Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Cloning and Characterization of Novel Glutamate-Gated Chloride Channel Subunits from Schistosoma mansoni

Cys-loop ligand-gated ion channels (LGICs) mediate fast ionotropic neurotransmission. They are proven drug targets in nematodes and arthropods, but are poorly characterized in flatworms. In this study, we characterized the anion-selective, non-acetylcholine-gated Cys-loop LGICs from Schistosoma mansoni. Full-length cDNAs were obtained for SmGluCl-1 (Smp_096480), SmGluCl-2 (Smp_015630) and SmGluCl-3 (Smp_104890). A partial cDNA was retrieved for SmGluCl-4 (Smp_099500/Smp_176730). Phylogenetic analyses suggest that SmGluCl-1, SmGluCl-2, SmGluCl-3 and SmGluCl-4 belong to a novel clade of flatworm glutamate-gated chloride channels (GluCl) that includes putative genes from trematodes and cestodes. The flatworm GluCl clade was distinct from the nematode-arthropod and mollusc GluCl clades, and from all GABA receptors. We found no evidence of GABA receptors in S. mansoni. SmGluCl-1, SmGluCl-2 and SmGluCl-3 subunits were characterized by two-electrode voltage clamp (TEVC) in Xenopus oocytes, and shown to encode Cl−-permeable channels gated by glutamate. SmGluCl-2 and SmGluCl-3 produced functional homomers, while SmGluCl-1 formed heteromers with SmGluCl-2. Concentration-response relationships revealed that the sensitivity of SmGluCl receptors to L-glutamate is among the highest reported for GluCl receptors, with EC50 values of 7–26 µM. Chloride selectivity was confirmed by current-voltage (I/V) relationships. SmGluCl receptors are insensitive to 1 µM ivermectin (IVM), indicating that they do not belong to the highly IVM-sensitive GluClα subtype group. SmGluCl receptors are also insensitive to 10 µM meclonazepam, a schistosomicidal benzodiazepine. These results provide the first molecular evidence showing the contribution of GluCl receptors to L-glutamate signaling in S. mansoni, an unprecedented finding in parasitic flatworms. Further work is needed to elucidate the roles of GluCl receptors in schistosomes and to explore their potential as drug targets.
Monetary utility functions

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Epitaxial La-doped SrTiO3 on silicon: A conductive template for epitaxial ferroelectrics on silicon

Use of an epitaxial conducting template has enabled the integration of epitaxial ferroelectric perovskites on silicon. The conducting template layer, LaxSr1−xTiO3 (LSTO), deposited onto (001) silicon wafers by molecular-beam epitaxy is then used to seed {001}-oriented epitaxial perovskite layers. We illustrate the viability of this approach using PbZr0.4Ti0. 6O3 (PZT) as the ferroelectric layer contacted with conducting perovskite La0.5Sr0. 5CoO3 (LSCO) electrodes. An important innovation that further facilitates this approach is the use of a low-temperature (450 °C) sol–gel process to crystallize the entire ferroelectric stack. Both transmission electron microscopy and x-ray diffraction analysis indicate the LSCO/PZT/LSCO/LSTO/Si heterostructures are epitaxial. The electrical response of ferroelectric capacitors (for pulse widths down to 1 μs) measured via the underlying silicon substrate is identical to measurements made using conventional capacitive coupling method, indicating the viability of this approach.
Towards identification of operating systems from the internet traffic: IPFIX monitoring with fingerprinting and clustering

This paper deals with identification of operating systems (OSs) from the Internet traffic. Every packet injected on the network carries a specific information in its packet header that reflects the initial settings of a host's operating system. The set of such features forms a fingerprint. The OS fingerprint usually includes an initial TTL time, a TCP initial window time, a set of specific TCP options, and other values obtained from IP and TCP headers. Identification of OSs can be useful for monitoring a traffic on a local network and also for security purposes. In our paper we focus on the passive fingerprinting using TCP SYN packets that is incorporated to a IPFIX probe. Our tool enhances standard IPFIX records by additional information about OSs. Then, it sends the records to an IPFIX collector where network statistics are stored and presented to the network administrator. If identification is not successful, a further HTTP header check is employed and the fingerprinting database in the probe is updated. Our fingerprinting technique can be extended using cluster analysis as presented in this paper. As we show the clustering adds flexibility and dynamics to the fingerprinting. We also discuss the impact of IPv6 protocol on the passive fingerprinting.
Long-term e-cigarette use and smoking cessation: a longitudinal study with US population

