Miracle-dz/UniFAR-FTUs huggingface dataset:
MapReduce-Based H-Mine Algorithm

Frequent Item set Mining (FIM) is a very effective method for knowledge acquisition from data, but with the advent of the era of big data, traditional algorithms based on memory are facing severe challenges such as the computation speed and storage capacity. Fortunately, Map Reduce model provides an efficient framework for distributed programming and operation framework. This paper proposes a novel Map Reduce-based H-mine algorithm (MRH-mine), a version of H-mine algorithm in the distributed operation environment. Experimental results show that MRH-mine algorithm has a better performance and scalability than traditional H-Mine when facing massive data growth.
Molecular Construction and Characterization of a Novel Exotoxin Fusion Protein that Selectively Blocks the B7:CD28 Costimulatory Signal System

An important strategy for specifically preventing and treating graft-versus-host and host-versus-graft diseases is to selectively block the B7:CD28/cytotoxic T-lymphocyte A4 costimulatory signal system for induced immune tolerance. In this study, a novel recombinant B7-2-L-PE40KDEL fusion protein was created to target the B7:CD28 system. We used a flexible linker sequence (Gly4Ser)4 and overlapping sequence extension to link the cDNAs encoding a human B7-2 extracellular domain and a mutant truncated form of Pseudomonas exotoxin A (PE), PE40KDEL. This B7-2-L-PE40KDEL fusion gene was then inserted into the pTYB4 expression vector, expressed in Escherichia coli, and purified through Ni-NTA mealty affinity→MonoQ anion exchange→Superdex75 gel filtration chromatography 3-step purification protocols. Western blotting demonstrated that the B7-2-L-PE40KDEL fusion protein specifically bound antihuman B7-2 monoclonal antibody and anti-pseudomonas exotoxin A antiserum. We used the Antheprot nucleic acid and protein analyzing software to predict the characteristics of this fusion protein, and showed that the fusion did not confer new antigenicities to the fusion protein. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide tests demonstrated that at doses ranging from 0.2 to 2 μg/mL, this fusion protein specifically killed CD28-overexpressing Jurkat cells but even at doses of 2 μg did not kill CD28-negative Hut28 cells. The results of a one-way mixed lymphocyte reaction demonstrated that the fusion protein has a range of suppressive effects on HLA class I and II matched related donors and recipients, and HLA class I and II mismatched unrelated donors. Taken together, these results demonstrate that we have developed a novel recombinant human B7-2-L-PE40KDEL exotoxin fusion protein that specifically blocks the B7:CD28 costimulatory signal system in a manner that may be of significant importance in preventing and treating graft-versus-host or host-versus-graft diseases.
AN OPTICAL SPECTROSCOPIC STUDY OF T TAURI STARS. I. PHOTOSPHERIC PROPERTIES

Estimates of the mass and age of young stars from their location in the H-R diagram are limited by not only the typical observational uncertainties that apply to field stars, but also by large systematic uncertainties related to circumstellar phenomena. In this paper, we analyze flux-calibrated optical spectra to measure accurate spectral types and extinctions of 281 nearby T Tauri stars (TTSs). The primary advances in this paper are (1) the incorporation of a simplistic accretion continuum in optical spectral type and extinction measurements calculated over the full optical wavelength range and (2) the uniform analysis of a large sample of stars, many of which are well known and can serve as benchmarks. Comparisons between the non-accreting TTS photospheric templates and stellar photosphere models are used to derive conversions from spectral type to temperature. Differences between spectral types can be subtle and difficult to discern, especially when accounting for accretion and extinction. The spectral types measured here are mostly consistent with spectral types measured over the past decade. However, our new spectral types are one to two subclasses later than literature spectral types for the original members of the TW Hya Association (TWA) and are discrepant with literature values for some well-known members of the Taurus Molecular Cloud. Our extinction measurements are consistent with other optical extinction measurements but are typically 1 mag lower than near-IR measurements, likely the result of methodological differences and the presence of near-IR excesses in most CTTSs. As an illustration of the impact of accretion, spectral type, and extinction uncertainties on the H-R diagrams of young clusters, we find that the resulting luminosity spread of stars in the TWA is 15%–30%. The luminosity spread in the TWA and previously measured for binary stars in Taurus suggests that for a majority of stars, protostellar accretion rates are not large enough to significantly alter the subsequent evolution.
Kaposi's Sarcoma-Associated Herpesvirus Noncoding Polyadenylated Nuclear RNA Interacts with Virus- and Host Cell-Encoded Proteins and Suppresses Expression of Genes Involved in Immune Modulation

