Miracle-dz/UniFAR-FTUs huggingface dataset:
Naturally occurring variants of human T-cell leukemia virus type I Tax protein impair its recognition by cytotoxic T lymphocytes and the transactivation function of Tax

There is a high degree of intraisolate sequence heterogeneity in the tax gene of human T-cell leukemia virus type I (HTLV-I), although the sequence variation between patients is small compared with that of human immunodeficiency virus type 1. In the present study, we investigated whether naturally occurring amino acid substitutions changed the properties of the Tax protein in two respects: first, recognition of the protein by cytotoxic T lymphocytes (CTL), and second, the ability of the Tax protein to transactivate various promoters. We found that (i) all of the observed amino acid substitutions that occur in known CTL epitopes abolished the recognition of the synthetic peptide representing the respective epitope; (ii) these substitutions occurred significantly more frequently in subjects carrying HLA-A2; and (iii) most of the amino acid substitutions severely reduced the ability of Tax protein to transactivate three promoters: the HTLV-I long terminal repeat, the c-fos promoter, and the interleukin-2 receptor alpha chain promoter.
Control of Spike Transfer at Hippocampal Mossy Fiber Synapses In Vivo by GABAA and GABAB Receptor-Mediated Inhibition

Despite extensive studies in hippocampal slices and incentive from computational theories, the synaptic mechanisms underlying information transfer at mossy fiber (mf) connections between the dentate gyrus (DG) and CA3 neurons in vivo are still elusive. Here we used an optogenetic approach in mice to selectively target and control the activity of DG granule cells (GCs) while performing whole-cell and juxtacellular recordings of CA3 neurons in vivo. In CA3 pyramidal cells (PCs), mf–CA3 synaptic responses consisted predominantly of an IPSP at low stimulation frequency (0.05 Hz). Upon increasing the frequency of stimulation, a biphasic response was observed consisting of a brief mf EPSP followed by an inhibitory response lasting on the order of 100 ms. Spike transfer at DG–CA3 interneurons recorded in the juxtacellular mode was efficient at low presynaptic stimulation frequency and appeared insensitive to an increased frequency of GC activity. Overall, this resulted in a robust and slow feedforward inhibition of spike transfer at mf–CA3 pyramidal cell synapses. Short-term plasticity of EPSPs with increasing frequency of presynaptic activity allowed inhibition to be overcome to reach spike discharge in CA3 PCs. Whereas the activation of GABAA receptors was responsible for the direct inhibition of light-evoked spike responses, the slow inhibition of spiking activity required the activation of GABAB receptors in CA3 PCs. The slow inhibitory response defined an optimum frequency of presynaptic activity for spike transfer at ∼10 Hz. Altogether these properties define the temporal rules for efficient information transfer at DG–CA3 synaptic connections in the intact circuit. SIGNIFICANCE STATEMENT Activity-dependent changes in synaptic strength constitute a basic mechanism for memory. Synapses from the dentate gyrus (DG) to the CA3 area of the hippocampus are distinctive for their prominent short-term plasticity, as studied in slices. Plasticity of DG–CA3 connections may assist in the encoding of precise memory in the CA3 network. Here we characterize DG–CA3 synaptic transmission in vivo using targeted optogenetic activation of DG granule cells while recording in whole-cell patch-clamp and juxtacellular configuration from CA3 pyramidal cells and interneurons. We show that, in vivo, short-term plasticity of excitatory inputs to CA3 pyramidal cells combines with robust feedforward inhibition mediated by both GABAA and GABAB receptors to control the efficacy and temporal rules for information transfer at DG–CA3 connections.
M line–deficient titin causes cardiac lethality through impaired maturation of the sarcomere

Titin, the largest protein known to date, has been linked to sarcomere assembly and function through its elastic adaptor and signaling domains. Titin's M-line region contains a unique kinase domain that has been proposed to regulate sarcomere assembly via its substrate titin cap (T-cap). In this study, we use a titin M line–deficient mouse to show that the initial assembly of the sarcomere does not depend on titin's M-line region or the phosphorylation of T-cap by the titin kinase. Rather, titin's M-line region is required to form a continuous titin filament and to provide mechanical stability of the embryonic sarcomere. Even without titin integrating into the M band, sarcomeres show proper spacing and alignment of Z discs and M bands but fail to grow laterally and ultimately disassemble. The comparison of disassembly in the developing and mature knockout sarcomere suggests diverse functions for titin's M line in embryonic development and the adult heart that not only involve the differential expression of titin isoforms but also of titin-binding proteins.
Methods for comparing center‐specific survival outcomes using direct standardization

