Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Factor H-Related Protein 5 Has Cofactor Activity, Inhibits C3 Convertase Activity, Binds Heparin and C-Reactive Protein, and Associates with Lipoprotein 1

Factor H-related protein 5 (FHR-5) is a recently discovered member of the factor H (fH)-related protein family. FHR proteins are structurally similar to the complement regulator fH, but their biological functions remain poorly defined. FHR-5 is synthesized in the liver and consists of 9 short consensus repeats (SCRs), which display various degrees of homology to those of fH and the other FHR proteins. FHR-5 colocalizes with complement deposits in vivo and binds C3b in vitro, suggesting a role in complement regulation or localization. The current study examined whether rFHR-5 exhibits properties similar to those of fH, including heparin binding, CRP binding, cofactor activity for the factor I-mediated degradation of C3b and decay acceleration of the C3 convertase. rFHR-5 bound heparin-BSA and heparin-agarose and a defined series of truncations expressed in Pichia pastoris localized the heparin-binding region to within SCRs 5–7. rFHR-5 bound CRP, and this binding was also localized to SCRs 5–7. FHR-5 inhibited alternative pathway C3 convertase activity in a fluid phase assay; however, dissociation of the convertase was not observed in a solid phase assay. rFHR-5 displayed factor I-dependent cofactor activity for C3b cleavage, although it was apparently less effective than fH. In addition, we demonstrate association of FHR-5 with high density lipid lipoprotein complexes in human plasma. These results demonstrate that FHR-5 shares properties of heparin and CRP binding and lipoprotein association with one or more of the other FHRs but is unique among this family of proteins in possessing independent complement-regulatory activity.
Future application of ontologies in e-Bioscience.

A method and apparatus for causing earthworms to come to the surface of soil in which electric pulses are applied to the soil. The pulses are characterized by high power during a brief burst followed by a relatively long rest period. The method requires a small power supply and may therefore be put into practice with portable equipment.
Structural Elements in the Transmembrane and Cytoplasmic Domains of the Metal Transporter SLC30A10 Are Required for Its Manganese Efflux Activity*

Homozygous mutations in SLC30A10 lead to the development of familial manganese-induced parkinsonism. We previously demonstrated that SLC30A10 is a cell surface-localized manganese efflux transporter, and parkinsonism-causing mutations block its trafficking and efflux activity. Interestingly, other transporters in the SLC30 family mediate zinc efflux. Determining the mechanisms that allow SLC30A10 to transport manganese, which are unclear, is essential to understand its role in parkinsonism. Here, we generated a predicted structure of SLC30A10, based on the structure of the bacterial zinc transporter YiiP, and performed functional studies. In YiiP, side chains of residues Asp-45 and Asp-49 in the second and His-153 and Asp-157 in the fifth transmembrane segments coordinate zinc and are required for transport. In SLC30A10, the corresponding residues are Asn-43 and Asp-47 in the second and His-244 and Asp-248 in the fifth transmembrane segments. Surprisingly, although alanine substitution of Asp-248 abolished manganese efflux, that of Asn-43 and Asp-47 did not. Instead, side chains of charged or polar residues adjacent to Asp-248 in the first (Glu-25) or fourth (Asn-127) transmembrane segments were required. Further analyses revealed that residues His-333 and His-350 in the cytoplasmic C-terminal domain were required for full activity. However, the C-terminal domain failed to transfer manganese transport capability to a related zinc transporter. Overall, our results indicate that residues in the transmembrane and C-terminal domains together confer optimal manganese transport capability to SLC30A10 and suggest that the mechanism of ion coordination in the transmembrane domain of SLC30A10 may be substantially different from that in YiiP/other SLC30 proteins.
An automated approach to quantify volumetric coronary plaque composition by multi-slice computed tomography: An ex-vivo feasibility study

