Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Dehydroaltenusin-C12 Derivative, a Selective DNA Polymerase α Inhibitor, on DNA Replication in Cultured Cells

Dehydroaltenusin is a selective inhibitor of mammalian DNA polymerase α (pol α) from a fungus (Alternaria tennuis). We have designed, synthesized, and characterized a derivative of dehydroaltenusin conjugated with a C12-alkyl side chain (dehydroaltenusin-C12 [C12]). C12 was the strongest pol α inhibitor in vitro. We introduced C12 into NIH3T3 cells with the help of a hypotonic shift, that is, a transient exposure of cultured cells in hypotonic buffer with small molecules which can not penetrate cells. The cells that took in C12 by hypotonic shift showed cell growth inhibition. At a low concentration (5 μM), DNA replication was inhibited and several large replication protein A (RPA) foci, which is different from dUTP foci. Furthermore, when C12 was incubated with aphidicolin, RPA foci were not observed in cells. Finally, these findings suggest that C12 inhibited DNA replication through pol α inhibition, and generated single-stranded DNA, resulted in uncoupling of the leading strand and lagging strand synthesis. These findings suggest that C12 could be more interesting as a molecule probe or anticancer agent than aphidicolin. C12 might provide novel markers for the development of antiproliferative drugs.
MLST reveals potentially high-risk international clones of Enterobacter cloacae.

OBJECTIVES To perform the first multinational Enterobacter cloacae clonality study, using the MLST scheme newly developed in Japan. METHODS The analysis included 195 rectal carriage E. cloacae isolates resistant to expanded-spectrum cephalosporins (ESCs), collected from patients in 12 hospital units across Europe and Israel. All of the isolates were typed by PFGE and 173 isolates were subjected to MLST. ESC resistance was analysed phenotypically; genes encoding ESBLs and carbapenemases were identified by PCR and sequencing. RESULTS MLST distinguished 88 STs, which correlated with the PFGE data. PFGE was more discriminatory, producing 129 pulsotypes (169 patterns). Numerous STs were observed in several countries each. The most widespread were ST66, ST78, ST108 and ST114, each having at least 10 isolates from three to five countries, diversified into multiple pulsotypes, with clusters of related isolates in one or more centres. Analysis of the STs against the MLST database revealed several epidemic clonal complexes, such as those with central genotypes ST74 (including ST78) or ST114 (including ST66). ESC resistance was equally related to overexpression of the AmpC cephalosporinase and to ESBL production. Among ESBL producers some spreading subclones were identified, including specific ST66, ST78 and ST114 pulsotypes, associated with CTX-M-15 production. Several isolates produced carbapenemase VIM-1 or KPC-2. CONCLUSIONS Together with the information available in the MLST database, our results suggest that, like Escherichia coli and Klebsiella pneumoniae, E. cloacae harbours clonal lineages of increased epidemic potential that may be associated with resistance spread.
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate ‘Patrocles DSPs’, including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on ‘Patrocles single nucleotide polymorphisms (pSNPs)’ in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep.
Disaster Narrative Emergent/cies: Performing Loss, Identity and Resistance

The essay investigates narratives of disaster experiences as performed in over five hundred oral histories, diaries, interviews, letters, and other sources drawn from US-related disasters over one hundred years’ time. Based on analysis of the stories, the study establishes disaster narratives as a specific type of cultural performance with characteristic aesthetic strategies and performative intents; articulates their reflexive and emergent qualities to be restoring/creating identity and social critique; and shows how ethnodramas of disaster narratives, particularly Playback Theatre, radically re-contextualize disaster narratives by opening them to new viewpoints and speakers, fostering dialogue, debate, and social action.
‘Two Eyes of a See-through’: Impaired and Intact Semantic Knowledge in a Case of Selective Deficit for Living Things

Abstract We report a patient, RC, with a category-specific semantic deficit for living things, who shows the following pattern of behaviour: (1) he has difficulty in distinguishing among individual exemplars for living thing categories, (2) he has no impairment in grouping living things according to their shared properties and (3) in property verification and definition tasks, RC shows good knowledge of shared but not distinctive properties of living things, (especially biological functional properties) and the reverse pattern for non-living things. These findings cannot be accounted for by selective damage to a particular type or category of information. We argue that RC's deficit is predicted by a unitary model of semantic memory in which the patterns of correlation among distinctive and shared perceptual and functional properties are different for concepts in the domains of living and non-living things. These differences in conceptual structure give rise to category-specific impairments when the semant.
Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction

