Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure maps for hcp metals from first-principles calculations

The ability to predict the existence and crystal type of ordered structures of materials from their components is a major challenge of current materials research. Empirical methods use experimental data to construct structure maps and make predictions based on clustering of simple physical parameters. Their usefulness depends on the availability of reliable data over the entire parameter space. Recent development of highthroughput methods opens the possibility to enhance these empirical structure maps by ab initio calculations in regions of the parameter space where the experimental evidence is lacking or not well characterized. In this paper we construct enhanced maps for the binary alloys of hcp metals, where the experimental data leaves large regions of poorly characterized systems believed to be phase separating. In these enhanced maps, the clusters of noncompound-forming systems are much smaller than indicated by the empirical results alone.
Mouse Homologue of a Novel Human Oncofetal Antigen, Glypican-3, Evokes T-Cell–Mediated Tumor Rejection without Autoimmune Reactions in Mice

Purpose and Experimental Design: We recently identified glypican-3 (GPC3) overexpressed specifically in human hepatocellular carcinoma, as based on cDNA microarray analysis of 23,040 genes, and we reported that GPC3 is a novel tumor marker for human hepatocellular carcinoma and melanoma. GPC3, expressed in almost all hepatocellular carcinomas and melanomas, but not in normal tissues except for placenta or fetal liver, is a candidate of ideal tumor antigen for immunotherapy. In this study, we attempted to identify a mouse GPC3 epitope for CTLs in BALB/c mice, and for this, we set up a preclinical study to investigate the usefulness of GPC3 as a target for cancer immunotherapy in vivo. Results: We identified a mouse GPC3-derived and Kd- restricted CTL epitope peptide in BALB/c mice. Inoculation of this GPC3 peptide-specific CTL into s.c. Colon26 cancer cells transfected with mouse GPC3 gene (C26/GPC3) led to rejection of the tumor in vivo, and i.v. inoculation of these CTLs into sublethally irradiated mice markedly inhibited growth of an established s.c. tumor. Inoculation of bone marrow-derived dendritic cells pulsed with this peptide prevented the growth of s.c. and splenic C26/GPC3 accompanied with massive infiltration of CD8+ T cells into tumors. Evidence of autoimmune reactions was never observed in surviving mice that had rejected tumor cell challenges. Conclusions: We found the novel oncofetal protein GPC3 to be highly immunogenic in mice and elicited effective antitumor immunity with no evidence of autoimmunity. GPC3 is useful not only for diagnosis of hepatocellular carcinoma and melanoma but also for possible immunotherapy or prevention of these tumors.
A comparison of academics' attitudes towards the rights protection of their research and teaching materials

This paper compares two JISC-funded surveys. The first was undertaken by the Rights MEtadata for Open Archiving (RoMEO) project and focused on the rights protection required by academic authors sharing their research outputs in an open-access environment. The second was carried out by the Rights and Rewards project and focused on the rights protection required by authors sharing their teaching materials in the same way. The data are compared. The study reports confusion amongst both researchers and teachers as to copyright ownership in the materials they produced. Researchers were more restrictive about the permissions they would allow, but were liberal about terms and conditions. Teachers would allow many permissions, but under stricter terms and conditions. The study concludes that a single rights solution could not be used for both research and teaching materials.
Enlarged Perivascular Spaces on MRI Are a Feature of Cerebral Small Vessel Disease

