Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the Contributions of Individual Viral Genes to Newcastle Disease Virus Virulence and Pathogenesis

ABSTRACT Naturally occurring Newcastle disease virus (NDV) strains vary greatly in virulence. The presence of multibasic residues at the proteolytic cleavage site of the fusion (F) protein has been shown to be a primary determinant differentiating virulent versus avirulent strains. However, there is wide variation in virulence among virulent strains. There also are examples of incongruity between cleavage site sequence and virulence. These observations suggest that additional viral factors contribute to virulence. In this study, we evaluated the contribution of each viral gene to virulence individually and in different combinations by exchanging genes between velogenic (highly virulent) strain GB Texas (GBT) and mesogenic (moderately virulent) strain Beaudette C (BC). These two strains are phylogenetically closely related, and their F proteins contain identical cleavage site sequences, 112RRQKR↓F117. A total of 20 chimeric viruses were constructed and evaluated in vitro, in 1-day-old chicks, and in 2-week-old chickens. The results showed that both the envelope-associated and polymerase-associated proteins contribute to the difference in virulence between rBC and rGBT, with the envelope-associated proteins playing the greater role. The F protein was the major individual contributor and was sometimes augmented by the homologous M and HN proteins. The dramatic effect of F was independent of its cleavage site sequence since that was identical in the two strains. The polymerase L protein was the next major individual contributor and was sometimes augmented by the homologous N and P proteins. The leader and trailer regions did not appear to contribute to the difference in virulence between BC and GBT. IMPORTANCE This study is the first comprehensive and systematic study of NDV virulence and pathogenesis. Genetic exchanges between a mesogenic and a velogenic strain revealed that the fusion glycoprotein is the major virulence determinant regardless of the identical virulence protease cleavage site sequence present in both strains. The contribution of the large polymerase protein to NDV virulence is second only to that of the fusion glycoprotein. The identification of virulence determinants is of considerable importance, because of the potential to generate better live attenuated NDV vaccines. It may also be possible to apply these findings to other paramyxoviruses.
Observer-based deadband control for discrete systems subject to external disturbance

This paper is concerned with designing the observer-based deadband output feedback controller for discrete-time systems subject to unknown but bounded external disturbance. Specifically, an augmentation method is utilized to estimate the system states and the disturbance, followed by designing the controller with the estimated states and disturbance. Moreover, a predefined updating instants scheduler is introduced to update the observer-based deadband controller thus designed. A theoretical analysis is provided for the stability and disturbance rejection properties of the resulting closed-loop system. A simulation example is presented to show the good performance of the designed observer-based deadband controller in terms of reduced frequency of updating the controller and disturbance rejection.
Low-Fat Dietary Pattern and Risk of Benign Proliferative Breast Disease: A Randomized, Controlled Dietary Modification Trial

Modifiable factors, including diet, might alter breast cancer risk. We used the Women's Health Initiative Dietary Modification trial to test the effect of the intervention on risk of benign proliferative breast disease, a condition associated with increased risk of, and considered to be on the pathway to, invasive breast cancer. The Women's Health Initiative Dietary Modification trial was a randomized, controlled, primary prevention trial conducted in 40 U.S. clinical centers from 1993 to 2005. A total of 48,835 postmenopausal women, ages 50 to 79 years, without prior breast cancer, were enrolled. Participants were randomly assigned to the dietary modification intervention group or to the comparison group. The intervention was designed to reduce total dietary fat intake to 20% of total energy intake, and to increase fruit and vegetable intake to ≥5 servings/d and intake of grain products to ≥6 servings/d, but resulted in smaller, albeit significant, changes in practice. Participants had biennial mammograms and regular clinical breast exams. We identified women who reported breast biopsies free of cancer, obtained the histologic sections, and subjected them to standardized central review. During follow-up (average, 7.7 years), 570 incident cases of benign proliferative breast disease were ascertained in the intervention group and 793 in the comparison group. The hazard ratio for the association between dietary modification and benign proliferative breast disease was 1.09 (95% confidence interval, 0.98-1.23). Risk varied by levels of baseline total vitamin D intake but it varied little by levels of other baseline variables. These results suggest that a modest reduction in fat intake and increase in fruit, vegetable, and grain intake do not alter the risk of benign proliferative breast disease.
Influence of Personality on Online Discussion.

Online collaborative learning has typically been studied within the context of learning communities. Little is known about the potential influence of students’ personalities on online communication, group interaction, and task engagement among members of a learning community. This study used a mixed-method, triangulation design, involving the collection and analysis of both quantitative and qualitative data, to investigate the effects of person ality on communication type and pattern, message length, task engagement, and student attitude toward online learning. Seventy students were organized into four personality-profile groups based on their Five Factor Personality Test scores, for the discussion of assigned case studies. Discussion messages were analyzed using Logistical Regressions for communication type and pattern, ANOVAs for message length, and Z-tests for pairwise comparisons for task engagement. The results indicate that personality affects communication type, pattern and task engagement but not message length. Students’ attitudes toward online discussion were generally positive. The results provide guidelines for forming groups and designing activities for online collaborative learning.
Population dynamics of salmon lice Lepeophtheirus salmonis on Atlantic salmon and sea trout

