Miracle-dz/UniFAR-FTUs huggingface dataset:
Multifaceted activity of HIV Vpr/Vpx proteins: the current view of their virological functions

Primate immunodeficiency viruses encode viral proteins that are uniquely auxiliary to their growth in host cells. Of these accessory proteins, those designated Vpr and Vpx are least well understood with respect to their functions in the viral replication cycle. Moreover, their assigned roles based on the results in published studies remain controversial. This review summarises current knowledge on human immunodeficiency virus (HIV) Vpr/Vpx proteins, and discusses their functional activities during the viral life cycle in macrophages and T lymphocytes, the two major target cells of HIV infection. Copyright © 2010 John Wiley & Sons, Ltd.
Enhancing the imperceptibility of image steganography for information hiding

In this paper, an image steganography approach is presented dividing the cover image into 2×2 non-overlapping pixel blocks. The upper-left pixel of that block embeds a certain number of bits of the secret bit stream. Whereas, the remaining pixels of the same block embed the secret data using a modified version of the pixel-value-differencing (PVD) method that considers embedding secret data into both horizontal and vertical edges; unlike traditional image steganography approaches. The experimental results show that the proposed approach perceptually outperforms competing approaches in terms of the standard PSNR and the complex wavelet SSIM index. In turn, the imperceptibility of the stego-image is improved with a comparable bit-embedding capacity.
Multilayer Obstacle-Avoiding X-Architecture Steiner Minimal Tree Construction Based on Particle Swarm Optimization

As the basic model for very large scale integration routing, the Steiner minimal tree (SMT) can be used in various practical problems, such as wire length optimization, congestion, and time delay estimation. In this paper, an effective algorithm based on particle swarm optimization is presented to construct a multilayer obstacle-avoiding X-architecture SMT (ML-OAXSMT). First, a pretreatment strategy is presented to reduce the total number of judgments for the routing conditions around obstacles and vias. Second, an edge transformation strategy is employed to make the particles have the ability to bypass the obstacles while the union-find partition is used to prevent invalid solutions. Third, according to the feature of ML-OAXSMT problem, we design an edge-vertex encoding strategy, which has the advantage of simple and effective. Moreover, a penalty mechanism is proposed to help the particle bypass the obstacles, and reduce the generation of via at the same time. Experimental results show that our algorithm from a global perspective of multilayer structure can achieve the best solution quality among the existing algorithms. Finally, to our best knowledge, we redefine the edge cost and then construct the obstacle-avoiding preferred direction X-architecture Steiner tree, which is the first work to address this problem and can offer the theory supports for chip design based on non-Manhattan architecture.
Inhibiting β-Catenin by β-Carboline-Type MDM2 Inhibitor for Pancreatic Cancer Therapy

The β-catenin and MDM2 oncoproteins are overexpressed and constitutively activated in human pancreatic cancer and contribute to its initiation, progression, and metastasis. The Wnt/β-catenin signaling pathway strongly interacts with the MDM2-p53 signaling pathway, accelerating the tumorigenesis and its development. Therefore, therapies inhibiting both β-catenin and MDM2 are suggested to be ideal treatments for patients with advanced pancreatic cancer. We have recently identified a novel class of β-carboline compounds as the specific and potent MDM2 inhibitors, including a lead compound SP141. In the present study, we utilized SP141 as an exemplary β-carboline compound to characterize β-catenin as a molecular target of the β-carboline compounds and to demonstrate an important role of β-catenin in the anticancer activity of β-carboline. We found that the silencing of either β-catenin or MDM2 largely reduced the anticancer activity of SP141 while the double silencing of both genes almost completely blocked SP141’s activity. SP141 directly bound to β-catenin and inhibited its expression and activity in pancreatic cancer cells in vitro and in vivo. The inhibitory effects of SP141 on β-catenin were mediated by the ubiquitin–proteasome system in an MDM2-independent manner. In conclusion, these results suggest that SP141 exerts its anticancer activity by dually inhibiting β-catenin and MDM2. We envision that β-carboline derivatives can be developed as promising dual inhibitors of β-catenin and MDM2 for the treatment of advanced pancreatic cancer.
Spatial Distribution and Sampling Plans for Mesoplatys ochroptera (Coleoptera: Chrysomelidae) on Sesbania

