Miracle-dz/UniFAR-FTUs huggingface dataset:
Many-Core Architectures: Hardware-Software Optimization and Modeling Techniques

During the last few decades an unprecedented technological growth has been at the center of the embedded systems design paramount, with Moore’s Law being the leading factor of this trend. Today in fact an ever increasing number of cores can be integrated on the same die, marking the transition from state-of-the-art multi-core chips to the new many-core design paradigm. Despite the extraordinarily high computing power, the complexity of many-core chips opens the door to several challenges. As a result of the increased silicon density of modern Systems-on-a-Chip (SoC), the design space exploration needed to find the best design has exploded and hardware designers are in fact facing the problem of a huge design space. Virtual Platforms have always been used to enable hardware-software co-design, but today they are facing with the huge complexity of both hardware and software systems. In this thesis two different research works on Virtual Platforms are presented: the first one is intended for the hardware developer, to easily allow complex cycle accurate simulations of many-core SoCs. The second work exploits the parallel computing power of off-the-shelf General Purpose Graphics Processing Units (GPGPUs), with the goal of an increased simulation speed. The term Virtualization can be used in the context of many-core systems not only to refer to the aforementioned hardware emulation tools (Virtual Platforms), but also for two other main purposes: 1) to help the programmer to achieve the maximum possible performance of an application, by hiding the complexity of the underlying hardware. 2) to efficiently exploit the high parallel hardware of many-core chips in environments with multiple active Virtual Machines. This thesis is focused on virtualization techniques with the goal to mitigate, and overtake when possible, some of the challenges introduced by the many-core design paradigm.
SMASH: A Next-Generation API for Programmable Graphics Accelerators

The SMASH API is a testbed for real-time, low-level graphics concepts. It is being developed to serve as a concrete target for the development of advanced extensions to OpenGL as well as a driver to test hardware architectures to support these extensions. SMASH is syntactically and conceptually similar to OpenGL but supports (along with other experimental features) a programmable shader sub-API that is compatible with both multi-pass and single-pass implementations of shaders. Arbitrary numbers of shader parameters of various types can be bound to vertices of geometric primitives using a simple immediatemode mechanism. Run-time specification, manipulation, and compilation of shaders is supported. The intermediate-level shading language includes integrated support for per-vertex and perfragment shaders under a common programming model. Implementation of real-time rendering effects using SMASH could be enhanced with metaprogramming toolkits and techniques, up to and including RenderMan-like textual shading languages and C++ toolkits with similar levels of compactness and functionality. We give several examples of how a two-term separable BRDF approximation could be implemented using such higher-level constructs.
Rhizospheric NO affects N uptake and metabolism in Scots pine (Pinus sylvestris L.) seedlings depending on soil N availability and N source.

We investigated the interaction of rhizospheric nitric oxide (NO) concentration (i.e. low, ambient or high) and soil nitrogen (N) availability (i.e. low or high) with organic and inorganic N uptake by fine roots of Pinus sylvestris L. seedlings by (15) N feeding experiments under controlled conditions. N metabolites in fine roots were analysed to link N uptake to N nutrition. NO affected N uptake depending on N source and soil N availability. The suppression of nitrate uptake in the presence of ammonium and glutamine was overruled by high NO. The effects of NO on N uptake with increasing N availability showed different patterns: (1) increasing N uptake regardless of NO concentration (i.e. ammonium); (2) increasing N uptake only with high NO concentration (i.e. nitrate and arginine); and (3) decreasing N uptake (i.e. glutamine). At low N availability and high NO nitrate accumulated in the roots indicating insufficient substrates for nitrate reduction or its storage in root vacuoles. Individual amino acid concentrations were negatively affected with increasing NO (i.e. asparagine and glutamine with low N availability, serine and proline with high N availability). In conclusion, this study provides first evidence that NO affects N uptake and metabolism in a conifer.
Risk of tuberculosis in rheumatoid arthritis patients on tumour necrosis factor-alpha inhibitor treatment in Taiwan

