Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of the Regulators SigB, Rot, SarA and sarS on the Toxic Shock Tst Promoter and TSST-1 Expression in Staphylococcus aureus

Staphylococcus aureus is an important pathogen manifesting virulence through diverse disease forms, ranging from acute skin infections to life-threatening bacteremia or systemic toxic shock syndromes. In the latter case, the prototypical superantigen is TSST-1 (Toxic Shock Syndrome Toxin 1), encoded by tst(H), and carried on a mobile genetic element that is not present in all S. aureus strains. Transcriptional regulation of tst is only partially understood. In this study, we dissected the role of sarA, sarS (sarH1), RNAIII, rot, and the alternative stress sigma factor sigB (σB). By examining tst promoter regulation predominantly in the context of its native sequence within the SaPI1 pathogenicity island of strain RN4282, we discovered that σB emerged as a particularly important tst regulator. We did not detect a consensus σB site within the tst promoter, and thus the effect of σB is likely indirect. We found that σB strongly repressed the expression of the toxin via at least two distinct regulatory pathways dependent upon sarA and agr. Furthermore rot, a member of SarA family, was shown to repress tst expression when overexpressed, although its deletion had no consistent measurable effect. We could not find any detectable effect of sarS, either by deletion or overexpression, suggesting that this regulator plays a minimal role in TSST-1 expression except when combined with disruption of sarA. Collectively, our results extend our understanding of complex multifactorial regulation of tst, revealing several layers of negative regulation. In addition to environmental stimuli thought to impact TSST-1 production, these findings support a model whereby sporadic mutation in a few key negative regulators can profoundly affect and enhance TSST-1 expression.
Effect of excess iron and copper on physiology of aquatic plant Spirodela polyrrhiza (L.) Schleid

To elucidate effect of chemical reagents addition on growth of aquatic plants in restoration of aquatic ecosystem, Spirodela polyrrhiza (L.) Schleid was used to evaluate its physiological responses to excess iron (Fe3+) and copper (Cu2+) in the study. Results showed that accumulation of iron and copper both reached maximum at 100 mg L−1 iron or copper after 24 h short‐term stress, but excess iron and copper caused plants necrosis or death and colonies disintegration as well as roots abscission at excess metal concentrations except for 1 mg L−1 iron. Significant differences in chlorophyll fluorescence (Fv/Fm) were observed at 1–100 mg L−1 iron or copper. The synthesis of chlorophyll and protein as well as carbohydrate and the uptake of phosphate and nitrogen were inhibited seriously by excess iron and copper. Proline content decreased with increasing iron or copper concentration, however, MDA content increased with increasing iron or copper concentration. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2010.
Local Adaptive SVM for Object Recognition

The Support Vector Machine (SVM) is an effective classification tool. Though extremely effective, SVMs are not a panacea. SVM training and testing is computationally expensive. Also, tuning the kernel parameters is a complicated procedure. On the other hand, the Nearest Neighbor (KNN) classifier is computationally efficient. In order to achieve the classification efficiency of an SVM and the computational efficiency of a KNN classifier, it has been shown previously that, rather than training a single global SVM, a separate SVM can be trained for the neighbourhood of each query point. In this work, we have extended this Local SVM (LSVM) formulation. Our Local Adaptive SVM (LASVM) formulation trains a local SVM in a modified neighborhood space of a query point. The main contributions of the paper are twofold: First, we present a novel LASVM algorithm to train a local SVM. Second, we discuss in detail the motivations behind the LSVM and LASVM formulations and its possible impacts on tuning the kernel parameters of an SVM. We found that training an SVM in a local adaptive neighborhood can result in significant classification performance gain. Experiments have been conducted on a selection of the UCIML, face, object, and digit databases.
Factors Related to Healthcare Service Quality in Long-term Care Hospitals in South Korea: A Mixed-methods Study