ABSTRACT During lytic infection, Kaposi's sarcoma-associated herpesvirus (KSHV) expresses a polyadenylated nuclear RNA (PAN RNA). This noncoding RNA (ncRNA) is localized to the nucleus and is the most abundant viral RNA during lytic infection; however, to date, the role of PAN RNA in the virus life cycle is unknown. Many examples exist where ncRNAs have a defined key regulatory function controlling gene expression by various mechanisms. Our goal for this study was to identify putative binding partners for PAN RNA in an effort to elucidate a possible function for the transcript in KSHV infection. We employed an in vitro affinity protocol where PAN RNA was used as bait for factors present in BCBL-1 cell nuclear extract to show that PAN RNA interacts with several virus- and host cell-encoded factors, including histones H1 and H2A, mitochondrial and cellular single-stranded binding proteins (SSBPs), and interferon regulatory factor 4 (IRF4). RNA chromatin immunoprecipitation (ChIP) assays confirmed that PAN RNA interacted with these factors in the infected cell environment. A luciferase reporter assay showed that PAN RNA expression interfered with the ability of IRF4/PU.1 to activate the interleukin-4 (IL-4) promoter, strongly suggesting a role for PAN RNA in immune modulation. Since the proteomic screen and functional data suggested a role in immune responses, we investigated if constitutive PAN RNA expression could affect other genes involved in immune responses. PAN RNA expression decreased expression of gamma interferon, interleukin-18, alpha interferon 16, and RNase L. These data strongly suggest that PAN RNA interacts with viral and cellular proteins and can function as an immune modulator.
Statistical evaluation of contraceptive methods.

A methodology for the statistical evaluation of the effectiveness and acceptability of 2 groups of contraceptive methods utilizing life-table procedures adapted for this purpose is described. 2 sets of illustrative tables one for clinical data on IUDs and the other for clinical data on oral medication which is also applicable to other methods of contraception that can be discontinued by the user at any time are presented. The procedures for the statistical analysis of use-effectiveness of which the 2 most important components are the antifertility effect expressed as the rate of accidental pregnancy and acceptability as reflected in the rate of continued use are described. To measure use-effectiveness by life-table procedures certain infomrati on is required: 1) the period covered by the study; 2) the number of women who accept the method (for IUDs the number of first insertions) by date of acceptance; and 3) for each termination the date of acceptance and the reason for discontinuing the contraceptive method by duration of use (ordinal months of use). Numerous self-checking features are included in the analysis.
Satisfaction with assistive technology device in relation to the service delivery process—A systematic review

ABSTRACT The service delivery process (SDP) of assistive technology devices (ATDs) is attracting interest, as the provision of ATDs is critical for the independence and participation in society of individuals with disabilities. The purpose of the current study was to investigate what impact the SDP has on satisfaction with ATDs in individuals with disabilities in relation to everyday activities. A systematic literature review was conducted, which resulted in 53 articles included. The results showed that there are factors in almost all the different steps of the SDP that affect the satisfaction with of the devices, which can lead to underutilization and abandonment of ATDs. Only a few studies have been conducted with a design robust enough to generalize the results; therefore, more research is needed. Therefore, the conclusion is the SDP as a whole contributes to the satisfaction with and usability of ATDs in individuals with disability in relation to achieving the desired goals of participation in everyday activities, for the articles included must be deemed as moderate. A client-centred approach in the process is advocated, and was found to be an important factor for an effective SDP and satisfied users.
A global non-parametric sampling based image matting