Abstract With the widespread introduction of the nitrogen-fixing legume sesbania, Sesbania sesban (L.) Merril, in agroforestry systems, the defoliating beetle Mesoplatys ochroptera Stål has become a serious pest of the trees in Africa. To determine within-field and within-plant spatial distribution of M. ochroptera on both seedlings and trees of sesbania, distribution statistics were computed using Iwao’s mean crowding regression model. In 1- to 3-mo-old seedlings, the model accounted for 29.8, 32.2, and 61.0% of the variation observed in mean crowding to mean relationships in egg masses, larvae and adults, respectively. The model slopes of the regression were greater than unity for all stages indicating aggregated spatial distribution. Values of the intercept were greater than zero for egg masses, larvae and adults indicating that the basic components of the population are groups of individuals. The highest density (>80%) of mating and feeding adults was found in the upper third of 1- to 2-mo-old seedlings, while most of the egg masses were found in the lower half of seedlings. In trees, >60% of the individuals of all stages were found in the lower third of the foliage canopy, while <10% were found in the upper third. Sampling adults was found to be easier and gave better density estimates of M. ochroptera population than egg masses and larvae. Therefore, sampling plans useful for population studies and decision-making in pest management were developed for adults.
Synthesis of divide and conquer parallelism for loops

Divide-and-conquer is a common parallel programming skeleton supported by many cross-platform multithreaded libraries, and most commonly used by programmers for parallelization. The challenges of producing (manually or automatically) a correct divide-and-conquer parallel program from a given sequential code are two-fold: (1) assuming that a good solution exists where individual worker threads execute a code identical to the sequential one, the programmer has to provide the extra code for dividing the tasks and combining the partial results (i.e. joins), and (2) the sequential code may not be suitable for divide-and-conquer parallelization as is, and may need to be modified to become a part of a good solution. We address both challenges in this paper. We present an automated synthesis technique to synthesize correct joins and an algorithm for modifying the sequential code to make it suitable for parallelization when necessary. This paper focuses on class of loops that traverse a read-only collection and compute a scalar function over that collection. We present theoretical results for when the necessary modifications to sequential code are possible, theoretical guarantees for the algorithmic solutions presented here, and experimental evaluation of the approach's success in practice and the quality of the produced parallel programs.
Roadmap Roadmap of ultrafast x-ray atomic and molecular physics

X-ray free-electron lasers (XFELs) and table-top sources of x-rays based upon high harmonic generation (HHG) have revolutionized the field of ultrafast x-ray atomic and molecular physics, largely due to an explosive growth in capabilities in the past decade. XFELs now provide unprecedented intensity (10W cm) of x-rays at wavelengths down to ∼1 Ångstrom, and HHG provides unprecedented time resolution (∼50 attoseconds) and a correspondingly large coherent bandwidth at longer wavelengths. For context, timescales can be referenced to the Bohr orbital period in hydrogen atom of 150 attoseconds and the hydrogen-molecule vibrational period of 8 femtoseconds; wavelength scales can be referenced to the chemically significant carbon K-edge at a photon energy of ∼280 eV (44 Ångstroms) and the bond length in methane of ∼1 Ångstrom. With these modern x-ray sources one now has the ability to focus on individual atoms, even when embedded in a complex molecule, and view electronic and nuclear motion on their intrinsic scales (attoseconds and Ångstroms). These sources have enabled coherent diffractive imaging, where one can image non-crystalline objects in three dimensions on ultrafast timescales, potentially with atomic resolution. The unprecedented intensity available with XFELs has opened new fields of multiphoton and nonlinear x-ray physics where behavior of matter under extreme conditions can be explored. The unprecedented time resolution and pulse synchronization provided by HHG sources has kindled fundamental investigations of time delays in photoionization, charge migration in molecules, and dynamics near conical intersections that are foundational to AMO physics and chemistry. This roadmap coincides with the year when three new XFEL facilities, operating at Ångstrom wavelengths, opened for users (European XFEL, Swiss-FEL and PAL-FEL in Korea) almost doubling the present worldwide number of XFELs, and documents the remarkable progress in HHG capabilities since its discovery roughly 30 years ago, showcasing experiments in AMO physics and other applications. Here we capture the perspectives of 17 leading groups and organize the contributions into four categories: ultrafast molecular dynamics, multidimensional x-ray spectroscopies; high-intensity x-ray phenomena; attosecond x-ray science.
Diseño de un nuevo procedimiento para calificar la prueba de la Figura Compleja de Rey: confiabilidad inter-evaluadores