Objectives The environment of long-term care hospitals (LTCHs) is critical to the management of the quality of their services and to patient safety, as highlighted by international studies. However, there is a lack of evidence on this topic in South Korea. This study aimed to examine the factors affecting healthcare quality in LTCHs and to explore the effectiveness of their quality management. Methods This study used a mixed methods approach with quantitative data collected in a national survey and qualitative data from semi-structured interviews with practice-based managers. The samples included 725 nationally representative LTCHs in South Korea for the quantitative analysis and 15 administrators for the in-depth interviews. Results A higher installation rate of patient-safety and hygiene-related facilities and staff with longer-tenures, especially nurses, were more likely to have better healthcare quality and education for both employees and patients. Conclusion The need for patient-safety- and hygiene-related facilities in LTCHs that serve older adults reflects their vulnerability to certain adverse events (e.g., infections). Consistent and skillful nursing care to improve the quality of LTCHs can be achieved by developing relevant educational programs for staff and patients, thereby strengthening the relationships between them.
A New Quantitative Quality Measure for Machine Translation Systems

In this paper, an objective quantitative quality measure is proposed to evaluate the performance of machine translation systems. The proposed method is to compare the raw translation output of an MT system with the final revised version for the customers, and then compute the editing efforts required to convert the raw translation to the final version. In contrast to the other proposals, the evaluation process can be done quickly and automatically. Hence, it can provide a quick response on any system change. A system designer can thus quickly find the advantages or faults of a particular performance dynamically. Application of such a measure to improve the system performance on-line on a parameterized and feedback-controlled system will be demonstrated. Furthermore, because the revised version is used directly as a reference, the performance measure can reflect the real quality gap between the system performance and customer expectation. A system designer can thus concentrate on practically important topics rather than on theoretically interesting issues.
A Generative Entity-Mention Model for Linking Entities with Knowledge Base

Linking entities with knowledge base (entity linking) is a key issue in bridging the textual data with the structural knowledge base. Due to the name variation problem and the name ambiguity problem, the entity linking decisions are critically depending on the heterogenous knowledge of entities. In this paper, we propose a generative probabilistic model, called entity-mention model, which can leverage heterogenous entity knowledge (including popularity knowledge, name knowledge and context knowledge) for the entity linking task. In our model, each name mention to be linked is modeled as a sample generated through a three-step generative story, and the entity knowledge is encoded in the distribution of entities in document P(e), the distribution of possible names of a specific entity P(s\e), and the distribution of possible contexts of a specific entity P(c\e). To find the referent entity of a name mention, our method combines the evidences from all the three distributions P(e), P(s\e) and P(c\e). Experimental results show that our method can significantly outperform the traditional methods.
Sequence Characterization and Comparative Analysis of Three Plasmids Isolated from Environmental Vibrio spp

ABSTRACT The horizontal transfer of genes by mobile genetic elements such as plasmids and phages can accelerate genome diversification of Vibrio spp. , affecting their physiology, pathogenicity, and ecological character. In this study, sequence analysis of three plasmids from Vibrio spp. previously isolated from salt marsh sediment revealed the remarkable diversity of these elements. Plasmids p0908 (81.4 kb), p23023 (52.5 kb), and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding sequences and G+C contents of 49.2%, 44.7%, and 42.4%, respectively. A phylogenetic tree based on concatenation of the host 16S rRNA and rpoA nucleotide sequences indicated p23023 and p09022 were isolated from strains most closely related to V. mediterranei and V. campbellii, respectively, while the host of p0908 forms a clade with V. fluvialis and V. furnissii. Many predicted proteins had amino acid identities to proteins of previously characterized phages and plasmids (24 to 94%). Predicted proteins with similarity to chromosomally encoded proteins included RecA, a nucleoid-associated protein (NdpA), a type IV helicase (UvrD), and multiple hypothetical proteins. Plasmid p0908 had striking similarity to enterobacteria phage P1, sharing genetic organization and amino acid identity for 23 predicted proteins. This study provides evidence of genetic exchange between Vibrio plasmids, phages, and chromosomes among diverse Vibrio spp.
Classification of heart sound signals based on AR model

