Miracle-dz/UniFAR-FTUs huggingface dataset:
nuBOINC: BOINC Extensions for Community Cycle Sharing

Currently, cycle sharing over the Internet is a one-way deal. Computer owners only have one role in the process: to donate their computers' idle time. This is due to the fact that it is difficult for an ordinary user to install the required infrastructure, develop the processing applications and gather enough computer cycle donors. In this paper we describe a set of BOINC extensions that allow any user to create and submit jobs that can take advantage of remote idle cycles. These jobs are processed by commonly available software (e.g. programming language interpreters or virtual machines, statistical software) that is installed in the remote donating computers. In order to submit their jobs, users only have to provide the input files, select the processing application and define the command line to provide to that application. Later, users of the same software packages will contact the server, receive a set of jobs, and process them using the already installed commodity application. These users can later take advantage of other peoplepsilas computer cycles.This system allows an expressive definition of jobs providing considerable speed gains, while leveraging a cyclesharing platform and widely available commodity applications, in a truly global communal computer cycle market.
A Technique for High-Throughput Protein Crystallization in Ionically Cross-Linked Polysaccharide Gel Beads for X-Ray Diffraction Experiments

A simple technique for high-throughput protein crystallization in ionically cross-linked polysaccharide gel beads has been developed for contactless handling of crystals in X-ray crystallography. The method is designed to reduce mechanical damage to crystals caused by physical contact between crystal and mount tool and by osmotic shock during various manipulations including cryoprotection, heavy-atom derivatization, ligand soaking, and diffraction experiments. For this study, protein crystallization in alginate and κ-carrageenan gel beads was performed using six test proteins, demonstrating that proteins could be successfully crystallized in gel beads. Two complete diffraction data sets from lysozyme and ID70067 protein crystals in gel beads were collected at 100 K without removing the crystals; the results showed that the crystals had low mosaicities. In addition, crystallization of glucose isomerase was carried out in alginate gel beads in the presence of synthetic zeolite molecular sieves (MS), a hetero-epitaxic nucleant; the results demonstrated that MS can reduce excess nucleation of this protein in beads. To demonstrate heavy-atom derivatization, lysozyme crystals were successfully derivatized with K2PtBr6 within alginate gel beads. These results suggest that gel beads prevent serious damage to protein crystals during such experiments.
‘Tragedy of the Commons’ in the Tourism Accommodation Industry

This paper models the interaction between the tourism accommodation industry and environmental quality – herein considered as a composite common pool resource. Results from the study show that open access generally leads to both economic and environmental overexploitation, that is ‘the tragedy of the commons’. This also affects the overall tourism industry since tourism accommodation and environmental quality perform central roles. This ultimately leads to mass tourism characterized by tourists with low willingness to pay. The results show that, apart from situations where positive externalities on other activities are very significant, or that open access faces binding restrictions (such as land availability), a firm's entry should be limited, based on both efficiency and sustainability.
Green function, quasi-classical Langevin and Kubo–Greenwood methods in quantum thermal transport

With the advances in fabrication of materials with feature sizes at the order of nanometers, it has been possible to alter their thermal transport properties dramatically. Miniaturization of device size increases the power density in general, hence faster electronics require better thermal transport, whereas better thermoelectric applications require the opposite. Such diverse needs bring new challenges for material design. Shrinkage of length scales has also changed the experimental and theoretical methods to study thermal transport. Unsurprisingly, novel approaches have emerged to control phonon flow. Besides, ever increasing computational power is another driving force for developing new computational methods. In this review, we discuss three methods developed for computing vibrational thermal transport properties of nano-structured systems, namely Green function, quasi-classical Langevin, and Kubo–Green methods. The Green function methods are explained using both nonequilibrium expressions and the Landauer-type formula. The partitioning scheme, decimation techniques and surface Green functions are reviewed, and a simple model for reservoir Green functions is shown. The expressions for the Kubo–Greenwood method are derived, and Lanczos tridiagonalization, continued fraction and Chebyshev polynomial expansion methods are discussed. Additionally, the quasi-classical Langevin approach, which is useful for incorporating phonon–phonon and other scatterings is summarized.
On the practicality of cryptographic defences against pollution attacks in wireless network coding