Background and Purpose— Enlarged perivascular spaces in the brain are common but generally overlooked and of uncertain pathophysiology. They may reflect underlying cerebral small vessel disease. We determined whether enlarged perivascular spaces were associated with lacunar stroke subtype and white matter hyperintensities, markers of established small vessel disease. Materials and Methods— We prospectively recruited patients with acute ischemic lacunar or cortical stroke. Age-matched nonstroke control subjects were also recruited. We rated basal ganglia and centrum semiovale enlarged perivascular spaces 0 to 4 (0=none, 4=>40) on T2-weighted MRI and white matter hyperintensities. We compared enlarged perivascular spaces between stroke subtypes and control subjects and assessed associations with vascular risk factors and white matter hyperintensities. Results— We recruited 350 patients; 129 lacunar, 124 cortical stroke, and 97 age-matched control subjects. Adjusting for vascular risk factors and white matter hyperintensities, total enlarged perivascular spaces were associated with lacunar stroke subtype (P=0.04) in the acute stroke group (n=253); basal ganglia enlarged perivascular spaces were associated with lacunar stroke subtype (P=0.003), deep (P=0.02) and periventricular white matter hyperintensities (P=0.01); in all 350 subjects, total enlarged perivascular spaces were associated with deep (P<0.001) and periventricular (P<0.001) white matter hyperintensities. Conclusions— Although prevalent in patients with vascular risk factors and stroke, enlarged perivascular spaces are specifically associated with lacunar ischemic stroke and white matter hyperintensities. Further studies should determine the mechanism of this association while including adequate controls to account for stroke and vascular risk factors. Enlarged perivascular spaces should not be overlooked in studies of small vessel disease.
Path planning through variational dynamic programming

This paper presents a novel approach to path planning. It is a variational technique, consisting of iteratively improving an initial path possibly colliding with obstacles. At each iteration, the path is improved by performing a dynamic programming search in a sub-manifold of the configuration space containing the current path. We call this method variational dynamic programming (VDP). The method can solve difficult high-dimensional path planning problems without using any problem-specific heuristics. More importantly, an extension of VDP can solve manipulator planning problems of unprecedented complexity. <<ETX>>
Does gender matter for lifelong learning activity

Development and maintaining skills in a life course through various lifelong learning activities is crucial to sustain employability, particularly in the context of longer working lives and more competitive economic environment. In the paper we investigate the determinants and obstacles in lifelong learning from a gender perspective. Based on the results of Labour Force Survey and Adult Education Survey we investigate the extent educational activity of adults in Europe as well as look barriers and obstacles to lifelong learning.
CrossCheck: Combining Crawling and Differencing to Better Detect Cross-browser Incompatibilities in Web Applications

One of the consequences of the continuous and rapid evolution of web technologies is the amount of inconsistencies between web browsers implementations. Such inconsistencies can result in cross-browser incompatibilities (XBIs)-situations in which the same web application can behave differently when run on different browsers. In some cases, XBIs consist of tolerable cosmetic differences. In other cases, however, they may completely prevent users from accessing part of a web application's functionality. Despite the prevalence of XBIs, there are hardly any tools that can help web developers detect and correct such issues. In fact, most existing approaches against XBIs involve a considerable amount of manual effort and are consequently extremely time consuming and error prone. In recent work, we have presented two complementary approaches, WEBDIFF and CROSST, for automatically detecting and reporting XBIs. In this paper, we present CROSSCHECK, a more powerful and comprehensive technique and tool for XBI detection that combines and adapts these two approaches in a way that leverages their respective strengths. The paper also presents an empirical evaluation of CROSSCHECK on a set of real-world web applications. The results of our experiments show that CROSSCHECK is both effective and efficient in detecting XBIs, and that it can outperform existing techniques.
Polyglutamine-Rich Suppressors of Huntingtin Toxicity Act Upstream of Hsp70 and Sti1 in Spatial Quality Control of Amyloid-Like Proteins