Heart sounds reflect information of the mechanical contraction of the heart in both of the physiological and pathological conditions. It is important to develop novel numerical algorithms to characterize the features of the heart sound as a helpful diagnostic tool of cardiovascular diseases. This study aims to develop an efficient algorithm for analyzing heart sound signals that can be used for cardiovascular disease monitoring. In the algorithms, wavelet analysis (coif5) with 5 decomposition levels was first applied to heart sound signals for noise eliminating by using a soft fixed threshold. Then, heart sound signals were decomposed by the wavelet method to reconstruct bands with different frequencies. Following this, the normalized Shannon energy of each frequency band within the same time duration was calculated to determine the position of the second heart sound (S2). Finally, the aortic valve closure (A2) of the S2 were extracted using the power spectrum analysis of Auto Regressive(AR) model, which were used to classify the normal and abnormal heart sound recordings. Results show that the modified Sensitivity (Se), Specificity (Sp) and overall score are respectively 0.87, 0.61, and 0.74.
Just-in-time aspects: efficient dynamic weaving for Java

Recent developments in service architectures suggest that run-time adaptations could be implemented with dynamic AOP. In this paper we discuss application requirements on run-time AOP support and present a system that addresses these requirements. We provide basic support for weaving using the Just-In-Time compiler, while the AOP system is treated as an exchangeable module on top of the basic support. This approach allows us to provide low run-time overhead, AOP system flexibility, and secure weaving. We provide an extensive empirical evaluation and discuss the tradeoffs resulting from using the JIT compiler and a modularized architecture.
Up-regulation and Sustained Activation of Stat1 Are Essential for Interferon-γ (IFN-γ)-induced Dual Oxidase 2 (Duox2) and Dual Oxidase A2 (DuoxA2) Expression in Human Pancreatic Cancer Cell Lines*

Dual oxidase 2 is a member of the NADPH oxidase (Nox) gene family that plays a critical role in the biosynthesis of thyroid hormone as well as in the inflammatory response of the upper airway mucosa and in wound healing, presumably through its ability to generate reactive oxygen species, including H2O2. The recently discovered overexpression of Duox2 in gastrointestinal malignancies, as well as our limited understanding of the regulation of Duox2 expression, led us to examine the effect of cytokines and growth factors on Duox2 in human tumor cells. We found that exposure of human pancreatic cancer cells to IFN-γ (but not other agents) produced a profound up-regulation of the expression of Duox2, and its cognate maturation factor DuoxA2, but not other members of the Nox family. Furthermore, increased Duox2/DuoxA2 expression was closely associated with a significant increase in the production of both intracellular reactive oxygen species and extracellular H2O2. Examination of IFN-γ-mediated signaling events demonstrated that in addition to the canonical Jak-Stat1 pathway, IFN-γ activated the p38-MAPK pathway in pancreatic cancer cells, and both played an important role in the induction of Duox2 by IFN-γ. Duox2 up-regulation following IFN-γ exposure is also directly associated with the binding of Stat1 to elements of the Duox2 promoter. Our findings suggest that the pro-inflammatory cytokine IFN-γ initiates a Duox2-mediated reactive oxygen cascade in human pancreatic cancer cells; reactive oxygen species production in this setting could contribute to the pathophysiologic characteristics of these tumors.
Drugs and Aggression Readily Mix; So What Now?

Intoxicated aggression is both a dangerous and a costly problem for society, with alcohol being involved in over 50% of violent crimes, and the cost of alcohol-consumption-related crime being estimated at $205 billion in the United States alone. First, the authors reviewed the substantial evidence for the connection between alcohol consumption and aggression, and then they examined the risk factors for this problem. These included societal/cultural factors, such as availability and alcohol expectancies, and individual factors, such as demographic characteristics, personality, comorbid disorders, individual differences in response to alcohol, and cognitive functioning. Finally, interventions were suggested focusing on policy, alcohol sellers, treatments for alcohol abuse and dependency, anger management, pharmacology, and low executive functioning. Further efforts are still needed to target interventions to specific risk factors.
Codon preference of Aedes aegypti and Aedes albopictus

