Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone arginine methylation in cocaine action in the nucleus accumbens

Significance We demonstrate that protein-R (arginine)-methyltransferase-6 (PRMT6) and its associated histone mark, asymmetric dimethylation of R2 on histone H3 (H3R2me2a), are decreased in the nucleus accumbens (NAc) of mice and rats after repeated cocaine exposure, as well as in the NAc of cocaine-addicted humans. We show that cocaine-induced PRMT6 down-regulation occurs selectively in NAc medium spiny neurons expressing dopamine D2 receptors (D2-MSNs) and serves to protect against cocaine-induced behavioral abnormalities. Furthermore, we provide the first, to our knowledge, genome-wide characterization of H3R2me2a within a specific brain region in vivo, and identify Src kinase signaling inhibitor 1 (Srcin1 or p140Cap) as a key target for this chromatin modification. Srcin1 induction in the NAc after cocaine exposure, which is associated with reduced Src signaling, decreases cocaine reward. Repeated cocaine exposure regulates transcriptional regulation within the nucleus accumbens (NAc), and epigenetic mechanisms—such as histone acetylation and methylation on Lys residues—have been linked to these lasting actions of cocaine. In contrast to Lys methylation, the role of histone Arg (R) methylation remains underexplored in addiction models. Here we show that protein-R-methyltransferase-6 (PRMT6) and its associated histone mark, asymmetric dimethylation of R2 on histone H3 (H3R2me2a), are decreased in the NAc of mice and rats after repeated cocaine exposure, including self-administration, and in the NAc of cocaine-addicted humans. Such PRMT6 down-regulation occurs selectively in NAc medium spiny neurons (MSNs) expressing dopamine D2 receptors (D2-MSNs), with opposite regulation occurring in D1-MSNs, and serves to protect against cocaine-induced addictive-like behavioral abnormalities. Using ChIP-seq, we identified Src kinase signaling inhibitor 1 (Srcin1; also referred to as p140Cap) as a key gene target for reduced H3R2me2a binding, and found that consequent Srcin1 induction in the NAc decreases Src signaling, cocaine reward, and the motivation to self-administer cocaine. Taken together, these findings suggest that suppression of Src signaling in NAc D2-MSNs, via PRMT6 and H3R2me2a down-regulation, functions as a homeostatic brake to restrain cocaine action, and provide novel candidates for the development of treatments for cocaine addiction.
Information Systems Research in Chinese Universities: an Examination of the Input Side

Along with the rapid growth of the Chinese economy over the past decades, information systems (IS) research in China has undergone a profound transformation. This exploratory study reports on a survey involving 107 university researchers, focusing on the input aspects of IS research and how institutional factors affect the input. In this paper, input mainly refers to research activities, effort, methods and reference disciplines. Data show researchers are withdrawing from IS development projects, while increasing their effort in academic research. Compared to the past, IS research topics are now more aligned to the international mainstream. A major hurdle for empirical research is the lack of familiarities with empirical research methodology, as indicated by nearly half of the respondents. Effort in academic research tends to correlate with the researchers’ income scheme, i.e., sources and proportion of base salary and benefits in their overall income. However, surprisingly, emphasis on quality of publication has not significantly influenced researchers’ effort yet, nor has the increased degree of internationalization affected the selection of research methods and the shift to empirical research. The underlying reasons are explored, and implications are also discussed.
Electrocardiography in women: taking the initiative.