Correspondence to: Wei-Ming Ke, Division of Drug Safety, Taiwan Drug Relief Foundation, Taipei, Taiwan. Tel: (+886) 2 2358 7343, extn 146. Fax: (+886) 2 2358 4100. e-mail: cliffke@tdrf.org. tw Article submitted 22 May 2013. Final version accepted 20 July 2013. O B J E C T I V E S : To quantify the incidence of tuberculosis (TB) in rheumatoid arthritis patients undergoing treatment with tumour necrosis factor-alpha inhibitors (TNFi). D E S I G N : In a retrospective cohort study conducted using data from Taiwan’s National Health Insurance claims databases, rheumatoid arthritis patients notified during the period 2006–2008 were recruited and classified based on types of TNFi treatment received. Active TB was the primary outcome. TB risk was estimated using Cox’s proportional hazard model. The TB screening rate within 30 days of initiating treatment with TNFi was examined. R E S U LT S : Respectively 5079 and 829 patients were included in the non-TNFi and TNFi groups. Active TB rates were respectively 1411.3 and 679.5 events per 100 000 person-years in patients treated with adalimumab and etanercept. Significant TB risk was noted in patients treated with TNFi (aHR 4.87, 95%CI 2.14– 11.06). No significant difference in active TB was observed between the TNFi subgroups (etanercept as reference, aHR 1.89, 95%CI 0.40–6.04). Only 8.7% (n = 9) of TNFi users underwent screening for TB before the first dose of TNFi. C O N C L U S I O N S : Patients on TNFi have a significantly greater risk of active TB than non-TNFi patients in the Taiwanese population. No difference in TB risk between the two available TNFi groups was noted. Screening for TB before initiating treatment with TNFi should be implemented. K E Y W O R D S : TB screening; pharmacovigilance; claims database
Principle component analysis on photoplethysmograms: Blood oxygen saturation estimation and signal segmentation

Most pulse oximeters determine blood oxygen saturation (SpO2) after calculating a coefficient, R, that represents the normalized ratiometric contributions of the pulsatile red and near-infrared photoplethysmograms (PPGs) acquired by the sensor. This paper presents a new approach that uses principle component analysis (PCA) to separate the signal and noise components of unfiltered PPGs and provide the determination of R. Also, rather than use peak-to-valley time intervals to obtain R, this technique uses eigenvalue and eigenvector data obtained during PCA to optimize these time intervals and improve the R calculation. Early analyses on unfiltered PPGs from 16 subjects indicate that these R values compare to those obtained from FFT-based methods and yield SpO2 values consistent with those reported by a commercial unit. All signal data are considered during the PCA process, so this technique shows promise to precisely segment clean versus noise-corrupted PPGs.
Constraints on Water Reservoir Lifetimes From Catchment‐Wide 10Be Erosion Rates—A Case Study From Western Turkey

The functionality and retention capacity of water reservoirs is generally impaired by upstream erosion and reservoir sedimentation, making a reliable assessment of erosion indispensable to estimate reservoir lifetimes. Widely used river gauging methods may underestimate sediment yield, because they do not record rare, high‐magnitude events and may underestimate bed load transport. Hence, reservoir lifetimes calculated from short‐term erosion rates should be regarded as maximum values. We propose that erosion rates from cosmogenic 10Be, which commonly integrate over hundreds to thousands of years, are useful to complement short‐term sediment yield estimates and should be employed to estimate minimum reservoir lifetimes. Here we present 10Be erosion rates for the drainage basins of six water reservoirs in Western Turkey, which are located in a tectonically active region with easily erodible bedrock. Our 10Be erosion rates for these catchments are high, ranging from ∼170 to ∼1,040 t/km2/yr. When linked to reservoir volumes, they yield minimum reservoir lifetimes between 25 ± 5 and 1,650 ± 360 years until complete filling, with four reservoirs having minimum lifespans of ≤110 years. In a neighboring region with more resistant bedrock and less tectonic activity, we obtain much lower catchment‐wide 10Be erosion rates of ∼33 to ∼95 t/km2/yr, illustrating that differences in lithology and tectonic boundary conditions can cause substantial variations in erosion even at a spatial scale of only ∼50 km. In conclusion, we suggest that both short‐term sediment yield estimates and 10Be erosion rates should be employed to predict the lifetimes of reservoirs.
A Comparison of Inference Techniques for Semi-supervised Clustering with Hidden Markov Random Fields