The evaluation of center‐specific outcomes is often through survival analysis methods. Such evaluations must account for differences in the distribution of patient characteristics across centers. In the context of censored event times, it is also important that the measure chosen to evaluate centers not be influenced by imbalances in the center‐specific censoring distributions. The practice of using center indicators in a hazard regression model is often invalid, inconvenient, or undesirable to carry out. We propose a semiparametric version of the standardized rate ratio (SRR) useful for the evaluation of centers with respect to a right‐censored event time. The SRR for center j can be interpreted as the ratio of the expected number of deaths in the total population (if the total population were in fact subject to the center j mortality hazard) to the observed number of events. The proposed measure is not affected by differences in center‐specific covariate or censoring distributions. Asymptotic properties of the proposed estimators are derived, with finite‐sample properties examined through simulation studies. The proposed methods are applied to national kidney transplant data. Copyright © 2014 John Wiley & Sons, Ltd.
Methylphenidate-Elicited Dopamine Increases in Ventral Striatum Are Associated with Long-Term Symptom Improvement in Adults with Attention Deficit Hyperactivity Disorder

Stimulant medications, such as methylphenidate, which are effective treatments for attention deficit hyperactivity disorder (ADHD), enhance brain dopamine signaling. However, the relationship between regional brain dopamine enhancement and treatment response has not been evaluated. Here, we assessed whether the dopamine increases elicited by methylphenidate are associated with long-term clinical response. We used a prospective design to study 20 treatment-naive adults with ADHD who were evaluated before treatment initiation and after 12 months of clinical treatment with a titrated regimen of oral methylphenidate. Methylphenidate-induced dopamine changes were evaluated with positron emission tomography and [11C]raclopride (D2/D3 receptor radioligand sensitive to competition with endogenous dopamine). Clinical responses were assessed using the Conners' Adult ADHD Rating Scale and revealed a significant reduction in symptoms of inattention and hyperactivity with long-term methylphenidate treatment. A challenge dose of 0.5 mg/kg intravenous methylphenidate significantly increased dopamine in striatum (assessed as decreases in D2/D3 receptor availability). In the ventral striatum, these dopamine increases were associated with the reductions in ratings of symptoms of inattention with clinical treatment. Statistical parametric mapping additionally showed dopamine increases in prefrontal and temporal cortices with intravenous methylphenidate that were also associated with decreases in symptoms of inattention. Our findings indicate that dopamine enhancement in ventral striatum (the brain region involved with reward and motivation) was associated with therapeutic response to methylphenidate, further corroborating the relevance of the dopamine reward/motivation circuitry in ADHD. It also provides preliminary evidence that methylphenidate-elicited dopamine increases in prefrontal and temporal cortices may also contribute to the clinical response.
Can Deep Neural Networks Match the Related Objects?: A Survey on ImageNet-trained Classification Models

Deep neural networks (DNNs) have shown the state-of-the-art level of performances in wide range of complicated tasks. In recent years, the studies have been actively conducted to analyze the black box characteristics of DNNs and to grasp the learning behaviours, tendency, and limitations of DNNs. In this paper, we investigate the limitation of DNNs in image classification task and verify it with the method inspired by cognitive psychology. Through analyzing the failure cases of ImageNet classification task, we hypothesize that the DNNs do not sufficiently learn to associate related classes of objects. To verify how DNNs understand the relatedness between object classes, we conducted experiments on the image database provided in cognitive psychology. We applied the ImageNet-trained DNNs to the database consisting of pairs of related and unrelated object images to compare the feature similarities and determine whether the pairs match each other. In the experiments, we observed that the DNNs show limited performance in determining relatedness between object classes. In addition, the DNNs present somewhat improved performance in discovering relatedness based on similarity, but they perform weaker in discovering relatedness based on association. Through these experiments, a novel analysis of learning behaviour of DNNs is provided and the limitation which needs to be overcome is suggested.
Roles of ozone depleting substances and solar activity in observed long-term trends in total ozone column over Indian region

