Miracle-dz/UniFAR-FTUs huggingface dataset:
Primate lentiviruses use at least three alternative strategies to suppress NF-κB-mediated immune activation

Primate lentiviruses have evolved sophisticated strategies to suppress the immune response of their host species. For example, HIV-2 and most simian immunodeficiency viruses (SIVs) use their accessory protein Nef to prevent T cell activation and antiviral gene expression by downmodulating the T cell receptor CD3. This Nef function was lost in HIV-1 and other vpu-encoding viruses suggesting that the acquisition of Vpu-mediated NF-κB inhibition reduced the selection pressure for inhibition of T cell activation by Nef. To obtain further insights into the modulation of NF-κB activity by primate lentiviral accessory factors, we analyzed 32 Vpr proteins from a large panel of divergent primate lentiviruses. We found that those of SIVcol and SIVolc infecting Colobinae monkeys showed the highest efficacy in suppressing NF-κB activation. Vpr-mediated inhibition of NF-κB resulted in decreased IFNβ promoter activity and suppressed type I IFN induction in virally infected primary cells. Interestingly, SIVcol and SIVolc differ from all other primate lentiviruses investigated by the lack of both, a vpu gene and efficient Nef-mediated downmodulation of CD3. Thus, primate lentiviruses have evolved at least three alternative strategies to inhibit NF-κB-dependent immune activation. Functional analyses showed that the inhibitory activity of SIVolc and SIVcol Vprs is independent of DCAF1 and the induction of cell cycle arrest. While both Vprs target the IKK complex or a factor further downstream in the NF-κB signaling cascade, only SIVolc Vpr stabilizes IκBα and inhibits p65 phosphorylation. Notably, only de-novo synthesized but not virion-associated Vpr suppressed the activation of NF-κB, thus enabling NF-κB-dependent initiation of viral gene transcription during early stages of the replication cycle, while minimizing antiviral gene expression at later stages. Our findings highlight the key role of NF-κB in antiviral immunity and demonstrate that primate lentiviruses follow distinct evolutionary paths to modulate NF-κB-dependent expression of viral and antiviral genes.
Dormancy as a Strategic Response to Detrimental Public Policy

Organizations in democratic societies often encounter detrimental public policies that are later reversed through rather predictable political cycles. The standard organizational responses to detrimental public policies examined in the literature include exiting the market altogether, attempting to change the public policy through various political strategies, or passively complying with the policy. However, these responses might not be suitable when a detrimental policy is likely to be reversed. In this paper, I consider organizational dormancy, which entails a temporary reduction in an organization’s level of activity, as a viable alternative response. I propose that some organizations might be able to undergo a period of strategic inactivity in response to the onset of a detrimental public policy and maintain this inactivity until a favorable public policy returns. I also propose that such dormancy is rewarded when the favorable policy returns. An investigation of a panel of private commercial banks in the Indian banking industry from 1981 to 2004 lends support to this proposal.
Assessment of Pain Expression in Infant Cry Signals Using Empirical Mode Decomposition

Summary Background:The presence of decoupling, i.e. the absence of coupling between fundamental frequency variation and intensity contour during phonetic crying, and its extent, reflects the degree of maturation of the central nervous system. Objectives: The aim of this work was to evaluate whether Empirical Mode Decomposition (EMD) is a suitable technique for analyzing infant cries. We hereby wanted to assess the existence and extent of decoupling in term neonates and whether an association between decoupling (derived from EMD) and clinical pain expression could be unveiled. Methods: To assess decoupling in healthy term neonates during procedural pain, 24 newborns were videotaped and crying was recorded during venous blood sampling. Besides acoustic analysis, pain expression was quantified based on the Modified Behavioral Pain Scale (MBPS). Fundamental frequency and the intensity contour of the cry signals were extracted by applying the EMD to the data, and the correlation between the two was studied. Results: Based on data collected in healthy term neonates, correlation coefficients varied between 0.39 and 0.83. The degree of decoupling displayed extended variability between the neonates and also in different cry bouts in a crying sequence within an individual neonate. Conclusion: When considering the individual ratio between the mean correlation of cry bouts during a crying sequence and their standard deviation, there seems to be a positive trend with increasing MBPS value. This might indicate that higher stressed subjects have less consistency in the investigated acoustic cry features, concluding that EMD has potential in the assessment of infant cry analysis.
Death of the Alpha: Within‐Community Lethal Violence Among Chimpanzees of the Mahale Mountains National Park