Recently, a number of methods have been proposed for semi-supervised clustering that employ supervision in the form of pairwise constraints. We describe a probabilistic model for semisupervised clustering based on Hidden Markov Random Fields (HMRFs) that incorporates relational supervision. The model leads to an EMstyle clustering algorithm, the E-step of which requires collective assignment of instances to cluster centroids under the constraints. We evaluate three known techniques for such collective assignment: belief propagation, linear programming relaxation, and iterated conditional modes (ICM). The first two methods attempt to globally approximate the optimal assignment, while ICM is a greedy method. Experimental results indicate that global methods outperform the greedy approach when relational supervision is limited, while their benefits diminish as more pairwise constraints are provided.
Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability

Abstract Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial cancer pathways. Recently, there is considerable evidence showing that, mutual exclusivity reflects alternative functions in tumor initiation and progression, or suggests adverse effects of their concurrence. Given its importance, numerous computational approaches have been proposed to study mutual exclusivity using genomic profiles alone, or by integrating networks and phenotypes. Some of them have been routinely used to explore genetic associations, which lead to a deeper understanding of carcinogenic mechanisms and reveals unexpected tumor vulnerabilities. Here, we present an overview of mutual exclusivity from the perspective of cancer genome. We describe the common hypothesis underlying mutual exclusivity, summarize the strategies for the identification of significant mutually exclusive patterns, compare the performance of representative algorithms from simulated data sets and discuss their common confounders.
Compressed sensing under optimal quantization

We consider the problem of recovering a sparse vector from a quantized or a lossy compressed version of its noisy random linear projections. We characterize the minimal distortion in this recovery as a function of the sampling ratio, the sparsity rate, the noise intensity and the total number of bits in the quantized representation. We first derive a singe-letter expression that can be seen as the indirect distortion-rate function of the sparse source observed through a Gaussian channel whose signal-to-noise ratio is derived from these parameters. Under the replica symmetry postulation, we prove that there exists a quantization scheme that attains this expression in the asymptotic regime of large system dimensions. In addition, we prove a converse demonstrating that the MMSE in estimating any fixed sub-block of the source from the quantized measurements at a fixed number of bits does not exceed this expression as the system dimensions go to infinity. Thus, under these conditions, the expression we derive describes the excess distortion incurred in encoding the source vector from its noisy random linear projections in lieu of the full source information.
Effect of litter decomposition on mowing and plant composition change during Solidago stand restoration

Decomposition of organic matter supports important soil ecosystem services. The rate of decomposition depends mostly on the type of plant material being decomposed and the abundance and diversity of organisms that process the organic matter. Consequently, any disturbance to the soil ecosystem will affect the decomposition process. Invasive plants, such as Solidago species, pose a serious ecological threat to natural habitats, so effective and environmentally safe methods of controlling their occurrence should be developed. In this study, decomposition rates were used as indicators of soil health during grassland restoration after Solidago invasion. Different seed mixtures (grasses, grasses with legumes, seeds collected from a seminatural meadow; use of fresh hay and no seeds) were sown during a field experiment and different mowing frequencies (1, 2 and 3 times per year) were established. Two hypotheses were tested: (1) plant species composition used in the restoration process affects litter decomposition rates, and (2) mowing regimes affect litter decomposition rates. It was found that decomposition rates were higher in plots with the highest species diversity. This indicates that an increase in species diversity has a positive effect on soil processes. Secondly, mowing two and three times per season has a positive effect on the decomposition process. In conclusion, decomposition rates can be used as a tool to identify adequate grassland management.
Enhanced selective gene delivery to neural stem cells in vivo by an adeno-associated viral variant

Neural stem cells (NSCs) are defined by their ability to self-renew and to differentiate into mature neuronal and glial cell types. NSCs are the subject of intense investigation, owing to their crucial roles in neural development and adult brain function and because they present potential targets for gene and cell replacement therapies following injury or disease. Approaches to specifically genetically perturb or modulate NSC function would be valuable for either motivation. Unfortunately, most gene delivery vectors are incapable of efficient or specific gene delivery to NSCs in vivo. Vectors based on adeno-associated virus (AAV) present a number of advantages and have proven increasingly successful in clinical trials. However, natural AAV variants are inefficient in transducing NSCs. We previously engineered a novel AAV variant (AAV r3.45) capable of efficient transduction of adult NSCs in vitro. Here, to build upon the initial promise of this variant, we investigated its in vitro and in vivo infectivity. AAV r3.45 was more selective for NSCs than mature neurons in a human embryonic stem cell-derived culture containing a mixture of cell types, including NSCs and neurons. It was capable of more efficient and selective transduction of rat and mouse NSCs in vivo than natural AAV serotypes following intracranial vector administration. Delivery of constitutively active β-catenin yielded insights into mechanisms by which this key regulator modulates NSC function, indicating that this engineered AAV variant can be harnessed for preferential modulation of adult NSCs in the hippocampus. The capacity to rapidly genetically modify these cells might greatly accelerate in vivo investigations of adult neurogenesis. SUMMARY: The adeno-associated virus variant r3.45 is used to efficiently and selectively transduce adult mouse, rat, and human neural stem cells both in vitro and in vivo.
Performance Analysis of Complex Communications Systems