In the just over 100 years since the first ECG was performed,1 the ECG has become the most extensively used noninvasive diagnostic and prognostic tool in cardiology. Used both at rest and during provocative exercise, the 12-lead ECG has impressive, if imperfect, utility for rhythm analysis, detection of ischemic and hypertrophic heart disease, and outcome prediction in a variety of clinical settings, with a large body of literature that illustrates and supports these applications. The first observation of gender differences in the ECG was published 85 years ago by Bazett,2 demonstrating that women have significantly longer QT intervals than men despite having higher heart rates. However, despite a growing body of literature demonstrating significant gender differences in QRS amplitudes and duration,3–6 QT intervals,5,7,8 ST-segment deviation,9,10 and novel, computer-based measurements of T-wave complexity,8,11 few ECG criteria routinely use gender-specific diagnostic criteria, and there has been a relative paucity of data on the prognostic performance of ECG variables in women. Articles pp 473 and 481 Two studies in the current issue of Circulation by Rautaharju and colleagues12,13 provide a wealth of new findings and impetus for further study of the ECG in women. Using well-validated computerized ECG methodology, the authors examined the value of a number of ECG variables for predicting incident coronary heart disease and its mortality, incident congestive heart failure, and total mortality in more than 38 000 women participating in the dietary modification trial of the Women’s Health Initiative. Although both studies reconfirm the predictive value of ECG evidence of prior Q-wave myocardial infarction (MI), the principle new findings are the strong predictive value of various ECG measures of repolarization, and in particular of the QRS/T angle,12,13 a measure of the spatial angle between mean QRS and T vectors. In the …
Evolution of the diverse biological roles of inositols.

Several of the nine hexahydroxycylohexanes (inositols) have functions in Biology, with myo-inositol (Ins) in most of the starring roles; and Ins polyphosphates are amongst the most abundant organic phosphate constituents on Earth. Many Archaea make Ins and use it as a component of diphytanyl membrane phospholipids and the thermoprotective solute di-L-Ins-1,1'-phosphate. Few bacteria make Ins or use it, other than as a carbon source. Those that do include hyperthermophilic Thermotogales (which also employ di-L-Ins-1,1'-phosphate) and actinomycetes such as Mycobacterium spp. (which use mycothiol, an inositol-containing thiol, as an intracellular redox reagent and have characteristic phosphatidylinositol-linked surface oligosaccharides). Bacteria acquired their Ins3P synthases by lateral gene transfer from Archaea. Many eukaryotes, including stressed plants, insects, deep-sea animals and kidney tubule cells, adapt to environmental variation by making or accumulating diverse inositol derivatives as 'compatible' solutes. Eukaryotes use phosphatidylinositol derivatives for numerous roles in cell signalling and regulation and in protein anchoring at the cell surface. Remarkably, the diradylglycerol cores of archaeal and eukaryote/bacterial glycerophospholipids have mirror image configurations: sn-2,3 and sn-1,2 respectively. Multicellular animals and amoebozoans exhibit the greatest variety of functions for PtdIns derivatives, including the use of PtdIns(3,4,5)P3 as a signal. Evolutionarily, it seems likely that (i) early archaeons first made myo-inositol approx. 3500 Ma (million years) ago; (ii) archeons brought inositol derivatives into early eukaryotes (approx. 2000 Ma? ); (iii) soon thereafter, eukaryotes established ubiquitous functions for phosphoinositides in membrane trafficking and Ins polyphosphate synthesis; and (iv) since approx. 1000 Ma, further waves of functional diversification in amoebozoans and metazoans have introduced Ins(1,4,5)P3 receptor Ca2+ channels and the messenger role of PtdIns(3,4,5)P3.
A bilateral filter in gradient domain

In this paper, a bilateral filter in gradient domain is first proposed. It is then applied to study detail enhancement via multi-light images and noise reduction of differently exposed low dynamic range images. These two applications show that the proposed filter can be applied to extract fine details from a set of images simultaneously and to provide flexibility for noise reduction from selected areas of an image.
The Lateral Superior Olive: A Functional Role in Sound Source Localization

Sound location in azimuth is signaled by differences in the times of arrival (interaural time difference, ITDs) and the amplitudes (interaural level differences, ILDs) of the stimuli at the ears. Psychophysical studies have shown that low- and high-frequency sounds are localized based on ITDs and ILDs, respectively, suggesting that dual mechanisms mediate localization. The anatomical and physiological bases for this “duplex theory” of localization are found in the medial (MSO) and lateral (LSO) superior olives, two of the most peripheral sites in the ascending auditory pathway receiving inputs from both ears. The MSO and LSO are believed to be responsible for the initial encoding of ITDs and ILDs, respectively. Here the author focuses on ILDs as a cue to location and the role of the LSO in encoding ILDs. Evidence from disparate fields of study supports the hypothesis that the LSO is the initial ILD processor in the mammalian auditory system. NEUROSCIENTIST 9(2): 127–143, 2003.
Database‐Assisted Object Retrieval for Real‐Time 3D Reconstruction