Chimpanzees (Pan troglodytes) are capable of extreme violence. They engage in inter‐group, sometimes lethal, aggression that provides the winners with an opportunity to enlarge their territory, increase their food supply and, potentially, attract more mates. Lethal violence between adult males also occurs within groups but this is rare; to date, only four cases (three observed and one inferred) have been recorded despite decades of observation. In consequence, the reasons for within‐group lethal violence in chimpanzees remain unclear. Such aggression may be rare due to the importance of coalitions between males during inter‐group encounters; cooperation between males is also thought to be key in the defense or advancement of social rank within the group. Previous accounts of within‐group lethal violence concern victims who were low‐ranking males; here we provide the first account of the killing of an incumbent alpha male by a coalition of adult males from the same community. We found no clear evidence that the alpha male's position was under threat during the months before the lethal attack: the male dominance hierarchy was highly stable, with low rates of male–male aggression, and there were no significant changes in social interactions (i.e. grooming and aggression) between the alpha male and the other adult males. Two of the four attackers were former alpha males and were the individuals with whom the victim appeared, in the period preceding his death, to be most strongly affiliated: his most frequent grooming partners and those with whom he spent most time in proximity. The lethal attack triggered a period of instability in the male hierarchy and was likely an opportunistic attempt to seize alpha status by the third‐ranking male. Am. J. Primatol. 75:789–797, 2013. © 2013 Wiley Periodicals, Inc.
Trends in US Contact Lens Prescribing 2002 to 2014

PurposeTo document contact lens prescribing patterns in the United States between 2002 and 2014. MethodsA survey of contact lens prescribing trends was conducted each year between 2002 and 2014, inclusive. Randomly selected contact lens practitioners were asked to provide information relating to 10 consecutive contact lens fits between January and March each year. ResultsOver the 13-year survey period, 1650 survey forms were received from US practitioners representing details of 7702 contact lens fits. The mean (±SD) age of lens wearers was 33.6 (±15.2) years, of whom 65.2% were female. Rigid lens new fits decreased from 13.0% in 2002 to 9.4% in 2014. Across this period, silicone hydrogels have replaced mid water contact lens hydrogels as the soft lens material of choice. Toric lenses represented about 25 to 30% of all soft lens fits. Multifocal soft lenses are generally preferred to monovision. Daily disposable lens fits have recently increased, and in 2014, they represented 27.1% of all soft lens fits. Most lenses are prescribed on 1 to 2 weekly or monthly lens replacement regimen. Extended wear remains a minority lens wearing modality. The vast majority of those wearing reusable lenses use multipurpose lens care solutions. Lenses are mostly worn 7 d/wk. ConclusionsThis survey has revealed prescribing trends and preferences in the United States over the past 13 years.
Application of compressive sensing for EEG source localization in Brain Computer Interfaces

Brain-Computer Interfaces (BCIs) provide a way to communicate without movement and can offer significant clinical benefits therefore. Electrical brain activity recorded using electroencephalography (EEG) can be automatically interpreted by supervised learning classifiers according to the descriptive features of the signal. Compressive sensing paradigm commonly used for array antenna design and signal processing can be used to solve the underdetermined EEG source localization problem in order to extract sparse cortical current topographies to be used as spatial features for classification. This paper investigates the performance of the novel feature extraction method based on sparse source localization.
Prediction of cutting parameters based on improved neural networks

The prediction and control of cutting process was a complicated problem and the suitable cutting parameters are instrumental to cutting process, the prediction models for cutting parameters realized with artificial neural networks was proposed in this paper. Artificial neural networks have strong non-linear modeling ability which can express the nonlinear mapping relation of input and output, but the traditional BP neural networks has many shortcomings such as easily step into local minimum, with weak generalization ability, especially the middle layer neuron are hard to determine, so the correlation pruning algorithm was applied to resolve the problem, the neural networks prediction models was created and the correlation of hidden layer nodes was analyzed and the algorithm was programmed, the simulation taken under MATLAB software which compared new algorithm with traditional BP algorithm, which shows the new methods is effective and can provide a guidance to optimizing turning parameters and turning process control.
The use of semi‐automated EBV IgG avidity determination for the diagnosis of infectious mononucleosis

