Miracle-dz/UniFAR-FTUs huggingface dataset:
The implementation of a Quality-Net as a part of the European project DIABCARE Q-Net

DIABCARE Q-Net is a European project with a consortium of partners in healthcare, industry, and research, which has the overall target of improvement in diabetes care by aggregation, evaluation, and feedback of anonymized patient data with the tools of modern telematics, resulting from the initiative of the St. Vincent-Declaration, St. Vincent, Italy. Based on standardized tools for quality improvement in diabetes care, i.e., the Basic Information Sheet (BIS) and recently developed data entry and feedback software (DIABCARE Data for Windows), DIABCARE Q-Net as a part of the Telematics Applications Program of the European Commission will improve diabetes care and disease management by the implementation of a quality network. Therefore, the project implements regional, national, and central nodes for processing of diabetes quality indicators. All participating centers (GPs and clinics in Europe) get feedback by standardized benchmarking. The pilot testing and the state of implementation of our network confirm the importance of improving the quality of life of diabetic patients in all participating countries.
Reactivation of Ocular Dominance Plasticity in the Adult Visual Cortex

In young animals, monocular deprivation leads to an ocular dominance shift, whereas in adults after the critical period there is no such shift. Chondroitin sulphate proteoglycans (CSPGs) are components of the extracellular matrix (ECM) inhibitory for axonal sprouting. We tested whether the developmental maturation of the ECM is inhibitory for experience-dependent plasticity in the visual cortex. The organization of CSPGs into perineuronal nets coincided with the end of the critical period and was delayed by dark rearing. After CSPG degradation with chondroitinase-ABC in adult rats, monocular deprivation caused an ocular dominance shift toward the nondeprived eye. The mature ECM is thus inhibitory for experience-dependent plasticity, and degradation of CSPGs reactivates cortical plasticity.
Applications of X-ray synchrotron microtomography for non-destructive 3 D studies of paleontological specimens

Paleontologists are quite recent newcomers among the users of X-ray synchrotron imaging techniques at the European Synchrotron Radiation Facility (ESRF). Studies of the external morphological characteristics of a fossil organism are not sufficient to extract all the information for a paleontological study. Nowadays observations of internal structures become increasingly important, but these observations should be non-destructive in order to preserve the important specimens. Conventional microtomography allows performing part of these investigations. Nevertheless, the best microtomographic images are obtained using third-generation synchrotrons producing hard X-rays, such as the ESRF. Firstly, monochromatisation avoids beam hardening that is frequently strong for paleontological samples. Secondly, the high beam intensity available at synchrotron radiation sources allows rapid data acquisition at very high spatial resolutions, resulting in precise mapping of the internal structures of the sample. Thirdly, high coherence leads to additional imaging possibilities: phase contrast radiography, phase contrast microtomography and holotomography. These methods greatly improve the image contrast and therefore allow studying fossils that cannot be investigated by conventional microtomography due to a high degree of mineralisation or low absorption contrast. Thanks to these different properties and imaging techniques, a synchrotron radiation source and the ESRF in particular appears as an almost ideal investigation tool for paleontology. PACS 01.30. Cc; 07.05. Hd; 68.37. Yz; 29.20. Lq; 81.70. Tx
The Next 10 , 000 BGP Gadgets : Lightweight Modeling for the Stable Paths Problem

For the past ten years, the de facto interdomain routing protocol, the Border Gateway Protocol (BGP), has been been studied in the framework of the Stable Paths Problem (SPP). The SPP approach revealed several combinations of node topologies and configurations in which BGP cannot converge to a stable solution. These misbehaving “gadgets” serve as counterexamples to desirable BGP behavior, which we would like to always converge on a stable solution. For just as long, researchers have been manually generating these gadgets by hand which is a labor intensive and incomplete process. We apply two different lightweight modeling techniques in order to automatically generate these misbehaving gadgets quickly and completely. We model the static Stable Paths Problem using Alloy and also the dynamic Stable Path Vector Protocol using the Promela/Spin platform. These two approaches serve as a case study both in the application of lightweight modeling to network protocols, but also as a comparison of two approaches to lightweight modeling. Using our approach we were able to generate over 10,000 instances of misbehaving gadgets.
Multi-Processor System-Level Synthesis for Multiple Applications on Platform FPGA

