation. We have previously shown that a molecular mimicry mechanism links antibodies against the human-cytomegalovirus-derived protein UL94 to the pathogenesis of systemic sclerosis. The UL94 epitope shows homology with NAG-2, a surface molecule highly expressed on endothelial cells. Anti-UL94 peptide antibodies purified from patients' sera induce apoptosis of endothelial cells upon engagement of the NAG-2–integrin complex. Methods and Findings We show here that NAG-2 is expressed on dermal fibroblasts and that anti-UL94 antibodies bind to fibroblasts. We have used the gene array strategy (Affimetrix oligonucleotide microarrays) to analyze the transcriptional profile in response to a 4-h and an 8-h treatment with antibodies against the UL94 peptide in endothelial cells and dermal fibroblasts. Exposure of endothelial cells to anti-UL94 antibodies had a profound impact on gene expression, resulting in the upregulation of 1,645 transcripts. Several gene clusters were upregulated including genes encoding adhesion molecules, chemokines, colony-stimulating factors (CSFs), growth factors, and molecules involved in apoptosis. Following antibody stimulation, dermal fibroblasts showed an upregulation of 989 transcripts and acquired a “scleroderma-like” phenotype. Indeed, genes involved in extracellular matrix deposition, growth factors, chemokines, and cytokines were upregulated. We confirmed the microarray results by real-time quantitative polymerase chain reaction and by measuring some of the corresponding proteins with ELISA and Western blotting. Conclusion Our results show that anti-human-cytomegalovirus antibodies may be linked to the pathogenesis of systemic sclerosis not only by inducing endothelial cell activation and apoptosis but also by causing activation of fibroblasts, one of the hallmarks of the disease.
CAD transactions best paper a ward "SPFD: a new method to express functional flexibility"

In this paper, we propose a unique way to express functional flexibility by using sets of pairs of functions called "Sets of Pairs of Functions to be Distinguished" (SPFDs) rather than traditional incompletely specified functions. This method was very naturally derived from a unique concept for distinguishing two logic functions, which we explain in detail in this paper. The flexibility represented by an SPFD assumes that the internal logic of a node in a circuit can be freely changed, SPFDs make good use of this assumption, and they can express larger flexibility than incompletely specified functions in some cases. Although the main subject of this paper is to explain the concept of SPFDs, we also present an efficient method for calculating the functional flexibilities by SPFDs because the concept becomes useful only if there is an efficient calculation method for it. Moreover, we present a method to use SPFDs for circuit transformation along with a proof of the correctness of the method, We further make a comparison between SPFDs and compatible sets of permissible functions (CSPFs), which express functional flexibility by incompletely specified functions. As an application of SPFDs, we show a method to optimize LUT (look-up table) networks and experimental results.
Linezolid in Prophylaxis against Experimental Aortic Valve Endocarditis Due to Streptococcus oralis or Enterococcus faecalis

ABSTRACT There are no experimental studies regarding the prophylactic efficacy of linezolid against infective endocarditis. Nonbacterial thrombotic endocarditis of the aortic valve was induced in rabbits by the insertion of a polyethylene catheter. Twenty-four hours later, animals were randomly assigned to a control group, and groups receiving either ampicillin (two doses of 40 mg/kg of body weight each, given intravenously, 2 h apart) or linezolid (a single per os dose of 75 mg/kg). The first dose of ampicillin and the single dose of linezolid were administered 0.5 and 1 h, respectively, prior to the intravenous inoculation of ∼107 CFU of Streptococcus oralis or Enterococcus faecalis. Linezolid peak levels in rabbit serum were similar to the peak serum levels in humans following a 600-mg oral dose of linezolid. Linezolid prevented endocarditis in 87% of S. oralis-challenged rabbits (P < 0.001 versus controls; P = 0.026 versus ampicillin). In rabbits challenged with E. faecalis, linezolid prevented endocarditis in 73% (P = 0.003 versus controls; P = 0.049 versus ampicillin). Ampicillin prevented endocarditis due to S. oralis or due to E. faecalis in 47% (P = 0.005 versus controls) and in 30% (P = not significant versus controls) of the challenged animals, respectively. In conclusion, linezolid was effective as prophylaxis against endocarditis caused by a strain of S. oralis and to a lesser degree against that caused by a strain of E. faecalis. Its prophylactic efficacy was superior to that of ampicillin.
Continued expression of recombination‐activating genes and TCR gene recombination in human peripheral T cells

It has been reported that a small population of peripheral T lymphocytes are capable of expressing V(D)J recombinase and initiating secondary V(D)J rearrangements. To determine whether RAG‐expression and secondary TCR gene recombination in peripheral T cells are an antigen‐driven process in secondary lymphoid tissues, we examined naive CD4+ T cells, activated/memory CD4+ T cells, and germinal center T cells from human tonsils. Our results showed that low levels of RAG‐1 and RAG‐2 mRNA were present in all T cell subpopulations except CD3+/CD4– T cells. LM‐PCR analyses for double‐strand DNA breaks showed that all the T cell subsets expressing RAG genes contain double‐strand signal break ends, indicating ongoing TCR gene recombination. Continued RAG gene expression, introducing and repairing of double‐strand DNA breaks at the TCR loci in the periphery may have significant implications in the development of some T cell neoplasms.
Analysis of pace‐maker and repolarization currents in frog atrial muscle.

