Miracle-dz/UniFAR-FTUs huggingface dataset:
A dynamic and component-based process scheduler framework for heterogeneous many-core systems

Since the first decade of the 21st century, improvements in computer performance are no longer achieved through increasing clock rates but parallelization and specialization. As a result, heterogeneous many-core systems are becoming more and more common. Leaving their niche in highly specialized computing, they have to be supported by a general purpose operating system. A major part of the support that has to be delivered will be done by the process scheduler as it has to tailor the task order and placement to those systems. Current approaches to scheduler architecture are not capable of coping with the resulting challenges. In particular, the state of the art falls short to provide ways and means to react to new developments in hardware technology quickly and lacks the capability to enable the adaptation of the scheduler to the changed environment. Therefore, the original contribution to the knowledge of this dissertation is a new approach to the architecture of the operating system’s process scheduler. This dissertation introduces a component-based approach to the process scheduler architecture that allows the decomposition of the scheduling problem into distinct parts rather than the monolithic approach as it is state of the art. Components are connected through Pipes that are an advanced form of runqueues suitable for the component-based approach. Besides Pipes, information is distributed among the components through a publish–subscribe-based message system. Components can change the order of tasks and distribute or merge tasks from or to several pipes. This allows a flexible scheduler design both during development and runtime: The developer can reuse existing components and build new schedulers from existing implementations. Through the explicit layout of the components code-paths, possible bottlenecks become easier to identify compared to a monolithic approach. Through the separation, it is also feasible to change the entire scheduling policy during runtime. This enables an optimal shaping of the scheduler to the needs of the current working set and the properties of the underlying hardware architecture. The components are embedded into a framework that allows a comprehensible development of schedulers that scale even in many-core systems. The framework approach permits the integration into several runtime systems without changing the actual scheduler implementation. This dissertation proves the feasibility through integrating the framework into major open source kernels: Linux and FreeBSD. Based on this exemplary implementation, the properties of the approach are evaluated. The studies show that the component-based scheduler framework is scalable for hundreds of cores, the overhead is quantified and the benefits of having well-defined interfaces are demonstrated. Finally, the advantages of a dynamic adaptation of scheduling strategies at runtime are shown.
Clinical measurement of corneal biomechanical properties : tangent elastic modulus

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Traceable Ring Signature

The ring signature allows a signer to leak secrets anonymously, without the risk of identity escrow. At the same time, the ring signature provides great flexibility: No group manager, no special setup, and the dynamics of group choice. The ring signature is, however, vulnerable to malicious or irresponsible signers in some applications, because of its anonymity. In this paper, we propose a traceable ring signature scheme. A traceable ring scheme is a ring signature except that it can restrict "excessive" anonymity. The traceable ring signature has a tag that consists of a list of ring members and an issue that refers to, for instance, a social affair or an election. A ring member can make any signed but anonymous opinion regarding the issue, but only once (per tag). If the member submits another signed opinion, possibly pretending to be another person who supports the first opinion, the identity of the member is immediately revealed. If the member submits the same opinion, for instance, voting "yes" regarding the same issue twice, everyone can see that these two are linked. The traceable ring signature can suit to many applications, such as an anonymous voting on a BBS. We formalize the security definitions for this primitive and show an efficient and simple construction in the random oracle model.
High Speed Imaging of Cavitation around Dental Ultrasonic Scaler Tips