The diagnosis of acute Epstein‐Barr virus (EBV) infection is based frequently on the combination of positive viral capsid antigen (VCA) IgM antibodies and negative EB viral nuclear antigen 1 (EBNA‐1) IgG antibodies. However, both VCA IgM and EBNA‐1 IgG can provide false positive and false negative results. Therefore, situations in which the EBV serology remains unclear are not uncommon. Determination of EBV IgG avidity can clarify the EBV status in these patients. So far, mainly immunofluorescence assays have been used for this purpose. These tests are laborious, their evaluation is subjective, and automation is difficult. Therefore, two commercially available microtiter plate enzyme immunoassays (EIA) were compared for their usefulness for semi‐automated EBV IgG avidity determination. One assay is based on a mixture of EBV antigens, the other assay uses a synthetic peptide of the VCA‐complex. Patient sera of confirmed acute and past EBV infections were tested for avidity by both assays. The results with the antigen mixture assay proved to be highly sensitive (100%) and specific (100%). Avidity index calculations on the basis of one‐point‐quantification titers gave better results than calculations using OD values. Determination of EBV IgG avidity by the peptide assay was complicated by the fact that it was less sensitive than the antigen mixture assay for IgG detection in acute EBV infections. On the other hand, about 30% of the samples had to be retested with the peptide assay in a higher dilution because the IgG units in initial testing fell outside the range covered by the standard curve. Using OD values of the peptide EIA, the sensitivity was 99% but the specificity of detection of acute EBV infections was only 86%. Thus, while the peptide EBV avidity assay is unsuitable as a confirmatory assay, avidity testing with the antigen mixture assay is a useful tool to resolve equivocal EBV serologies. Avidity assays on the basis of EIA can be automated which should lead to wider use of this methodology. J. Med. Virol. 54:145–153, 1998. © 1998 Wiley‐Liss,Inc.
A Multi‐center Study of Intrathecal Neostigmine for Analgesia following Vaginal Hysterectomy

Background Intrathecal neostigmine injection produces analgesia in volunteers and reduces hypotension from intrathecal bupivacaine in animals. Initial clinical trials with neostigmine studied doses of more than 100 [micro sign]g, but animal studies suggest that smaller doses may be effective. In addition, all controlled clinical trials of neostigmine have come from one Brazilian university. This multicenter, placebo‐controlled trial investigated the effects of 25‐75 [micro sign]g intrathecal neostigmine on analgesia and blood pressure in women undergoing vaginal hysterectomy. Methods After institutional review board approval was obtained at the three university centers, and after patients gave informed consent, 92 women scheduled for vaginal hysterectomy were randomized to receive an intrathecal injection of 2 ml bupivacaine, 0.75%, in dextrose plus either 1 ml saline or 25, 50, or 75 [micro sign]g neostigmine. Blood pressure, heart rate, pain and nausea (both assessed by visual analog scale), and intravenous morphine use were recorded during surgery and at specified intervals afterward. Results Morphine use was reduced similarly by all doses of neostigmine. Only the 75‐[micro sign]g dose of neostigmine increased the nausea score in the recovery room. The incidence of treatment for nausea was greater in patients receiving neostigmine (61%) than in those receiving saline placebo (29%) and was unaffected by neostigmine dose. Neostigmine did not reduce the incidence of hypotension from bupivacaine. Conclusion These data in patients after vaginal hysterectomy suggest that analgesia from intrathecal neostigmine may occur at doses less than 50 [micro sign]g. In these doses, neostigmine does not reduce spinal bupivacaine‐induced hypotension but may increase the need for treatment of nausea.
Acute Cellular Rejection Predominated by Monocytes Is a Severe Form of Rejection in Human Renal Recipients With or Without Campath‐1H (Alemtuzumab) Induction Therapy