Image matting is a process of separating the foreground objects from an image along with opacity values for each pixel. It is an under-constraint problem hence a user interaction is required to identify the definite foreground, background and semi-transparent pixels. In general the information in the definite foreground and background regions is modeled locally to estimate the foreground and background color of the pixels in the semi-transparent region which are then used to estimate opacity values. A global non-parametric sampling based approach is presented which incorporates not only the color information in the foreground and background regions but also utilizes the local structure of an image to improve the quality of the estimate matte. This global sampling approach reduces the segmentation mis-classification that is incorporated in the resulting alpha matte by considering only the local color information. The results obtained are comparable to the state of the art image matting techniques on a standard dataset.
Robust generalized H2 filtering for uncertain discrete-time linear systems

This paper considers the problem of robust generalized H2 filtering for discrete-time linear systems with polytopic uncertainties. Based on parameter-dependent Lyapunov functions combined with Finsler's lemma, new conditions for the solvability of the problem are given in terms of linear matrix inequalities (LMIs). Compared to the existing results, more slack variables are introduced to provide extra freedom for the generalized H2 optimization which lead to improving the performance and reducing the conservatism further. An example is give to illustrate the effectiveness of the proposed method.
ARDS: refinement of concept and redefinition.

AMERICAN REVIEW OF RESPIRATORY DISEASE who wrote "The Adult Respiratory Distress Syndrome (May it Rest in Peace)" (2). In the interim, we have each continued both clinical and basic research designed to unravel some of the many remaining mysteries about the pathogenesis of ARDS and factors associated with the prognosis. Gradually, a fairly standard approach to supportive therapy has emerged that involves mechanical ventilation, use of positive end expiratory pressure (PEEP), blood and fluid replacement, treatment ofpresumed or identified infections, and nutritional and psychological support. Still today more than 50070 ofpatients die ofARDS in either the early or late stages of disease. Also this interval has seen the definition of many of the risk factors associated with ARDS (3, 4) and the factors associated with prognosis once ARDS is established (5). On the bright side is the favorable outcome of patients who can be weaned from mechanical ventilation and can leave the hospital (6). Those investigators who have continued to observe their patients over many years have marvelled at the potential of the lung to remodel itself and reestablish good or even normal ventilatory and gas transfer function of the lung. Many patients have minimal or no symptoms at all in the late recovery phase. The expanded definition of the adult respiratorydistress syndrome proposed by John Murray and associates in this issue has considerable merit in my opinion (7). Wecertainly need a grading system for severity of lung injury. Stratifying patients by the degree of impaired oxygenation along with PEEP requirements is both reasonable and practical. It will be potentially useful to identify causal factors related to the initiation of this syndrome. I am personally delighted at the suggestion that ARDS not be defined in terms of measurements made by a flow-directed catheter. After all, the flow-directed catheter didn't even exist when we offered our three early papers on ARDS (8-10). Certainly hemodynamic measurements will play a strategic role in selected patients as a guide to therapy and for clinical research purposes in certain patients with informed consent. I believe stratification by bedside measurements of overall compliance is also reasonable and practical. These measurements will be available and can be made serially in all patients requiring mechanical ventila-
Inhibition of the Emergence of Ciprofloxacin Resistance in Streptococcus pneumoniae by the Multidrug Efflux Inhibitor Reserpine

ABSTRACT Recent evidence supports the contribution of a multidrug efflux mechanism to fluoroquinolone resistance in Streptococcus pneumoniae. In this paper I show that reserpine, an inhibitor of multidrug transporters in gram-positive bacteria, dramatically suppresses the in vitro emergence of ciprofloxacin-resistant variants of S. pneumoniae, suggesting that the combination of a fluoroquinolone with an inhibitor of multidrug transport may help preserve the efficacy of this class of antibiotics.
Expression and purification of GST-LMP-1 extracellular domain fusion protein of EB virus