This study explores the possibility to use the Hounsfield unit (HU) distribution of a coronary plaque to quantify its composition when imaged with multi-slice computed tomography (MSCT). Explanted left anterior descending specimens were imaged with different contrast strengths. In one specimen, 5 sections of 0.9 to 1.4 mm long were 3D-quantitatively evaluated against quantitative volumetric histopathology. There were no substantial differences found between the two quantitative methodologies. Both quantitative methodologies showed a remarkable positive correlation. This ex-vivo multi-modality imaging study shows encouraging results for quantitative MSCT-CA based plaque composition measurements compared against quantitative histopathology.
PENGARUH PENGEMBANGAN KARIR TERHADAP KINERJA PEGAWAI PADA PT. POS INDONESIA (Persero) KABUPATEN JEMBRANA TAHUN 2014

Penelitian ini bertujuan untuk mengetahui (1) pengaruh parsial antara latar belakang pendidikan, pelatihan dan pengalaman kerja terhadap kinerja pegawai pada PT. Pos Indonesia Kabupaten Jembrana, (2) pengaruh simultan seluruh dimensi pengembangan karir terhadap kinerja pegawai pada PT. Pos Indonesia Kabupaten Jembrana. Penelitian ini merupakan penelitian kausalitas dan dilaksanakan di PT. Pos Indonesia Kabupaten Jembarana dengan jumlah responden sebanyak 38 orang. Data yang dikumpulkan dengan metode kuesioner yang dianalisis menggunakan analisis regresi berganda. Hasil penelitian menunjukkan bahwa (1) latar belakang pendidikan berpengaruh terhadap kinerja pegawai PT. Pos Indonesia Kabupaten Jembrana. Hal ini ditunjukkan dengan nilai thitung = 2.522 > ttabel = 1,6909 atau p-value 0,017 ttabel = 1,6909 atau p-value 0,001 ttabel = 1,6909 atau p-value 0,000 Ftabel = 0,339 atau p-value 0,000 Kata Kunci : pengembangan karir dan kinerja pegawai This study aims to determine (1) the partial influence of education background, trainee and work experience on employee performance at PT. Pos Indonesia regency Jembrana, (2) the simultaneous influence of all dimensions of career development on employee performance PT. Pos Indonesia regency Jembrana. This is a causalitas research conducted at PT. Pos Indonesia regency Jembrana with 38 respondents. The data was colleted by questionnaire which analyzed by technique used is multiple regression analyze. The results showed that (1) education background has influence on employee performance at PT. Pos Indonesia regency Jembrana. It was showed by the value of tvalue = 2,522 > ttable = 1,6909 or p-value 0.017 ttable = 1,6909 or p-value = 0.001 ttable = 1,6909 or p-value = 0,000 Ftable = 0,339 or p-value = 0.000 keyword : career development and employee performance
Joint Secure Beamforming for Cognitive Radio Networks with Untrusted Secondary Users

In this paper, we consider a cognitive radio network (CRN) consisting of a primary transmitter-receiver pair and an untrusted secondary transmitter-receiver pair, and each pair is a multiple-input single-output (MISO) link. We consider two transmission schemes, namely underlay scheme and cooperative scheme. For the underlay scheme, the secondary user (SU) is allowed to transmit simultaneously in the presence of primary transmission. For the cooperative scheme, the secondary transmitter acts as a relay node to increase the secrecy rate of primary transmission in exchange for its own transmission. For both schemes, the SU is untrusted and considered as a potential eavesdropper. Our goal is to minimize the total power consumption while satisfying the primary user (PU)'s required secrecy rate and SU's required information rate. By suitable optimization tools, we design the joint secure beamforming for both schemes. The simulation results show that in the considered system model, the underlay scheme performs better than the cooperative scheme, especially with high rate requirements and large number of antennas at secondary transmitter.
Shapira -thank You for Fruitful Collaboration and Joyful Joint Work

