Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Copy Number Variation and Gene Expression Analyses Reveal the Implication of Specific Oncogenes and Genes in GBM

To understand the pathogenesis of glioblastoma multiforme (GBM) we used high-resolution comparative genomic hybridization arrays and gene expression microarrays to identify DNA copy number alterations and gene expression changes in comparable sets of GBM samples. Gains were detected at chromosomes 1, 2, 7, 9, 12, 19, and 20 and losses at 6, 9, and 10. Gene expression analyses identified specific genes overexpressed in GBM mapping at amplified chromosomal regions. Among these genes we found genes involved in angiogenesis, extracellular matrix remodeling and several oncogenes. DNA copy number analysis along with gene expression profiles provides a powerful strategy to understand tumor progression and identification of genes involved in GBM pathogenesis.
The Capacity Region of the Three Receiver Less Noisy Broadcast Channel

We determine the capacity region of a 3-receiver less noisy broadcast channel. The difficulty in extending the two-receiver result to three-receivers involves extending the Csiszar-sum lemma to three or more sequences, a standard difficulty in this area. In this work we bypass the difficulty by using a new information inequality, for less noisy receivers, that is employed in the converse. We also generalize our result to obtain the capacity region for a class of less noisy receivers.
Carboniferous Post‐collisional Rift Volcanism of the Tianshan Mountains, Northwestern China

Abstract The Tianshan Carboniferous post‐collisional rift volcanic rocks occur in northwestern China as a large igneous province. Based on petrogeochemical data, the Tianshan Carboniferous post‐collisional rift basic lavas can be classified into two major magma types: (1) the low‐Ti/Y type situated in the eastern‐central Tianshan area, which exhibits low Ti/Y (<500), Ce/Yb (<15) and SiO2 (43–55%), and relatively high Fe2O3T (6.4–11.5%); (2) the high‐Ti/Y type situated in the western Tianshan area, which has high Ti/Y (>500), Ce/Yb (>11) and SiO2 (49–55%), and relatively low Fe2O3T (5.8–7.8%). Elemental data suggest that chemical variations of the low‐Ti/Y and high‐Ti/Y lavas cannot be explained by fractional crystallization from a common parental magma. The Tianshan Carboniferous basic lavas originated most likely from an OIB‐like asthenospheric mantle source (87Sr/86Sr(t) ∼ 0.703–0.705, εNd(t) ∼ +4 to +7). The crustal contamination and continental lithospheric mantle have also contributed significantly to the formation of the basic lavas of the Tianshan Carboniferous post‐collisional rift. The silicic lavas were probably generated by partial melting of the crust. The data of this study show that spatial petrogeochemical variations exist in the Carboniferous post‐collisional rift volcanics province in the Tianshan region. Occurrence of the thickest volcanics dominated by tholeiitic lavas may imply that the center of the mantle‐melting anomaly (mantle plume) was in the eastern Tianshan area at that time. The basic volcanic magmas in the eastern Tianshan area were generated by a relatively high degree of partial melting of the mantle source around the spinel‐garnet transition zone, whereas the alkaline basaltic lavas are of the dominant magma type in the western Tianshan area, which were generated by a low degree of partial melting of the mantle source within the stable garnet region, thus the basic lavas of the western Tianshan area might have resulted from relatively thick lithosphere and low geothermal gradient.
Observation of the smectic-C-smectic-I critical point.

We report the first observation of the smectic C--smectic I (C--I) critical point by Xray diffraction studies on a binary system. This is in confirmity with the theoretical idea of Nelson and Halperin that coupling to the molecular tilt should induce hexatic order even in the C phase and as such both C and I (a tilted hexatic phase) should have the same symmetry. The results provide evidence in support of the recent theory of Defontaines and Prost proposing a new universality class for critical points in layered systems.
Transfer and Counterconditioning of Conditional Control in the Rabbit Nictitating Membrane Response