1. A quantitative analysis of the time‐dependent component of outward membrane current in atrial wall trabeculae from Rana catesbeiana and Rana ridibunda has been carried out using a double sucrose gap technique. 2. Separation of the different components of delayed outward current was hampered by the sigmoid onset of one of the outward current systems ixfast and by the development of potassium ion accumulation which prevented current activation from reaching a steady state at positive membrane potentials. Semilogarithmic analysis of positive current decay tails recorded immediately following square voltage clamp depolarizations was therefore used to separate the two membrane conductance components ixfast and ixslow and the third component, attributable to potassium ion accumulation, which was almost invariably present in the tails. 3. It is shown that inaccuracies in this method of semilogarithmic separation of components caused by visual assessment of the i3 (accumulation) line are minor compared with the large changes in the time constants of ixfast and more especially of ixslow which would result from ignoring the potassium accumulation component. 4. Such semilogarithmic separation of the three components of outward current gave separate activation curves for each of the two membrane conductance components, ixfast and ixslow. 5. Measurement of 'total' activation curves in which all components of outward current were represented could be made more easily and fairly reliably. The position and shape of these activation curves on the voltage axis were found to closely resemble those obtained by three component separation. It is therefore suggested that such a simplified analysis reflects the properties of the individual currents sufficiently well for it to be of use in preliminary studies of, for example, drug action. 6. The kinetic properties of the atrial outward currents have been investigated over a wide potential range. Because of the presence of potassium ion accumulation, an indirect method of obtaining the average value of 1/gamma for outward current decay at negative potentials had to be employed. 7. It is shown that some degree of inward‐going rectification is associated with the outward current systems of frog atrium. 8. The possible reasons for the differences between the analysis presented here and those presented earlier by us (Brown & Noble, 1969a, b) and by Ojeda & Rougier (1974) are discussed.
Eigenvalue Dynamics of a Central Wishart Matrix With Application to MIMO Systems

We investigate the dynamic behavior of the stationary random process defined by a central complex Wishart matrix W(t) as it varies along a certain dimension t. We characterize the second-order joint cumulative distribution function (cdf) of the largest eigenvalue, and the second-order joint cdf of the smallest eigenvalue of this matrix. We show that both cdfs can be expressed in exact closed-form in terms of a finite number of well-known special functions in the context of communication theory. As a direct application, we investigate the dynamic behavior of the parallel channels associated with multiple-input multiple-output (MIMO) systems in the presence of Rayleigh fading. Studying the complex random matrix that defines the MIMO channel, we characterize the second-order joint cdf of the signal-to-noise ratio (SNR) for the best and worst channels. We use these results to study the rate of change of MIMO parallel channels, using different performance metrics. For a given value of the MIMO channel correlation coefficient, we observe how the SNR associated with the best parallel channel changes slower than the SNR of the worst channel. This different dynamic behavior is much more appreciable when the number of transmit (NT) and receive (NR) antennas is similar. However, as NT is increased while keeping NR fixed, we see how the best and worst channels tend to have a similar rate of change.
Effect of Glucose or Fat Challenge on Aspirin Resistance in Diabetes

Aspirin has lower antiplatelet activity in diabetic patients. Our aim is to study the roles of acute hyperglycemia and hyperlipidemia on aspirin function in diabetic subjects with and without cardiovascular disease. Using urine thromboxane (pg/mg creatinine) and VerifyNow (Aspirin Resistance Measures-ARU), we investigated diabetic subjects during a 2-hour glucose challenge (n = 49) or a 4-hour fat challenge (n = 11). All subjects were currently taking aspirin (81 or 325 mg). After fat ingestion, urine thromboxane increased in all subjects (Mean ± SE before: after) (1209 ± 336: 1552 ± 371, P = .01), while we noted a trend increase in VerifyNow measures (408 ± 8: 431 ± 18, P = .1). The response to glucose ingestion was variable. Diabetic subjects with cardiac disease and dyslipidemia increased thromboxane (1693 ± 364: 2799 ± 513, P < .05) and VerifyNow (457.6 ± 22.3: 527.1 ± 25.8, P < .05) measures after glucose. We conclude that saturated fat ingestion increases in vivo thromboxane production despite aspirin therapy.
Distributed under Creative Commons Cc-by 4.0 the Concept of Watson's Carative Factors in Nursing and Their (dis)harmony with Patient Satisfaction