To all my parents, sisters and brothers and to Anat. Acknowledgment To my advisor Muli Safra, whose prolific ideas and lucid views on math, the universe, and everything guided me through this research. His enthusiastic, optimistic, easygoing approach to settling fundamental hard problems, and his constant patience, were more than I could hope for. To my advisor Amnon Ta-Shma, whose ability to know the right thing to say and do, when tackling theoretical problems and when dealing with earthly dilemmas, have been so enlightening and valuable to me. To Noga Alon for his encouragement, support and sound advice, that made the difference. To Hanoch Levy, for putting the fun in fundamental course teaching. you for making difficult times easier and for insightful and far-reaching advice. To all my parents, sisters and brothers, thank you for everything. And to Anat, for all the love and support. Abstract Expanders are graphs that are sparse, yet highly connected. In this thesis, we consider an elementary algorithm for constructing expanders, how to use them for proving hardness of approximation , how to utilize expanders for obtaining better approximations and their relation to the parallel-repetition technique. In Chapter 2 we presents two variants of the Parallel-Repetition. One that preserves uniqueness but works only for good expanders and union of disjoint expanders, and the other that works for any instance but does not preserve uniqueness. We show that the two variants of the Parallel-Repetition technique perform " optimally " , i.e, the success probability decays exponentially fast with k, regardless of the alphabet size and with no power on ε, albeit only down to some constant error probability of the generated instance. Such analysis also has algorithmic consequences: it allows converting an approximation algorithm of expander instances for one set of parameters (error, size of alphabet and approximation ratio) into another, so that an optimal algorithm for one such set of parameters suffices to obtain optimal approximations for all the others. This chapter is based on the paper [SS07]. In Chapter 3 we describe a short and easy to analyze construction of constant-degree ex-panders. Expanders are some of the most widely used objects in theoretical computer science. Many algorithm were suggested for constructing such graphs (see Chapter 3 for further discussion). Our construction relies on the replacement product, applied by [RVW02] to give an iterative construction of bounded-degree expanders. Here we give a simpler construction, which …
Socio-Behavioral Challenges to HIV Vaccine Trials : Literature Review

Introduction: Social and behavioral factors have the potential to affect and inform both the implementation of HIV vaccine trials and the uptake of an eventual HIV vaccine. The growing number of ongoing phase I/II HIV vaccine trials underscores the need for a review of factors affecting the conduct of these trials. Methods: Major databases (PubMed, Cochrane, and Google Search Engine) were searched for relevant articles published in English in the last 10 years on social and behavioral issues affecting HIV vaccine trials. Key search terms applied included: HIV/AIDS, vaccine, microbicides, and recruitment, participation in trials, social harm, adolescent, community, ethics, consent, sexual behavior, acceptability, feasibility, motivation, key populations, vaccine-induced seropositivity, and vaccine trials. The review process was further informed by searches of the reference lists from publications
Towards autonomic computing: effective event management

Autonomic computing is emerging as a significant new approach for the design of computing systems. Its goal is the production of systems that are self-managing, self-healing, self-protecting and self-optimizing. Achieving this goal involve techniques from both software engineering and artificial intelligence. We discuss one particular aspect of autonomic computing: event management. It considers the range of event handling techniques in use, particularly in relation to distributed systems. Intelligent approaches are illustrated using the example of event handling in telecommunication systems. In particular, the telecom survivable network architecture is analyzed to identify lessons and potential pitfalls for autonomic computing.
General estimation and evaluation of compositional distributional semantic models

In recent years, there has been widespread interest in compositional distributional semantic models (cDSMs), that derive meaning representations for phrases from their parts. We present an evaluation of alternative cDSMs under truly comparable conditions. In particular, we extend the idea of Baroni and Zamparelli (2010) and Guevara (2010) to use corpus-extracted examples of the target phrases for parameter estimation to the other models proposed in the literature, so that all models can be tested under the same training conditions. The linguistically motivated functional model of Baroni and Zamparelli (2010) and Coecke et al. (2010) emerges as the winner in all our tests.
Gain limiting processes in Er-doped Si nanocrystal waveguides in SiO2