Quantitative real-time polymerase chain reactions (qRT-PCR) have become the method of choice for rapid, sensitive, quantitative comparison of RNA transcript abundance. Useful data from this method depend on fitting data to theoretical curves that allow computation of mRNA levels. Calculating accurate mRNA levels requires important parameters such as reaction efficiency and the fractional cycle number at threshold (CT) to be used; however, many algorithms currently in use estimate these important parameters. Here we describe an objective method for quantifying qRT-PCR results using calculations based on the kinetics of individual PCR reactions without the need of the standard curve, independent of any assumptions or subjective judgments which allow direct calculation of efficiency and CT. We use a four-parameter logistic model to fit the raw fluorescence data as a function of PCR cycles to identify the exponential phase of the reaction. Next, we use a three-parameter simple exponent model to fit the exponential phase using an iterative nonlinear regression algorithm. Within the exponential portion of the curve, our technique automatically identifies candidate regression values using the P-value of regression and then uses a weighted average to compute a final efficiency for quantification. For CT determination, we chose the first positive second derivative maximum from the logistic model. This algorithm provides an objective and noise-resistant method for quantification of qRT-PCR results that is independent of the specific equipment used to perform PCR reactions.
Ubiquitous Redirection as Access Control Response

Rule-based access control mechanisms, network firewalls and application input validation all serve to enforce security policy. When violating the acceptable conditions these defenses mandate, an unauthorized requester is generally turned away. We make an argument for a modification to traditional access limitation through redirection and deceptive completion across many layers of data communication. Ubiquitous redirection provides additional information on attacker behavior, consumes attacker resources, improving defender awareness and, ultimately, site security. We describe a variety of network-based techniques for deception implemented in our honeypots, and undertake a study of OS-level deception practiced by rootkit writers with the view towards prospective use of similar techniques for defensive applications.
Performance analysis and odometry improvement of an omnidirectional mobile robot for outdoor terrain

In this paper an omnidirectional mobile robot that possesses high mobility in rough terrain is presented. The omnidirectional robot has four active split offset caster (ASOC) modules, enabling the robot to move in any planar direction. It also possesses passive suspension articulation, allowing the robot to conform to uneven terrain. The agility of the robot is experimentally evaluated in various configurations. In addition, an odometry method that mitigates position estimation error due to wheel slippage is proposed. A key aspect of the proposed method is to utilize sensory data of wheel velocity, and turning rate around each ASOC pivot shaft, along with kinematic constraints of the robot configuration. Experimental odometry tests with different maneuvers in rough terrain are presented that confirm the utility of the proposed method.
Social Anxiety and the Post-Event Processing of Socially Distressing Events

The correlation between social anxiety, as measured by the Social Phobia Scale, and negative post-event processing of socially distressing events, as measured by a diary record, was studied in a sample of 62 undergraduate students during a 1-week period. Of the participants, 55 individuals reported the experience of at least 1 socially distressing event during this time; only 24 of the participants, however, reported distressing events of a negative-evaluational character during the recording week. Although the Social Phobia Scale did not correlate with post-event processing of socially distressing events in general, it showed moderate to strong correlations with post-event processing of negative-evaluational events both on the same day and on the following day. Furthermore, the degree of negative post-event processing that was reported the same day was strongly predictive of the degree of such processing that was reported the following day. The results confirm that negative post-event processing is a real phenomenon with regard to socially distressing situations, and that high social anxiety is associated with higher degrees of such post-event processing of negative-evaluational events. The results also suggest that social anxiety is only one of several forms of interpersonal distress that are characterized by such negative post-event processing; other forms of such distress involve other fears (fears of separation or loneliness, fears of hurting others, etc.) or other kinds of feelings (e.g. guilt and anger).
Docetaxel-Resistant Prostate Cancer Cells Remain Sensitive to S-Trityl-l-Cysteine–Mediated Eg5 Inhibition

Castrate-resistant prostate cancer remains a major clinical challenge. Due to the toxicity profile of taxane-based chemotherapy and treatment failure in some patients, novel agents with improved efficacy to side effect profiles are urgently needed. Eg5, a member of the kinesin-5 family, controls the formation of the bipolar spindle during cell division, and suppressed Eg5 function leads to mitotic arrest. S-Trityl-l-cysteine (STLC) is a novel Eg5-specific small-molecule inhibitor. Here, we report the first study to evaluate its use in prostate cancer. In a panel of prostate cancer cells, LNCaP and PC3 cells were the most and least sensitive to STLC treatment, with a 7.2-fold difference in their respective GI50 values: 250 nmol/L and 1.8 μmol/L. In LNCaP cells, treatment with either STLC or docetaxel resulted in transient G2-M arrest and subsequent caspase-mediated cell death. However, STLC- and docetaxel-treated PC3M cells have distinct fates: STLC induced a transient G2-M arrest, followed by polyploidy; in contrast, docetaxel-treated PC3M cells progressed to apoptosis after a transient G2-M arrest. Docetaxel-resistant LNCaP-derived (LDocR) cells respond to STLC in a similar manner to the parental cells. Although the docetaxel-resistant PC3M-derived (PDocR) cell line and its parental PC3M cells have similar GI50 to STLC treatment, PDocR cells showed significantly more G2-M arrest and less apoptosis. Hence, although docetaxel-resistant prostate cancer cells remain responsive to Eg5 inhibition with STLC, there are key differences at the cell cycle level, which may have implication in future development. Mol Cancer Ther; 9(6); 1730–9. ©2010 AACR.
Physiological Characterization of Two Genes for Na+ Exclusion in Durum Wheat, Nax1 and Nax21