Cavitation occurs around dental ultrasonic scalers, which are used clinically for removing dental biofilm and calculus. However it is not known if this contributes to the cleaning process. Characterisation of the cavitation around ultrasonic scalers will assist in assessing its contribution and in developing new clinical devices for removing biofilm with cavitation. The aim is to use high speed camera imaging to quantify cavitation patterns around an ultrasonic scaler. A Satelec ultrasonic scaler operating at 29 kHz with three different shaped tips has been studied at medium and high operating power using high speed imaging at 15,000, 90,000 and 250,000 frames per second. The tip displacement has been recorded using scanning laser vibrometry. Cavitation occurs at the free end of the tip and increases with power while the area and width of the cavitation cloud varies for different shaped tips. The cavitation starts at the antinodes, with little or no cavitation at the node. High speed image sequences combined with scanning laser vibrometry show individual microbubbles imploding and bubble clouds lifting and moving away from the ultrasonic scaler tip, with larger tip displacement causing more cavitation.
Arabidopsis Methionine γ-Lyase Is Regulated According to Isoleucine Biosynthesis Needs But Plays a Subordinate Role to Threonine Deaminase1[W][OA]

The canonical pathway for isoleucine biosynthesis in plants begins with the conversion of threonine to 2-ketobutyrate by threonine deaminase (OMR1). However, demonstration of methionine γ-lyase (MGL) activity in Arabidopsis (Arabidopsis thaliana) suggested that production of 2-ketobutyrate from methionine can also lead to isoleucine biosynthesis. Rescue of the isoleucine deficit in a threonine deaminase mutant by MGL overexpression, as well as decreased transcription of endogenous Arabidopsis MGL in a feedback-insensitive threonine deaminase mutant background, shows that these two enzymes have overlapping functions in amino acid biosynthesis. In mgl mutant flowers and seeds, methionine levels are significantly increased and incorporation of [13C]Met into isoleucine is decreased, but isoleucine levels are unaffected. Accumulation of free isoleucine and other branched-chain amino acids is greatly elevated in response to drought stress in Arabidopsis. Gene expression analyses, amino acid phenotypes, and labeled precursor feeding experiments demonstrate that MGL activity is up-regulated by osmotic stress but likely plays a less prominent role in isoleucine biosynthesis than threonine deaminase. The observation that MGL makes a significant contribution to methionine degradation, particularly in reproductive tissue, suggests practical applications for silencing the expression of MGL in crop plants and thereby increasing the abundance of methionine, a limiting essential amino acid.
Sequence-Based Prediction of Type III Secreted Proteins

The type III secretion system (TTSS) is a key mechanism for host cell interaction used by a variety of bacterial pathogens and symbionts of plants and animals including humans. The TTSS represents a molecular syringe with which the bacteria deliver effector proteins directly into the host cell cytosol. Despite the importance of the TTSS for bacterial pathogenesis, recognition and targeting of type III secreted proteins has up until now been poorly understood. Several hypotheses are discussed, including an mRNA-based signal, a chaperon-mediated process, or an N-terminal signal peptide. In this study, we systematically analyzed the amino acid composition and secondary structure of N-termini of 100 experimentally verified effector proteins. Based on this, we developed a machine-learning approach for the prediction of TTSS effector proteins, taking into account N-terminal sequence features such as frequencies of amino acids, short peptides, or residues with certain physico-chemical properties. The resulting computational model revealed a strong type III secretion signal in the N-terminus that can be used to detect effectors with sensitivity of ∼71% and selectivity of ∼85%. This signal seems to be taxonomically universal and conserved among animal pathogens and plant symbionts, since we could successfully detect effector proteins if the respective group was excluded from training. The application of our prediction approach to 739 complete bacterial and archaeal genome sequences resulted in the identification of between 0% and 12% putative TTSS effector proteins. Comparison of effector proteins with orthologs that are not secreted by the TTSS showed no clear pattern of signal acquisition by fusion, suggesting convergent evolutionary processes shaping the type III secretion signal. The newly developed program EffectiveT3 (http://www.chlamydiaedb.org) is the first universal in silico prediction program for the identification of novel TTSS effectors. Our findings will facilitate further studies on and improve our understanding of type III secretion and its role in pathogen–host interactions.
ADAPT: Automated De-coupled Adaptive Program Transformation

