Miracle-dz/UniFAR-FTUs huggingface dataset:
The anatomy of a search and mining system for digital humanities

Samtla (Search And Mining Tools with Linguistic Analysis) is an online integrated research environment designed in collaboration with historians and linguists to facilitate the study of digitised texts written in any language. It currently supports the research of two corpora: the Genizah collection held by the Taylor-Schechter Genizah Research Unit in Cambridge University, and a collection of Aramaic incantation texts from late antiquity. In contrast to standard search engines and text mining systems that rely on the bag-of-words representation of text, Samtla provides the retrieval and discovery of fuzzy text patterns/motifs (aka “formulae” to historians), which is achieved through applying a character-based n-gram statistical language model built on top of a powerful generalised suffix tree data structure. This paper brie y describes the major components of Samtla and their underlying techniques.
Sublocales in formal topology

Abstract The paper studies how the localic notion of sublocale transfers to formal topology. For any formal topology (not necessarily with positivity predicate) we define a sublocale to be a cover relation that includes that of the formal topology. The family of sublocales has set-indexed joins. For each set of base elements there are corresponding open and closed sublocales, boolean complements of each other. They generate a boolean algebra amongst the sublocales. In the case of an inductively generated formal topology, the collection of inductively generated sublocales has coframe structure. Overt sublocales and weakly closed sublocales are described, and related via a new notion of “rest closed” sublocale to the binary positivity predicate. Overt, weakly closed sublocales of an inductively generated formal topology are in bijection with “lower powerpoints”, arising from the impredicative theory of the lower powerlocale. Compact sublocales and fitted sublocales are described. Compact fitted sublocales of an inductively generated formal topology are in bijection with “upper powerpoints”, arising from the impredicative theory of the upper powerlocale.
Parallel evolution and ecological selection: replicated character displacement in spadefoot toads

Ecological character displacement—trait evolution stemming from selection to lessen resource competition between species—is most often inferred from a pattern in which species differ in resource-use traits in sympatry but not in allopatry, and in which sympatric populations within each species differ from conspecific allopatric populations. Yet, without information on population history, the presence of a divergent phenotype in multiple sympatric populations does not necessarily imply that there has been repeated evolution of character displacement. Instead, such a pattern may arise if there has been character displacement in a single ancestral population, followed by gene flow carrying the divergent phenotype into multiple, derived, sympatric populations. Here, we evaluate the likelihood of such historical events versus ongoing ecological selection in generating divergence in trophic morphology between multiple populations of spadefoot toad (Spea multiplicata) tadpoles that are in sympatry with a heterospecific and those that are in allopatry. We present both phylogenetic and population genetic evidence indicating that the same divergent trait, which minimizes resource competition with the heterospecific, has arisen independently in multiple sympatric populations. These data, therefore, provide strong indirect support for competition's role in divergent trait evolution.
Numerical simulation of microring resonator biosensor with FDTD algorithm based on GPU and CPU architectures

In this paper we present numerical simulations of microring resonator biosensor with FDTD algorithm based on GPU and CPU architectures. High quality factor and high sensitivity microring resonator with implemented hallow core defects is analysed. Since defects are small compared to overall microring dimensions, small grid size is required to describe them accurately using FDTD scheme. This in turn greatly increases simulation time. One way to reduce computational time is to perform calculations on GPU. Here we compare two freely available FDTD implementations: one based on CPU (MEEP) and one - on GPU (B-CALM). Comparisons between these two implementations in computational time and accuracy are made.
Protected interactive 3D graphics via remote rendering

Valuable 3D graphical models, such as high-resolution digital scans of cultural heritage objects, may require protection to prevent piracy or misuse, while still allowing for interactive display and manipulation by a widespread audience. We have investigated techniques for protecting 3D graphics content, and we have developed a remote rendering system suitable for sharing archives of 3D models while protecting the 3D geometry from unauthorized extraction. The system consists of a 3D viewer client that includes low-resolution versions of the 3D models, and a rendering server that renders and returns images of high-resolution models according to client requests. The server implements a number of defenses to guard against 3D reconstruction attacks, such as monitoring and limiting request streams, and slightly perturbing and distorting the rendered images. We consider several possible types of reconstruction attacks on such a rendering server, and we examine how these attacks can be defended against without excessively compromising the interactive experience for non-malicious users.
MALTectomy (appendectomy/tonsillectomy) does not influence the occurrence or mode of presentation of adult celiac disease.