Durum wheat (Triticum turgidum L. subsp. durum Desf.) Line 149 contains two novel major genes for excluding Na+ from leaf blades, named Nax1 and Nax2. The genes were separated into families containing a single gene and near-isogenic homozygous lines were selected. Lines containing either Nax1 or Nax2 had lower rates of Na+ transport from roots to shoots than their near-isogenic pairs due to lower rates of net loading of the xylem, not to lower rates of net uptake from the soil or higher rates of retranslocation in the phloem. Nax1 and Nax2 lines also had higher rates of K+ transport from root to shoot, resulting in an enhanced discrimination of K+ over Na+. Lines containing Nax1 differed from those containing Nax2 by unloading Na+ from the xylem as it entered the shoot so that Na+ was retained in the base of the leaf, leading to a high sheath to blade ratio of Na+ concentration. Gradients in tissue concentrations of Na+ along the leaf suggested that Na+ was continually removed from the xylem. The Nax2 line did not retain Na+ in the base of the leaf, suggesting that it functioned only in the root. The Nax2 gene therefore has a similar function to Kna1 in bread wheat (Triticum aestivum).
Global Register Alias Table: Executing Sequential Program on Multi-Core

Executing sequential program on multi-core is crucial for accommodating instruction level parallelism (ILP) in chip multiprocessor (CMP) architecture. One widely used method of steering instructions across cores is based on dependency. However, this method requires a sophisticated steering mechanism and brings much hardware complexity and area overhead. This paper presents the Global Register Alias Table (GRAT), a structure which can be used in CMP architecture to facilitate sequential program execution across cores. The GRAT also reduces the area and complexity for steering instructions greatly without introducing additional programming effort and compiler support. In our evaluation, the result shows that our work performs within 5.9% of Core Fusion, a recent proposal which requires a complex steering unit.
A Spanish translation of Mehrabian and Russell's emotionality scales for environmental consumer psychology

The development of a translation of Mehrabian and Russell's scales for the measurement of pleasure, arousal and dominance from the original English to a Spanish version for use in Venezuela is described. The translated scales were administered to two samples of middle-class Venezuelan consumers (n = 127,n = 127) between the ages of 20 and 50, among whom males and females were represented approximately equally. Internal reliability (measured by Cronbach's alpha) and scale validity (measured by factor analysis) indicate that the translated scales are suitable for consumer and other social psychological research in Spanish.
Audio-visual large vocabulary continuous speech recognition in the broadcast domain

Considers the problem of combining visual cues with audio signals for the purpose of improved automatic machine recognition of speech. Although significant progress has been made in the machine transcription of large-vocabulary continuous speech (LVCSR) over the last few years, the technology to date is most effective only under controlled conditions, such as low noise, speaker-dependent recognition, read speech (as opposed to conversational speech), etc. On the other hand, while augmenting the recognition of speech utterances with visual cues has attracted the attention of researchers over the last couple of years, most efforts in this domain can be considered to be only preliminary in the sense that, unlike LVCSR efforts, tasks have been limited to small vocabularies (e.g. commands, digits) and often to speaker-dependent training or isolated word speech, where word boundaries are artificially well-defined.
Fungicide Sensitivity and Characterization of Cobweb Disease on a Pleurotus eryngii Mushroom Crop Caused by Cladobotryum mycophilum

In 2009–2010, unusual symptoms were observed on Pleurotus eryngii grown in mushroom farms in Gyeongnam Province, Republic of Korea. One of the main symptoms was a cobweb-like growth of fungal mycelia over the surface of the mushroom. The colonies on the surface rapidly overwhelmed the mushrooms and developed several spores within 3–4 days. The colonized surface turned pale brown or yellow. The fruit body eventually turned dark brown and became rancid. Koch’s postulates were completed by spraying and spotting using isolated strains. The phylogenetic tree obtained from the internal transcribed spacer sequence analysis showed that the isolated fungal pathogen corresponded to Cladobotryum mycophilum (99.5%). In the fungicide sensitivity tests, the ED50 values for the isolate with respect to benomyl and carbendazim were from 0.29 to 0.31 ppm. Benzimidazole fungicides were most effective against C. mycophilum, a causal agent of cobweb disease in P. eryngii.
Natural Killer Cell Cytotoxicity Against SKOV3 after HLA-G Downregulation by shRNA.