In recent years, real‐time 3D scanning technology has developed significantly and is now able to capture large environments with considerable accuracy. Unfortunately, the reconstructed geometry still suffers from incompleteness, due to occlusions and lack of view coverage, resulting in unsatisfactory reconstructions. In order to overcome these fundamental physical limitations, we present a novel reconstruction approach based on retrieving objects from a 3D shape database while scanning an environment in real‐time. With this approach, we are able to replace scanned RGB‐D data with complete, hand‐modeled objects from shape databases. We align and scale retrieved models to the input data to obtain a high‐quality virtual representation of the real‐world environment that is quite faithful to the original geometry. In contrast to previous methods, we are able to retrieve objects in cluttered and noisy scenes even when the database contains only similar models, but no exact matches. In addition, we put a strong focus on object retrieval in an interactive scanning context — our algorithm runs directly on 3D scanning data structures, and is able to query databases of thousands of models in an online fashion during scanning.
Involvement of the Anterior Cingulate Cortex in the Expression of Remote Spatial Memory

Although the hippocampus plays a crucial role in the formation of spatial memories, as these memories mature they may become additionally (or even exclusively) dependent on extrahippocampal structures. However, the identity of these extrahippocampal structures that support remote spatial memory is currently not known. Using a Morris water-maze task, we show that the anterior cingulate cortex (ACC) plays a key role in the expression of remote spatial memories in mice. To first evaluate whether the ACC is activated after the recall of spatial memory, we examined the expression of the immediate early gene, c-fos, in the ACC. Fos expression was elevated after expression of a remote (1 month old), but not recent (1 d old), water-maze memory, suggesting that ACC plays an increasingly important role as a function of time. Consistent with the gene expression data, targeted pharmacological inactivation of the ACC with the sodium channel blocker lidocaine blocked expression of remote, but spared recent, spatial memory. In contrast, inactivation of the dorsal hippocampus disrupted expression of spatial memory, regardless of its age. We further showed that inactivation of the ACC blocked expression of remote spatial memory in two different mouse strains, after training with either a hidden or visible platform in a constant location, and using the AMPA receptor antagonist CNQX. Together, our data provide evidence that circuits supporting spatial memory are reorganized in a time-dependent manner, and establish that activity in neurons intrinsic to the ACC is critical for processing remote spatial memories.
Towards a Biocatalyst for (S)-Styrene Oxide Production: Characterization of the Styrene Degradation Pathway of Pseudomonas sp. Strain VLB120

ABSTRACT In order to design a biocatalyst for the production of optically pure styrene oxide, an important building block in organic synthesis, the metabolic pathway and molecular biology of styrene degradation inPseudomonas sp. strain VLB120 was investigated. A 5.7-kbXhoI fragment, which contained on the same strand of DNA six genes involved in styrene degradation, was isolated from a gene library of this organism in Escherichia coli by screening for indigo formation. T7 RNA polymerase expression experiments indicated that this fragment coded for at least five complete polypeptides, StyRABCD, corresponding to five of the six genes. The first two genes encoded the potential carboxy-terminal part of a sensor, named StySc, and the complete response regulator StyR. Fusion of the putative styAp promoter to a lacZreporter indicated that StySc and StyR together regulate expression of the structural genes at the transcriptional level. Expression ofstyScR also alleviated a block that prevented translation of styA mRNA when a heterologous promoter was used. The structural genes styA and styBproduced a styrene monooxygenase that converted styrene to styrene oxide, which was then converted to phenylacetaldehyde by StyC. Sequence homology analysis of StyD indicated a probable function as a phenylacetaldehyde dehydrogenase. To assess the usefulness of the enzymes for the production of enantiomerically pure styrene oxide, we investigated the enantiospecificities of the reactions involved. Kinetic resolution of racemic styrene oxide by styrene oxide isomerase was studied with E. coli recombinants carryingstyC, which converted styrene oxide at a very high rate but with only a slight preference for the S enantiomer. However, recombinants producing styrene monooxygenase catalyzed the formation of (S)-styrene oxide from inexpensive styrene with an excellent enantiomeric excess of more than 99% at rates up to 180 U g (dry weight) of cells−1.
A trainable spoken language understanding system for visual object selection