OBJECTIVE Recent reports suggest that appendectomy may protect against the development of ulcerative colitis. Depletion of mucosal helper T-cells is the suggested mechanism. Because mucosal T-cell activity has an even more critical role in the pathogenesis of celiac disease, our objective was to determine whether the development or mode of presentation of this disorder is influenced by appendectomy and/or tonsillectomy. METHODS One hundred fifty consecutive adult celiac patients were compared with 138 consecutive patients examined at orthopedic clinics. One hundred twenty consecutive patients with ulcerative colitis from the same ethnogeographic population were included as positive disease control. RESULTS Contrary to the previous findings in ulcerative colitis, which were again confirmed in this study, appendectomy and/or tonsillectomy did not influence the occurrence of celiac disease. In addition, presenting features, predefined in the study protocol, did not differ significantly in the appendectomy and nonappendectomy celiac patients. CONCLUSION Resection of mucosa-associated lymphoid tissue (MALT) does not influence the occurrence or the mode of presentation of adult celiac disease. Therefore, in this classical example of a T-cell-mediated disorder, the hypothesis that surgical depletion of mucosal T-cells has a protective effect or influences the clinical manifestations cannot be supported.
Combined Spatial Multiplexing and STBC to Provide Throughput Enhancements to Next Generation WLANs

— Recently, there has been an explosion of growth in research on MIMO (Multiple Input Multiple Output) systems. Current WLAN systems such as IEEE 802.11a and 802.11g Wireless Local Area Networks (WLANs) employ Coded Orthogonal Frequency Division Multiplexing (COFDM) and provide data rates of up to 54 Mbps in a 20MHz bandwidth. In this paper, space-time block coding (STBC) and spatial multiplexing MIMO techniques are considered as a means of enhancing the performance of COFDM WLANs. A hybrid 4x4 scheme is presented that combines spatial multiplexing and STBC to provide both increased throughput and diversity. Results showed that the proposed scheme can provide good performance even under correlated channels.
A Robust Class of Context-Sensitive Languages

We define a new class of languages defined by multi-stack automata that forms a robust subclass of context-sensitive languages, with decidable emptiness and closure under boolean operations. This class, called multi-stack visibly pushdown languages (MVPLs), is defined using multi-stack pushdown automata with two restrictions: (a) the pushdown automaton is visible, i.e. the input letter determines the operation on the stacks, and (b) any computation of the machine can be split into k stages, where in each stage, there is at most one stack that is popped. MVPLs are an extension of visibly pushdown languages that captures noncontext free behaviors, and has applications in analyzing abstractions of multithreaded recursive programs, signifi- cantly enlarging the search space that can be explored for them. We show that MVPLs are closed under boolean operations, and problems such as emptiness and inclusion are decidable. We characterize MVPLs using monadic second-order logic over appropriate structures, and exhibit a Parikh theorem for them.
Differential Phosphorylation of RNA Polymerase III and the Initiation Factor TFIIIB in Saccharomyces cerevisiae