Objective:To express structural GST-LMP-1 fusion protein in E.coli,detecting and analyzing its antibodies in NPC patients’ sera of EBV associated malignancies with Western-blot. Methods:The plasmid pMD18-LMP1 containing the recombinant extracellular peptide gene of LMP1 of EBV was digested with BamHⅠ and EcoRⅠ,and cloned into expression vector pGEX-4T-2. The constructed vector which had been identified by enzyme digestion and nucleotide sequence analysis was transformed into BL21(DE3). After induced with IPTG,the recombinant protein was purified with GST affinity chromatography,and confirmed by Western blot. Results:The recombinant plasmid was constructed correctly. SDS-PAGE analysis showed that the recombinant protein was about 32.2 ku. The purified protein could be used as an antigen to detect specific antibodies in the sera of patients with NPC by Western blot. Conclusion:The recombinant extracellular peptide gene of LMP1 of EBV could be expressed with high performance,and the antigenicity of the purified protein was certificated in sera of patients with NPC,which was associated with EBV.
Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor

A fundamental challenge to the study of oxidative stress responses of Mycobacterium tuberculosis (Mtb) is to understand how the protective host molecules are sensed and relayed to control bacilli gene expression. The genetic response of Mtb to hypoxia and NO is controlled by the sensor kinases DosS and DosT and the response regulator DosR through activation of the dormancy/NO (Dos) regulon. However, the regulatory ligands of DosS and DosT and the mechanism of signal sensing were unknown. Here, we show that both DosS and DosT bind heme as a prosthetic group and that DosS is rapidly autooxidized to attain the met (Fe3+) form, whereas DosT exists in the O2-bound (oxy) form. EPR and UV-visible spectroscopy analysis showed that O2, NO, and CO are ligands of DosS and DosT. Importantly, we demonstrate that the oxidation or ligation state of the heme iron modulates DosS and DosT autokinase activity and that ferrous DosS, and deoxy DosT, show significantly increased autokinase activity compared with met DosS and oxy DosT. Our data provide direct proof that DosS functions as a redox sensor, whereas DosT functions as a hypoxia sensor, and that O2, NO, and CO are modulatory ligands of DosS and DosT. Finally, we identified a third potential dormancy signal, CO, that induces the Mtb Dos regulon. We conclude that Mtb has evolved finely tuned redox and hypoxia-mediated sensing strategies for detecting O2, NO, and CO. Data presented here establish a paradigm for understanding the mechanism of bacilli persistence.
Serologic Evidence of Fruit Bat Exposure to Filoviruses, Singapore, 2011–2016

To determine whether fruit bats in Singapore have been exposed to filoviruses, we screened 409 serum samples from bats of 3 species by using a multiplex assay that detects antibodies against filoviruses. Positive samples reacted with glycoproteins from Bundibugyo, Ebola, and Sudan viruses, indicating filovirus circulation among bats in Southeast Asia.
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes

Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both aquatic and terrestrial plants. In this study we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algal and three plant species. Algal species were broadly selected from green and red algae, glaucophytes, oomycetes, diatoms and other microalgal groups. The results were deposited in the Algal Protein Annotation Suite database (Alga-PrAS; http://alga-pras.riken.jp/), which can be freely accessed online.
Heterogeneity of smooth muscle alpha adrenoceptors in rat tail artery in vitro.

Vascular smooth muscle alpha adrenoceptors in the proximal end of the rat isolated tail artery have been classified by determining pA2 values and -log KB values for the antagonists prazosin, corynanthine and idazoxan (RX 781094, a new synthetic alpha-2 adrenoceptor antagonist) against norepinephrine. The effects of the antagonists on responses to intramural sympathetic nerve stimulation were also assessed. Artery segments were perfused and superfused with Krebs' solution containing cocaine (4 microM) and propranolol (1 microM). Maximum responses to KCl, norepinephrine and nerve stimulation were not significantly different from one another. Corynanthine (0.1-100 microM), prazosin (10 nM-1 microM) and idazoxan (1-100 microM) caused competitive antagonism of norepinephrine responses with pA2 values consistent with the presence of alpha-1 adrenoceptors. However, idazoxan (10-100 nM) also caused parallel shifts in the concentration-response curves to norepinephrine with -log KB values higher than those consistent with the presence of alpha-1 adrenoceptors. The results have been interpreted to suggest a predominance of smooth muscle alpha-1 adrenoceptors in addition to a subpopulation of smooth muscle alpha-2 adrenoceptors which also contribute to vasoconstrictor responses to norepinephrine. In contrast to the results obtained with exogenous norepinephrine, responses to electrical stimulation were exquisitely sensitive to blockade by prazosin but resistant to idazoxan , suggesting an involvement of an alpha-1 adrenoceptor in these responses. It is concluded that idazoxan may be used to distinguish alpha-1 and alpha-2 adrenoceptors on vascular smooth muscle in vitro and that the results favor the existence of alpha-1 and alpha-2 adrenoceptors in terms of the existing subclassification scheme for alpha adrenoceptor subtypes. (ABSTRACT TRUNCATED AT 250 WORDS)
Prostate stem‐cell antigen gene is associated with diffuse and intestinal gastric cancer in Caucasians: Results from the EPIC‐EURGAST study