Erbium-doped Si nanocrystal based optical waveguides were formed by Er and Si ion implantation into SiO2. Optical images of the waveguide output facet show a single, well-confined optical mode. Transmission measurements reveal a clear Er related absorption of 2.7 dB/cm at 1.532 μm, corresponding to a cross section of 8×10−20 cm2. The Si nanocrystals act as sensitizers for Er but under high doping conditions (∼50 Er ions per nanocrystals) no pump-induced change in the Er related absorption is observed under optical pumping (λ=458 nm), which is ascribed to an Auger quenching effect. For very high pump powers, a broad absorption feature is observed, attributed to free carrier absorption.
Software model checking using languages of nested trees

While model checking of pushdown systems is by now an established technique in software verification, temporal logics and automata traditionally used in this area are unattractive on two counts. First, logics and automata traditionally used in model checking cannot express requirements such as pre/post-conditions that are basic to analysis of software. Second, unlike in the finite-state world, where the μ-calculus has a symbolic model-checking algorithm and serves as an “assembly language” to which temporal logics can be compiled, there is no common formalism—either fixpoint-based or automata-theoretic—to model-check requirements on pushdown models. In this article, we introduce a new theory of temporal logics and automata that addresses the above issues, and provides a unified foundation for the verification of pushdown systems. The key idea here is to view a program as a generator of structures known as nested trees as opposed to trees. A fixpoint logic (called NT-μ) and a class of automata (called nested tree automata) interpreted on languages of these structures are now defined, and branching-time model-checking is phrased as language inclusion and membership problems for these languages. We show that NT-μ and nested tree automata allow the specification of a new frontier of requirements usable in software verification. At the same time, their model checking problem has the same worst-case complexity as their traditional analogs, and can be solved symbolically using a fixpoint computation that generalizes, and includes as a special case, “summary”-based computations traditionally used in interprocedural program analysis. We also show that our logics and automata define a robust class of languages—in particular, just as the μ-calculus is equivalent to alternating parity automata on trees, NT-μ is equivalent to alternating parity automata on nested trees.
Symmetry and Approximability of Submodular Maximization Problems

A number of recent results on optimization problems involving submodular functions have made use of the "multilinear relaxation" of the problem. We present a general approach to deriving inapproximability results in the value oracle model, based on the notion of "symmetry gap". Our main result is that for any fixed instance that exhibits a certain "symmetry gap" in its multilinear relaxation, there is a naturally related class of instances for which a better approximation factor than the symmetry gap would require exponentially many oracle queries. This unifies several known hardness results for submodular maximization, e.g. the optimality of (1-1/e)-approximation for monotone submodular maximization under a cardinality constraint, and the impossibility of (1/2+epsilon)-approximation for unconstrained (non-monotone) submodular maximization. It follows from our result that (1/2+epsilon)-approximation is also impossible for non-monotone submodular maximization subject to a (non-trivial) matroid constraint. On the algorithmic side, we present a 0.309-approximation for this problem, improving the previously known factor of 1/4-o(1). As another application, we consider the problem of maximizing a non-monotone submodular function over the bases of a matroid. A (1/6-o(1))-approximation has been developed for this problem, assuming that the matroid contains two disjoint bases. We show that the best approximation one can achieve is indeed related to packings of bases in the matroid. Specifically, for any k≫=2, there is a class of matroids of fractional base packing number nu = k/(k-1), such that any algorithm achieving a better than (1-1/nu)-approximation for this class would require exponentially many value queries. On the positive side, we present a 1/2 (1-1/nu-o(1))-approximation algorithm for the same problem. Our hardness results hold in fact for very special symmetric instances. For such symmetric instances, we show that the approximation factors of 1/2 (for submodular maximization subject to a matroid constraint) and 1-1/nu (for a matroid base constraint) can be achieved algorithmically and hence are optimal.
Evaluating the performance of legacy applications on emerging parallel architectures