El presente trabajo propone un sistema original de calificacion de la figura compleja de Rey, basado, tanto en el marco teorico neuropsicologico y de la psicologia experimental, como en un amplio proceso de muestreo, en 937 sujetos de entre 4 y 15 anos. Se presenta el estudio de confiabilidad inter-jueces, llevado a cabo con la participacion de 18 evaluadores, que calificaron la copia y la reproduccion de memoria de 20 sujetos en forma indepediente, en el que se demuestra que este sistema es muy confiable.
A Role for Extracellular Na+ in the Channel Gating of Native and Recombinant Kainate Receptors

Ionotropic glutamate receptors of the kainate and AMPA subtypes share a number of structural features, both topographical and in terms of stoichiometry. In addition, AMPA and kainate receptors share similar pharmacological and biophysical properties in that they are activated by common agonists and display rapid activation and desensitization characteristics. However, we show here that in contrast to AMPA receptor-mediated responses (native or recombinant GluR3 receptor), the response of native and recombinant (GluR6) kainate receptors to glutamate was drastically reduced in the absence of extracellular Na+ (i.e., when replaced by Cs+). Removal of Na+ increases the rate of desensitization, indicating that external Na+ modulates channel gating. Whereas the size of the substituting cation is important in mimicking the action of Na+ (Li+>K+>Cs+), modulation was voltage independent. These results indicate the existence of different gating mechanisms for AMPA and kainate receptors. By using chimeric AMPA-kainate receptors derived from GluR3 and GluR6, we have identified a key residue in the S2 segment of GluR6 (M770) that is largely responsible for the sensitivity of the receptor to external Na+. Thus, these results show the existence of a specific kainate receptor gating mechanism that requires external Na+ to be operative.
Capacitance–Frequency Estimates of Border-Trap Densities in Multifin MOS Capacitors

We use capacitance–frequency (<inline-formula> <tex-math notation="LaTeX">$C$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">$f$ </tex-math></inline-formula>) measurements to provide lower bound estimates of border-trap densities in multifin MOS capacitors with high-K dielectrics built in Ge and InGaAs fin field effect transistor (FinFET) technologies before and after X-ray irradiation. The <inline-formula> <tex-math notation="LaTeX">$C$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">$f$ </tex-math></inline-formula> method is illustrated for SiO<sub>2</sub>-based planar MOS capacitors and compared with high-frequency capacitance–voltage measurements. Lower effective border-trap densities are found before and after irradiation for multifin capacitors built in a strained Ge <inline-formula> <tex-math notation="LaTeX">$p$ </tex-math></inline-formula>MOS FinFET technology than for similar devices built using an early-developmental stage InGaAs MOS technology. These results show the utility of <inline-formula> <tex-math notation="LaTeX">$C$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">$f$ </tex-math></inline-formula> measurements in characterizing defect densities in MOS capacitors, particularly when large border-trap densities exist.
Sound–meaning association biases evidenced across thousands of languages