Background E-cigarettes have grown popular. The most common pattern is dual use with conventional cigarettes. Dual use has raised concerns that it might delay quitting of cigarette smoking. This study examined the relationship between long-term use of e-cigarettes and smoking cessation in a 2-year period. Methods A nationally representative sample of 2028 US smokers were surveyed in 2012 and 2014. Long-term e-cigarette use was defined as using e-cigarettes at baseline and follow-up. Use of e-cigarettes only at baseline or at follow-up was defined as short-term use. Non-users did not use e-cigarettes at either survey. Quit attempt rates and cessation rates (abstinent for 3 months or longer) were compared across the three groups. Results At 2-year follow-up, 43.7% of baseline dual users were still using e-cigarettes. Long-term e-cigarette users had a higher quit attempt rate than short-term or non-users (72.6% vs 53.8% and 45.5%, respectively), and a higher cessation rate (42.4% vs 14.2% and 15.6%, respectively). The difference in cessation rate between long-term users and non-users remained significant after adjusting for baseline variables, OR=4.1 (95% CI 1.5 to 11.4) as did the difference between long-term users and short-term users, OR=4.8 (95% CI 1.6 to 13.9). The difference in cessation rate between short-term users and non-users was not significant, OR=0.9 (95% CI 0.5 to 1.4). Among those making a quit attempt, use of e-cigarettes as a cessation aid surpassed that of FDA-approved pharmacotherapy. Conclusions Short-term e-cigarette use was not associated with a lower rate of smoking cessation. Long-term use of e-cigarettes was associated with a higher rate of quitting smoking.
Effects Of Gaze-Contingent Stimuli On Eye Movements

Although we are mostly unaware of the fact that our eyes move several times per second, the way we perceive the world depends to a large extent on the exact scan paths our eyes describe. Indeed, recent studies have impressively shown that even substantial changes to a visual display can go unnoticed if the observer’s attention is directed somewhere else. Therefore, one of the goals of the Information technology for active perception (Itap) project is to improve communication systems by guiding the scan path of an observer. In this thesis, a system was implemented that allows to perform first experiments towards this goal. This system consists of a workstation that is connected to an eye-tracking device. High resolution movies can be displayed and manipulated in real time. The manipulation depends on the structure of the image sequence and on the gaze of the observer. To reduce the overall latency was a major design goal so that the system is capable of reacting to an eye movement within less than 30 ms. Results will be presented for experiments where image sequence manipulations were designed to attract the gaze of an observer. One of these manipulations was the sudden onset of a red square, the other stimulus type simulated the optical flow of an object moving towards the observer. The results show that it is possible to influence the gaze of an observer, but the strength of this effect seems to depend on the underlying image sequence.
Design and implementation of user-oriented video streaming service based on machine learning

We propose a method to determine appropriate quality of service (QoS) dynamically required by users for video streaming services in this paper. In the proposed method, the QoS parameters for the video streaming are determined based on the machine learning algorithm, by using a regression analysis in particular, according to the user requirements, computational/network resources and service provisioning environments. In this paper, we describe the design and implementation of our method. Furthermore, we confirm the feasibility of our proposed method through an experiment of a prototype system.
Fine scale genetic structure in the wild ancestor of maize (Zea mays ssp. parviglumis)