Campath‐1H has been used successfully for induction and has resulted in a low rate of acute cellular rejection (ACR) in renal transplantation in combination with various postoperative immunosuppression regimens. This study was undertaken to investigate the extent of monocyte involvement in ACR, with or without Campath‐1H induction. We found that monocytes represented the majority of inflammatory cells in grades Ib or higher ACR, but not with Ia type of ACR, regardless of the status of Campath‐1H induction. Cases of ACR, following Campath‐1H induction, appear to demonstrate a ‘pure form’ of monocytic ACR, whereas monocytes were mixed with many other types of inflammatory cells in the cases of ACR in the absence of Campath‐1H induction. In addition with Campath‐1H induction, the cases of monocyte‐predominant ACR were found to uniformly exhibit a good response to corticosteroid treatment. We conclude that monocyte‐predominate ACR may represent a severe form of rejection, with or without Campath‐1H treatment.
200GHz broadband proximity coupled patch antenna

In this paper, we have successfully designed a broadband elevated patch antenna using a new feeding technique. The antenna scheme offers a large operational bandwidth, compatibly with MMICs, eliminates the undesired substrate effects, and maximizes antenna performance on high dielectric substrates. A rectangular patch, elevated above the high dielectric substrate (semi-insulating-GaAs), is used as the main radiator. The patch is excited by electromagnetic coupling using a loop slot, which is formed in the antenna ground plane and located below the patch at the end of the 50 Ω CPW feed line. With this configuration a broadband patch antenna can be realized, and a low dielectric substrate constant can be created, since the antenna substrate is essentially air which is the lowest possible dielectric constant. The antenna was designed to operate at 200GHz for G-band applications. The simulation and measurement data have shown superior performance over conventional designs with a 10dB bandwidth of about 13GHz, from 190.8GHz to 203.8GHz, with nearly constant broadside radiation pattern over antenna bandwidth.
Breakthroughs in Analog and RF Circuit Performance through Steep Slope FinFETs

Abstract : Fin-shaped Field-Effect Transistors} (FinFETs) with ThreeIndependent Gates (TIG) have been recently demonstratedcapable of an ultra-steep-slope operation down to 3.4mV/dec. Inthis paper, we explore their opportunities in the domain ofanalog design and terahertz detectors. We see that they couldresult in analog circuits with 25 power efficiency improvementand in THz detectors with 2 orders of magnitude highersensitivity.
RNA Secondary Structure Analysis Using The RNAshapes Package

This unit shows how to use the RNAshapes package for the prediction of the secondary structure of a single RNA sequence using either minimum free energy methods or weighted ensemble information. It also includes a protocol for the consensus prediction of a set of related sequences. Curr. Protoc. Bioinform. 26:12.8. 1‐12.8. 17. © 2009 by John Wiley & Sons, Inc.
The Temperature Dependence of Mismatch in Deep-Submicrometer Bulk MOSFETs

We present a study of the temperature dependence of transistor mismatch in a 65-nm CMOS platform over a temperature range of 0degC to 125degC. We show that the relative-drain-current-mismatch fluctuation properties improve marginally in strong inversion, while they are strongly affected in the subthreshold region. This is compared and explained with a commonly used model. Furthermore, we analyze the change over temperature of the ION mismatch of individual matched pairs. This analysis shows, for the first time, that although relative-current-mismatch fluctuation standard deviations estimated on whole populations are reduced at higher temperatures, the current mismatch of individual pairs can change substantially over temperature.
Effect of tris buffer on free cytosolic calcium in myocardial cells.