Background. Constant reviews of the caring behavior of nurses and patient satisfaction help to improve the quality of nursing. The aim of our research was to explore relationships between the level of nursing education, the perception of nurses and nursing assistants of Watson's carative factors, and patient satisfaction. Methods. A questionnaire survey using a convenience sample of 1,098 members of nursing teams and a purposive sample of 1,123 patients in four health care institutions in Slovenia was conducted in August 2012. A demographic questionnaire and the Caring Nurse-Patient Interactions Scale (nurse version) were delivered to the nurses. A Hospital Consumer Assessment of Health Plans Survey was delivered to discharged patients. Data were analyzed using descriptive and inferential statistics. Results. Carative factor sensibility was related to the level of nursing education. Patients were satisfied with the care received from nurses, nursing assistants and hospitals, although we found differences between the perceptions of nurses and nursing assistants of carative factors and patient satisfaction. By comparing only the perceptions of nurses and nursing assistants of carative factors in health care institutions, differences were found for seven out of ten carative factors. Discussion. We did not find major significant differences between carative factors and level of nurse education, except in one carative factor. Differences in perceptions of carative factors between health care institutions are probably the result of different institutional factors. The results can be of great benefit to nurse administrators and educators, indicating the factors that must be taken into account for enhancing patient satisfaction. Emphasis on caring theories should be placed in nursing education and their application in nursing practice.
Optimization of the Oertli CataRhex 3® phacoemulsification machine

Purpose The aim of this study was to determine optimal bottle height, vacuum, aspiration rate, and power settings of the Oertli CataRhex 3® phacoemulsification machine. Methods Porcine lens nuclei were hardened with formalin and cut into 2.0 mm cubes. Lens cubes were emulsified using the easyTip® 2.2 mm at 30°. Fragment removal time (efficiency) and fragment bounces off the tip (chatter) were measured. Settings tested included bottle height of 60, 80, 100 and 120 cm; aspiration rate of 40, 45, and 50 mL/min; vacuum of 400, 500, and 600 mmHg; and power of 50, 60, 70, 80, 90, and 100%. Results Efficiency and chatter increased in a linear fashion with increasing vacuum to 600 mmHg (P=0.017, P=0.046, respectively). The most efficient aspiration rate was 50 mL/min, although this finding lacked statistical significance (P=0.66). Increasing power increased efficiency up to 80% without increasing chatter (P=0.042, P=0.71, respectively). Compared to all other power settings, chatter was increased at 100% (P=0.014). Conclusion The most efficient machine settings were vacuum at 600 mmHg, aspiration rate at 50 mL/min, and power at 80%.
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out. We characterized the features of mammalian tissue transcriptomes at the gene level through analysis of RNA deep sequencing (RNA-Seq) data across human and mouse tissues and cell lines. We observed that roughly 8,000 protein-coding genes were ubiquitously expressed, contributing to around 75% of all mRNAs by message copy number in most tissues. These mRNAs encoded proteins that were often intracellular, and tended to be involved in metabolism, transcription, RNA processing or translation. In contrast, genes for secreted or plasma membrane proteins were generally expressed in only a subset of tissues. The distribution of expression levels was broad but fairly continuous: no support was found for the concept of distinct expression classes of genes. Expression estimates that included reads mapping to coding exons only correlated better with qRT-PCR data than estimates which also included 3′ untranslated regions (UTRs). Muscle and liver had the least complex transcriptomes, in that they expressed predominantly ubiquitous genes and a large fraction of the transcripts came from a few highly expressed genes, whereas brain, kidney and testis expressed more complex transcriptomes with the vast majority of genes expressed and relatively small contributions from the most expressed genes. mRNAs expressed in brain had unusually long 3′UTRs, and mean 3′UTR length was higher for genes involved in development, morphogenesis and signal transduction, suggesting added complexity of UTR-based regulation for these genes. Our results support a model in which variable exterior components feed into a large, densely connected core composed of ubiquitously expressed intracellular proteins.
Effects of soil tillage and crop rotation on the development of wheat stem base diseases

Abstract Wheat stem base disease (WSD) is an important disease complex which can be caused by various pathogens with variable life cycles, ecological requirements and sensitivities to fungicides. Agronomic practices are considered important tools to control this disease complex and influence the spectrum of fungal communities in infected wheat stems. The aim of the present study was to determine the impact of crop rotation schemes and soil tillage methods on the development of WSD and to elucidate the spectrum of causal agents of this disease. The development of WSD was assessed in a two-factorial (soil tillage practice and crop rotation) experiment. The incidence of WSD was evaluated at the BBCH growth stages 83–85. Causal agents of WSD and other fungi were identified using molecular methods. The soil tillage method did not influence the development of WSD, but the impact of crop rotation was significant, and the cropping system where oilseed rape, barley and faba beans were included decreased disease levels. Members of the genera Oculimacula and Fusarium were the most prevalent fungi associated with WSD. Moreover, fungi from other taxonomic groups were detected, with Phaeosphaeria spp. being prevalent. An increasing occurrence of Microdochium spp. was also observed. In conclusion, agronomic practices influenced the level of WSD, but no distinct impact on the fungal spectrum was identified. Further investigation is required to clarify the roles that pathogens and fungi from other taxonomic groups play in the fungal–wheat relationship.
CT identification of coeliac ganglia.