Protein conformational maladies such as Huntington Disease are characterized by accumulation of intracellular and extracellular protein inclusions containing amyloid-like proteins. There is an inverse correlation between proteotoxicity and aggregation, so facilitated protein aggregation appears cytoprotective. To define mechanisms for protective protein aggregation, a screen for suppressors of nuclear huntingtin (Htt103Q) toxicity was conducted. Nuclear Htt103Q is highly toxic and less aggregation prone than its cytosolic form, so we identified suppressors of cytotoxicity caused by Htt103Q tagged with a nuclear localization signal (NLS). High copy suppressors of Htt103Q-NLS toxicity include the polyQ-domain containing proteins Nab3, Pop2, and Cbk1, and each suppresses Htt toxicity via a different mechanism. Htt103Q-NLS appears to inactivate the essential functions of Nab3 in RNA processing in the nucleus. Function of Pop2 and Cbk1 is not impaired by nuclear Htt103Q, as their respective polyQ-rich domains are sufficient to suppress Htt103Q toxicity. Pop2 is a subunit of an RNA processing complex and is localized throughout the cytoplasm. Expression of just the Pop2 polyQ domain and an adjacent proline-rich stretch is sufficient to suppress Htt103Q toxicity. The proline-rich domain in Pop2 resembles an aggresome targeting signal, so Pop2 may act in trans to positively impact spatial quality control of Htt103Q. Cbk1 accumulates in discrete perinuclear foci and overexpression of the Cbk1 polyQ domain concentrates diffuse Htt103Q into these foci, which correlates with suppression of Htt toxicity. Protective action of Pop2 and Cbk1 in spatial quality control is dependent upon the Hsp70 co-chaperone Sti1, which packages amyloid-like proteins into benign foci. Protein:protein interactions between Htt103Q and its intracellular neighbors lead to toxic and protective outcomes. A subset of polyQ-rich proteins buffer amyloid toxicity by funneling toxic aggregation intermediates to the Hsp70/Sti1 system for spatial organization into benign species.
CHAPTER 12 L-PEACH , AN L-SYSTEM-BASED MODEL FOR SIMULATING ARCHITECTURE , CARBOHYDRATE SOURCE – SINK INTERACTIONS AND PHYSIOLOGICAL RESPONSES OF GROWING TREES

Carbohydrate partitioning is closely coupled with plant growth and architecture, and therefore constitutes an important aspect of the functional-structural modelling of plants. L-PEACH is an L-systembased tree simulation model that combines supply/demand concepts of carbon partitioning with a developmental model of tree architecture. The model is expressed in terms of modules that represent plant organs. An organ may correspond to one or more elementary sources or sinks for carbohydrates. The whole plant is modelled as a branching network of these sources and sinks, connected by conductive elements. An analogy to an electric network is used to calculate the flow and partitioning of carbohydrates between the individual components. It can simulate multiple years of tree growth while capturing the effects of irrigation, crop load and pruning on carbon partitioning and the dynamics of architectural development. The growing tree can be visualized in a schematic or semi-realistic manner, while quantitative data characterizing individual organs, organ types or the whole tree can be output for visualization and analysis to an external program, such as MATLAB.
Probabilistic deduplication for cluster-based storage systems

The need to backup huge quantities of data has led to the development of a number of distributed deduplication techniques that aim to reproduce the operation of centralized, single-node backup systems in a cluster-based environment. At one extreme, stateful solutions rely on indexing mechanisms to maximize deduplication. However the cost of these strategies in terms of computation and memory resources makes them unsuitable for large-scale storage systems. At the other extreme, stateless strategies store data blocks based only on their content, without taking into account previous placement decisions, thus reducing the cost but also the effectiveness of deduplication. In this work, we propose, Produck, a stateful, yet light-weight cluster-based backup system that provides deduplication rates close to those of a single-node system at a very low computational cost and with minimal memory overhead. In doing so, we provide two main contributions: a lightweight probabilistic node-assignment mechanism and a new bucket-based load-balancing strategy. The former allows Produck to quickly identify the servers that can provide the highest deduplication rates for a given data block. The latter efficiently spreads the load equally among the nodes. Our experiments compare Produck against state-of-the-art alternatives over a publicly available dataset consisting of 16 full Wikipedia backups, as well as over a private one consisting of images of the environments available for deployment on the Grid5000 experimental platform. Our results show that, on average, Produck provides (i) up to 18% better deduplication compared to a stateless minhash-based technique, and (ii) an 18-fold reduction in computational cost with respect to a stateful Bloom-filter-based solution.
Phrase Model Training for Statistical Machine Translation with Word Lattices of Preprocessing Alternatives

