gebhart/patrepeval huggingface dataset:
Performance analysis of a parallel and distributed simulation framework for large scale wireless systems (2004)

The simulation of ad hoc and sensor networks often requires a large amount of computation, memory and time to obtain significant results. The parallel and distributed simulation approach can be a valuable solution to reduce the computation time, and to support model components' modularity and reuse. In this work we perform a testbed evaluation of a new middleware for the simulation of large scale wireless systems. The proposed middleware has been designed to adapt and to scale over a heterogeneous distributed execution infrastructure. To realize a testbed evaluation of the considered framework we implemented and investigated a set of wireless systems' models. Specifically, we identified two classes of widely investigated wireless models: mobile ad hoc, and static sensor networks. In this work we present the performances of the simulation framework, with respect to the heterogeneous set of execution architectures, and the modeled systems' characteristics. Results demonstrate that the framework leads to increased model scalability and speed-up, by transparently adapting and managing at runtime the communication and synchronization overheads, and the load balancing.
Forecasting Sclerotinia Disease on Lettuce: Toward Developing a Prediction Model for Carpogenic Germination of Sclerotia (2004)

ABSTRACT The feasibility of developing a forecasting system for carpogenic germination of Sclerotinia sclerotiorum sclerotia was investigated in the laboratory by determining key relationships among temperature, soil water potential, and carpogenic germination for sclerotia of two S. sclerotiorum isolates. Germination of multiple burials of sclerotia to produce apothecia also was assessed in the field with concurrent recording of environmental data to examine patterns of germination under different fluctuating conditions. Carpogenic germination of sclerotia occurred between 5 and 25 degrees C but only for soil water potentials of >/=-100 kPa for both S. sclerotiorum isolates. Little or no germination occurred at 26 or 29 degrees C. At optimum temperatures of 15 to 20 degrees C, sclerotia buried in soil and placed in illuminated growth cabinets produced stipes after 20 to 27 days and apothecia after 27 to 34 days. Temperature, therefore, had a significant effect on both the rate of germination of sclerotia and the final number germinated. Rate of germination was correlated positively with temperature and final number of sclerotia germinated was related to temperature according to a probit model. Thermal time analysis of field data with constraints for temperature and water potential showed that the mean degree days to 10% germination of sclerotia in 2000 and 2001 was 285 and 279, respecttively, and generally was a good predictor of the observed appearance of apothecia. Neither thermal time nor relationships established in the laboratory could account for a decline in final percentage of germination for sclerotia buried from mid-May compared with earlier burials. Exposure to high temperatures may explain this effect. This, and other factors, require investigation before relationships derived in the laboratory or thermal time can be incorporated into a forecasting system for carpogenic germination.
Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding (2001)

We have identified the mammalian orthologs of yCCR4 and have shown that the human member binds to the human yPOP2 homologs, thus strongly suggesting conservation of the CCR4-NOT complex from yeast to human. All members of the four identified yCCR4-related protein families show stricking conservation of the endonuclease-like catalytic motifs of the yCCR4 C-terminal domain and therefore constitute a new family of potential deadenylases in mammals.
Cytokine-based Cancer Immunotherapy: Challenges and Opportunities for IL-10 (2021)

Cancer immunotherapy is an evolving field of research. Cytokines have been conceptualized as an anticancer therapy for longer than most other cancer immunotherapy modalities. Yet, to date, only two cytokines are FDA-approved: IFN-α and IL-2. Despite the initial breakthrough, both agents have been superseded by other, more efficacious agents such as immune checkpoint inhibitors. Several issues persist with cytokine-based cancer therapies; these are broadly categorised into a) high toxicity and b) low efficacy. Despite the only moderate benefits with early cytokine-based cancer therapies, advances in molecular engineering, genomics, and molecular analysis hold promise to optimise and reinstate cytokine-based therapies in future clinical practice. This review considers five important concepts for the successful clinical application of cytokine-based cancer therapies including: (i) improving pharmacokinetics and pharmacodynamics, (ii) improving local administration strategies, (iii) understanding context-dependent interactions in the tumour-microenvironment, (iv) elucidating the role of genetic polymorphisms, and (v) optimising combination therapies. IL-10 has been the focus of attention in recent years and is discussed herein as an example.
A Diet Mimicking Fasting Promotes Regeneration and Reduces Autoimmunity and Multiple Sclerosis Symptoms (2016)