BACKGROUND HLA-G is a nonclassical HLA class I molecule which, when elevated in tumor cells, is one of the main factors involved in tumor evasion of immune responses including NK and T cells. OBJECTIVE To evaluate the effect of HLA-G downregulation on NK cell cytotoxicity in tumor cell lines. METHODS The expression level of HLA-G was measured by real-time PCR and flowcytometry after transfection of SKOV3 by shRNA.1, which targets specific sequences in exon 4, or shRNA.2, which targets both exons 4 and 6. NK-92MI cell cytotoxicity against transfected or untransfected target cell lines was measured with the lactate dehydrogenase (LDH) release assay. The Jeg-3 cell line was used as a positive control. RESULTS Membrane-bound HLA-G expression levels decreased significantly in both cell lines after transfection with both shRNAs compared to their corresponding untransfected cells (p<0.05). Jeg-3 cells were better lysed than SKOV3 cells by NK cells during the first 48 h after transfection with both shRNAs. Compared to untransfected cells, shRNA.1-transfected SKOV3 cells were significantly more lysed by NK cells 24 h post-transfection (p=0.043). CONCLUSION As a clinical approach, HLA-G downregulation with shRNA may be effective in cancer therapy by improving immune cell activation.
Applying the Multiple Cause Mixture Model to Text Categorization

This paper introduces the use of the Multiple Cause Mixture Model to automatic text category assign- ment. Although much research has been done on text categorization, this algorithm is novel in that is unsu- pervised, that is, does not require pre-labeled training examples, and it can assign multiple category labels to documents. In this paper we present very preliminary results of the application of this model to a standard test collection, evaluating it in supervised mode in or- der to facilitate comparison with other methods, and showing initial results of its use in unsupervised mode.
Statistical Reconstruction of Material Decomposed Data in Spectral CT

Photon-counting detector technology has enabled the first experimental investigations of energy-resolved computed tomography (CT) imaging and the potential use for K-edge imaging. However, limitations in regards to detecter technology have been imposing a limit to effective count rates. As a consequence, this has resulted in high noise levels in the obtained images given scan time limitations in CT imaging applications. It has been well recognized in the area of low-dose imaging with conventional CT that iterative image reconstruction provides a superior signal to noise ratio compared to traditional filtered backprojection techniques. Furthermore, iterative reconstruction methods also allow for incorporation of a roughness penalty function in order to make a trade-off between noise and spatial resolution in the reconstructed images. In this work, we investigate statistically-principled iterative image reconstruction from material-decomposed sinograms in spectral CT. The proposed reconstruction algorithm seeks to minimize a penalized likelihood-based cost functional, where the parameters of the likelihood function are estimated by computing the Fisher information matrix associated with the material decomposition step. The performance of the proposed reconstruction method is quantitatively investigated by use of computer-simulated and experimental phantom data. The potential for improved K-edge imaging is also demonstrated in an animal experiment.
Analysis of the performance of cooperative spectrum sensing over correlated Log-Normal shadowing with the moment generation function

A method is proposed for analyzing the performance of cooperative spectrum sensing in correlated Log-Normal shadow-fading environment. The probability density function (PDF) of Log-Normal sum is approximated by improving Schwartz-Yeh (I-SY), in which mean and derivation are obtained by moment generation function (MGF) instead of recursive Log-Normal approximation in Schwartz-Yeh (SY). The extension to the correlated scenario is made. Then an expression for calculating the average detection probability is obtained with the derivatives of MGF of Log-Normal RVs sum. Finally the performance of cooperative spectrum sensing is investigated using the method. Simulation results prove the reliability of the method.
Risky decision-making in HIV-associated neurocognitive disorders (HAND)

Individuals infected with HIV show moderate deficits in decision-making, but the ecological relevance of such deficits on everyday functioning has not previously been described. This study sought to examine the magnitude, cognitive correlates, and everyday functioning impact of risky decision-making impairment in HIV-associated neurocognitive disorders (HAND). Participants included 68 HIV+ individuals with HAND, 78 HIV+ individuals without HAND, and 51 HIV− comparison participants, who were administered the Iowa Gambling Task (IGT) alongside a comprehensive neuropsychological test battery and self-report measures assessing aspects of everyday functioning. HIV+ individuals with HAND performed more poorly on the IGT relative to the other two groups, most notably during the last three trial blocks. Within the HIV+ group, IGT performance during the last three trial blocks was most strongly associated with cognitive flexibility, but was not significantly related to declines in instrumental activities of daily living (IADLs), unemployment, or medication non-adherence. While overall IGT performance across the last three trial blocks may be helpful diagnostically in identifying decision-making impairment in HAND, examination of alternate, more specific metrics (e.g., individual deck selections across trial blocks) may be more useful in delineating the role of poor decision-making in HIV-related disability, and should be examined in future research.