In statistical machine translation, word lattices are used to represent the ambiguities in the preprocessing of the source sentence, such as word segmentation for Chinese or morphological analysis for German. Several approaches have been proposed to define the probability of different paths through the lattice with external tools like word segmenters, or by applying indicator features. We introduce a novel lattice design, which explicitly distinguishes between different preprocessing alternatives for the source sentence. It allows us to make use of specific features for each preprocessing type and to lexicalize the choice of lattice path directly in the phrase translation model. We argue that forced alignment training can be used to learn lattice path and phrase translation model simultaneously. On the news-commentary portion of the German→English WMT 2011 task we can show moderate improvements of up to 0.6% Bleu over a state-of-the-art baseline system.
Effect of rotation on the tachoclinic transport

Aims. We study the effect of rotation on sheared turbulence due to differential rotation in the solar tachocline. Methods. By solving quasi-linear equations for the fluctuating fields, we derive turbulence amplitude and turbulent transport coefficients (turbulent viscosity and diffusivity), taking into account the effects of shear and rotation on turbulence. We focus on the regions of the tachocline near the equator and the poles where rotation and shear are perpendicular and parallel, respectively. Results. For parameter values typical of the tachocline, we show that the shear reduces both turbulence amplitude and transport, more strongly in the radial direction (parallel to the shear) than in the horizontal one, resulting in anisotropic turbulence. Rotation further reduces turbulence amplitude and transport at the equator whereas it does not have much effect near the pole. The interaction between shear and rotation is shown to give rise to a novel non-diffusive flux of angular momentum (known as the Λ -effect), possibly offering a mechanism for the occurrence of a strong shear region in the solar interior. Further implications for the transport in the tachocline are discussed.
Amino Acid Residues Required for Physical and Cooperative Transcriptional Interaction of STAT3 and AP-1 Proteins c-Jun and c-Fos

ABSTRACT Cooperation between STAT3 and c-Jun in driving transcription during transfection of reporter constructs is well established, and both proteins are present on some interleukin-6 (IL-6) STAT3-dependent promoters on chromosomal loci. We report that small interfering RNA knockdown of c-Jun or c-Fos diminishes IL-6 induction of some but not all STAT3-dependent mRNAs. Specific contact sites in STAT3 responsible for interaction of a domain of STAT3 with c-Jun were known. Here we show that the B-zip domain of c-Jun interacts with STAT3 and that c-Jun mutation R261A or R261D near but not in the DNA binding domain blocks in vitro STAT3-c-Jun interaction and decreases costimulation of transcription in transfection assays. Cooperative binding to DNA of tyrosine-phosphorylated STAT3 and both wild-type and R261A mutant c-Jun was observed. Even c-Jun mutant R261D, which on its own did not bind DNA, bound DNA weakly in the presence of STAT3. We conclude that a functional interaction between STAT3 and c-Jun while bound to chromosomal DNA elements exists and is necessary for driving transcription on at least some STAT3 target genes. Identifying such required interactive protein interfaces should be a stimulus to search for compounds that could ultimately inhibit the activity of STAT3 in tumors dependent on persistently active STAT3.
Lateral diffusion of rhodopsin in photoreceptor membrane: a reappraisal