Dietary interventions have not been effective in the treatment of multiple sclerosis (MS). Here, we show that periodic 3-day cycles of a fasting mimicking diet (FMD) are effective in ameliorating demyelination and symptoms in a murine experimental autoimmune encephalomyelitis (EAE) model. The FMD reduced clinical severity in all mice and completely reversed symptoms in 20% of animals. These improvements were associated with increased corticosterone levels and regulatory T (Treg) cell numbers and reduced levels of pro-inflammatory cytokines, TH1 and TH17 cells, and antigen-presenting cells (APCs). Moreover, the FMD promoted oligodendrocyte precursor cell regeneration and remyelination in axons in both EAE and cuprizone MS models, supporting its effects on both suppression of autoimmunity and remyelination. We also report preliminary data suggesting that an FMD or a chronic ketogenic diet are safe, feasible, and potentially effective in the treatment of relapsing-remitting multiple sclerosis (RRMS) patients (NCT01538355).
Inhibition of rate of tumour growth in rodent species by inoculation of herpesviruses and encephalomyocarditis virus (1990)

Inoculation of herpesviruses and encephalomyocarditis virus into subcutaneous tumours in hamsters and mice reduced the rate of tumour growth compared to untreated tumours or secondary tumours which had arisen following surgical excision of the primary tumour; in addition, survival times were increased in animals whose tumours were inoculated with virus. It is suggested that the role of virus in the modification of tumour growth merits further exploration.
Optimizing the Maximum Recovery of Dihydromyricetin from Chinese Vine Tea, Ampelopsis grossedentata, Using Response Surface Methodology (2017)

This work provides an optimized extraction approach intended to maximize the recovery of dihydromyricetin (DHM) from Chinese vine tea (<i>Ampelopsis grossedentata</i>) leaves. The presented work adopts a Box-Behnken design as a response surface methodology to understand the role and influence of specific extraction parameters including: time, temperature, and solvent composition/ethanol (%) on DHM final yields. Initially, single factor experiments were used to delineate the role of above factors (temperature, time, and solvent composition) before proceeding with three factors-three levels Box-Behnken design with 17 separate runs to assess the effect of multifactorial treatments on DHM recovery rates. The collected data shows that independent variables (solvent composition, time, and temperature) can significantly affect DHM recovery rates with maximum yields resulting from a combined 60 °C, 60% aqueous ethanol, and 180 min treatment. From the empirical point of view, the above optimized extraction protocol can substantially enhance processing and profitability margins with a minimum need of interventions or associated costs.
Gesture-based control and EMG decomposition (2006)

This paper presents two probabilistic developments for the use with electromyograms (EMGs). First described is a neuroelectric interface for virtual device control based on gesture recognition. The second development is a Bayesian method for decomposing EMGs into individual motor unit action potentials (MUAPs). This Bayesian decomposition method allows for distinguishing individual muscle groups with the goal of enhancing gesture recognition. All examples presented rely upon sampling EMG data from a subject's forearm. The gesture-based recognition uses pattern recognition software that has been trained to identify gestures from among a given set of gestures. The pattern recognition software consists of hidden Markov models, which are used to recognize the gestures as they are being performed in real time from moving averages of EMGs. Two experiments were conducted to examine the feasibility of this interface technology. The first replicated a virtual joystick interface, and the second replicated a keyboard. Moving averages of EMGs do not provide an easy distinction between fine muscle groups. To better distinguish between different fine motor skill muscle groups, we present a Bayesian algorithm to separate surface EMGs into representative MUAPs. The algorithm is based on differential variable component analysis, which was originally developed for electroencephalograms. The algorithm uses a simple forward model representing a mixture of MUAPs as seen across multiple channels. The parameters of this model are iteratively optimized for each component. Results are presented on both synthetic and experimental EMG data. The synthetic case has additive white noise and is compared with known components. The experimental EMG data were obtained using a custom linear electrode array designed for this study.
Particle acceleration at a three-dimensional reconnection site in the solar corona (2005)