The authors achieved the "in vivo" identification of the coeliac ganglia (C.G.), using computerised tomography (CT). This result was confirmed by autopsies and by CT scans of an anatomical specimen in which the coeliac ganglia had been previously marked. CT allows an exact location of the coeliac ganglia and can be very useful for a precise alcoholic neurolysis of the coeliac plexus.
Characterization of glycogen synthetases and phosphorylases in transplantable rat hepatomas.

Summary A study of the chemical and kinetic properties of a series of transplantable, chemically induced rat hepatomas has revealed profound alterations in isozyme patterns of glycogen synthetase and phosphorylase. Highly differentiated, slow-growing hepatomas retain the liver-type isozymes, but with decreased differentiation and increased growth rate these are largely or entirely replaced by nonhepatic isozymes. The phosphorylase of poorly differentiated hepatomas was a third form, shown by isoelectric focusing and by immunochemical criteria to be different from either the liver or muscle isozymes. This form was also present in 21-day fetal liver, together with the adult liver isozyme. All of the hepatomas contained the phosphatases and kinases that interconvert the a and b forms, and preliminary data indicate that the synthetase phosphatase of the poorly differentiated hepatomas also is different from the liver phosphatase. Total synthetase activity was high in liver and muscle, lower in the well- to highly differentiated hepatomas, and very low in poorly differentiated tumors, except for the Novikoff ascites hepatoma, the only one of the poorly differentiated tumors that stored appreciable glycogen. In all tissues, b form predominated. Total phosphorylase activity was highest in muscle, predominantly in the b form; lower in liver; and still lower in tumors. There was no correlation between the activity of tumor phosphorylase and the degree of differentiation or the storage of glycogen, and most of the liver and hepatoma phosphorylase was in the a form.
Enhancing object, action, and effect recognition using probabilistic affordances

Recent advances in deep learning, in particular in convolutional neural networks (CNNs), have been widely used in robotics for object classification and action recognition, among others, with very high performance. Nevertheless, this high performance, mostly in classification tasks, is rarely accompanied by reasoning processes that consider the relationships between objects, actions, and effects. In this article, we used three CNNs to classify objects, actions, and effects that were trained with the CERTH-SOR3D dataset that has more than 20,000 RGB-D videos. This dataset involves 14 objects, 13 actions, and in this article was augmented with seven effects. The probabilistic vector output of each trained CNN was combined into a Bayesian network (BN) to capture the relationships between objects, actions, and effects. It is shown that by probabilistically combining information from the three classifiers, it is possible to improve the classification performance of each CNN or to level the same performance with less training data. In particular, the recognition performance improved from 71.2% to 79.7% for actions, 85.0%–86.7% for objects, and 77.0%–82.1% for effects. In the article, it is also shown that with missing information, the model can still produce reasonable classification performance. In particular, the system can be used for reasoning purposes in robotics, as it can make action planning with information from object and effects or it can predict effects with information from objects and actions.
A PEDF-Derived Peptide Inhibits Retinal Neovascularization and Blocks Mobilization of Bone Marrow-Derived Endothelial Progenitor Cells

Proliferative diabetic retinopathy is characterized by pathological retinal neovascularization, mediated by both angiogenesis (involving mature endothelial cells) and vasculogenesis (involving bone marrow-derived circulating endothelial progenitor cells (EPCs)). Pigment epithelium-derived factor (PEDF) contains an N-terminal 34-amino acid peptide (PEDF-34) that has antiangiogenic properties. Herein, we present a novel finding that PEDF-34 also possesses antivasculogenic activity. In the oxygen-induced retinopathy (OIR) model using transgenic mice that have Tie2 promoter-driven GFP expression, we quantified Tie2GFP+ cells in bone marrow and peripheral blood by fluorescence-activated cell sorting (FACS). OIR significantly increased the number of circulating Tie2-GFP+ at P16, correlating with the peak progression of neovascularization. Daily intraperitoneal injections of PEDF-34 into OIR mice decreased the number of Tie2-GFP+ cells in the circulation at P16 by 65% but did not affect the number of Tie2-GFP+ cells in the bone marrow. These studies suggest that PEDF-34 attenuates EPC mobilization from the bone marrow into the blood circulation during retinal neovascularization.