Numerous practical systems based on network coding have been proposed in recent years demonstrating the wide range of benefits of network coding, such as increased throughput, reliability, and energy efficiency. However, network coding systems are inherently vulnerable to a severe attack, known as packet pollution, which presents a key obstacle to the deployment of such systems. Several cryptographic schemes have been proposed to defend against pollution attacks. We conduct a detailed analysis and an experimental evaluation in a realistic wireless network coding setting of a set of representative cryptographic defenses against pollution attacks. Our analysis identifies severe limitations of asymmetric-based schemes, which impose high communication overhead by placing constraints on the basic network coding parameters and high computation overhead by relying on numerous operations over large fields. Our analysis also shows that symmetric cryptographic schemes, while having better performance than asymmetric cryptographic-based schemes, impose prohibitive overhead in the presence of multiple byzantine adversaries. We further evaluate these schemes by using a set of typical network coding system parameters on a realistic topology. Our experimental evaluation shows that all the schemes we compare induce a throughput degradation that negates the performance benefits of network coding in the presence of multiple colluding adversaries.
Acute Hypoxia Profile is a Stronger Prognostic Factor than Chronic Hypoxia in Advanced Stage Head and Neck Cancer Patients

Hypoxic head and neck tumors respond poorly to radiotherapy and can be identified using gene expression profiles. However, it is unknown whether treatment outcome is driven by acute or chronic hypoxia. Gene expression data of 398 head and neck cancers was collected. Four clinical hypoxia profiles were compared to in vitro acute and chronic hypoxia profiles. Chronic and acute hypoxia profiles were tested for their association to outcome using Cox proportional hazard analyses. In an initial set of 224 patients, scores of the four clinical hypoxia profiles correlated with each other and with chronic hypoxia. However, the acute hypoxia profile showed a stronger association with local recurrence after chemoradiotherapy (p = 0.02; HR = 3.1) than the four clinical (chronic hypoxia) profiles (p = 0.2; HR = 0.9). An independent set of 174 patients confirmed that acute hypoxia is a stronger prognostic factor than chronic hypoxia for overall survival, progression-free survival, local and locoregional control. Multivariable analyses accounting for known prognostic factors substantiate this finding (p = 0.045; p = 0.042; p = 0.018 and p = 0.003, respectively). In conclusion, the four clinical hypoxia profiles are related to chronic hypoxia and not acute hypoxia. The acute hypoxia profile shows a stronger association with patient outcome and should be incorporated into existing prediction models.
Proteasome Activator REGγ Enhances Coxsackieviral Infection by Facilitating p53 Degradation

ABSTRACT Coxsackievirus B3 (CVB3) is a small RNA virus associated with diseases such as myocarditis, meningitis, and pancreatitis. We have previously demonstrated that proteasome inhibition reduces CVB3 replication and attenuates virus-induced myocarditis. However, the underlying mechanisms by which the ubiquitin/proteasome system regulates CVB replication remain unclear. In this study, we investigated the role of REGγ, a member of the 11S proteasome activator, in CVB3 replication. We showed that overexpression of REGγ promoted CVB3 replication but that knockdown of REGγ led to reduced CVB3 replication. We further demonstrated that REGγ-mediated p53 proteolysis contributes, as least in part, to the proviral function of REGγ. Although total protein levels of REGγ remained unaltered after CVB3 infection, virus infection induced a redistribution of REGγ from the nucleus to the cytoplasm, rendering an opportunity for a direct interaction of REGγ with viral proteins and/or host proteins (e.g., p53), which controls viral growth and thereby enhances viral infectivity. Further analyses suggested a potential modification of REGγ by SUMO following CVB3 infection, which was verified by both in vitro and in vivo sumoylation assays. Sumoylation of REGγ may play a role in its nuclear export during CVB3 infection. Taken together, our results present the first evidence that the host REGγ pathway is utilized and modified during CVB3 infection to promote efficient viral replication.
A low-jitter skew-calibrated multi-phase clock generator for time-interleaved applications

Time-interleaved architectures employ multiple signal processing paths in parallel to achieve high overall speed while maintaining relaxed speed requirements on individual channels. This type of architecture requires a precise multi-phase clock generator to implement the interleaving function with the performance of the system depending upon the uniformity of the clock signals. This work implements an on-chip dynamic skew calibration multi-phase clock generator with ultra-low jitter. This scheme does not require any additional calibration cycle and therefore does not interrupt the clock output at any time.
An oncogenic virus carried by hamster kidney cells.