The gap between a supercomputer's theoretical maximum (\peak") oatingpoint performance and that actually achieved by applications has grown wider over time. Today, a typical scientific application achieves only 5{20% of any given machine's peak processing capability, and this gap leaves room for significant improvements in execution times. This problem is most pronounced for modern \accelerator" architectures { collections of hundreds of simple, low-clocked cores capable of executing the same instruction on dozens of pieces of data simultaneously. This is a significant change from the low number of high-clocked cores found in traditional CPUs, and effective utilisation of accelerators typically requires extensive code and algorithmic changes. In many cases, the best way in which to map a parallel workload to these new architectures is unclear. The principle focus of the work presented in this thesis is the evaluation of emerging parallel architectures (specifically, modern CPUs, GPUs and Intel MIC) for two benchmark codes { the LU benchmark from the NAS Parallel Benchmark Suite and Sandia's miniMD benchmark { which exhibit complex parallel behaviours that are representative of many scientific applications. Using combinations of low-level intrinsic functions, OpenMP, CUDA and MPI, we demonstrate performance improvements of up to 7x for these workloads. We also detail a code development methodology that permits application developers to target multiple architecture types without maintaining completely separate implementations for each platform. Using OpenCL, we develop performance portable implementations of the LU and miniMD benchmarks that are faster than the original codes, and at most 2x slower than versions highly-tuned for particular hardware. Finally, we demonstrate the importance of evaluating architectures at scale (as opposed to on single nodes) through performance modelling techniques, highlighting the problems associated with strong-scaling on emerging accelerator architectures.
Annotating Corpora from Various Sources in the Humanities Domain

  Voula Giouli  Annotating corpora from various sources in the humanities domain: shortcomings and issues  In this paper, we present work aimed at the linguistic annotation of Greek corpora that belong to the humanities domain, the focus being on the methodological principles as well as the implementation framework adopted. This framework builds on an existing XML annotation platform that was initially developed in an Information Extraction setting and in order to cope with texts that pertain to domains such as news, administrative, economics, etc.; we elaborate on the initial steps taken towards customization of the tools.
A Fast Active Set Block Coordinate Descent Algorithm for ℓ1-Regularized Least Squares

The problem of finding sparse solutions to underdetermined systems of linear equations arises in several applications (e.g., signal and image processing, compressive sensing, statistical inference). A standard tool for dealing with sparse recovery is the $\ell_1$-regularized least squares approach that has been recently attracting the attention of many researchers. In this paper, we describe an active set estimate (i.e., an estimate of the indices of the zero variables in the optimal solution) for the considered problem that tries to quickly identify as many active variables as possible at a given point, while guaranteeing that some approximate optimality conditions are satisfied. A relevant feature of the estimate is that it gives a significant reduction of the objective function when setting to zero all those variables estimated to be active. This enables us to easily embed it into a given globally converging algorithmic framework. In particular, we include our estimate into a block coordinate descent a.
Altered Brain Functional Connectivity in Small-Cell Lung Cancer Patients after Chemotherapy Treatment: A Resting-State fMRI Study

Previous studies in small-cell lung cancer (SCLC) patients have mainly focused on exploring neurocognitive deficits associated with prophylactic cranial irradiation (PCI). Little is known about functional brain alterations that might occur due to chemotherapy treatment in this population before PCI is administered. For this reason, we used resting-state functional Magnetic Resonance Imaging (fMRI) to examine potential functional connectivity disruptions in brain networks, including the Default Mode Network (DMN), the Sensorimotor Network, and the Task-Positive Network (TPN). Nineteen SCLC patients after platinum-based chemotherapy treatment and thirteen controls were recruited in the current study. ROI-to-ROI and Seed-to-Voxel analyses were carried out and revealed functional connectivity deficits in patients within all the networks investigated demonstrating the possible negative effect of chemotherapy in cognitive functions in SCLC populations.
Gravitational wave bursts from cosmic superstrings with Y-junctions

Cosmic superstring loops generically contain strings of different tensions that meet at Y-junctions. These loops evolve nonperiodically in time, and have cusps and kinks that interact with the junctions. We study the effect of junctions on the gravitational wave signal emanating from cosmic string cusps and kinks. We find that earlier results on the strength of individual bursts from cusps and kinks on strings without junctions remain largely unchanged, but junctions give rise to additional contributions to the gravitational wave signal coming from strings expanding at the speed of light at a junction and kinks passing through a junction.