The production of ribosomes and tRNAs for protein synthesis has a high energetic cost and is under tight transcriptional control to ensure that the level of RNA synthesis is balanced with nutrient availability and the prevailing environmental conditions. In the RNA polymerase (pol) III system in yeast, nutrients and stress affect transcription through a bifurcated signaling pathway in which protein kinase A (PKA) and TORC1 activity directly or indirectly, through downstream kinases, alter the phosphorylation state and function of the Maf1 repressor and Rpc53, a TFIIF-like subunit of the polymerase. However, numerous lines of evidence suggest greater complexity in the regulatory network including the phosphoregulation of other pol III components. To address this issue, we systematically examined all 17 subunits of pol III along with the three subunits of the initiation factor TFIIIB for evidence of differential phosphorylation in response to inhibition of TORC1. A relatively high stoichiometry of phosphorylation was observed for several of these proteins and the Rpc82 subunit of the polymerase and the Bdp1 subunit of TFIIIB were found to be differentially phosphorylated. Bdp1 is phosphorylated on four major sites during exponential growth and the protein is variably dephosphorylated under conditions that inhibit tRNA gene transcription. PKA, the TORC1-regulated kinase Sch9 and protein kinase CK2 are all implicated in the phosphorylation of Bdp1. Alanine substitutions at the four phosphosites cause hyper-repression of transcription indicating that phosphorylation of Bdp1 opposes Maf1-mediated repression. The new findings suggest an integrated regulatory model for signaling events controlling pol III transcription.
Validation of a Virtual Sound Environment System for Hearing Aid Testing

Hearing aid (HA) users typically benefit a lot from their HAs in simple acoustic situations like a one-toone conversation in a quiet room, but they have difficulties following a conversation in challenging listening situations involving multiple talkers, background noise and reverberation [1]. The processing power of HAs has increased dramatically over the last 10 years and advanced signal processing strategies have been applied to help the users, particularly in more complex listening situations. To assess and evaluate the performance of such modern HAs, the test scenarios should be as realistic as possible. Until recently, however, most testing was done either in very basic conditions with simple loudspeaker setups in acoustically dampened rooms or in field studies, where end users wear certain types of HAs for a while and report back via questionnaires after the testing period. The first approach offers much control over the test conditions, but only very limited flexibility regarding the acoustic conditions. In field tests, the participants experience the HAs in their everyday life, but the experimental conditions are difficult to control.
The Effect of Soil Moisture Level on Growing of Two Common Bean (Phaseolus Vulgaris L) Cultivars

The amounts of water use efficiency vary with climatic, soils and crop ability to extract water in the soil. It has been frequently reported, lack of water availability reduce the amount and yield of common bean. The aim of study was to determine the effect of soil moisture level on growth of two common bean cultivars. The study was conducted in greenhouse. The design was factorial arrangement in randomized complete block design. Forty eight treatment pots were used for two common bean cultivars.
Orientation determination in the 3D reconstruction of icosahedral viruses using a parallel computer

Three dimensional image reconstruction from cryoelectron micrographs allows the capsid structures of icosahedral viruses to be studied. The most computationally demanding stages of the reconstruction process are those that find and refine the orientations of the virus particles. We have devised and implemented parallel solutions to the problem of determining these orientations. By enabling determination of the orientations of far more particles than previously had been possible, parallel processing methods have contributed to improvements in the quality of recent reconstructions. <<ETX>>
Preparation and in vitro and in vivo characterization of cyclosporin A-loaded, PEGylated chitosan-modified, lipid-based nanoparticles