We study test particle trajectories in the vicinity of a three-dimensional (3D) magnetic null point during spine reconnection. Particles are injected into the steady-state non-uniform magnetic and electric fields derived by Priest & Titov (1996), and the equations of motion numerically integrated. We use input parameters typical of the solar corona, for which reconnection has been suggested as the fundamental mechanism responsible for particle acceleration in flare events. We show that substantial acceleration is possible in the 3D spine reconnection configuration, in the strong electric field regime. The energy gain is strongly dependent on the location of injection into the simulation box, as was the case in 2D X-point configurations. In our 3D geometry, we first vary the location of injection within a plane through the spine, and derive an analytical value for the injection angle for which maximum energy gain is achieved. Secondly we vary the azimuthal location of particle injection and show that as one moves away from the plane with maximum electric field magnitude, higher final energies can be achieved, though this requires substantially longer times.
Closing the Circle on the Discovery of Genes Encoding Hrp Regulon Members and Type III Secretion System Effectors in the Genomes of Three Model <i>Pseudomonas syringae</i> Strains (2006)

Pseudomonas syringae strains translocate large and distinct collections of effector proteins into plant cells via the type III secretion system (T3SS). Mutations in T3SS-encoding hrp genes are unable to elicit the hypersensitive response or pathogenesis in nonhost and host plants, respectively. Mutations in individual effectors lack strong phenotypes, which has impeded their discovery. P. syringae effectors are designated Hop (Hrp outer protein) or Avr (avirulence) proteins. Some Hop proteins are considered to be extracellular T3SS helpers acting at the plant-bacterium interface. Identification of complete sets of effectors and related proteins has been enabled by the application of bioinformatic and high-throughput experimental techniques to the complete genome sequences of three model strains: P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a. Several recent papers, including three in this issue of Molecular Plant-Microbe Interactions, address the effector inventories of these strains. These studies establish that active effector genes in P. syringae are expressed by the HrpL alternative sigma factor and can be predicted on the basis of cis Hrp promoter sequences and N-terminal amino-acid patterns. Among the three strains analyzed, P. syringae pv. tomato DC3000 has the largest effector inventory and P. syringae pv. syringae B728a has the smallest. Each strain has several effector genes that appear inactive. Only five of the 46 effector families that are represented in these three strains have an active member in all of the strains. Web-based community resources for managing and sharing growing information on these complex effector arsenals should help future efforts to understand how effectors promote P. syringae virulence.
An authoring toolkit design for educational game content (2008)

A new way of teaching using multimedia presentations or game-based technologies are urgently needed in order to engage and sustain students’ learning interests in their learning materials. To achieve that, teachers should be able to produce interactive multimedia learning materials (e.g. educational games) themselves. However, current authoring tools such as Adobe Flash and Macromedia Director are too complex to use by teachers with no computing backgrounds. We would like to address this issue by proposing a simple to use authoring toolkit that will enable teachers to create their own educational game contents. The proposed toolkit operates by using games templates i.e. akin to producing presentation slides using Microsoft Power Point. In this paper, we present the framework in designing such toolkit. Based on this framework, an authoring tool will be developed to enable teachers in Malaysia to author educational game content for teaching basic Jawi words for the primary school children.
The use of gonadotrophin releasing hormone agonists for in vitro fertilization and other assisted procreation techniques: Experience from three centres (1992)