Multiprocessor systems-on-chip (MPSoC) are being developed in increasing numbers to support the high number of applications running on modern embedded systems. Designing and programming such systems prove to be a major challenge. Most of the current design methodologies rely on creating the design by hand, and are therefore error-prone and time-consuming. This also limits the number of design points that can be explored. While some efforts have been made to automate the flow and raise the abstraction level, these are still limited to single-application designs. In this paper, we present a design methodology to generate and program MPSoC designs in a systematic and automated way for multiple applications. The architecture is automatically inferred from the application specifications, and customized for it. The flow is ideal for fast design space exploration (DSE) in MPSoC systems. We present results of a case study to compute the buffer-throughput trade-offs in real-life applications, H263 and JPEG decoders. The generation of the entire project takes about 100 ms, and the whole DSE was completed in 45 minutes, including the FPGA mapping and synthesis.
Nonparametric Function Estimation of the Relationship between two Repeatedly Measured Variables

We describe methods for estimating the regression function nonparametrically and for estimating the variance components in a simple variance component model which is sometimes used for repeated measures data or data with a simple clustered structure. We consider a number of different ways of estimating the regression function. The main results are that the simple pooled estimator which treats the data as independent performs very well asymptotically but that we can construct estimators which perform better asymptotically in some circumstances.
Effect of Phonon Dispersion on Thermal Conduction Across Si/Ge Interfaces

We report finite-volume simulations of the phonon Boltzmann transport equation (BTE) for heat conduction across the heterogeneous interfaces in SiGe superlattices. The diffuse mismatch model incorporating phonon dispersion and polarization is implemented over a wide range of Knudsen numbers. The results indicate that the thermal conductivity of a Si/Ge superlattice is much lower than that of the constitutive bulk materials for superlattice periods in the submicron regime. We report results for effective thermal conductivity of various material volume fractions and superlattice periods. Details of the nonequilibrium energy exchange between optical and acoustic phonons that originate from the mismatch of phonon spectra in silicon and germanium are delineated for the first time. Conditions are identified for which this effect can produce significantly more thermal resistance than that due to boundary scattering of phonons. [DOI: 10.1115/1.4004429]
Reduced Bone Mass and Muscle Strength in Male 5α-Reductase Type 1 Inactivated Mice

Androgens are important regulators of bone mass but the relative importance of testosterone (T) versus dihydrotestosterone (DHT) for the activation of the androgen receptor (AR) in bone is unknown. 5α-reductase is responsible for the irreversible conversion of T to the more potent AR activator DHT. There are two well established isoenzymes of 5α-reductase (type 1 and type 2), encoded by separate genes (Srd5a1 and Srd5a2). 5α-reductase type 2 is predominantly expressed in male reproductive tissues whereas 5α-reductase type 1 is highly expressed in liver and moderately expressed in several other tissues including bone. The aim of the present study was to investigate the role of 5α-reductase type 1 for bone mass using Srd5a1−/− mice. Four-month-old male Srd5a1 −/− mice had reduced trabecular bone mineral density (−36%, p<0.05) and cortical bone mineral content (−15%, p<0.05) but unchanged serum androgen levels compared with wild type (WT) mice. The cortical bone dimensions were reduced in the male Srd5a1 −/− mice as a result of a reduced cortical periosteal circumference compared with WT mice. T treatment increased the cortical periosteal circumference (p<0.05) in orchidectomized WT mice but not in orchidectomized Srd5a1 −/− mice. Male Srd5a1 −/− mice demonstrated a reduced forelimb muscle grip strength compared with WT mice (p<0.05). Female Srd5a1 −/− mice had slightly increased cortical bone mass associated with elevated circulating levels of androgens. In conclusion, 5α-reductase type 1 inactivated male mice have reduced bone mass and forelimb muscle grip strength and we propose that these effects are due to lack of 5α-reductase type 1 expression in bone and muscle. In contrast, the increased cortical bone mass in female Srd5a1 −/− mice, is an indirect effect mediated by elevated circulating androgen levels.
Bi-elastic Neighbourhood Models