Dynamic program optimization offers performance improvements far beyond those possible with traditional compile-time optimization. These gains are due to the ability to exploit both architectural and input data set characteristics that are unknown prior to execution time. In this paper, we propose a novel framework for dynamic program optimization, ADAPT (Automated De-coupled Adaptive Program Transformation), that builds on the strengths of existing approaches. The key to our framework is the de-coupling of the dynamic compilation of new code variants from the dynamic selection of these variants at their points of use. This allows code generation to occur concurrently with program execution, removing dynamic compilation overheads from the critical path. We present a compilation system, based on the Polaris optimizing compiler, that automatically applies this framework to general "plugged-in" optimization techniques. We evaluate our system on three programs from the SPEC floating point benchmark suite by dynamically applying loop distribution, loop unrolling, loop tiling and automatic parallelization. We show that our techniques can improve performance by as much as 70% over statically optimized code.
In Vivo Significance of ITK-SLP-76 Interaction in Cytokine Production

ABSTRACT In vitro data have suggested that activation of the inducible T-cell kinase (ITK) requires an interaction with the adaptor protein SLP-76. One means for this interaction involves binding of the ITK SH3 domain to the polyproline-rich (PR) region of SLP-76. However, the biological significance of this association in live cells and the consequences of its disruption have not been demonstrated. Here, we utilized a polyarginine-rich, cell-permeable peptide that represents the portion of the SLP-76 PR region that interacts with the ITK SH3 domain as a competitive inhibitor to disrupt the association between ITK and SLP-76 in live cells. We demonstrate that treatment of cells with this peptide, by either in vitro incubation or intraperitoneal injection of the peptide in mice, inhibits the T-cell receptor (TCR)-induced association between ITK and SLP-76, recruitment and transphosphorylation of ITK, actin polarization at the T-cell contact site, and expression of Th2 cytokines. The inhibition is specific, as indicated by lack of effects by the polyarginine vehicle alone or a scrambled sequence of the cargo peptide. In view of the role of ITK as a regulator of Th2 cytokine expression, the data underscore the significance of ITK as a target for pharmacological intervention.
The geometry of graphs and some of its algorithmic applications

AbstractIn this paper we explore some implications of viewing graphs asgeometric objects. This approach offers a new perspective on a number of graph-theoretic and algorithmic problems. There are several ways to model graphs geometrically and our main concern here is with geometric representations that respect themetric of the (possibly weighted) graph. Given a graphG we map its vertices to a normed space in an attempt to (i) keep down the dimension of the host space, and (ii) guarantee a smalldistortion, i.e., make sure that distances between vertices inG closely match the distances between their geometric images.In this paper we develop efficient algorithms for embedding graphs low-dimensionally with a small distortion. Further algorithmic applications include:•A simple, unified approach to a number of problems on multicommodity flows, including the Leighton-Rao Theorem [37] and some of its extensions. We solve an open question in this area, showing that the max-flow vs. min-cut gap in thek-commodities problem isO(logk). Our new deterministic polynomial-time algorithm finds a (nearly tight) cut meeting this bound. •For graphs embeddable in low-dimensional spaces with a small distortion, we can find low-diameter decompositions (in the sense of [7] and [43]). The parameters of the decomposition depend only on the dimension and the distortion and not on the size of the graph. •In graphs embedded this way, small balancedseparators can be found efficiently. Given faithful low-dimensional representations of statistical data, it is possible to obtain meaningful and efficientclustering. This is one of the most basic tasks in pattern-recognition. For the (mostly heuristic) methods used in the practice of pattern-recognition, see [20], especially chapter 6.Our studies of multicommodity flows also imply that every embedding of (the metric of) ann-vertex, constant-degree expander into a Euclidean space (of any dimension) has distortion Ω(logn). This result is tight, and closes a gap left open by Bourgain [12].
Thermographic visualization of cell death in tobacco and Arabidopsis