The codon bias of two Aedes mosquito species was examined using a sign test. In general, there appeared to be some preference for C + G at the third base position, although this was not statistically significant. While amino acids such as phenylalanine and tyrosine clearly displayed biases, others such as valine and serine appeared to have little or no bias for any particular codon. Three homologous genes of Aedes aegypti and Drosophila melanogaster were compared using the chi‐square test and the codon bias of the two species compared. Drosophila melanogaster was found to have a much stronger bias for C + G at the third base position compared to Aedes. The implications and usefulness of the codon bias are discussed.
Soft Error Tolerant Asynchronous Circuits Based on Dual Redundant Four State Logic

The continuing downscaling of integrated circuits makes modern devices more susceptible to soft errors. This paper investigates the possibility of using Four-State Logic (FSL) to improve the fault tolerance of digital circuits. FSL is a possible implementation of asynchronous Quasi Delay Insensitive (QDI) logic using a more efficient encoding and handshake protocol. The behavior of asynchronous circuits designed with FSL when subjected to transient faults is analyzed. We present methods based on dual redundancy that allow to detect as well as correct soft errors autonomously. The concept is demonstrated by fault injection experiments. Keywords-Asynchronous Logic; Four-State Logic; Soft Error; Dual-Redundancy; Fault Tolerance I. INTRODUCTION
PREDICTION OF MODULUS OF RUPTURE OF CONCRETE

Tensile strength of concrete is an important parameter for determining deflection and minimum flexural reinforcement. Many design codes use the modulus of rupture as the cracking strength. Relations giving the modulus of rupture as a function of concrete compressive strength are based on tests on concrete with a compressive strength lower than 40 MPa. This study presents a statistical study on 395 data points from a large number of research programs with concrete compressive strength ranging from 20 MPa to 130 MPa. It further reveals that the data are largely scattered and that minimum, mean, and maximum values for the modulus of rupture should be defined. New relations are proposed by giving the modulus of rupture as a function of the square root of the compressive cylinder strength of concrete and the compressive cylinder strength of concrete raised to the 2/3 power. The use of the new relations in design codes is illustrated.
T Lymphocyte Proliferative Responses Induced by Recombinant Factor VIII in Hemophilia A Patients with Inhibitors

Summary In this study we sought to determine whether factor VUI-reactive T lymphocytes were present in hemophilia A patients with inhibitor antibodies. Peripheral blood mononuclear cells (MNC) were obtained from 12 severe hemophilia A patients having high titer inhibitors, 4 severe hemophilia A patients without inhibitors and 5 normal male subjects. B cell-depleted MNC were cultured in serum-free medium in the absence or presence of 2 µg of recombinant human factor VIII (rFVIII) per ml, and cellular proliferation was assessed after 5 days of culture by measuring 3H-thymidine incorporation. rFVIII induced marked cellular proliferation in cultures of 4 of 12 inhibitor-positive hemophilia patients: fold increase over background (stimulation index, SI) of 7.8 to 23.3. The remaining 8 inhibitor-positive patients, the 4 hemophilia patients without inhibitors and the 5 normal subjects, all had lower proliferative responses to rFVIII, SI range = 1.6 to 6.0. As a group, the inhibitor-positive subjects had significantly higher proliferative responses to rFVIII than did the inhibitor-negative and normal subjects (p < 0.05 by t-test). Cell fractionation experiments showed that T lymphocytes were the rFVIII-responsive cell type, and that monocytes were required for T cell proliferation. Thus, rFVIII-reactive T lymphocytes are present in the peripheral circulation of some inhibitor-positive hemophilia A patients. These T cells may recognize FVIII in an antigen-specific manner and play a central role in the regulation of inhibitor antibody production
Energy Efficient In-network RFID Data Filtering Scheme in Wireless Sensor Networks

RFID (Radio frequency identification) and wireless sensor networks are backbone technologies for pervasive environments. In integration of RFID and WSN, RFID data uses WSN protocols for multi-hop communications. Energy is a critical issue in WSNs; however, RFID data contains a lot of duplication. These duplications can be eliminated at the base station, but unnecessary transmissions of duplicate data within the network still occurs, which consumes nodes’ energy and affects network lifetime. In this paper, we propose an in-network RFID data filtering scheme that efficiently eliminates the duplicate data. For this we use a clustering mechanism where cluster heads eliminate duplicate data and forward filtered data towards the base station. Simulation results prove that our approach saves considerable amounts of energy in terms of communication and computational cost, compared to existing filtering schemes.
Epstein-Barr virus latent membrane protein transactivates the human immunodeficiency virus type 1 long terminal repeat through induction of NF-kappa B activity