We extend Buja’s concept of “pseudo-capacities”, which comprises the neighbourhood models for classical probabilities commonly used in robust statistics. Although systematically developing various directions for generalizing that model, we especially show that robust statistics can be freed from the severe restriction to 2-monotone capacities by employing the more natural framework of coherent or F-probabilities. Our main new tool for doing this is to use bi-elastic instead of convex functions.
Parametric Model Study of Microstructure Effects on Damage Behavior of Asphalt Samples

This paper presents a computational modeling study of the microstructural influence on damage behavior of asphalt materials. Computer generated asphalt samples were created for numerical simulation in indirect tension and compression testing geometries. Our previously developed micromechanical finite element model was used in the simulations. This model uses a special purpose finite element that incorporates the mechanical load-carrying response between neighboring aggregates. The element was developed from an approximate elasticity solution of the stress and displacement field in a cementation layer between particle pairs. The computational model establishes a network of such elements to simulate an asphalt mass. Continuum damage mechanics was then incorporated within this scheme leading to the construction of a micro-damage model capable of predicting typical global inelastic behavior found in asphalt materials. A series of model asphalt samples have been generated and simulated with controllable microstructure variation in an effort to determine the effects of particular microstructural variables on the material response. These simulations explored the relationship between microstructure parameters and damage behavior of particular asphalt samples.
Genetic analysis of low survival rate of pups in RR/Sgn inbred mice

Newborn offspring of the inbred mouse RR/Sgn strain have a low survival rate prior to weaning. We hypothesized that this is a consequence of an inferior nurturing ability of RR/Sgn mothers and that RR/Sgn mothers have a tendency to lose their pups. We performed quantitative trait locus (QTL) mapping for inferior nurturing ability and tendency to lose pups in RR/Sgn mothers. The number of pups was adjusted to 6 per dam on the day of delivery, and the number of surviving pups and their total weight (litter weight) were scored at 12 days after birth. Nurturing ability was evaluated by litter weight, and tendency to lose pups was evaluated by scoring whether or not the mothers lost their pups. For litter weight, we identified one significant QTL on chromosome 4 and three suggestive QTLs on chromosomes 7, 9 and 17. The RR/Sgn allele was associated with lower litter weight at all loci. For the tendency to lose pups, we identified three suggestive QTLs on chromosomes 4, 9 and 16. The RR/Sgn allele was associated with an increased tendency to lose pups at all loci. These results supported our hypothesis that the low survival rate phenotype was attributable, at least in part, to a phenotype whereby mothers display inferior nurturing ability and a tendency to lose pups. Thus, it suggests that these two traits share genetic basis.
Cytoplasmic Polyadenylation Element Binding Protein 1-Mediated mRNA Translation in Purkinje Neurons Is Required for Cerebellar Long-Term Depression and Motor Coordination

The ability of neurons to modify synaptic connections is critical for proper brain development and function in the adult. It is now clear that changes in synaptic strength are often accompanied by changes in synaptic morphology. This synaptic plasticity can be maintained for varying lengths of time depending on the type of neuronal activity that first induced the changes. Long-term synaptic plasticity requires the synthesis of new proteins, and one mechanism for the regulation of experience-induced protein synthesis in neurons involves cytoplasmic polyadenylation element binding protein (CPEB1). CPEB1 can bidirectionally regulate mRNA translation, first repressing translation, and then activating translation after the phosphorylation of two critical residues (T171 and S177). To determine the full extent of CPEB1-mediated protein synthesis in synaptic function, we engineered a line of mice expressing CPEB1 with these phosphorylation sites mutated to alanines (mCPEB1-AA) exclusively in cerebellar Purkinje neurons (PNs). Thus, mRNAs bound by mCPEB1-AA would be held in a translationally dormant state. We show that mCPEB1-AA localizes to synapses in cerebellum and resulted in a loss of protein synthesis-dependent phase of parallel fiber–PN long-term depression. This was accompanied by a change in spine number and spine length that are likely attributable in part to the dysregulation of IRSp53, a protein known to play a role in synaptic structure. Finally, mCPEB1-AA mice displayed a significant impairment of motor coordination and a motor learning delay.
Common cancer-associated imbalances in the DNA damage response confer sensitivity to single agent ATR inhibition