Significance The independence between sound and meaning is believed to be a crucial property of language: across languages, sequences of different sounds are used to express similar concepts (e.g., Russian “ptitsa,” Swahili “ndege,” and Japanese “tori” all mean “bird”). However, a careful statistical examination of words from nearly two-thirds of the world’s languages reveals that unrelated languages very often use (or avoid) the same sounds for specific referents. For instance, words for tongue tend to have l or u, “round” often appears with r, and “small” with i. These striking similarities call for a reexamination of the fundamental assumption of the arbitrariness of the sign. It is widely assumed that one of the fundamental properties of spoken language is the arbitrary relation between sound and meaning. Some exceptions in the form of nonarbitrary associations have been documented in linguistics, cognitive science, and anthropology, but these studies only involved small subsets of the 6,000+ languages spoken in the world today. By analyzing word lists covering nearly two-thirds of the world’s languages, we demonstrate that a considerable proportion of 100 basic vocabulary items carry strong associations with specific kinds of human speech sounds, occurring persistently across continents and linguistic lineages (linguistic families or isolates). Prominently among these relations, we find property words (“small” and i, “full” and p or b) and body part terms (“tongue” and l, “nose” and n). The areal and historical distribution of these associations suggests that they often emerge independently rather than being inherited or borrowed. Our results therefore have important implications for the language sciences, given that nonarbitrary associations have been proposed to play a critical role in the emergence of cross-modal mappings, the acquisition of language, and the evolution of our species’ unique communication system.
Sub-second lookups on a large-scale Kademlia-based overlay

Previous studies of large-scale (multimillion node) Kademlia-based DHTs have shown poor performance, measured in seconds; in contrast to the far more optimistic results from theoretical analysis, simulations and testbeds. In this paper, we unexpectedly find that in the Mainline BitTorrent DHT (MDHT), probably the largest DHT overlay on the Internet, many lookups already yield results in less than a second, albeit not consistently. With our backwards-compatible modifications, we show that not only can we reduce median latencies to between 100 and 200 ms, but also consistently achieve sub-second lookups. These results suggest that it is possible to deploy latency-sensitive applications on top of large-scale DHT overlays on the Internet, contrary to what some might have concluded based on previous results reported in the literature.
Interplay between the alpharetroviral Gag protein and SR proteins SF2 and SC35 in the nucleus

Retroviruses are positive-sense, single-stranded RNA viruses that reverse transcribe their RNA genomes into double-stranded DNA for integration into the host cell chromosome. The integrated provirus is used as a template for the transcription of viral RNA. The full-length viral RNA can be used for the translation of the Gag and Gag-Pol structural proteins or as the genomic RNA (gRNA) for encapsidation into new virions by the Gag protein. The mechanism by which Gag selectively incorporates unspliced gRNA into virus particles is poorly understood. Although Gag was previously thought to localize exclusively to the cytoplasm and plasma membrane where particles are released, we found that the Gag protein of Rous sarcoma virus, an alpharetrovirus, undergoes transient nuclear trafficking. When the nuclear export signal of RSV Gag is mutated (Gag.L219A), the protein accumulates in discrete subnuclear foci reminiscent of nuclear bodies such as splicing speckles, paraspeckles, and PML bodies. In this report, we observed that RSV Gag.L219A foci appeared to be tethered in the nucleus, partially co-localizing with the splicing speckle components SC35 and SF2. Overexpression of SC35 increased the number of Gag.L219A nucleoplasmic foci, suggesting that SC35 may facilitate the formation of Gag foci. We previously reported that RSV Gag nuclear trafficking is required for efficient gRNA packaging. Together with the data presented herein, our findings raise the intriguing hypothesis that RSV Gag may co-opt splicing factors to localize near transcription sites. Because splicing occurs co-transcriptionally, we speculate that this mechanism could allow Gag to associate with unspliced viral RNA shortly after its transcription initiation in the nucleus, before the viral RNA can be spliced or exported from the nucleus as an mRNA template.
Ghrelin Receptor Inverse Agonists: Identification of an Active Peptide Core and Its Interaction Epitopes on the Receptor