Purpose In a series of works between 1972 and 1984, it was established that rhodopsin undergoes rotational and lateral Brownian motion in the plane of photoreceptor membrane. The concept of free movement of proteins of phototransduction cascade is an essential principle of the present scheme of vertebrate phototransduction. This has recently been challenged by findings that show that in certain conditions rhodopsin in the membrane may be dimeric and form extended areas of paracrystalline organization. Such organization seems incompatible with earlier data on free rhodopsin diffusion. Thus we decided to reinvestigate lateral diffusion of rhodopsin and products of its photolysis in photoreceptor membrane specifically looking for indications of possible oligomeric organization. Methods Diffusion exchange by rhodopsin and its photoproducts between bleached and unbleached halves of rod outer segment was traced using high-speed dichroic microspectrophotometer. Measurements were conducted on amphibian (frog, toad, and salamander) and gecko rods. Results We found that the curves that are supposed to reflect the process of diffusion equilibration of rhodopsin in nonuniformly bleached outer segment largely show production of long-lived bleaching intermediate, metarhodopsin III (Meta III). After experimental elimination of Meta III contribution, we observed rhodopsin equilibration time constant was threefold to tenfold longer than estimated previously. However, after proper correction for the geometry of rod discs, it translates into generally accepted value of diffusion constant of approximately 5×10−9 cm2 s−1. Yet, we found that there exists an immobile rhodopsin fraction whose size can vary from virtually zero to 100%, depending on poorly defined factors. Controls suggest that the formation of the immobile fraction is not due to fragmentation of rod outer segment discs but supposedly reflects oligomerization of rhodopsin. Conclusions Implications of the new findings for the present model of phototransduction are discussed. We hypothesize that formation of paracrystalline areas, if controlled physiologically, could be an extra mechanism of cascade regulation.
Fuhr's challenge: conceptual research, or bust

In his 2012 Salton Award acceptance speech, Norbert Fuhr challenged the IR research community to develop IR into an engineering science. In this note, I elaborate on the implications of this challenge, which I interpret as a call for more conceptualization in IR research. The stakes are high, because failing this transition, IR research may never be able to produce generalizable, long--term performance gains, and IR risks losing its significance as a research field.
Fully and partially interpolated adaptive Volterra filters

This paper presents two simplified algorithms to implement adaptive Volterra filters. The central idea of the proposed approach is the use of sparse adaptive filters to reduce the number of coefficients to be adapted, which is the major drawback of adaptive Volterra filters. Such filters are obtained by removing some coefficients and then recreating them through an interpolating scheme. A second interpolated structure exploits also the block-size structure of the Volterra filter for coefficient reduction. Numerical simulation results are shown to ratify the good MSE behavior of the proposed structures.
Rotational Linear Discriminant Analysis Using Bayes Rule for Dimensionality Reduction

Linear discriminant analysis (LDA) finds an orientation that projects high dimensional feature vectors to reduced dimensional feature space in such a way that the overlapping between the classes in this feature space is minimum. This overlapping is usually finite and produces finite classification error which is further minimized by rotational LDA technique. This rotational LDA technique rotates the classes individually in the original feature space in a manner that enables further reduction of error. In this paper we present an extension of the rotational LDA technique by utilizing Bayes decision theory for class separation which improves the classification performance even further.
High Connectivity Between Reduced Cortical Thickness and Disrupted White Matter Tracts in Long-Standing Type 1 Diabetes

OBJECTIVE Previous studies have observed disruptions in brain white and gray matter structure in individuals with type 1 diabetes, and these structural differences have been associated with neurocognitive testing deficiencies. This study investigated the relationship between cerebral cortical thickness reductions and white matter microstructural integrity loss in a group of patients with type 1 diabetes and in healthy control subjects using diffusion tensor imaging (DTI). RESEARCH DESIGN AND METHODS Twenty-five subjects with type 1 diabetes for at least 15 years and 25 age- and sex-matched control subjects underwent structural T1 and proton-density and DTI on a 3.0 Tesla scanner. Fractional anisotropy measurements were made on major cerebral white matter tracts, and DTI tractography was performed to identify cortical regions with high connectivity to these tracts. RESULTS Posterior white matter tracts with reduced fractional anisotropy (optic radiations, posterior corona radiata, and the splenium region of the corpus callosum) were found to have high connectivity with a number of posterior cortical regions, including the cuneus, precuneus, fusiform, and posterior parietal cortical regions. A significant reduction in cortical thickness in the diabetic group was observed in the regions with high connectivity to the optic radiations and posterior corona radiata tracts (P < 0.05). CONCLUSIONS The direct relationship between white and gray matter structural pathology has not been previously demonstrated in subjects with long-standing type 1 diabetes. The relationship between posterior white matter microstructural integrity disruption and lower cortical thickness demonstrated using a novel DTI connectivity technique suggests a common or interrelated pathophysiological mechanism in type 1 diabetes.