ATRis an attractive target in cancer therapy because it signals replication stress and DNA lesions for repair and to S/G2 checkpoints. Cancer-specific defects in the DNA damage response (DDR) may render cancer cells vulnerable to ATR inhibition alone. We determined the cytotoxicity of the ATR inhibitor VE-821 in isogenically matched cells with DDR imbalance. Cell cycle arrest, DNA damage accumulation and repair were determined following VE-821 exposure. Defectsin homologous recombination repair (HRR: ATM, BRCA2 and XRCC3) and baseexcision repair (BER: XRCC1) conferred sensitivity to VE-821. Surprisingly, the loss of different components of the trimeric non-homologous end-joining (NHEJ) protein DNA-PK had opposing effects. Loss of the DNA-binding component, Ku80, caused hypersensitivity to VE-821, but loss of its partner catalytic subunit, DNA-PKcs, did not. Unexpectedly, VE-821 was particularly cytotoxic to human and hamster cells expressing high levels of DNA-PKcs. High DNA-PKcs was associated with replicative stress and activation of the DDR. VE-821 suppressed HRR, determined by RAD51 focus formation, to a greater extent in cells with high DNA-PKcs. Defects in HRR and BER and high DNA-PKcs expression, that are common in cancer, confer sensitivity to ATR inhibitor monotherapy and may be developed as predictive biomarkers for personalised medicine.
Using same-language machine translation to create alternative target sequences for text-to-speech synthesis

Modern speech synthesis systems attempt to produce speech utterances from an open domain of words. In some situations, the synthesiser will not have the appropriate units to pronounce some words or phrases accurately but it still must attempt to pronounce them. This paper presents a hybrid machine translation and unit selection speech synthesis system. The machine translation system was trained with English as the source and target language. Rather than the synthesiser only saying the input text as would happen in conventional synthesis systems, the synthesiser may say an alternative utterance with the same meaning. This method allows the synthesiser to overcome the problem of insufficient units in runtime.
THE IMPACT OF F0 EXTRACTION ERRORS ON THE CLASSIFICATION OF PROMINENCE AND EMOTION

Traditionally, it has been assumed that pitch is the most important prosodic feature for the marking of prominence, and of other phenomena such as the marking of boundaries or emotions. This role has been put into question by recent studies. As nowadays larger databases are always being processed automatically, it is not clear up to what extent the possibly lower relevance of pitch can be attributed to extraction errors or to other factors. We present some ideas as for a phenomenological difference between pitch and duration, and compare the performance of automatically extracted F0 values and of manually corrected F0 values for the automatic recognition of prominence and emotion in spontaneous speech (children giving commands to a pet robot). The difference in classification performance between corrected and automatically extracted pitch features turns out to be consistent but not very pronounced.
Stereo Vision Library for Obstacle Avoidance Applications

With this report we want to propose a new stereo algorithm, which is especially conceived to be used for robot navigation applications. It is fast and very robust, and allows to suppress the need of empirically set threshold values. The stereo library is self adapting and is able to manage environment luminosity modifications. A texture quality filter is used to drop those image portions which probably yield to a mismatch. This technique increase the algorithm performance and its reliability. We also propose a new consistency check which is especially conceived to allow close objects detection. To overcome the algorithm limits a detection model based on neural networks is proposed. Neural networks are used to identify very close objects which are out of range, and no more detectable by the stereo algorithm. A floor detection filter is also introduced, its purpose is to filter out all floor depth measurement which can confuse the obstacle avoidance algorithm. In this report we also explain the problematic of doing dynamic stereo vision having a passively moved binocular vision system. How we conceived the hardware and it related drivers. We explain the need to have two perfectly synchronize frames (left and right cameras images) and how to achieve it. Finally in the report the reader can find a description of all utility tools we developed for this project.
NMR Structure of Integrin α4 Cytosolic Tail and Its Interactions with Paxillin