Two experiments using the rabbit nictitating membrane response investigated whether training in one conditional discrimination (A→X+, B→X-), enabled the feature cues (A and B) to modulate responding to another CS (Y) trained as a target stimulus in a second conditional discrimination (C→Y+, D→Y-). There was near-complete transfer of the feature cue's conditional control, indicating that the feature cue's ability to modulate responding is not based on an association specific to the training target. Experiment 2 also revealed that the role of a stimulus to act as a conditional cue is affected by its ability to act as a simple conditioned excitor or inhibitor. Following initial acquisition of two conditional discriminations, two feature cues were reinforced in a pattern consistent with the initial conditional discrimination (A→+, B→-), whereas the other two feature cues were reinforced in the reverse pattern to that of the original conditional discrimination (C→-, D→+). Subsequent tests revealed that the reversed training of the feature cues interfered with the original conditional discriminations. The results are consistent with theories that the feature cue gains an association with a representation of the emotional attributes of the US, which acts to modulate responding to the target stimulus through a diffuse change in motivational level. However, hierarchical theories of conditional discriminations that assume a lack of CS-specificity may also be able to explain the findings.
Structural Evolution of North—East Newfoundland: comparison with that of the British Caledonides

The British Caiedonides and the Newfoundland Appalachian systems have in common: a northwestern foreland region composed of pre-Cambrian gneisses, overlain by Cambro-Ordovician carbonate rocks containing a typical North American fauna; a north-central orthotectonic belt of intensely deformed garnet-grade metamorphic rocks; a south-central belt of Ordovician and Silurian elastic and volcanic rocks; and a south-eastern foreland region composed dominantly of pre-Cambrian volcanics overlain by Upper Proterozoic rocks followed by Cambro-Ordovician elastic rocks bearing a typical European fossil fauna.
Personalized smart TV program recommender based on collaborative filtering and a novel similarity method

The viewing set-based method has difficulties ensuring that a user will enjoy recommended programs, and the model-based collaborative filtering method contains system-side real-time recommendation problems because most recent ratings cannot be applied in the recommendations and it has increased calculating costs due to the training process. In this paper, we propose a personalized program recommender for smart TVs using memory-based collaborative filtering with a novel similarity method that is robust to cold-start conditions and faster than the often-used, existing similarity method. The proposed method can improve the recommendation performance of electronic program guides and recommender applications for smart TVs. We determined the prediction accuracy of the ratings under various conditions in order to evaluate the proposed method. As a result, we confirmed that the proposed method is effective for cold-start conditions.
Risk Scores of Common Genetic Variants for Lipid Levels Influence Atherosclerosis and Incident Coronary Heart Disease

Objective—Circulating levels of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides are recognized risk factors for cardiovascular disease. We tested the hypothesis that the cumulative effects of common genetic variants for lipids are collectively associated with subclinical atherosclerosis and incident coronary heart disease. Approach and Results—Participants were drawn from the Erasmus Rucphen Family Study (n=2269) and the Rotterdam Study (n=8130). Linear regression and Cox proportional hazards models were applied to assess the influence of 4 risk scores derived from common genetic variants for lipids (total cholesterol, LDL-C, high-density lipoprotein cholesterol, and triglycerides) on carotid plaque, intima-media thickness, incident myocardial infarction, and coronary heart disease. Adjusted for age and sex, all 4 risk scores were associated with carotid plaque. This relationship was the strongest for the LDL-C score, which increased plaque score by 0.102 per SD increase in genetic risk score (P=3.2×10−8). The LDL-C score was also nominally associated with intima-media thickness, which increased 0.006 mm per SD increase in score (P=0.05). Both the total cholesterol and LDL-C scores were associated with incident myocardial infarction and coronary heart disease with hazard ratios between 1.10 and 1.13 per SD increase in score. Inclusion of additional risk factors as covariates minimally affected these results. Conclusions—Common genetic variants with small effects on lipid levels are, in combination, significantly associated with subclinical and clinical cardiovascular outcomes. As knowledge of genetic variation increases, preclinical genetic screening tools might enhance the prediction and prevention of clinical events.
Connectivity-Guided Adaptive Lifting Transform for Image Like Compression of Meshes