We present a trainable, visually-grounded, spoken language understanding system. The system acquires a grammar and vocabulary from a “show-and-tell” procedure in which visual scenes are paired with verbal descriptions. The system is embodied in a table-top mounted active vision platform. During training, a set of objects is placed in front of the vision system. Using a laser pointer, the system points to objects in random sequence, prompting a human teacher to provide spoken descriptions of the selected objects. The descriptions are transcribed and used to automatically acquire a visually-grounded vocabulary and grammar. Once trained, a person can interact with the system by verbally describing objects placed in front of the system. The system recognizes and robustly parses the speech and points, in real-time, to the object which best fits the visual semantics of the spoken description.
Single methyl group determines prion propagation and protein degradation activities of yeast heat shock protein (Hsp)-70 chaperones Ssa1p and Ssa2p

Organisms encode multiple homologous heat shock protein (Hsp)-70s, which are essential protein chaperones that play the major role in cellular protein “quality control. ” Although Hsp70s are functionally redundant and highly homologous, many possess distinct functions. A regulatory motif underlying such distinctions, however, is unknown. The 98% identical cytoplasmic Hsp70s Ssa1p and Ssa2p function differently with regard to propagation of yeast [URE3] prions and in the vacuolar-mediated degradation of gluconeogenesis enzymes, such as FBPase. Here, we show that the Hsp70 nucleotide binding domain (NBD) regulates these functional specificities. We find little difference in ATPase, protein refolding, and amyloid inhibiting activities of purified Ssa1p and Ssa2p, but show that interchanging NBD residue alanine 83 (Ssa1p) and glycine 83 (Ssa2p) switched functions of Ssa1p and Ssa2p in [URE3] propagation and FBPase degradation. Disrupting the degradation pathway did not affect prion propagation, however, indicating these are two distinct processes where Ssa1/2p chaperones function differently. Our results suggest that the primary evolutionary pressure for Hsp70 functional distinctions is not to specify interactions of Hsp70 with substrate, but to specify the regulation of this activity. Our data suggest a rationale for maintaining multiple Hsp70s and suggest that subtle differences among Hsp70s evolved to provide functional specificity without affecting overall enzymatic activity.
Differentiation-specific transcriptional regulation of the hepatitis B virus large surface antigen gene in human hepatoma cell lines

The transcriptional activities of the four hepatitis B virus promoters were compared in three differentiated hepatoma cell lines, HepG2, Hep3B, and PLC/PRF/5; a dedifferentiated subline of HepG2, HepG2.1; a human cervical carcinoma cell line, HeLa S3; and a mouse fibroblast cell line, NIH 3T3. The plasmid constructs, which contain the complete hepatitis B virus genome directing the expression of the luciferase reporter gene, were analyzed by transient transfection assays. The relative orders of the levels of the transcriptional activities of the four promoters were similar in each of the cell lines. The major surface antigen and X-gene promoters displayed the highest activity levels, the core promoter activity level was less than or similar to the activity levels of these two promoters, and the large surface antigen promoter had the lowest activity level in all of the cell lines examined. The core promoter demonstrated an approximately 2- to 20-fold higher relative level of expression in the differentiated hepatoma cell lines, suggesting that this promoter might be preferentially active in these cells. The relative level of activity of the large surface antigen promoter in the differentiated hepatoma cell lines was approximately 5 to 90 times greater than that observed in the other cell lines, indicating that the activity of this promoter is highly specific for differentiation state and cell type. Deletion analysis of the large surface antigen promoter demonstrated that the sequence element responsible for the differentiation state-specific expression from this promoter is located between nucleotides 2719 and 2733 (-90 and -76). Within this sequence element is a binding site (GTTAATCATTACT) for the liver-specific transcription factor hepatocyte nuclear factor 1 (HNF1). This indicates that the preferential expression from the large surface antigen promoter in the differentiated hepatoma cell lines is probably mediated by HNF1 or an HNF1-related transcription factor.
A Particle Model for State Estimation in Real-Time Strategy Games