A genome‐wide study performed in a Japanese population identified a strong association between SNP rs2294008 (Met1Thr) in the Prostate Stem Cell Antigen gene (PSCA) and diffuse‐type gastric cancer (GC). This association was validated in different Asian populations, and, very recently, a study has been published in Caucasians. In this study, we analyzed the association between PSCA variation and GC risk in Caucasians from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Six tagSNPs covering the PSCA gene region were genotyped in 411 incident gastric adenocarcinoma cases and 1530 matched controls from a nested case–control study in the EPIC cohort. Associations were analyzed by unconditional logistic regression, adjusting for age, sex and country. The T allele of rs2294008 in PSCA was found to be a highly significant risk factor for GC (per allele OR = 1.42, 95% CI: 1.23–1.66, p‐value = 6.5 × 10−6), particularly of the noncardia‐type (per allele OR = 1.47, 95% CI: 1.19–1.81, p‐value = 3 × 10−4). At contrast with previous studies, no significant differences were observed between the diffuse (per allele OR = 1.54, 95% CI: 1.20–1.96, p‐value = 5 × 10−4) and the intestinal (per allele OR = 1.52, 95% CI: 1.20–1.93, p‐value = 5 × 10−4) GC histological subtypes. Although rs12155758 and rs9297976 were also found associated with GC, this association appeared to be due to linkage disequilibrium with rs2294008. Haplotype analysis did not provide additional information. These results confirm the association between variation in the promoter region of PSCA and GC risk in Caucasians and also indicate that the rs2294008 variant is a similar risk factor for both the diffuse and intestinal‐types of GC.
Some remarks on Arc-connectivity, vertex splitting, and orientation in graphs and digraphs

We apply proof techniques developed by L. Lovasz and A. Frank to obtain several results on the arc-connectivity of graphs and digraphs. The first results concern the operation of splitting two arcs from a vertex of an Eulerian graph or digraph in such a way as to preserve local connectivity conditions. The final result is concerned with orienting the edges of a mixed graph (consisting of vertices, undirected edges, and directed arcs) in such a way that the resulting digraph is as arc-connected as possible.
Comparative study of four adaptive frequency trackers

We study and compare four algorithms for adaptive retrieval of slowly time-varying multiple cisoids in noise: the adaptive notch filter, the multiple frequency tracker, the adaptive estimation scheme, and the hyperstable adaptive line enhancer. The local behavior of the algorithms in a neighborhood of their equilibrium state [assuming high signal-to-noise ratio (SNR) and large data sample] for a two-cisoid signal is treated in a similar way to the linear filter approximation technique used for a single-cisoid case. The validity of the results is confirmed by computer simulations.
Two algorithms for adaptive retrieval of slowly time-varying multiple cisoids in noise

Two algorithms for tracking parameters of slowly varying multiple complex sine waves (cisoids) in noise (the multiple frequency tracker and the adaptive notch filter) are described. For high signal-to-noise ratio (SNR), the properties of the algorithms (i.e., stability, noise rejection, and tracking speed) are studied analytically using a linear filter approximation technique. The tradeoff between noise rejection and tracking error for both algorithms is shown to be similar. Different choices of the design variables are discussed, namely (i) minimal mean-square estimation error for random walk modeled frequency variations and (ii) minimal stationary estimation variance subject to a given tracking delay. >