We propose a new connectivity-guided adaptive wavelet transform based mesh compression framework. The 3D mesh is first transformed to 2D images on a regular grid structure by performing orthogonal projections onto the image plane. Then, this image-like representation is wavelet transformed using a lifting structure employing an adaptive predictor that takes advantage of the connectivity information of mesh vertices. Then the wavelet domain data is encoded using "Set Partitioning In Hierarchical Trees" (SPIHT) method or JPEG2000. The SPIHT approach is progressive because the resolution of the reconstructed mesh can be changed by varying the length of the ID data stream created by the algorithm. In JPEG2000 based approach, quantization of the coefficients determines the quality of the reconstruction. The results of the SPIHT based algorithm is observed to be superior to JPEG200 based mesh coder and MPEG-3DGC in rate-distortion.
Lamina-specific deficits in parvalbumin-immunoreactive varicosities in the prefrontal cortex of subjects with schizophrenia: evidence for fewer projections from the thalamus.

OBJECTIVE Neuronal number in the mediodorsal thalamic nucleus, the principal source of thalamic projections to the prefrontal cortex, has been reported to be lower in subjects with schizophrenia. The authors tested the hypothesis that schizophrenia is associated with a selective deficit in a marker of thalamic axon terminals in the middle layers of the prefrontal cortex, the primary zone of termination of thalamic axons. METHOD The densities of parvalbumin-immunoreactive varicosities (putative axon terminals) were determined in the superficial and middle layers of prefrontal cortex area 9 from 20 matched pairs of subjects with schizophrenia and normal comparison subjects. In order to determine the specificity of these observations, similar studies were conducted in subjects with major depressive disorder and in monkeys after 9-12 months of haloperidol treatment. RESULTS The relative densities of parvalbumin-immunoreactive varicosities did not differ between schizophrenic and comparison subjects in the superficial layers. However, in the middle layers, mean varicosity density was significantly lower (24% difference) in the subjects with schizophrenia. In contrast, neither subjects with major depressive disorder nor haloperidol-treated monkeys exhibited a middle-layer density of parvalbumin-immunoreactive varicosities that was lower than that of their matched comparison groups. CONCLUSIONS Although not definitive, these findings are consistent with the hypothesis of fewer projections from the mediodorsal thalamic nucleus to the prefrontal cortex in schizophrenic subjects and thus converge with other lines of evidence demonstrating an abnormality in thalamo-prefrontal cortical circuitry in persons with schizophrenia.
Machine learning techniques for autonomous agents in military simulations — Multum in parvo

In military simulations, software agents are used to represent individuals, weapon platforms or aggregates thereof. Modeling the behavioral capabilities and limitations of such agents may be time-consuming, requiring extensive interaction with subject matter experts and complicated scripts, but nevertheless resulting in rigid, predictable performance. Autonomous agents that learn desired behaviors themselves using Machine Learning (ML) techniques can overcome these shortcomings. However, such techniques are not yet widely used and perhaps underappreciated. In this context, the latin expression "multum in parvo" ("much in little") denotes that ML agents are able to yield a large variety of behavior, despite their compactness in terms of code and usage of physical memory. This paper attempts to provide some background on applicable Machine Learning solutions and their potential military application. The paper is based on the work of the NATO Research Task Group IST-121 Machine Learning Techniques for Autonomous Computer Generated Entities.
Design, Implementation and Performance Evaluation of a Stochastic Gradient Descent Algorithm on CUDA