Summary A filterable oncogenic factor was isolated from ascitic tumors induced in X-irradiated hamsters by inoculation of BHK 21 clone 13 cells. This agent reproduces a tumor in hamsters 22 days after inoculation. Its oncogenic characteristics are preserved even after the ascitic tumor cells have been subcultured in vitro . The occurrence of R or H virus-like particles, both in tumor cells and in cultures, suggests a probable participation of such structures in the oncogenetic mechanisms of the aforementioned neoplasm.
Overview of my work on Multi-word expressions and Semantic Role Labeling

In this paper, I present the two problems on which I am working currently. The first work is a study of the relative compositionality of multi-word expressions of V-N type. The second work is semantic role labeling. Multi-word expressions (MWEs) are those whose structure and meaning cannot be derived from their component words, as they occur independently. Recognition of Multiword Expressions (MWEs) and their relative compositionality are crucial to Natural Language Processing, especially in applications like Machine translation. Various statistical techniques have been proposed to recognize MWEs. We integrate all the existing statistical techniques and investigate a range of classifiers for their suitability for recognizing the non-compositional Verb-Noun (V-N) collocations. In the task of ranking the V-N collocations based on their relative compositionality, we show that the correlation between the ranks computed by the classifier and human ranking is significantly better than the correlation between ranking of individual classifier and human ranking. Semantic role labeling is the task of assigning appropriate semantic roles to the participants of an action. Recognizing and labeling semantic arguments is a key task for Machine translation, answering “who”, “when”, “what”, “where”, “why”, etc. questions in Information extraction, Question answering and in Summarization. We present a generative model (adapted from [18]) which can infer roles of the various verbs in the sentence called predicators. Our model uses maximum entropy model for smoothing. 1. Relative compositionality of multi-word expressions: a study of verb-noun (V-N) collocations This section presents my study on the relative compositionality of multi-word expressions of V-N type. 1.
Increased risk of migraine in patients with psoriasis

Abstract Both psoriasis and migraine are associated with inflammatory diseases. However, few studies have been conducted the increased risk of migraine in psoriasis patients. The aim of this study was to identify whether the psoriasis increases the risk of migraine. This study used the national cohort study data collected by the Korean Health Insurance Review and Assessment from 2002 to 2013. Patients with psoriasis (n = 11,071) and control participants (n = 44,284) were selected and matched 1:4 by age, sex, income, region of residence, and past medical history of hypertension, diabetes, and dyslipidemia. This study used Cox-proportional hazard model for calculating hazard ratio (HR) with crude and adjusted model. Stratification by age and sex was analyzed. Migraines occurred significantly more frequently in psoriasis patients than in control participants (adjusted HR = 1.16, 95% confidence interval (CI) = 1.04–1.31, P <. 05). In the stratification analysis, migraines occurred significantly more frequently in psoriasis patients than in control participants only in the group of middle-aged males (adjusted HR = 1.62 95% CI = 1.22–2.13, P = .001). In conclusion, psoriasis might increase the risk of migraine.
Application of Dynamic Voltage Restorer for Voltage Balancing with ASD Load Using DQO Transformation

Dynamic voltage restorer has been considered the very effective solution for the mitigation of voltage sags and swells in the distribution network. DVR has other added features such as harmonics and power factor correction capability due to which it has gained a widespread importance. In this paper, the effectiveness of dynamic voltage restorer for voltage balancing is presented. The dqo based control algorithm is considered. The system is connected to the adjustable speed drive load. The MATLAB/Simulink demonstrates the validity and superiority of proposed control strategy during various voltage unbalancing conditions on low voltage distribution system.
The Pfam protein families database

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is ∼100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11 912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).
Hepatitis B virus strains in Thailand: Genomic variants in chronic carriers

Genetic heterogeneity of the hepatitis B virus (HBV) has been shown to influence the serological pattern and clinical picture in HBV infection. Thailand has a high transmission rate of HBV, but the molecular epidemiology of HBV strains circulating in this region was hitherto unknown. In this study, the HBV strains from 34 Thai HBsAg‐positive patients were investigated. In a proportion of these samples, an antigenically important region of the S gene (n = 181, and the pre‐S2 and precore genes (n = 15) were sequenced after PCR amplification. Four strains had in‐frame deletions of an upstream region of the pre‐S2 gene, with all deletions ending at the same nucleotide. In one of three anti‐HBe positive strains without a translational stop at codon 28 of the precore gene, there was a one nucleotide insertion in the precore gene. This insertion would cause a frame shift and result in a nonsense protein being expressed, thus providing one explanation for the lack of HBeAg in this patient. Several rare or unique amino acid changes in the region between residues 120 and 161 of the S protein were found. Glycine 145 was changed to alanine in one strain, and this position showed an apparent mixture of glycine and arginine in another. In total, 10 strains displayed unexpected changes that were not related to the normal variability between subtypes or genetic subgroups. It is concluded that there is considerable heterogeneity in HBV strains in Thailand and that this could have clinical and epidemiological importance in a region with high HBV transmission rates. © Wiley‐Liss, Inc.
Limitations of MLLR adaptation with Spanish-accented English: an error analysis

