Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of the Transcription Factor TFIID with Simian Virus 40 (SV40) Large T Antigen Interferes with Replication of SV40 DNA In Vitro

ABSTRACT Simian virus 40 (SV40) large tumor (T) antigen is the major regulatory protein that directs the course of viral infection, primarily by interacting with host cell proteins and modulating their functions. Initiation of viral DNA replication requires specific interactions of T antigen bound to the viral origin of DNA replication with cellular replication proteins. Transcription factors are thought to stimulate initiation of viral DNA replication, but the mechanism of stimulation is poorly understood. Since the transcription factor TATA-binding protein (TBP) binds to sequences within the origin of replication and interacts specifically with T antigen, we examined whether TBP complexes stimulate SV40 DNA replication in vitro. On the contrary, we found that depletion of TBP complexes from human cell extracts increased their ability to support viral DNA replication, and readdition of TBP complexes to the depleted extracts diminished their activity. We have mapped the sites of interaction between the proteins to residues 181 to 205 of T antigen and 184 to 220 of TBP. Titration of fusion proteins containing either of these peptides into undepleted cell extracts stimulated their replication activity, suggesting that they prevented the T antigen-TBP interaction that interfered with replication activity. TBP complexes also interfered with origin DNA unwinding by purified T antigen, and addition of either the T antigen or the TBP fusion peptide relieved the inhibition. These results suggest that TBP complexes associate with a T-antigen surface that is also required for origin DNA unwinding and viral DNA replication. We speculate that competition among cellular proteins for T antigen may play a role in regulating the course of viral infection.
Cortical evoked potentials to semantic stimuli.

The influence of affective meaning on the photically evoked response was studied in male college students. Three sets of stimuli were used: taboo words, neutral words, and blank flashes. Two blocks of trials were run for each stimulus, one in which the S responded by calling the stimulus presented, and a second in which the S was not required to respond. The late components of the evoked potential were significantly related to both the stimulus and response conditions. Amplitude 2 was larger for the taboo words than for either the neutral words or the blank flash. The taboo words had a significantly greater amplitude 3 than neutral words, and both sets of words had higher amplitude 3 than the blank flash. The stimulus effect was discussed in terms of the possible influence of anatomical structures involved in emotional behavior on the visual evoked response. The response effect was felt to be the result of the increased attention required under the response condition.
Sperm preference in Drosophila melanogaster.

A mating is described in which the females appear actively to discriminate against one of the genotypes of sperm. The males in the mating carry T(1;4)BS, and the sperm type selected against is the BS+4-bearing segregant. Prior exposure of the reproductive tract of the females to BS+4-bearing sperm seems to enhance the ability of the females to subsequently discriminate against BS+4-bearing sperm. Thus it appears that at least some females of Drosophila melanogaster do possess a mechanism whereby different types of sperm can be distinguished—the sperm preference observed in this system appears to be independent of the meiotic drive in the T(1;4)BS males.
Oct-1 modifies S100A4 exchange between intra- and extracellular compartments in Namalwa cells and increases their sensitivity to glucocorticoids

ABSTRACT S100A4, a small intra- and extracellular Ca2+-binding protein, is involved in tumor progression and metastasis with S100A4 level shown to be correlated with tumor cells metastatic potential. Simultaneously, Octamer transcription factor 1 (Oct-1) regulates a wide range of genes and participates in tumor cell progression with high Oct-1 level associated with a poor prognosis for different tumors. In this study, following the establishment of Oct-1 binding site, we used Burkit lymphoma B cells (Namalwa cells) which express different isoforms of Oct-1 (Oct-1A, Oct-1L and Oct-1X) to investigate the role of Oct-1 in S100A4 expression and sustaining intra- and extra-cellular S100A4 levels. As antitumor agents, we used dexamethasone which effect is mediated by the activation of intracellular glucocorticoid receptors and camptothecin which molecular target is nuclear DNA topoisomerase I (TOP1). We established that, firstly, the most significant increase in S100A4 gene expression has been demonstrated in the cells transfected with Oct-1A. Secondly, we have established that high level of Oct-1 and decreased intracellular S100A4 level decline the survival of Namalwa cells under dexamethasone treatment. Thirdly, we have shown that the tumor cells transformation by different Oct-1 isoforms retained those cells' sensitivity to the antitumor effect of combined dexamethasone and camptothecin. In contrast, in the non-transformed Namalwa cells, dexamethasone decreased the camptothecin effect on the cells survivorship, thus, emphasizing Oct-1 role in the regulation of cell response to different antitumor agents. The results identify a necessity to consider Oct-1 level for combined chemotherapeutic drug treatment.
Cooperative Caching in Disruption Tolerant Networks with Security