This paper discusses the designing of complex teleprocessing systems using a discrete simulation modeling tool, the Systems Network Analysis Program/Simulated Host Overview Technique (internally and informally called SNAP/SHOT). This modeling tool aids in designing computer communications systems composed of local and remote terminals, teleprocessing lines, host processors that control the teleprocessing lines, and interconnected communications systems. The model is capable of analyzing both tree- and mesh-structured networks.
How pairs interact over a multimodal digital table

Co-located collaborators often work over physical tabletops using combinations of expressive hand gestures and verbal utterances. This paper provides the first observations of how pairs of people communicated and interacted in a multimodal digital table environment built atop existing single user applications. We contribute to the understanding of these environments in two ways. First, we saw that speech and gesture commands served double duty as both commands to the computer, and as implicit communication to others. Second, in spite of limitations imposed by the underlying single-user application, people were able to work together simultaneously, and they performed interleaving acts: the graceful mixing of inter-person speech and gesture actions as commands to the system. This work contributes to the intricate understanding of multi-user multimodal digital table interaction.
The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs) that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.
New tendencies in the application of altitude training in sport preparation

Competitive athletes frequently use altitude training (AT) to improve sea-level performance. AT became interesting for sport scientists and athletes since Olympic Games in Mexico City in 1968. Exercise at altitude may increase the training stimulus and enlarge the effects of endurance training. The first noted adaptation induced by staying at altitude is an increase in red blood cell mass that improves aerobic power and sea-level performance. Currently, there are several types of AT modalities: traditional ‘live high-train high’, contemporary ‘live high-train low’, intermittent hypoxic exposure during rest, live low-train high and intermittent hypoxic exposure during continuous session. Despite several substantial differences between these methods of hypoxic all of them have the same goal: to stimulate an improvement in athletic performance at sea level. A proper distinction must be made between altitude acclimatization during preparation for competitions at altitude and AT and acclimatization for improvement of the sea-level performances. Former scientific researches identified two longer phases of enhanced work capacity after AT. First phase of enhanced work capacity occurring between days 3-7 and 12-13, while the best results are achieved during 18 and 20 days after AT. Second phase of enhanced work capacity is reported between days 36 and 48 after AT. The further development of practical knowledge in area of AT should predominantly include recommendations about application of different AT methods in training periodization in different sports. Improvement of the work capacity and duration of enhanced work capacity at the sea level after AT stimuli are the main questions opened for future scientific researches.
Entity linking in media content and user comments: Connecting data to wikipedia and other knowledge bases

This paper presents an approach to entity linking in the domain of Social TV on two different knowledge bases: Wikipedia and our own ontology of media assets. We provide insights into the main challenges posed by this task, together with a description of different tools and related projects in the field. Since the system described is part of a platform intended for commercial exploitation, licensing issues are described in order to help small and medium-sized enterprises (SME) willing to develop systems for entity linking to take decisions on the best choice. The paper also presents information about business benefits of these technologies for both end users and companies. The approach described includes an evaluation of three different disambiguation methods and two different entity candidate selection processes.
A Ground-Based Prototype of a CMOS Navigational Star Camera for Small Satellite Applications

Small satellites are now capable of performing missions that require accurate attitude determination and control. However, low size, power, and cost requirements limit the types of attitude sensors that can be used on a small craft, making attitude estimation difficult. In particular, star trackers—often the attitude sensors of choice for larger spacecraft—are not practical for small satellites. This paper describes a miniature navigational star camera based on CMOS sensor technology that is appropriate for small satellite applications. A ground-based prototype version has been built to demonstrate the technology. Hardware design and algorithms for star-pattern recognition and attitude estimation are discussed, along with simulation results and hardware test results.