Background Integrins are a group of transmembrane signaling proteins that are important in biological processes such as cell adhesion, proliferation and migration. Integrins are α/β hetero-dimers and there are 24 different integrins formed by specific combinations of 18 α and 8 β subunits in humans. Generally, each of these subunits has a large extracellular domain, a single pass transmembrane segment and a cytosolic tail (CT). CTs of integrins are important in bidirectional signal transduction and they associate with a large number of intracellular proteins. Principal Findings Using NMR spectroscopy, we determined the 3-D structure of the full-length α4 CT (Lys968-Asp999) and characterize its interactions with the adaptor protein paxillin. The α4 CT assumes an overall helical structure with a kink in its membrane proximal region. Residues Gln981-Asn997 formed a continuous helical conformation that may be sustained by potential ionic and/or hydrogen bond interactions and packing of aromatic-aliphatic side-chains. 15N-1H HSQC NMR experiments reveal interactions of the α4 CT C-terminal region with a fragment of paxillin (residues G139-K277) that encompassed LD2-LD4 repeats. Residues of these LD repeats including their adjoining linkers showed α4 CT binding-induced chemical shift changes. Furthermore, NMR studies using LD-containing peptides showed predominant interactions between LD3 and LD4 of paxillin and α4 CT. Docked structures of the α4 CT with these LD repeats suggest possible polar and/or salt-bridge and non-polar packing interactions. Significance The current study provides molecular insights into the structural diversity of α CTs of integrins and interactions of integrin α4 CT with the adaptor protein paxillin.
For Personal Use. Only Reproduce with Permission from the Lancet Publishing Group. Population Stratification and Spurious Allelic Association

Prevalence of many complex human diseases such as asthma, cardiovascular disease, and diabetes has risen greatly over the past two decades in developed countries. During the same period, the genetic causes of such diseases have been increasingly emphasised as a means to better understand their pathogenesis, with the ultimate goal of improvement of preventive strategies, diagnostic tools, and treatment. 3–8 Considerable effort is being expended in attempts to detect genetic loci contributing to complex diseases. 9 Association and linkage studies comprise the two dominant strategies: association studies aim to find disease-predisposing alleles at the population level; and linkage studies focus on familial segregation. Although both strategies have compelling strengths, association analyses are more widely done and likely to spread even further in the future, especially in the pharmacogenetics domain. 5 Technical developments in molecular genetics facilitate these studies, as does use of gene-specific variants derived from the human genome sequencing project. 10 Furthermore, extensive catalogues of anonymous DNA sequence variants across the human genome are being compiled. 11,12 Some large-scale, population-based human samples have been, or are expected to be, gathered (eg, and use of DNA variants in drug development is expanding. 4 Coupling of high-throughput molecular technology, many genetic variants, and population-based samples offers unique opportunities for understanding the cause of common diseases. Genetic variants—or polymorphisms—arise from new mutations. The simplest type of polymorphism is a single base mutation, which substitutes one nucleotide for another, referred to as a single nucleotide polymorphism (SNP). SNPs do not necessarily have any relevance to disease or outcome; they can be anonymous variants within or between genes (ie, uncharacterised with respect to protein coding or gene function), or could be functional, causal mutations. More SNPs are thought to exist in the human genome than any other type of polymorphism. 20 Nearly three million variants have been reported and are catalogued in a public database In this review, we restrict our attention to SNPs, owing to their widespread presence and use, but the issues and principles described are general and apply to other DNA polymorphisms. Genetic association studies aim to correlate differences in disease frequencies between groups (or in trait levels for continuously varying characters) with differences in allele frequencies at an SNP. Thus, the frequencies of the two variant forms (alleles) of an SNP are of primary interest for identification of genes affecting disease. The simplest study design for assessment of genotype-phenotype correlation …