Disruption Tolerant Networks (DTNs) are considered to be a successful solution to allow communication between nodes in extreme networking environments. Cooperative caching is one of the best methods of data access in such conditions. One of the major challenges in this scenario is secure and efficient data transfer between nodes. Due to random nature of DTNs, harmful intruders can launch attacks, which may cause misrouting, drop or alteration of packets. Thus, it is imperative to detect such intruders and respond to these intruders in a timely and effective way. The traditional security mechanisms mainly focus on intrusion detection capability only. Incorporating a firewall based intrusion response scheme called smart intrusion blocker, along with the conventional detection method will reduce the complexity of overall security system. This response scheme can create a quick virtual barrier between the data nodes and the intruder, which blocks further communication with the intruder nodes.
Crystal structure of a phosphotransacetylase from Streptococcus pyogenes

Introduction. The Berkeley Structural Genomics Center (BSGC) pursues an integrated structural genomics program designed to obtain a near-complete structural representation of two minimal genomes: Mycoplasma genitalium (MG) and Mycoplasma pneumoniae (MP), two related human and animal pathogens. The MP gene MPN428 (gi:1674097) encodes an enzyme with unknown three-dimensional (3-D) structure and no sequence homologues are found in Protein Data Bank (PDB) structure database. For technical expediency, a sequence homologue of MPN428, SP1324 (gi:15675108) from Streptococcus pyogenes, was selected as a target based on sequence homology to MPN428: [log(EPSI-BLAST ) 53, sequence identity 43.09%, chain length coverage 97.19%]. Both MPN428 and SP1324 genes were annotated as phosphotransacetylase (EC 2.3.1.8), an enzyme that catalyzes the reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA): CH3COOPO3 2 CoASH 7 CH3COSCoA HPO4 2 . This sequence annotation is awaiting experimental verification. Phosphotransacetylase and acetate kinase are present in nearly all anaerobic prokaryotes, playing a major role in the energy-yielding metabolism. Here, we report the crystal structure of SP1324 at 2.7 Å resolution determined by multiwavelength anomalous diffraction (MAD) method.
Input isolated sense amplifiers

The paper describes new types of sense amplifiers called the input isolated sense amplifier (IISA) for high-speed VLSI applications. The inputs of the sense amplifier are isolated from the incoming signals during the operation. The IISA has totally two positive feedback paths to the inputs and outputs nodes, respectively. Thus the voltage gain can be largely increased In this work, the IISA is used as the receiver of the long interconnection to reduce the RC delay in deep sub-micron process. The simulation in a 0.35-/spl mu/m CMOS process shows that the novel design has 31-58% delay improvement compared to the prior arts. The IISA can also be applied to the memory design and the receiving of large capacitive load signals.
An Integrative Approach to Accurate Vehicle Logo Detection