We studied the effect of MLLR adaptation with Spanishaccented English to understand the strengths and weaknesses of MLLR with unseen foreign accents. We trained a global MLLR transform on 10 adaptation sentences per speaker, giving a 3.4% absolute decrease in phone error rate. We then studied the pattern of improvements across phones and phone classes. Phones that improved the least tended to be those that do not exist in Spanish. Results suggest the poorer performance is related to increased insertion and substituter rates during the adaptation phase, as well as greater acoustic variability.
A fault tolerant signal processing computer

A fault tolerant computer has been designed for radiation environments which employs COTS components. The use of radiation-tolerant but not fully hardened COTS devices provides significantly higher performance than specialty, fully hardened parts. The computer architecture consists of multiple, redundant processing nodes, each containing levels of internal redundancy, and multiple point-to-point communication ports on a crossbar switch. The nodes are linked together via ports to form a distributed crossbar network with inherent fault tolerance. A key attribute of the architecture is the provision for selectable levels of error detection and recovery. The trade-offs between performance and degree of fault tolerance can be dynamically adjusted to meet specific system needs and parts selection at any particular time.
A Human Condensin Complex Containing hCAP-C–hCAP-E and CNAP1, a Homolog of Xenopus XCAP-D2, Colocalizes with Phosphorylated Histone H3 during the Early Stage of Mitotic Chromosome Condensation

ABSTRACT Structural maintenance of chromosomes (SMC) family proteins play critical roles in structural changes of chromosomes. Previously, we identified two human SMC family proteins, hCAP-C and hCAP-E, which form a heterodimeric complex (hCAP-C–hCAP-E) in the cell. Based on the sequence conservation and mitotic chromosome localization, hCAP-C–hCAP-E was determined to be the human ortholog of theXenopus SMC complex, XCAP-C–XCAP-E. XCAP-C–XCAP-E is a component of the multiprotein complex termed condensin, required for mitotic chromosome condensation in vitro. However, presence of such a complex has not been demonstrated in mammalian cells. Coimmunoprecipitation of the endogenous hCAP-C–hCAP-E complex from HeLa extracts identified a 155-kDa protein interacting with hCAP-C–hCAP-E, termed condensation-related SMC-associated protein 1 (CNAP1). CNAP1 associates with mitotic chromosomes and is homologous toXenopus condensin component XCAP-D2, indicating the presence of a condensin complex in human cells. Chromosome association of human condensin is mitosis specific, and the majority of condensin dissociates from chromosomes and is sequestered in the cytoplasm throughout interphase. However, a subpopulation of the complex was found to remain on chromosomes as foci in the interphase nucleus. During late G2/early prophase, the larger nuclear condensin foci colocalize with phosphorylated histone H3 clusters on partially condensed regions of chromosomes. These results suggest that mitosis-specific function of human condensin may be regulated by cell cycle-specific subcellular localization of the complex, and the nuclear condensin that associates with interphase chromosomes is involved in the reinitiation of mitotic chromosome condensation in conjunction with phosphorylation of histone H3.
Constructed product result analysis for Haskell

Compilers for ML and Haskell typically go to a good deal of trouble to arrange that multiple arguments can be passed efficiently to a procedure. For some reason, less effort seems to be invested in ensuring that multiple results can also be returned efficiently. In the context of the lazy functional language Haskell, we describe an analysis, Constructed Product Result (CPR) analysis, that determines when a function can profitably return multiple results in registers. The analysis is based only on a function's definition, and not on its uses (so separate compilation is easily supported) and the results of the analysis can be expressed by a transformation of the function definition alone. We discuss a variety of design issues that were addressed in our implementation, and give measurements of the effectiveness of our approach across a substantial benchmark set. Overall, the price/performance ratio is good: the benefits are modest in general (though occasionally dramatic), but the costs in both complexity and compile time, are low.
Following the ontogeny of retinal waves: pan-retinal recordings of population dynamics in the neonatal mouse

Novel pan‐retinal recordings of mouse retinal waves were obtained at near cellular resolution using a large‐scale, high‐density array of 4096 electrodes to investigate changes in wave spatiotemporal properties from postnatal day 2 to eye opening. Early cholinergic waves are large, slow and random, with low cellular recruitment. A developmental shift in GABAA signalling from depolarizing to hyperpolarizing influences the dynamics of cholinergic waves. Glutamatergic waves that occur just before eye opening are focused, faster, denser, non‐random and repetitive. These results provide a new, deeper understanding of developmental changes in retinal spontaneous activity patterns, which will help researchers in the investigation of the role of early retinal activity during wiring of the visual system.