Background and methods: A new cyclosporin A-loaded, PEGylated chitosan-modified lipid-based nanoparticle was developed to improve upon the formulation of cyclosporin A. PEGylated chitosan, synthesized in three steps using mild reaction conditions, was used to modify the nanoparticles. Cyclosporin A-loaded, PEGylated chitosan-modified nanoparticles were prepared using an emulsification/solvent evaporation method. The drug content and encapsulation efficiency of the cyclosporin A-loaded, PEGylated chitosan-modified nanoparticles were measured by high-performance liquid chromatography. The average size of the nanoparticles was determined by transmission electron microscopy and dynamic light scattering. The pharmacokinetic behavior of the nanoparticles was investigated in rabbits after intravenous injection. Cyclosporin A concentrations in a whole blood sample were analyzed by high-performance liquid chromatography using tamoxifen as the internal standard. The pharmacokinetic parameters were calculated using the 3p87 software program. Results: Fourier transform infrared spectroscopy and nuclear magnetic resonance confirmed the structure of PEGylated chitosan. The drug content and encapsulation efficiency of the cyclosporin A-loaded, PEGylated chitosan-modified nanoparticles were 37.04% and 69.22%, respectively. The average size of the nanoparticles was 89.4 nm. The nanoparticles released 30% cyclosporin A-loaded in 48 hours in vitro, with no initial burst release. The mode of release in vitro was prone to bulk erosion. The in vivo results showed the biological half-life of the elimination phase (t1/2β) of the nanoparticles was 21 times longer than that of the cyclosporin A solution, and the area under the curve for the nanoparticles was 25.8 times greater than that of the cyclosporin A solution. Conclusion: Modification of PEGylated chitosan prolonged the retention time of the nanoparticles in the circulatory system and improved the bioavailability of cyclosporin A.
Failure mode assumptions and assumption coverage

A method is proposed for the formal analysis of failure mode assumptions and for the evaluation of the dependability of systems whose design correctness is conditioned on the validity of such assumptions. Formal definitions are given for the types of errors that can affect items of service delivered by a system or component. Failure node assumptions are then formalized as assertions on the types of errors that a component may induce in its enclosing system. The concept of assumption coverage is introduced to relate the notion of partially-ordered assumption assertions to the quantification of system dependability. Assumption coverage is shown to be extremely important in systems requiring very high dependability. It is also shown that the need to increase system redundancy to accommodate more severe modes of component failure can sometimes result in a decrease in dependability. <<ETX>>
Targeting the Cell Broadband Engine for constraint‐based local search

We investigated the use of the Cell Broadband Engine (Cell/BE) for constraint‐based local search and combinatorial optimization applications. We presented a parallel version of a constraint‐based local search algorithm that was chosen because it fits very well the Cell/BE architecture because it requires neither shared memory nor communication among processors. The performance study on several large optimization benchmarks shows mostly linear time speedups, sometimes even super linear. These experiments were carried out on a dual‐Cell IBM (Armonk, NY, USA) blade with 16 processors. Besides getting speedups, the execution times exhibit a much smaller variance that benefits applications where a timely reply is critical. Copyright © 2011 John Wiley & Sons, Ltd.
[Cytokines and osteoporosis].

During the last few years, progress has been made towards the understanding of local regulation of bone remodelling especially in relation to osteoporosis. Cytokines have shown to be powerful regulators of bone resorption and formation, though under superior control from oestrogen/testosterone, parathyroidhormone and 1,25(OH)2D3. Some of the cytokines primarily enhance osteoclastic bone resorption e.g. IL-1 (Interleukin-1), TNF (Tumor Necrosis Factor) and IL-6 (Interleukin-6), while others primarily stimulate bone formation e.g. TGF-beta (Transforming Growth Factor), IGF (Insulin-like Growth Factor) and PDGF (Platelet Derived Growth Factor). Another category has complex functions with stimulation of bone formation in vitro but stimulation of bone resorption in vivo; IFN-gamma (Interferon-gamma) belongs to this category. The bone remodelling cycle is delicately regulated, and even a slight disturbance in this regulation can cause a pathological state in the bone such as osteoporosis. This paper will try to give a survey of some of the processes that regulate bone metabolism and hopefully contribute to understanding the changes in the remodelling related to osteoporosis.
SPREPI: Selective Prediction and REplay for predicated Instructions