Stochastic Gradient Descent, a stochastic optimization of Gradient Descent, is an algorithm that is used in different topics,like for example for linear regression or logistic regression. After the Netflix prize, SGD start to be used also in recommender systems to compute matrix factorization. Considering the large amounts of data that this kind of system has to elaborate, adapt the algorithm on a distributed system or parallelize it is a good idea to improve performance. One way to do this is by using GPGPU, that thanks to its characteristics itâ€™s now days a good solution for parallelize an application.With this work, we are interested in analyze how SGD works on a GPGPU environment that is designed with a CUDA architecture, starting from an existing implementation for parallel environments and then adapting it to exploits all characteristics that a GPU of this kind provide.
Corporate Governance , Performance and Management Turnover : An Empirical Analysis of Chinese Listed Companies

This paper provides an empirical analysis of corporate governance (CG) efficiencies among Chinese listed companies (CLCs) under different types of ownership. Employing the data of over 700 CLCs in 2006, this study looks specifically into the effects of separation of controlling and residual claim rights upon CG (specifically management turnover) and firm performance under different shareholding patterns. The results under two sample firms are different, suggesting that state-owned enterprises (SOEs) and non-SOEs are subject to dissimilar pressures for corporate performance and management changing. It suggests that owing to the separation of controlling rights and residual claim rights the agency problem between major shareholders and minority shareholders is more serious among non-SOEs.
A Turbulence Dissipation Correction to the k-epsilon Model and Its Effect on Turbulence Length Scales in Engine Flows

Non-equilibrium turbulence considerations from rapid distortion theory have been utilized to derive a correction to the turbulence dissipation rate, which then has been implemented in combination with the RNG k-epsilon model in a KIVA-based code. This correction reflects the time delay between changes in the turbulent kinetic energy due to changes in the mean flow and its turbulence dissipation rate, and it is shown that this time delay is controlled by the turbulence Reynolds number. This dissipation rate correction has been validated with experimental turbulence measurements of a small diesel engine operated in motored mode. Improvements in the turbulence length scales have then been obtained by means of this model correction for the compression and the combustion phase of two heavy-duty DI diesel engines.
Proneurotrophin-3 promotes cell cycle withdrawal of developing cerebellar granule cell progenitors via the p75 neurotrophin receptor

Cerebellar granule cell progenitors (GCP) proliferate extensively in the external granule layer (EGL) of the developing cerebellum prior to differentiating and migrating. Mechanisms that regulate the appropriate timing of cell cycle withdrawal of these neuronal progenitors during brain development are not well defined. The p75 neurotrophin receptor (p75NTR) is highly expressed in the proliferating GCPs, but is downregulated once the cells leave the cell cycle. This receptor has primarily been characterized as a death receptor for its ability to induce neuronal apoptosis following injury. Here we demonstrate a novel function for p75NTR in regulating proper cell cycle exit of neuronal progenitors in the developing rat and mouse EGL, which is stimulated by proNT3. In the absence of p75NTR, GCPs continue to proliferate beyond their normal period, resulting in a larger cerebellum that persists into adulthood, with consequent motor deficits. DOI: http://dx.doi. org/10.7554/eLife.16654. 001
Thermooptic effect in chloroplast thylakoid membranes. Thermal and light stability of pigment arrays with different levels of structural complexity.