Pending cell death was visualized by thermographic imaging in bacterio-opsin transgenic tobacco plants. Cell death in these plants was characterized by a complex lesion phenotype. Isolated cell death lesions were preceded by a colocalized thermal effect, as previously observed at sites infected by tobacco mosaic virus (TMV) (Chaerle et al. 1999 Nature Biotechnology 17, 813‐816). However, in most cases, a coherent front of higher temperature, trailed by cell death, initiated at the leaf base and expanded over the leaf lamina. In contrast to the homogenous thermal front, cell death was first visible close to the veins, and subsequently appeared as discrete spots on the interveinal tissue, as cell death spread along the veins. Regions with visible cell death had a lower temperature because of water evaporation from damaged cells. In analogy with previous observations on the localized tobacco‐TMV interaction (Chaerle et al. 1999), the kinetics of thermographic and continuous gas exchange measurements indicated that stomatal closure preceded tissue collapse. Localized spontaneous cell death could also be presymptomatically visualized in the Arabidopsis lsd2 mutant.
Quantum-aided solutions in wireless systems

The past, the current state-of-the-art and the future of wireless communications was briefly summarized in [1], [2]. Against this background, this presentation briefly reports on some of the recent quantum-aided design examples in the field of wireless communications. The high complexity of numerous optimal classic communication schemes, such as that of the Maximum Likelihood (ML) Multi-User Detector (MUD) often prevents their practical implementation [3], [4]. Fortunately the parallel-processing capability of quantum-domain algorithms is capable of potentially circumventing this limitation. In our first design example [5] we follow a quantum-aided approach to achieve the same performance as the optimal soft-input soft-output classic detectors by replacing them with a quantum algorithm which estimates the weighted sum of a function's evaluations. We propose a soft-input soft-output Quantum-assisted MUD (QMUD) scheme, which is the quantum-domain equivalent of the Maximum Likelihood (ML) MUD. We then demonstrate its application using the design example of a Direct-Sequence Code Division Multiple Access (DS-CDMA) system employing Bit-Interleaved Coded Modulation (BICM) relying on Iterative Decoding (ID), and compare it to the optimal ML MUD in terms of its performance and complexity. Both our EXtrinsic Information Transfer (EXIT) charts and Bit Error Ratio (BER) curves show that the performance of the proposed QMUD and that of the optimal classic MUD are equivalent, but the QMUD’s computational complexity is significantly lower. In our second design example [6] we have conceived a near-capacity code design for entanglement-assisted classical communication over the quantum depolarizing channel. The proposed system relies on efficient near-capacity classical code designs [7] for approaching the entanglement-assisted classical capacity of a quantum depolarizing channel. It incorporates an Irregular Convolutional Code (IRCC), a Unity Rate Code (URC) and a soft-decision aided Superdense Code (SD), which is hence referred to as an IRCC-URC-SD arrangement. Furthermore, the entanglement-assisted classical capacity of an N-qubit superdense code transmitted over a depolarizing channel is invoked for benchmarking. It is demonstrated that the proposed system operates within 0.4 dB of the achievable noise limit for both 2-qubit as well as 3-qubit SD schemes. More specifically, our design exhibits a deviation of only 0.062 and 0.031 classical bits per channel use from the corresponding 2-qubit and 3-qubit capacity limits, respectively. The proposed system is also benchmarked against the classical convolutional and turbo codes.
A Semantics for Abstraction

The goal of this paper is to propose a model-theoretic formalization of abstraction, where abstraction is modeled as two representations, the ground and the abstract representation, modeling the same phenomenon at different levels of detail. Using the framework of Local Models Semantics, the ground and abstract representations are modeled as two sets of (local) first order models, while the relations holding between them are captured by an appropriate "compatibility relation". The tuning of the compatibility relation allows for the definition of the many different kinds of abstraction.
Clinical practice. Initial management of epilepsy.