ARM ISA-based processors are no longer low-cost low-power processors. Nowadays ARM ISA based processor manufacturers are struggling to implement medium-end to high-end processor cores, and this implies implementing a state-of-the-art out-of-order execution engine. Unfortunately providing efficient out-of-order execution on legacy ARM codes may be quite challenging due to predicated instructions. In this paper, we propose a new hardware solution, Selective Prediction and REplay for Predicated Instructions (SPREPI), to provide efficient out-of-order execution of codes featuring predicated instructions. Predicting the predicated instructions addresses the so-called multiple definition problem. Predicated instructions are predicted using either a global branch-and-predicate history predictor or a global history predictor. But systematic usage of predicate prediction sometimes impairs the performance dramatically. Efficient filters are proposed to disable predicate prediction uses when they are likely to be counter-productive. Moreover predicate misprediction penalty can be as high as the branch mispenalty. To reduce this penalty we introduce a specific selective replay hardware component targeting mispredicted predicated instructions. SPREPI is shown to allow high out-order execution performance on ARM codes generated even with a compiler applying if-conversion only to very short branches. Moreover since SPREPI predicts most of the predicated instructions, a relatively inefficient hardware solution is sufficient for executing the few predicated instructions on which prediction is not used.
Incremental Constraint-Posting Algorithms in Interleaved Planning and Scheduling

In this paper we examine a collection of related incremental constraint-posting algorithms for temporal planning and for planning with continuous processes. The basis for these algorithms is an incremental version of the Bellman-Ford single-source shortest-path algorithm for consistency checking Simple Temporal Networks (STNs). We extend an existing incremental algorithm for STNs and then proceed to show how this algorithm plays a key role in temporal planning by a forward-chaining strategy, interleaving action choice with action scheduling. We go on to consider the more complex problem of temporal planning with continuous linear processes and show how the incremental STN algorithm can be integrated with a linear program (LP) solver, to achieve an efficient incremental constraint-posting algorithm for use in a forward-search planner. We demonstrate empirically that the incremental algorithms improve performance in both temporal and temporal and numeric settings.
EFFECTS OF MEMBRANE POTENTIAL ON SODIUM AND POTASSIUM FLUXES IN SQUID AXONS

The potential difference across the membranes of most excitable cells is of the order of 50 to 100 mV inside negative. Although this potential difference may seem rather small in absolute magnitude, it occurs across an interface of such extreme thinness that the resultant electric field ( 1 00,000 V/cm) approaches the dielectric breakdown point of many lipid materials. Since many of the constituents of the membrane are either charged particles or polar molecules, their orientation in the membrane might be affected by the presence of such large potential gradients, and it seems reasonable to suppose that the macromolecules responsible for ion transport as well as parameters of the transport system such as magnitude and/or sensitivity to internal and external ions might also be a function of the field strength. The experiments to be described were designed to test this hypothesis by altering the potential gradient across the membrane in two ways: (1 ) by passing hyperpolarizing electrical currents across the membrane and (2) by changing [ K ] i or [ K ] o , procedures that are known to change the membrane potential since the membrane is highly permeable to this ion. Brief reports of the effects of hyperpolarizations on sodium efflux from cephalopod axons have appeared p r e v i o ~ s l y . ~ * ' ~ In addition to the general orienting effect that an electrical field might be expected to have on any polar macromolecule, membrane potential might have a specific effect on Na : K transport in squid axons because of the electrogenic character of the pump (one cycle of pump operation moves more positive charges outward than inward). Because pumping extrudes a net charge from the cell, changing the potential gradient must change the amount of work that the pump does per cycle and thus might be expected to change either therate of pumping (i.e., magnitudes of the Na or K fluxes) or their sensitivity to external ions.
A 0.5 V, 80-nW pseudo-differential two-stage OTA in 0.18µm CMOS technology

This paper presents the design of a miller compensated two-stage fully differential pseudo operational transconductance amplifier (OTA) for ultra low-voltage and low-power mixed-signal applications. The circuit was designed using standard 0. 18μm digital CMOS process with bulk biasing of PMOS transistor to reduce the threshold voltage(Vth). The OTA operated at a supply voltage of 0.5V and consumes only 80nW of power. The OTA has simulated with a load of 5pF, which gives a DC gain 87.5 dB and a phase margin 62° at unity gain frequency 35 kHz. The proposed OTA figure of merit improved for unity gain frequency and slew-rate as compared to the state of art.