A big challenge for creating human-level game AI is building agents capable of operating in imperfect information environments. In real-time strategy games the technological progress of an opponent and locations of enemy units are partially observable. To overcome this limitation, we explore a particle-based approach for estimating the location of enemy units that have been encountered. We represent state estimation as an optimization problem, and automatically learn parameters for the particle model by mining a corpus of expert StarCraft replays. The particle model tracks opponent units and provides conditions for activating tactical behaviors in our StarCraft bot. Our results show that incorporating a learned particle model improves the performance of EISBot by 10% over baseline approaches.
Feasibility-Seeking and Superiorization Algorithms Applied to Inverse Treatment Planning in Radiation Therapy

We apply the recently proposed superiorization methodology (SM) to the inverse planning problem in radiation therapy. The inverse planning problem is represented here as a constrained minimization problem of the to- tal variation (TV) of the intensity vector over a large system of linear two-sided inequalities. The SM can be viewed conceptually as lying between feasibility- seeking for the constraints and full-edged constrained minimization of the objective function subject to these constraints. It is based on the discovery that many feasibility-seeking algorithms (of the projection methods variety) are perturbation-resilient, and can be proactively steered toward a feasible so- lution of the constraints with a reduced, thus superiorized, but not necessarily minimal, objective function value.
Analyzing the Use of Character-Level Translation with Sparse and Noisy Datasets

This paper provides an analysis of character-level machine translation models used in pivot-based translation when applied to sparse and noisy datasets, such as crowdsourced movie subtitles. In our experiments, we find that such characterlevel models cut the number of untranslated words by over 40% and are especially competitive (improvements of 2-3 BLEU points) in the case of limited training data. We explore the impact of character alignment, phrase table filtering, bitext size and the choice of pivot language on translation quality. We further compare cascaded translation models to the use of synthetic training data via multiple pivots, and we find that the latter works significantly better. Finally, we demonstrate that neither word- nor character-BLEU correlate perfectly with human judgments, due to BLEU’s sensitivity to length.
Serotype-Specific Entry of Dengue Virus into Liver Cells: Identification of the 37-Kilodalton/67-Kilodalton High-Affinity Laminin Receptor as a Dengue Virus Serotype 1 Receptor

ABSTRACT Dengue virus, the causative agent of dengue fever, dengue shock syndrome, and dengue hemorrhagic fever, infects susceptible cells by initially binding to a receptor(s) located on the host cell surface. Evidence to date suggests that receptor usage may be cell and serotype specific, and this study sought to identify dengue virus serotype 1 binding proteins on the surface of liver cells, a known target organ. By using a virus overlay protein binding assay (VOPBA), in both nondenaturing and denaturing gel systems, a putative dengue virus serotype 1 binding protein of approximately 37 kDa expressed on the surface of liver (HepG2) cells was identified. Mass spectrometry analysis identified a candidate protein, the 37/67-kDa high-affinity laminin receptor. Entry of the dengue virus serotype 1 was significantly inhibited in a dose-dependent manner by both antibodies directed against the 37/67-kDa high-affinity laminin receptor and soluble laminin. No inhibition of virus entry was seen with dengue virus serotypes 2, 3, or 4, demonstrating that the 37/67-kDa high-affinity laminin receptor is a serotype-specific receptor for dengue virus entry into liver cells.
Characterizations of function spaces on the sphere using frames

In this paper we introduce a polynomial frame on the unit sphere S d-1 of R d , for which every distribution has a wavelet-type decomposition. More importantly, we prove that many function spaces on the sphere S d-1 , such as L p , H p and Besov spaces, can be characterized in terms of the coefficients in the wavelet decompositions, as in the usual Euclidean case R d . We also study a related nonlinear m-term approximation problem on S d-1 . In particular, we prove both a Jackson-type inequality and a Bernstein-type inequality associated to wavelet decompositions, which extend the corresponding results obtained by R. A. DeVore, B. Jawerth and V. Popov ("Compression of wavelet decompositions", Amer. J. Math. 114 (1992), no. 4, 737-785).