(62%), the cause is unknown. Stroke (9.0%), head trauma (9.0%), alcohol (6.0%), neurodegenerative disease (4.0%), static encephalopathy (3.5%), brain tumors (3.0%), and infection (2.0%) account for most remaining cases. 4 Although cerebrovascular causes are more common in the elderly, the cause is still unknown in 25 to 40% of patients who are 65 years of age or older. 5
Hidden information recognition based on multitask convolution neural network

With the continuous application of big data technology, machine learning is playing an increasingly important role in enterprise applications. User information, such as gender, age and educational level are the core factors for the research and application in the field of computer psychology, personalized search and social business promotion. This paper proposes a method for automatically inferring user information based on the search terms of users. We establish a multi task convolution neural network model based on word vectors. After the process of data cleaning, user search word segmentation, we use the word2vec to transform words into vector representation, and then build a multi task convolutional neural network model. This model is compared with other models based on word frequency, LDA methods. Experimental results show that our proposed multitasking based convolutional neural network approach works better than other methods.
Predictive Factors of Secondary Normocalcemic Hyperparathyroidism after Roux-en-Y Gastric Bypass

Objective Aim of this study is to evaluate determinants of secondary normocalcemic hyperparathyroidism (SNHPT) persistence in patients who have undergone Roux-en-Y gastric bypass on vertical-banded gastroplasty. Methods 226 consecutive patients submitted to bariatric surgery were prospectively enrolled and divided in two groups on the basis of preoperative presence of SNHPT. For each patient, we evaluated anthropometric and laboratory parameters. Calcium metabolism (calcemia, PTH, and 25-hydroxy vitamin D serum levels) was studied before surgery and at 6-month intervals (6, 12, and 18 months) as surgical follow-up. Results Based on presurgical SNHPT presence or absence, we defined group 1—201 patients and group 2—25 patients, respectively. Among the group 1, 153 (76%) recovered from this endocrinopathy within 6 months after surgery (group 3), while the remaining 48 patients (24%) had persistent SNHPT (group 4). Comparing the anthropometric and laboratory data of group 3 with group 2, the only statistically significant factor was the elapsed time since a prior effective medically controlled diet that led to a steady and substantial weight loss. We found also a statistically significant difference (p < 0.05) between group 3 and group 4 in term of % of weight loss and PTH levels. Conclusions Patients suitable for bariatric surgery must have history of at least one efficient medically controlled diet, not dating back more than 5 years before surgery. This elapsed time represent the cut-off time within which it is possible to recover from SNHPT in the first semester after Roux-en-Y gastric bypass on vertical-banded gastroplasty. The treatment of vitamin D insufficiency and the evaluation of SNHPT before bariatric surgery should be recommended. The clinical significance of preoperative SNHPT and in particular SNHPT after bariatric surgery remains undefined and further studies are required.
An Evaluation of the Crystal Structure of C-terminal Truncated Apolipoprotein A-I in Solution Reveals Structural Dynamics Related to Lipid Binding*

Apolipoprotein (apo) A-I mediates many of the anti-atherogenic functions attributed to high density lipoprotein. Unfortunately, efforts toward a high resolution structure of full-length apoA-I have not been fruitful, although there have been successes with deletion mutants. Recently, a C-terminal truncation (apoA-IΔ185–243) was crystallized as a dimer. The structure showed two helical bundles connected by a long, curved pair of swapped helical domains. To compare this structure to that existing under solution conditions, we applied small angle x-ray scattering and isotope-assisted chemical cross-linking to apoA-IΔ185–243 in its dimeric and monomeric forms. For the dimer, we found evidence for the shared domains and aspects of the N-terminal bundles, but not the molecular curvature seen in the crystal. We also found that the N-terminal bundles equilibrate between open and closed states. Interestingly, this movement is one of the transitions proposed during lipid binding. The monomer was consistent with a model in which the long shared helix doubles back onto the helical bundle. Combined with the crystal structure, these data offer an important starting point to understand the molecular details of high density lipoprotein biogenesis.