Vehicle logo detection from images captured by surveillance cameras is an important step towards the vehicle recognition that is required for many applications in intelligent transportation systems and automatic surveillance. The task is challenging considering the small target of logos and the wide range of variability in shape, color, and illumination. A fast and reliable vehicle logo detection approach is proposed following visual attention mechanism from the human vision. Two prelogo detection steps, that is, vehicle region detection and a small RoI segmentation, rapidly focalize a small logo target. An enhanced Adaboost algorithm, together with two types of features of Haar and HOG, is proposed to detect vehicles. An RoI that covers logos is segmented based on our prior knowledge about the logos' position relative to license plates, which can be accurately localized from frontal vehicle images. A two-stage cascade classier proceeds with the segmented RoI, using a hybrid of Gentle Adaboost and Support Vector Machine (SVM), resulting in precise logo positioning. Extensive experiments were conducted to verify the efficiency of the proposed scheme.
miRNA-141, Downregulated in Pancreatic Cancer, Inhibits Cell Proliferation and Invasion by Directly Targeting MAP4K4

miRNAs are associated with various types of cancer due to their ability to affect expression of genes that modulate tumorigenesis. In this study, we explored the role of miR-141 in pancreatic cancer. The analysis of clinical characteristics showed that miR-141 was significantly downregulated in tissues and cell lines of pancreatic cancer. Moreover, the decreased miR-141 level was significantly associated with tumor size and TNM stage, as well as lymph node and distant metastasis. Meanwhile, both Kaplan–Meier and multivariate survival analysis showed decreased miR-141 were associated with overall survival. Overexpression of miR-141 in pancreatic cancer cells inhibited cell proliferation, clonogenicity, and invasion; induced G1 arrest and apoptosis; and enhanced chemosensitivity. To understand how miR-141 mediates the phenotype of pancreatic cancer cells, a bioinformatics tool was used to identify MAP4K4 as a potential target of miR-141. The Dual-Luciferase reporter gene assay showed that miR-141 binds directly to the 3′-untranslated region (3′UTR) of MAP4K4 to inhibit MAP4K4 expression. Western blot and quantitative real-time PCR (qRT-PCR) analyses revealed that MAP4K4 expression was inversely correlated with miR-141 expression both in pancreatic cancer samples and cell lines. Knockdown of MAP4K4 inhibited cell proliferation, clonogenicity, and invasion, induced G1 arrest and apoptosis, and enhanced chemosensitivity. In a nude mouse xenograft model, both overexpression of miR-141 and knockdown of MAP4K4 significantly repressed pancreatic cancer cell growth. Therefore, we conclude that miR-141 targets MAP4K4, acts as a tumor suppressor in pancreatic cancer cells, and may serve as a novel therapeutic agent for miRNA-based pancreatic cancer therapy. Mol Cancer Ther; 12(11); 2569–80. ©2013 AACR.
Shunt Active Power Filter with Dynamic Output Current Limitation

This paper presents a shunt active filter with a controller able to dynamically limit the output current, which allows an effective protection of the inverter semiconductors without diminishing the active filter performance. The control strategy is based on the p-q theory expanded for three-phase four-wire systems and the power stage of the active filter is composed by a two-level four-leg inverter. Simulation results on PSCADreg/EMTDCtrade are presented to demonstrate the performance of the dynamic current limitation.
Evaluation of antitumor effects following tumor necrosis factor‐α gene delivery using nanobubbles and ultrasound