ABSTRACT An additive time-series decomposition analysis was performed on the Multi Sensor Reanalysis-2 (MSR-2) monthly mean total ozone column (TOC) time-series dataset spanning over 34 years (January 1979–December 2012) for Indian region (0.0–40.0 °N; 67.5–97.5° E). Statistically significant (p-value <0.05) long-term trends in TOC were estimated in the deseasonalized TOC time series. The role of multiple natural and anthropogenic factors: quasi biennial oscillations (QBO), El-Nino Southern Oscillations (ENSO), cyclic variation in solar activity (SA), and ozone depleting substances (ODS) was investigated to explain the long-term trends in TOC over Indian region. Over sub-tropical Indian region (25.0° N– 40.0° N), declining long-term linear trends were estimated, which varied from −0.30% to −1.10% per decade. Interestingly a positive long-term linear-trend (0.10–0.30% per decade) was observed over equatorial-tropical part of Indian region. No statistically significant long-term trend was observed for 30mb Equatorial Zonal Winds and Nino 3.4 index – indicators for QBO and ENSO; however, a positive long-term linear trend of magnitude 17.00 ± 1.18% per decade was observed in effective equivalent stratospheric chlorine – a proxy for ODS, and a negative long-term linear trend of magnitude 12.72 ± 2.86% per decade was observed in 10.7 cm Solar Radio Flux – a representative for SF. It is inferred that over the Indian region above tropic of cancer, about 85.00% of the estimated negative long-term linear trend in TOC can be explained by the increase in the stratospheric concentration of ODS; whereas, decrease in the solar activity accounted for 15.00% of the estimated negative long-term linear trend in TOC over sub-tropical Indian region.
Learning to Prune: Context-Sensitive Pruning for Syntactic MT

We present a context-sensitive chart pruning method for CKY-style MT decoding. Source phrases that are unlikely to have aligned target constituents are identified using sequence labellers learned from the parallel corpus, and speed-up is obtained by pruning corresponding chart cells. The proposed method is easy to implement, orthogonal to cube pruning and additive to its pruning power. On a full-scale Englishto-German experiment with a string-totree model, we obtain a speed-up of more than 60% over a strong baseline, with no loss in BLEU.
Planar Geometric Projections and Viewing Transformations

In computer graphics one is often concerned with representing three-dimensional objects on a two-dimensional display surface. The choice of such a representation depends on several factors, including the purpose for which the representation is intended, the visual effects tha t are desired, and the shape of the object. This paper describes how twodimensional views can be obtained using planar geometric projections such as perspective and parallel projections. It discusses how these projections can be generated from a threedimensional representation of an object in a manner suitable for computer graphics systems. In particular, it shows how these projections can be generated using the viewing transformations of the Core Graphics System. The factors tha t affect the choice of projection are also discussed, and some guidelines for making such a choice are given.
The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry

The effective fragment potential (EFP) method is described and its capabilities illustrated using several applications. The original method, EFP1, was primarily developed to describe aqueous solvation, by representing Coulombic, induction and repulsive interactions via one-electron terms in the ab initio Hamiltonian. It is demonstrated, using water clusters, the Menshutkin reaction and the glycine neutral/zwitterion equilibrium, that agreement with both fully ab initio calculations and experiment are excellent. More recently, the model has been extended so that it can treat any solvent, as well as more difficult links across covalent bonds.
ATPG for Crosstalk using Hybrid Structural SAT

As technology evolves into the deep sub-micron era, signal integrity problems are growing into a major challenge. An important source of signal integrity problems is the crosstalk noise generated by coupling capacitances between wires. Test vectors that activate and propagate crosstalk noise effects are becoming an essential part of design verification and manufacturing test. However, deriving such vectors is a complex task. In this paper, we propose HyAC, a fast yet accurate hybrid ATPG method targeting multiple-aggressor induced crosstalk errors. Given a victim and a set of aggressors, the proposed ATPG method searches for test vectors to activate and propagate a crosstalk error for the victim. Due to logic constraints, it may not be possible to trigger all aggressors simultaneously. Therefore, firstly we use an implication graph (IG) that consists of logic variables and structural information to check for logic conflicts. If the current set of aggressors is not feasible, our algorithm automatically searches for the next-best subset of aggressors (resulting in the largest noise). After a set of feasible aggressors is identified, we use a modified PODEM [21] algorithm to search for test vectors. This hybrid structural SAT-based ATPG method inherits advantages from both Boolean– satisfiabilitity based methods and structural-based methods to achieve flexibility and efficiency. We demonstrate the accuracy, high quality, and run time efficiency of HyAC through experiments conducted on several benchmark circuits as well as a circuit from a commercial processor.
On the divergence of potential and actual evapotranspiration trends: An assessment across alternate global datasets

Evapotranspiration is a key variable in hydrology, playing an important role in water and energy balance of the land surface. There has been speculation on the direction of trend in potential and actual evapotranspiration (PET and AET) resulting from rising global temperatures, in both observational and derived records representing the historical climate. In this study, PET and AET trends of eight different global model datasets where analyzed over two time periods: from 2003 to 2012 (short term) and from 1980 to 2012 (multidecadal), to identify regions where the trends coincide or differ and to study the reasons behind these changes. The short‐term analysis showed considerable uncertainty exists on the detection and direction of significant trends on both PET and AET. There was little agreement among the datasets about the direction of the global trends. The multidecadal study showed much more consistent trends throughout the datasets, particularly in relation to positive significant PET trends. During this period, the global PET mean increased 0.091 mm month−1 yr−1, while the global AET rose at 0.045 mm month−1 yr−1. Much of the opposite PET/AET trends can be attributed to changes in the precipitation. Most of the regions which present these trends are water‐limited and present strong correlations between AET and precipitation trends. Some energy‐limited regions showed an increasing gap between PET and AET, suggesting the influence of additional variables controlling AET.
Dietary protein level affects iridescent coloration in Anna's hummingbirds, Calypte anna