[d-Arg1,d-Phe5,d-Trp7,9,Leu11]Substance P functions as a low-potency antagonist but a high-potency full inverse agonist on the ghrelin receptor. Through a systematic deletion and substitution analysis of this peptide, the C-terminal carboxyamidated pentapeptide wFwLX was identified as the core structure, which itself displayed relatively low inverse agonist potency. Mutational analysis at 17 selected positions in the main ligand-binding crevice of the ghrelin receptor demonstrated that ghrelin apparently interacts only with residues in the middle part of the pocket [i.e., between transmembrane (TM)-III, TM-VI and TM-VII]. In contrast, the inverse agonist peptides bind in a pocket that extends all the way from the extracellular end of TM-II (AspII:20) across between TM-III and TM-VI/VII to TM-V and TM-IV. The potency of the main inverse agonist could be improved up to 20-fold by a number of space-generating mutants located relatively deep in the binding pocket at key positions in TM-III, TM-IV and TM-V. It is proposed that the inverse agonists prevent the spontaneous receptor activation by inserting relatively deeply across the main ligand-binding pocket and sterically blocking the movement of TM-VI and TM-VII into their inward-bend, active conformation. The combined structure-functional analysis of both the ligand and the receptor allowed for the design of a novel, N-terminally Lys-extended analog of wFwLL, which rescued the high-potency, selective inverse agonism that was dependent upon both AspII:20 and GluIII:09. The identified pharmacophore can possibly serve as the basis for targeted discovery of also nonpeptide inverse agonists for the ghrelin receptor.
Reducing SMT Rule Table with Monolingual Key Phrase

This paper presents an effective approach to discard most entries of the rule table for statistical machine translation. The rule table is filtered by monolingual key phrases, which are extracted from source text using a technique based on term extraction. Experiments show that 78% of the rule table is reduced without worsening translation performance. In most cases, our approach results in measurable improvements in BLEU score.
The depressed child and adolescent: Historical aspects of mood and its disorders in young people

The rapid growth of clinical and research interest in mood disorders in juveniles over the last 20 years was preceded by a long period in which these conditions were discussed only cursorily, or not at all, in textbooks of psychiatry, child psychiatry or paediatrics. This chapter provides evidence about the wider historical background and sets some current clinical and research issues in perspective. It discusses the growth of interest in juvenile mental disorder, changing theories of child mental development, and changing conceptions of childhood. With the subsequent return to near-Kraepelinian concern for descriptive diagnosis and the search for organic causes, fostered by new knowledge and pharmacological treatments, clinical and scientific interest in mood disorders and their pathophysiology began to surface. The historical study of mood disorders in children and adolescents draws attention to many of the issues and questions that continue to call for clinical and research attention.
Enriched Expression of GluD1 in Higher Brain Regions and Its Involvement in Parallel Fiber–Interneuron Synapse Formation in the Cerebellum

Of the two members of the δ subfamily of ionotropic glutamate receptors, GluD2 is exclusively expressed at parallel fiber–Purkinje cell (PF–PC) synapses in the cerebellum and regulates their structural and functional connectivity. However, little is known to date regarding cellular and synaptic expression of GluD1 and its role in synaptic circuit formation. In the present study, we investigated this issue by producing specific and sensitive histochemical probes for GluD1 and analyzing cerebellar synaptic circuits in GluD1-knock-out mice. GluD1 was widely expressed in the adult mouse brain, with high levels in higher brain regions, including the cerebral cortex, striatum, limbic regions (hippocampus, nucleus accumbens, lateral septum, bed nucleus stria terminalis, lateral habenula, and central nucleus of the amygdala), and cerebellar cortex. In the cerebellar cortex, GluD1 mRNA was expressed at the highest level in molecular layer interneurons and its immunoreactivity was concentrated at PF synapses on interneuron somata. In GluD1-knock-out mice, the density of PF synapses on interneuron somata was significantly reduced and the size and number of interneurons were significantly diminished. Therefore, GluD1 is common to GluD2 in expression at PF synapses, but distinct from GluD2 in neuronal expression in the cerebellar cortex; that is, GluD1 in interneurons and GluD2 in PCs. Furthermore, GluD1 regulates the connectivity of PF–interneuron synapses and promotes the differentiation and/or survival of molecular layer interneurons. These results suggest that GluD1 works in concert with GluD2 for the construction of cerebellar synaptic wiring through distinct neuronal and synaptic expressions and also their shared synapse-connecting function.