The antitumor effects of tumor necrosis factor (TNF‐α) were evaluated following transfection of TNF‐α plasmid DNA into solid mouse tumors using the nanobubbles (NBs) and ultrasound (US) gene delivery system. Murine breast carcinoma (EMT6) cells expressing luciferase (1 × 106 cells) were injected intradermally into the flanks of 6–7‐week‐old male SCID mice on day 0. Ten microliters of TNF‐α (5 μg/μL) or TNF‐α mock plasmid DNA (5 μg/μL) with/without NBs (15 μL) and saline was injected intratumorally in a total volume of 30 μL, and tumors were exposed to US (frequency, 1 MHz; intensity, 3.0 W/cm2; duty cycle, 20%; number of pulses, 200; and exposure time, 60 s) on days 2, 4, 7, and 9. Changes in tumor size were measured with an in vivo bioluminescent imaging system and a mechanical caliper. Changes in tumor vessel area were quantified using contrast‐enhanced US imaging with Sonazoid and a high frequency US imaging system (40 MHz) and immunohistochemistry (CD31). At the mRNA level, expression of TNF‐α, caspase‐3, and p53 were quantified using real‐time quantitative RT‐PCR. At the protein level, expression of caspase‐3 and p53 were confirmed by immunohistochemistry. We show that repeated TNF‐α gene delivery using NBs and US can lead to the local production of TNF‐α. This results in antitumor effects, including activation of p53‐dependent apoptosis, decrease in tumor vessel density, and suppression of tumor size. In this study, we showed the effectiveness of using NBs and US for TNF‐α gene delivery into tumor cells. (Cancer Sci 2011; 102: 2082–2089)
EBQUAL: A Success Model of E-Business

E-business is a new type of promising business model in the Internet era. However, there have been not many researches on what are the success factors of e-business. In this paper, it is assumed that building trust is one of the most important success factors. Based on the assumption, among others, the quality of e-business is proposed to be the source of trust in business-to-customer e-markets. In other words, it is assumed that increasing the quality of ebusiness is one of the most important critical success factors in the competitive business-to-customer e-markets. Based on the assumption, the quality of e-business is analyzed, including the relationships with other factors such as trust and discontinuity. A conceptual framework is introduced to propose that the quality of e-business is a source of trust in e-markets. In addition, discontinuity is proposed to negatively affect the quality of e-business and trust. Recovery is proposed to moderate the impact of discontinuity on quality and trust.
Implementation of Switchable Pins in Chip Multiprocessor

Transistor scaling and voltage scaling promote the development of VLSI chip design and modern portable devices. However, transistor scaling brings dark silicon to chips. Lowering supply voltage also results in many transistors to work in near threshold voltage region in which transistors are very sensitive to voltage variation. The paper analyzes the influence of IR drop in a chip multiprocessor (CMP) architecture. Based on our previous work, we focus on the circuit implementation of the proposed switchable pin in CMP using I/O pads with on-chip low cost control circuit; and to let the microprocessor work in data mode or power mode according to various requirements. Using six of eight traditional data pins in an 8-bit RISC microprocessor as switchable pins, the entire current in power mode can be boosted by 72% compared to normal data mode. For data transmission, relative signal-to-noise ratio (rSNR) are tested and the performance of the DRAM is also discussed. Keywords—Dark silicon; IR drop; Switchable pins
The field emission properties of diamond-like carbon film prepared by filtered cathodic vacuum arc

The diamond-like carbon films were prepared by filtered cathodic vacuum arc system. Surface morphology and microstructure of the films were investigated by atomic force microscope and Raman spectrum. The field emission properties of the film were tested under vacuum condition, and the turn-on field was found to be 1.3V/μm.
Mechanisms and Efficacy of Immunobiologic Therapies for Inflammatory Bowel Diseases

Current advances in understanding of the pathogenesis of inflammatory bowel disease have encouraged the development of many new therapies targeted at specific and non-specific mediators of the inflammatory bowel disease inflammatory pathway. Crohn's disease and ulcerative colitis, two common inflammatory bowel diseases likely result from interaction of multiple genetic and environmental risk and protective factors, deregulation of mucosal immunity in gut and breakdown of delicate balance of proinflammatory and anti-inflammatory cytokines. Immunobiologic agents targeted against TNF, leukocyte adhesion, Th1 polarization, T cell activation, nuclear factor-kappaB (NF-κB), and others are being assessed and will open exciting perspectives on development of therapies for inflammatory bowel disease.
Acroangiodermatitis mimicking Kaposi’s sarcoma in an HIV-positive man

Kaposi’s sarcoma (KS) is the commonest human immunodeficiency virus (HIV)-related malignancy with its characteristic cutaneous morphological appearance and histopathological features. However, it can be simulated by other co-morbid opportunistic infections and unrelated dermatological conditions. We describe such a case of acroangiodermatitis in an HIV co-infected man, based on exclusion of KS histologically and the absence of human herpesvirus 8, the causative agent of KS.
Predictors of late asthmatic response. Logistic regression and classification tree analyses.