Analysis of fine scale genetic structure in continuous populations of outcrossing plant species has traditionally been limited by the availability of sufficient markers. We used a set of 468 SNPs to characterize fine‐scale genetic structure within and between two dense stands of the wild ancestor of maize, teosinte (Zea mays ssp. parviglumis). Our analyses confirmed that teosinte is highly outcrossing and showed little population structure over short distances. We found that the two populations were clearly genetically differentiated, although the actual level of differentiation was low. Spatial autocorrelation of relatedness was observed within both sites but was somewhat stronger in one of the populations. Using principal component analysis, we found evidence for significant local differentiation in the population with stronger spatial autocorrelation. This differentiation was associated with pronounced shifts in the first two principal components along the field. These shifts corresponded to changes in allele frequencies, potentially due to local topographical features. There was little evidence for selection at individual loci as a contributing factor to differentiation. Our results demonstrate that significant local differentiation may, but need not, co‐occur with spatial autocorrelation of relatedness. The present study represents one of the most detailed analyses of local genetic structure to date and provides a benchmark for future studies dealing with fine scale patterns of genetic diversity in natural plant populations.
Has the Rate of Job Loss Increased in the Nineties

I examine changes in the incidence of job loss between 1981 and 1995 using data from the Displaced Workers Surveys (DWS) from 1984-1996. The rate of job loss followed a cyclical pattern between 1981 and 1991, starting at a high level in the slack labor market of the early 1980's, falling during the economic expansion of the middle and late 1980s, and rising during the weak labor market at the end of the 1980's and early 1990's. A puzzle is that the overall rate of job loss has increased in the 1990's despite the sustained expansion. I document these facts and address the possibility that the elevated rates of job loss in the 1990's are a statistical artifact resulting from changes in the wording of key questions in the DWS in 1994 and 1996 exacerbating a problem of misclassification of some workers as displaced. Using additional data from a debriefing of respondents to the the February 1996 DWS to adjust rates of job loss to estimate a consistent time series of job loss rates, I find 1) that the overall rate of job loss has not declined in the 1993-95 time period, despite the strong labor market and 2) the overall rate of job loss in the 1993-95 period may be as high as it was during the slack labor market of 1989-91 and almost as high as it was during the very slack labor market of 1981-83.
Optimising Natural Language Generation Decision Making For Situated Dialogue

Natural language generators are faced with a multitude of different decisions during their generation process. We address the joint optimisation of navigation strategies and referring expressions in a situated setting with respect to task success and human-likeness. To this end, we present a novel, comprehensive framework that combines supervised learning, Hierarchical Reinforcement Learning and a hierarchical Information State. A human evaluation shows that our learnt instructions are rated similar to human instructions, and significantly better than the supervised learning baseline.
Quantitative Analysis of UDP-Glucuronosyltransferase (UGT) 1A and UGT2B Expression Levels in Human Livers

UDP-glucuronosyltransferases (UGTs) catalyze glucuronidation of a variety of xenobiotics and endobiotics. UGTs are divided into two families, UGT1 and UGT2. The purpose of this study was to estimate the absolute expression levels of each UGT isoform in human liver and to evaluate the interindividual variability. Real-time reverse transcriptase-polymerase chain reaction analysis was performed to determine the copy numbers of nine functional UGT1A isoforms and seven UGT2B isoforms. We noticed that not only primers but also templates as a standard for quantification should prudently be selected. Once we established appropriate conditions, the mRNA levels of each UGT isoform in 25 individual human livers were determined. UGT1A1 (0.9–138.5), UGT1A3 (0.1–66.6), UGT1A4 (0.1–143.3), UGT1A6 (1.0–70.4), UGT1A9 (0.3–132.4), UGT2B4 (0.3–615.0), UGT2B7 (0.2–97.4), UGT2B10 (0.7–253.2), UGT2B15 (0.3–107.8), and UGT2B17 (0.5–157.1) were substantially expressed (×104 copy/μg RNA) with large interindividual variability. Abundant isoforms were UGT2B4 and UGT2B10, followed by UGT1A1, UGT2B15, and UGT1A6. The sum of the UGT2B mRNA levels was higher than that of UGT1A mRNA levels. It is interesting to note that the mRNA levels normalized with glyceraldehyde-3-phosphate dehydrogenase mRNA for almost UGT isoforms that are substantially expressed in liver showed significant correlations to each other. Western blot analysis was performed using antibodies specific for UGT1A1, UGT1A4, UGT1A6, or UGT2B7. Correlation between the protein and mRNA levels was observed in only UGT1A1 (r = 0.488; p < 0.01). In conclusion, this study comprehensively determined the absolute values of mRNA expression of each UGT isoform in human livers and found considerable interindividual variability.
The Folk Theorem for Repeated Games