Gonadotrophin releasing hormone (GnRH) agonists have had a profound impact on infertility treatment by in vitro fertilization and related procreation techniques. Its combination with human menopausal gonadotrophin (HMG) for superovulation has increased the success rate in patients with premature luteinizing hormone (LH) surges, a poor response, endometriosis or polycystic ovarian disease. Although most in vitro fertilization (IVF) centres routinely use GnRH agonists for reasons of a better planning of activities, its superiority as a first-line treatment over the more conventional regimes of clomiphene citrate (CC)/HMG or HMG alone is still debated. An increase of the number and maturity of recovered oocytes was reported by most groups, but an inverse relationship between the number of oocytes and embryo quality and pregnancy rate after cryopreservation has been frequently mentioned. The possible complications of the combined use of a GnRH agonist with HMG include the formation of ovarian 'follicle' cysts and ovarian hyperstimulation syndrome; luteal phase defects are also common. Routine luteal phase support with progesterone and oestradiol valerate or human chorionic gonadotrophin (HCG) is required. GnRH agonists have proved to be safe drugs, side-effects are minor and sporadic and the congenital malformation rate in GnRHa/HMG treatment is comparable to the spontaneous rates reported in national IVF registers.
Unraveling Molecular Complexity of Phosphorylated Human Cardiac Troponin I by Top Down Electron Capture Dissociation/Electron Transfer Dissociation Mass Spectrometry (2008)

Cardiac troponin I (cTnI), the inhibitory subunit of the thin filament troponin-tropomyosin regulatory complex, is required for heart muscle relaxation during the cardiac cycle. Expressed only in cardiac muscle, cTnI is widely used in the clinic as a serum biomarker of cardiac injury. In vivo function of cTnI is influenced by phosphorylation and proteolysis; therefore analysis of post-translational modifications of the intact protein should greatly facilitate the understanding of cardiac regulatory mechanisms and may improve cTnI as a disease biomarker. cTnI (24 kDa, pI approximately 9.5) contains twelve serine, eight threonine, and three tyrosine residues, which presents a challenge for unequivocal identification of phosphorylation sites and quantification of positional isomers. In this study, we used top down electron capture dissociation and electron transfer dissociation MS to unravel the molecular complexity of cTnI purified from human heart tissue. High resolution MS spectra of human cTnI revealed a high degree of heterogeneity, corresponding to phosphorylation, acetylation, oxidation, and C-terminal proteolysis. Thirty-six molecular ions of cTnI were detected in a single ESI/FTMS spectrum despite running as a single sharp band on SDS-PAGE. Electron capture dissociation of monophosphorylated cTnI localized two major basal phosphorylation sites: a well known site at Ser(22) and a novel site at Ser(76)/Thr(77), each with partial occupancy (Ser(22): 53%; Ser(76)/Thr(77): 36%). Top down MS(3) analysis of diphosphorylated cTnI revealed occupancy of Ser(23) only in diphosphorylated species consistent with sequential (or ordered) phosphorylation/dephosphorylation of the Ser(22/23) pair. Top down MS of cTnI provides unique opportunities for unraveling its molecular complexity and for quantification of phosphorylated positional isomers thus allowing establishment of the relevance of such modifications to physiological functions and disease status.
Pretreatment of dyestuff wastewater by internal microelectrolysis (2011)

Internal microelectrolysis is an effective pretreatment technology for poor biodegradable industrial wastewater contaminated with dyestuffs, pesticides, pharmaceuticals, etc. In internal microelectrolysis system, numerous microscopic galvanic cells are formed between iron and carbon in wastewater, resulting in galvanic cell reaction. Products released from the galvanic cell reaction include hydroxyl, atomic hydrogen and Fe(II) which have high capacity to decompose contaminants. In this paper, the effects of internal microelectrolysis pretreatment for dyestuff wastewater were firstly studied. The degradation mechanism and influence factors of internal microelectrolysis were also investigated. Experimental results indicated that the weight ratio of iron to carbon is a key parameter during internal microelectrolysis. The optimum ratio of Fe/C was found to be 5. To obtain the maximum removal efficiency with low operation costs, reaction time of microelectrolysis was about 2 hours and the pertinent pH of influent was 2∼3. Under these optimum conditions, different concentrations of dyestuff wastewater were treated by internal microelectrolysis. In the end, the removal efficiency of COD was over 45 percent, and B/C of wastewater was increased obviously from 0.2 to about 0.4.
Synthesis and physical performance of indole and benzimidazole cyanine dyes (1996)