To identify predictors of the late asthmatic response (LAR), we reviewed data from 60 asthmatic subjects who had undergone allergen challenge over the past 5 yr (33 females, age 31.4 +/- 6.7 yr [mean +/- SD], FEV(1) 90% +/- 14% predicted). Variables considered likely predictors of LAR included baseline FEV(1), PC(20) methacholine (PC(20)), sputum eosinophil percent, and the decrease in FEV(1) within 20 min of allergen challenge. A LAR (FEV(1) >/= 15% fall between 3 and 7 h after challenge) was documented in 57% of subjects. A variety of logistic regression methods revealed a significant inverse association between LAR and PC(20) (odds ratio [OR] = 0.14 [95% CI = 0.03-0.66]) and a positive association between LAR and the decrease in FEV(1) at 20 min (OR = 1.18 [1.04 -1.33]). Classification tree analysis revealed that a threshold of 0.25 mg/ml for PC(20) was most predictive of LAR; LAR developed in 87% of those with PC(20) </= 0.25 mg/ml (n = 23) and in 38% of those with PC(20) > 0.25 mg/ml (n = 37). Notably, in subjects with PC(20) > 0.25 mg/ml, the incidence of LAR increased from 38% to 57% if the allergen-induced decline in FEV(1) at 20 min was >/= 27%. Surprisingly, baseline FEV(1) and percent eosinophils in induced sputum were not significantly associated with LAR. We conclude that a threshold value of 0.25 mg/ml for PC(20) methacholine is a good predictor of LAR. Measuring the PC(20) methacholine may be useful as a screening method to improve the efficiency of identifying asthmatic subjects with a LAR.
The relationship between export assistance and performance improvement in Portuguese export ventures: An empirical test of the mediating role of pricing strategy adaptation

Purpose – The article aims to test how pricing strategy adaptation to the foreign market mediates the relationship between export assistance and annual export performance improvement. It also aims to consider the effects of management international experience and export market competition.Design/methodology/approach – Structural equation modelling with WLS estimation is used to test the direct and indirect influences of the variables on short‐term export performance.Findings – Surprisingly, the findings reveal that the total effects of export assistance on annual export performance improvement are non‐significant, because although export assistance has a direct positive impact on performance, there is a negative indirect impact through export pricing strategy adaptation.Research limitations/implications – These surprising results suggest that future research is required to incorporate and test the intervening and indirect effects among variables.Practical implications – The findings also indicate that bot.
What Captures Liquidity Risk? Order Based Versus Trade Based Liquidity Measures

Is the effect of liquidity risk on asset prices sensitive to the choice of liquidity proxy? In our study we achieve three main results. First, we extract three factors from a broad range of trade- and order based liquidity variables, and find that an order based liquidity factor is not related to realized returns while a trade based liquidity factor tied to information risk is. Second, we find evidence that the factor related to information risk explains expected returns when we estimate the theoretical liquidity-adjusted CAPM. Third, when we estimate a liquidity-augmented factor model, the Fama-French model does well in pricing stocks relative to each individual liquidity factor, but a CAPM model augmented with all our liquidity factors outraces the Fama-French model.
A clinico-pathological study of some factors influencing survival in cancer of the oesophagus: a survey of ten years' experience.

Three hundred and thirty-two patients with histologically proved carcinoma of the œesophagus, admitted over a ten-year period to the Royal Prince Alfred Hospital, Sydney, were studied according to the site, histological type, stage and grading of their malignancies. The survival rates after resection and palliative treatments, including radiotherapy, were correlated with these factors.