The Fudenberg and Maskin (1986) folk theorem for discounted repeated games assumes that the set of feasible payoffs is full dimensional. We obtain the same conclusion using a weaker condition. This condition is that no pair of players has equivalent von Neumann-Morgenstern utilities over outcomes. We term this condition NEU "non-equivalent utilities". The condition is weak, easily interpreted, and also almost necessary for the result.
A Critical Discourse Analysis of the Obama Administration's Education Speeches

This qualitative study examined 45 education speeches presented by President Obama and leaders of the U.S. Department of Education from January 2009 through December 2010. These speeches were interpreted with the use of critical discourse analysis and reviewed through the lens of interest convergence theory. The first aim of the researcher was to uncover the underlying ideologies represented in the Obama Administration’s education speeches. The second objective was to understand how those ideologies impacted the Administration’s proposed reform ideas. Specifically, the researcher was interested in how the underpinning ideologies and proposed solutions affected the education of poor students of color. The researcher found four primary ideologies in the education speeches. First, every speech was coupled with an economic agenda. Second, the speakers displayed great concern over America’s ability to remain a global economic leader. Third, there was an emphasis on the role of education in promoting equal opportunity and a belief in the American Dream. Finally, the speakers showed a deficit-oriented perception of students of color. The researcher discovered that economic ideologies inspired the Obama Administration’s proposed solutions. As such, the author argues that the Obama Administration utilized interest convergence by focusing on the economic self-interests of white policymakers. This study concludes with the author’s recommendations for change in the education of poor students of color. The author calls for strategic alliances throughout group identities in order to achieve educational equity.
Visual Data Mining

Never before in history has data been generated at such high volumes as it is today. Exploring and analyzing the vast volumes of data has become increasingly difficult. Information visualization and visual data mining can help to deal with the flood of information. The advantage of visual data exploration is that the user is directly involved in the data mining process. There are a large number of information visualization techniques that have been developed over the last two decades to support the exploration of large data sets. In this star report, we provide an overview of information visualization and visual data mining techniques, and illustrate them using a few examples.
Improved assembly accuracy by integrating base-calling, error correction and assembly

Motivation. With the recent advent of a multitude of next-generation sequencing (NGS) technologies (characterized by high throughput but relatively shorter read length), de novo DNA sequence assembly has become again one of the most prominent problems in Genomics and Computational Biology. Although algorithmic improvements play an important role in sequence assembly, the complexity of the problem is strongly reduced if higher quality (low error rate) sequences can be generated. For this reason, base-calling and error correction tools, together with novel assembly strategies, have begun to play a significant role in generating more accurate sequence assemblies. Methods. We present a new de novo assembly pipeline that integrates, in a Bayesian manner, two of our recent tools: TotalReCaller (for base-calling and error correction) and SUTTA (for sequence assembly). TotalReCaller was designed to improve base-calling quality by interpreting the analog signals from sequencing machines while simultaneously aligning the sequence reads to a source reference (draft or finished) genome, whenever available, to reduce the error rate. SUTTA is an accurate sequence assembler, based on a flexible branch-and-bound framework that forcefully and quickly eliminates incorrect solutions (i.e., implausible layouts). To achieve this goal SUTTA relies on technology agnostic score functions that enable combining data from multiple sources and distinct technologies. Results. This novel pipeline is demonstrated to improve the assembly quality significantly, when compared to the standard SUTTA pipeline (without error correction). Extensive comparison results with respect to some of the best state-of-the-art assembly algorithms (e.g., SOAPdenovo, ABySS and Velvet) for short read next-generation technologies are presented. The results point to a competitive performance improvement, achievable by combining an insightful base-caller with a foresighted assembler.
Image Completion from Low-Level Learning