OBJECTIVE To study the effect of tris buffer on free cytosolic calcium in vitro. DESIGN Open, randomized, control trial of dispersed rat myocardial cells. SETTING Experimental laboratory in a large university hospital. SUBJECTS Dispersed myocardial cells from Sprague-Dawley rats. INTERVENTIONS The influences of pure trometamol (tris) and a tris butter mixture, as well as conventional sodium bicarbonate on free cytosolic calcium in suspended rat myocardial cells were studied with the fluorescent intracellular probe fura-2. MEASUREMENTS AND MAIN RESULTS Addition of pure trometamol (tris) resulted in a significant increase of free cytosolic calcium in myocardial cells suspended in a buffer containing 1.25 mM of ionized calcium. The actions of trometamol display a dose-dependency in relation to the concentration of external ionized calcium since the ionized calcium response was reduced in a buffer with 0.5 mM of extracellular ionized calcium. Furthermore, removal of external ionized calcium totally prevented trometamol induced increases of ionized calcium, indicating that this increase is dependent on transmembrane ionized calcium fluxes. When tris buffer mixture was investigated in 1.25 mM of calcium, as well as 0.5 mM of external ionized calcium, a decrease of ionized calcium was noted initially, followed by an increase during the observation period. Addition of sodium bicarbonate to the two experimental settings resulted in a more prominent initial decrease of ionized calcium, followed by a slower increase which did not reach the initial values during the 20-min observation period. Extracellular pH was also included as a variable. When the cells were suspended in a buffer containing 1.25 mM of ionized calcium with a pH of 6.80 instead of 7.40 (as above), addition of pure trometamol also resulted in an increase of ionized calcium; however, after 20 mins this increase was smaller as compared with the results above. When tris buffer mixture as well as sodium bicarbonate was added, initial decreases of ionized calcium were recorded, followed by smaller increases during the observation period, compared with the increase in buffers with a pH of 7.40. CONCLUSIONS Pure trometamol (tris) induces an increase in free cytosolic calcium in suspended myocardial cells.
Downregulation and aberrant promoter methylation of p16INK4A: A possible novel heritable susceptibility marker to retinoblastoma

RB loss has long been recognized as the causative genetic alteration underlying retinoblastoma but it is increasingly evident that other alterations are required for the tumor to develop. Therefore, we set out to identify additional inheritable susceptibility markers and new potential preventive and therapeutic targets for retinoblastoma. We focused on the p16INK4A tumor suppressor gene because of its possible role in retinoblastoma pathogenesis and its involvement in predisposition to familial cancer. p16INK4A expression was analyzed in tumor samples from retinoblastoma patients by immunohistochemistry and in peripheral blood cells from both patients and their parents by real‐time quantitative reverse transcription‐PCR (qRT‐PCR). Since promoter methylation is a common mechanism regulating p16INK4A expression, the methylation status of its promoter was also analyzed in blood samples from patients and their parents by methylation‐specific PCR. A downregulation of p16INK4A was observed in 55% of retinoblastoma patients. Interestingly, in 56% of the cases showing p16INK4A downregulation at least one of the patients' parents bore the same alteration in blood cells. Analysis of p16INK4A promoter methylation showed hypermethylation in most patients with p16INK4A downregulation and in the parents with the same alteration in p16INK4A expression. The finding that p16INK4A was downregulated both in patients and their parents suggests that this alteration could be a novel inheritable susceptibility marker to retinoblastoma. The observation that p16INK4A downregulation seems to be due to its promoter hypermethylation opens the way for the development of new preventive and therapeutic strategies using demethylating agents. J. Cell. Physiol. 223: 143–150, 2010. © 2009 Wiley‐Liss, Inc.
Dehydrogenase GRD1 Represents a Novel Component of the Cellulase Regulon in Trichoderma reesei (Hypocrea jecorina)

ABSTRACT Trichoderma reesei (Hypocrea jecorina) is nowadays the most important industrial producer of cellulase and hemicellulase enzymes, which are used for pretreatment of cellulosic biomass for biofuel production. In this study, we introduce a novel component, GRD1 (glucose-ribitol dehydrogenase 1), which shows enzymatic activity on cellobiose and positively influences cellulase gene transcription, expression, and extracellular endo-1,4-β-d-glucanase activity. grd1 is differentially transcribed upon growth on cellulose and the induction of cellulase gene expression by sophorose. The transcription of grd1 is coregulated with that of cel7a (cbh1) under inducing conditions. GRD1 is further involved in carbon source utilization on several carbon sources, such as those involved in lactose and d-galactose catabolism, in several cases in a light-dependent manner. We conclude that GRD1 represents a novel enhancer of cellulase gene expression, which by coregulation with the major cellulase may act via optimization of inducing mechanisms.