The Epstein-Barr virus latent membrane protein (LMP) is an integral membrane protein that is expressed in cells latently infected with the virus. LMP is believed to play an important role in Epstein-Barr virus transformation and has been shown to induce expression of several cellular proteins. We performed a series of experiments that demonstrated that LMP is an efficient transactivator of expression from the human immunodeficiency virus type 1 long terminal repeat (HIV-1 LTR). Mutation or deletion of the NF-kappa B elements in the LTR abolished the transactivation, indicating that the LMP effect on HIV expression was due to induction of NF-kappa B activity. Experiments in which the HIV-1 Tat protein was coexpressed in cells together with LMP showed that Tat was able to potentiate the transactivation. Surprisingly, a synergistic effect of the two proteins was observed even in the absence of the recognized target region for Tat (TAR) in the HIV-1 LTR.
Forsythoside A Inhibits BVDV Replication via TRAF2-Dependent CD28–4-1BB Signaling in Bovine PBMCs

Bovine viral diarrhea virus (BVDV), the causative agent of bovine viral diarrhea/mucosal disease (BVD/MD), is an important pathogen of cattle and other wild animals throughout the world. BVDV infection typically leads to an impaired immune response in cattle. In the present study, we investigated the effect of Forsythoside A (FTA) on BVDV infection of bovine peripheral blood mononuclear cells (PBMCs). We found that Forsythoside A could not only promote proliferation of PBMCs and T cells activation but also inhibit the replication of BVDV as well as apoptosis induced by BVDV. FTA treatment could counteract the BVDV-induced overproduction of IFN-γ to maintain the immune homeostasis in bovine PBMCs. At same time, FTA can enhance the secretion of IL-2. What’s more, BVDV promotes the expression of CD28, 4-1BB and TRAF-2, which can be modulated by FTA. Our data suggest that FTA protects PBMCs from BVDV infection possibly via TRAF2-dependent CD28–4-1BB signaling, which may activate PBMCs in response to BVDV infection. Therefore, this aids in the development of an effective adjuvant for vaccines against BVDV and other specific FTA-based therapies for preventing BVDV infection.
A systematic review of graft materials and biological agents for periodontal intraosseous defects.

OBJECTIVES To determine the adjunctive effect of grafting biomaterials/biological agents with open flap debridement (OFD) in the treatment of deep intraosseous defects. BACKGROUND No systematic review of treatment outcomes in patients who received graft biomaterials or biological agents have been published. METHODS A rigorous systematic review of randomized controlled trials of at least 6-month duration was conducted comparing grafting biomaterials/biological agents (alone or in combination) + OFD (test group) to OFD alone or in combination with a placebo (control group). RESULTS The difference in CAL change between test and control groups varied from -1.45 mm to 1.40 mm with respect to different biomaterials/biological agents. Meta-analysis showed that CAL change significantly improved after treatment for coralline calcium carbonate (weighted mean difference 0.90 mm; 95% CI: 0.53-1.27), bioactive glass (weighted mean difference 1.04 mm; 95% CI: 0.31-1.76), hydroxyapatite (weighted mean difference 1.40 mm, 95% CI 0.64-2.16), and enamel matrix proteins (weighted mean difference 1.33 mm, 95% CI 0.78-1.88). However, heterogeneity in results between studies was highly statistically significant for most of biomaterials/biologicals and could not be fully explained. CONCLUSIONS Overall, the use of specific biomaterials/biologicals was more effective than OFD in improving attachment levels in intraosseous defects. Difference in CAL gain varied greatly with respect to different biomaterial/biological agent. Due to a significant heterogeneity in results between studies in most treatment groups, general conclusions about the expected clinical benefit of graft biomaterials/biologicals need to be interpreted with caution. Further research should focus on understanding this variability.