Nine indole and benzimidazole cyanine dyes, used as green-sensitizing dyes in photographic emulsions, are synthesized. The compounds are characterized from mass spectrometric and NMR spectroscopic data, and elemental analysis. FAB mass spectrometry proved to be an efficient method for determining the structure of the compounds. From UV–VIS data of the compounds the sensitizing properties of the cyanine dyes are predicted. The reflection spectrum of Gs2-9 coated in photographic emulsions showed J-aggregation behaviour at λ= 560 nm. Unsymmetric benzimidazole–indole cyanine dyes showed good to excellent green sensitizing properties in photographic emulsions, whereas symmetric indole cyanine dyes showed heavy residual colour and no sensitizing properties.
Video camera system using fuzzy logic (1992)

Fuzzy logic was applied to the AE (automatic exposure), AF (automatic focus), and AWB (automatic white balance) controls in a video camera. A unified fuzzy control system for the basic functions of a video camera was developed. High performance was realized with a simple hardware construction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Pharmacokinetics and in vivo activity of liposome-encapsulated gentamicin (1990)

Gentamicin sulfate was encapsulated in liposomes composed solely of egg phosphatidylcholine and administered via intravenous injection to rats and mice. The total gentamicin activity (regardless of whether it was free or liposome associated) in serum and selected tissues was determined for 24 h (serum) or up to 15 weeks (tissues) by using a microbiological assay. The mean half-lives in serum of a single 20-mg/kg dose of free (nonencapsulated) gentamicin in mice and rats were estimated to be 1.0 and 0.6 h, respectively, whereas a similar dose of encapsulated drug had apparent mean half-lives of 3.8 h in mice and 4.0 h in rats. In both species, the apparent half-life in serum of the liposomal formulation increased as the dose increased. Liposome encapsulation resulted in higher and more prolonged activity in organs rich in reticuloendothelial cells (especially spleen and liver). In acute septicemia infections in mice, the liposomal formulation showed enhanced prophylactic activity (as determined by calculation of the 50% protective dose). In a model of murine salmonellosis, liposomal gentamicin greatly enhanced survival when given as a single dose (10 mg/kg) at 1 or 2 days after infection as well as up to 7 days before infection.
Parallel Tabu Search for Real-Time Vehicle Routing and Dispatching (1999)

An abundant literature about vehicle routing and scheduling problems is available in the scientific community. However, a large fraction of this work deals with static problems where all data are known before the routes are constructed. Recent technological advances now create environments where decisions are taken quickly, using new or updated information about the current routing situation. This paper describes such a dynamic problem, motivated from courier service applications, where customer requests with soft time windows must be dispatched in real time to a fleet of vehicles in movement. A tabu search heuristic, initially designed for the static version of the problem, has been adapted to the dynamic case and implemented on a parallel platform to increase the computational effort. Numerical results are reported using different request arrival rates, and comparisons are established with other heuristic methods.
An efficient recursive algorithm and an explicit formula for calculating update vectors of running walsh-hadamard transform (2007)

Walsh-Hadamard transform (WHT) has many applications in digital signal processing including bioinformatics. While there are efficient algorithms for implementing this transform such as fast WHT (FWHT), performing WHT continuously on a sliding window over a long sequence is time consuming. As it is not reasonable to compute a separate WHT upon arrival of every new sample, another implementation named running WHT (RWHT) has been introduced in (G. Deng and A. Ling, 1996) which needs to have some update vectors pre-calculated. In this paper we report on an efficient recursive algorithm to find these vectors. Also we propose an easy-to-compute explicit formula for computing coefficients of these update vectors in a computation time independent of the vector size. A proof of the formula and a comparison between the proposed recursive algorithm and an algorithm based on the formula are also given.