We present a learning-based approach to complete the missing parts of an image. Besides the conventional adopted image continuity and coherency heuristics, learnt image patches are used to better regularize the completion result. Through the learning process from a collection of commonly encountered natural images, we built a synthetic world consisting of scenes and their corresponding images. We further model the inter-patch relationships with a Markov Network. A belief propagation scheme is then used to choose and update a latent scene structure based on a maximal posterior probability estimation of the given image. The above operation usually converges within a few iterations. The obtained image is visually realistic.
Penrose limits and maximal supersymmetry

We show that the maximally supersymmetric pp-wave of IIB superstring and M-theories can be obtained as a Penrose limit of the supersymmetric AdS × S solutions. In addition, we find that in a certain large tension limit, the geometry seen by a brane probe in an AdS × S background is either Minkowski space or a maximally supersymmetric pp-wave.
EWS Knockdown and Taxifolin Treatment Induced Differentiation and Removed DNA Methylation from p53 Promoter to Promote Expression of Puma and Noxa for Apoptosis in Ewing’s Sarcoma

Ewing’s sarcoma is a pediatric tumor that mainly occurs in soft tissues and bones. Malignant characteristics of Ewing’s sarcoma are correlated with expression of EWS oncogene. We achieved knockdown of EWS expression using a plasmid vector encoding EWS short hairpin RNA (shRNA) to increase anti-tumor mechanisms of taxifolin (TFL), a new flavonoid, in human Ewing’s sarcoma cells in culture and animal models. Immunofluorescence microscopy and flow cytometric analysis showed high expression of EWS in human Ewing’s sarcoma SK-N-MC and RD-ES cell lines. EWS shRNA plus TFL inhibited 80% cell viability and caused the highest decreases in EWS expression at mRNA and protein levels in both cell lines. Knockdown of EWS expression induced morphological features of differentiation. EWS shRNA plus TFL caused more alterations in molecular markers of differentiation than either agent alone. EWS shRNA plus TFL caused the highest decreases in cell migration with inhibition of survival, angiogenic and invasive factors. Knockdown of EWS expression was associated with removal of DNA methylation from p53 promoter, promoting expression of p53, Puma, and Noxa. EWS shRNA plus TFL induced the highest amounts of apoptosis with activation of extrinsic and intrinsic pathways in both cell lines in culture. EWS shRNA plus TFL also inhibited growth of Ewing’s sarcoma tumors in animal models due to inhibition of differentiation inhibitors and angiogenic and invasive factors and also induction of activation of caspase-3 for apoptosis. Collectively, knockdown of EWS expression increased various anti-tumor mechanisms of TFL in human Ewing’s sarcoma in cell culture and animal models.
YORUBA VOWEL PATTERNS: DERIVING ASYMMETRIES BY THE TENSION BETWEEN OPPOSING CONSTRAINTS

It is frequently the case that phonological patterns exhibit asymmetric properties with respect to their featural content. Such asymmetries may involve a variety of properties including stability, level of activity, nature of assimilatory target , nature of assimilatory trigger , and nature of epenthetic segment . Consider examples of these properties briefly. With regard to stability, it may be the case, for example, that high tones are stable under deletion while nonhigh tones are not (e.g. Pulleyblank 1986), or that nasality is stable while orality is not (e.g. Prunet 1986). Some features may play an ctive role in the phonology, while a second feature may be relatively or completely inert. For example, some tongue root harmony systems exhibit active advancement (A TR) while others exhibit active retraction (RTR) (Archangeli & Pulleyblank 1994). Recurrent patterns where one segment type acts as the targe of assimilation and another acts as the trigger are attested. For example, coronals are frequently observed to function as assimilation targets while noncoronals frequently function as assimilation triggers (Paradis & Prunet 1991). As a final example, certain features may more typically characterise penthetic segments (Archangeli 1988): high vowels may be more frequently epenthesised than mid, front more frequently than back, oral more frequently than nasal, and so on.