SUMMARY Many animal displays involve colorful ornamental traits that signal an individual's quality as a mate or rival. Brilliant iridescent ornaments are common, but little is currently known about their production cost and signaling value. One potential cost of colorful ornaments is the acquisition of limited dietary resources that may be involved, directly or indirectly, in their production. Protein, the primary component of bird feathers and of many nanostructural components of iridescent traits, is naturally restricted in hummingbird diets (comprised mostly of sugars), suggesting that iridescent coloration may be especially challenging to produce in these animals. In this study, we experimentally investigated the effect of dietary protein availability during molt on iridescent color expression in male Anna's hummingbirds (Calypte anna). We fed captive birds either a 6% (high) or a 3% (low) protein diet and stimulated molt by plucking half the gorget and crown ornaments on each bird as well as the non-ornamental iridescent green tail feathers. We found that birds receiving more protein grew significantly more colorful crown feathers (higher red chroma and redder hue) than those fed the low-protein diet. Diet did not affect gorget coloration, but regrowth of feathers in captivity affected both gorget and crown coloration. Additionally, birds on the high-protein diet grew yellower (higher hue) green tail feathers than birds on the low-protein diet. These results indicate that iridescent ornamental feathers are sensitive to diet quality and may serve as honest signals of nutrition to mates or rivals. Further, because both ornamental and non-ornamental iridescent coloration were affected by conditions during their growth, iridescent color in these birds appears to be generally condition dependent.
A Transmission Scheme for Continuous ARQ Protocols over Underwater Acoustic Channels

Due to the half-duplex property of the underwater acoustic channels, the classic stop-and-wait ARQ (SW-ARQ) and its variants are generally thought to be the only class of ARQ protocols that can be applied in underwater. When combined with the large propagation delay property of the underwater acoustic channels, the use of SW-ARQ and its variants makes the throughput performance of underwater acoustic communication systems very inefficient. In this paper, we propose a transmission scheme that takes advantage of the long propagation delay in underwater to enable the use of continuous ARQ protocols over underwater acoustic channels. Simulation results show that our proposed transmission scheme allows much higher throughput to be achieved than both the classic SW-ARQ and its variants, even when simple continuous ARQ protocols are used.
Higher-order nonlinear priors for surface reconstruction

For surface reconstruction problems with noisy and incomplete range data, a Bayesian estimation approach can improve the overall quality of the surfaces. The Bayesian approach to surface estimation relies on a likelihood term, which ties the surface estimate to the input data, and the prior, which ensures surface smoothness or continuity. This paper introduces a new high-order, nonlinear prior for surface reconstruction. The proposed prior can smooth complex, noisy surfaces, while preserving sharp, geometric features, and it is a natural generalization of edge-preserving methods in image processing, such as anisotropic diffusion. An exact solution would require solving a fourth-order partial differential equation (PDE), which can be difficult with conventional numerical techniques. Our approach is to solve a cascade system of two second-order PDEs, which resembles the original fourth-order system. This strategy is based on the observation that the generalization of image processing to surfaces entails filtering the surface normals. We solve one PDE for processing the normals and one for refitting the surface to the normals. Furthermore, we implement the associated surface deformations using level sets. Hence, the algorithm can accommodate very complex shapes with arbitrary and changing topologies. This paper gives the mathematical formulation and describes the numerical algorithms. We also show results using range and medical data.
A hybrid algorithm for the point to multipoint routing problem

The process of nding optimal routing for a set of circuit connection requests through a communications network is known as call request scheduling or message scheduling Each request has a single source and multiple destinations and dif ferent requests may have di erent source and di erent des tination nodes Finding optimal routing for a set of requests is called the Point to Multipoint Routing Problem PMRP Current practice takes each point to multipoint request and treats it as a collection of point to point requests which is very costly This paper presents an algorithm for the Point to Multipoint Routing Problem that uses a genetic algo rithm and a heuristic Steiner tree algorithm Our hybrid algorithm allows the scheduler to nd an optimal or near optimal path through the network for each request In our algorithm each request is treated as a whole and not as a col lection of point to point requests We ran our hybrid PMRP algorithm on several test cases with excellent results