In chloroplast thylakoid membranes, chiral macrodomains, i.e., large arrays of pigment molecules with long-range chiral order, have earlier been shown to undergo light-induced reversible and irreversible structural changes; such reorganizations did not affect the short-range, excitonic pigment-pigment interactions. These structural changes and similar changes in lamellar aggregates of the main chlorophyll a/b light-harvesting complexes exhibited a linear dependence on the intensity of light that was not utilized in photosynthesis. It has been hypothesized that the light-induced rearrangements are driven by a thermooptic effect, i.e., thermal fluctuations due to the dissipation of excess excitation energies [Barzda, V. , et al. (1996) Biochemistry 35, 8981-8985]. To test this hypothesis, we have utilized circular dichroism (CD) spectroscopy to investigate the structural stability of the chiral macrodomains and the constituent bulk pigment-protein complexes of granal thylakoid membranes against heat and prolonged, intense illumination. (i) In intact thylakoid membranes, the chiral macrodomains displayed high stability below 40 degrees C, but they were gradually disassembled between 50 and 60 degrees C; the thermal stability of the chiral macrodomains could be decreased substantially by suspending the membranes in reaction media that were hypotonic or had low ionic strength. (ii) The chiral macrodomains were also susceptible to high light: prolonged illumination with intense white light (25 min, 2500 microE m(-)(2) s(-)(1), 25 degrees C) induced similar, irreversible disassembly to that observed at high temperatures; in different preparations, lower thermal stability was coupled to lower light stability. (iii) The light stability depended significantly on the temperature: between about 5 and 15 degrees C, the macrodomains in the intact thylakoids were virtually not susceptible to high light; in contrast, the same preillumination at 35-40 degrees C almost completely destroyed the chiral macrodomains. (iv) As testified by the excitonic CD bands, the molecular organization of the pigment-protein complexes in all samples exhibited very high thermal stability between about 15 and 65 degrees C, and virtually total immunity against intense illumination. These data are fully consistent with the hypothesis of a thermooptic effect, and are interpreted within the frame of a simple model.
All-Integer Dual Simplex for Binate Cover Problems (Draft)

All-integer dual simplex, int-dual, first introduced around 1960, has not received much attention recently because, in most situations, it does not perform well when the goal is to obtain optimal solutions. This paper presents experimental results for int-dual in a limited context. First instead of seeking optimality int-dual is only required to run long enough to match an upper bound obtained by stochastic local search. If both procedures are run simultaneously or concurrently, the maximum time for the two determines when they will “meet in the middle”. Second, the problem domain is limited to binate cover problems, set cover problems with some side constraints, arising in design automation. While initial results are encouraging, the algorithm exhibits extreme sensitivity to row and column permutations with one of the benchmark instances. The paper gives important implementation details, experimental results, and a thorough analysis.
Directing learner attention with manipulation styles

This paper investigates what aspects of a pupil’s interaction with educational software are determinants of their learning. The work reported here considers whether the computer interface can be designed to encourage people to plan, to think more deeply about relevant information, and hence to learn more successfully. Findings reported here challenge the universal welcome given to graphical user interfaces. A number of pedagogical issues involved in designing educational software are raised. These suggest that designing with considerations other than ease-of-use is paramount.
Educational Question Answering based on Social Media Content

We analyze the requirements for an educational Question Answering (QA) system operating on social media content. As a result, we identify a set of advanced natural language processing (NLP) technologies to address the challenges in educational QA. We conducted an inter-annotator agreement study on subjective question classification in the Yahoo! Answers social Q&A site and propose a simple, but effective approach to automatically identify subjective questions. We also developed a two-stage QA architecture for answering learners' questions. In the first step, we aim at re-using human answers to already answered questions by employing question paraphrase identification [1]. In the second step, we apply information retrieval techniques to perform answer retrieval from social media content. We show that elaborate techniques for question preprocessing are crucial.
"NEW MEMBRANE" FORMATION IN AMOEBA PROTEUS UPON INJURY OF INDIVIDUAL CELLS

Changes in the plasma membrane complex following the injury of single cells of Amoeba proteus were examined with the electron microscope. Two types of injury were employed in this study; cells were either pinched ("cut") in half or speared with a glass microneedle, and quickly fixed. Speared cells, when fixed in the presence of the ruthenium violet (a derivative of ruthenium red), revealed the presence of an extra trilaminar structure outside of each cell. This structure, called the "new membrane," was separated from the plasma membrane complex by a distance of less than a micron. The trilaminar structure of the new membrane strikingly resembled the image of the plasma membrane in all cells examined, except for its increased width (30%). This new membrane appeared nearly to surround the injured amebae. Attempts were made to demonstrate the possible origin of the new membrane, its reality, and its sensitivity to calcium. Also, some evidence is shown concerning the role of the small dense droplets (100–1200 A in diameter) normally present in the cytoplasm of amebae. Their frequent contact with the plasma membrane of the cell as the result of injury is interpreted as indicating their involvement in the formation and expansion of the plasma membrane.