The salmon louse Lepeophtheirus salmonis is a common ectoparasite of both farmed and wild salmonids in the marine environment, and can have a significant negative effect on the sur- vival and growth of its host. To facilitate development of models of salmon lice population dynamics, we review the available experimental information on its demographic rates and highlight areas where further research is needed. For all stages, the reduced minimum development time of a stage with increasing water temperature (T) was well described by Belehradek's function. However, detailed experimental studies of the development of the parasitic stages at low (T 15°C) water temperatures are needed to cover the whole range of water temperatures experi- enced in the wild. Little information was available on mortality rates and distributions of develop- mental times after the initial minimum developmental times. These parameters could only be esti- mated for a narrow temperature range, but the available estimates suggested that distributions of development times may be assumed to be constant with respect to temperature. Factors affecting female fecundity are presently poorly understood, with a level of unexplained variability in both average egg numbers per string and egg viability, which demands further investigations. In addition, experiments on possible density-dependent effects on salmon lice fecundity and survival are required.
MAX ONES GENERALISED TO LARGER DOMAINS

We study a family of problems, called Maximum Solution, where the objective is to maximise a linear goal function over the feasible integer assignments to a set of variables subject to a set of constraints. When the domain is Boolean (i.e. restricted to {0, 1}), the maximum solution problem is identical to the well-studied Max Ones problem, and the approximability is completely understood for all restrictions on the underlying constraints [Khanna et al., SIAM J. Comput. , 30 (2001), pp. 1863-1920]. We continue this line of research by considering domains containing more than two elements. We present two main results: a complete classification for the approximability of all maximal constraint languages over domains of cardinality at most 4, and a complete classification of the approximability of the problem when the set of allowed constraints contains all permutation constraints. Under the assumption that a conjecture due to Szczepara holds, we give a complete classification for all maximal constraint languages. These classes of languages are well-studied in universal algebra and computer science; they have, for instance, been considered in connection with machine learning and constraint satisfaction. Our results are proved by using algebraic results from clone theory and the results indicates that this approach is very powerful for classifying the approximability of certain optimisation problems.
Trust me, i'm partially right: incremental visualization lets analysts explore large datasets faster

Queries over large scale (petabyte) data bases often mean waiting overnight for a result to come back. Scale costs time. Such time also means that potential avenues of exploration are ignored because the costs are perceived to be too high to run or even propose them. With sampleAction we have explored whether interaction techniques to present query results running over only incremental samples can be presented as sufficiently trustworthy for analysts both to make closer to real time decisions about their queries and to be more exploratory in their questions of the data. Our work with three teams of analysts suggests that we can indeed accelerate and open up the query process with such incremental visualizations.
Co‐localization of PARP‐1 and lamin B in the nuclear architecture: A halo‐fluorescence‐ and confocal‐microscopy study

A functional interaction between poly(ADP‐ribose) polymerase‐1 (PARP‐1) and lamin B has recently been proposed by nuclear fractionation, crosslinking, and immunoprecipitation experiments. Here we use fluorescence microscopy to verify and extend these findings. We analyze nuclear halo preparations by fluorescence in situ immuno staining (FISIS), which shares attributes with traditional nuclear fractionation techniques, and by confocal laser scanning microscopy (CLSM). The results agree in that a major part of the enzyme co‐localizes with lamin B under physiological conditions, where PARP‐1 only has basal activity. After DNA damage and the associated activation of PARP‐1, and during the subsequent entry into apoptosis, dramatic changes occur: a gradual release of the enzyme from the lamina, accompanied by its accumulation in nucleoli. Our observations are in line with biochemical evidence for lamin B‐PARP‐1 interactions under physiological conditions and suggest ways by which these interactions are modified to support PARP‐functions in damage and its fate in apoptosis. © 2005 Wiley‐Liss, Inc.
Modeling the Transmission of al-Mubashshir Ibn Fātik’s Mukhtār al-Ḥikam in Medieval Europe: Some Initial Data-Driven Explorations

This article addresses the transmission of a mid-eleventh century Arabic compilation of Hellenic wisdom, al-Mubashshir Ibn F ā tik’s Mukht ā r al- Ḥ ikam wa-ma ḥ ā sin al-kalim , into medieval European languages. It documents new archival evidence for the scope of this textual tradition. The combination of digital textual and archival evidence provides important clues for building hypotheses for an expanded reception history of the Arabic text in Europe. Using corpora built in three languages—Castilian, Latin and French—it leverages stylometric analysis to explore the discursive communities in which the translations may have emerged and where they took on new meanings. The article puts medium-scale stylometry into practice in the field of comparative literature and translation studies for the exploration of large text collections, and suggests how quantitative methods could be deployed in translingual corpus-level literary research. It also argues for the use of stylometry at early stages of literary historical research to discover new paths of inquiry.
An interconnect-driven design of a DFT processor

A new interconnect-driven DFT implementation is proposed in this paper. The normal way to implement the DFT is to use the FFT algorithm since it is computationally favorable. However, the increased speed comes at the cost of increased communications which give a higher power consumption. If the DFT algorithm is directly implemented instead, each channel becomes independent of all other channels and consequently communications and hence power consumption are reduced. Other benefits of using the DFT directly are the possibility to calculate a spectrum of any length, not only a power of two, and to have an irregular frequency step between channels. A number of ad hoc processing-element (PE) and system-level solutions are also proposed to reduce the power consumption even further.
P2X Receptor Intermediate Activation States Have Altered Nucleotide Selectivity

Purinergic P2X receptors are widely distributed in the nervous system and are known to play roles in primary afferent transmission and central respiratory regulation. They are trimeric membrane proteins, with the extracellular domain that provides three intersubunit ATP binding sites. We expressed the rat P2X7 receptor in human embryonic kidney cells and measured membrane currents before and after photo-affinity labeling with the agonist 2′(3′)-O-(4-benzoylbenzoyl)-ATP (BzATP). After tethering BzATP with ultraviolet light, a persistent current remained after washing out the agonist. Additional current could now be elicited by other nucleotides (CTP and ADP) that are not normally effective as P2X receptor agonists. Similar results were obtained at P2X2 receptors even without previous agonist tethering: exposure to low concentrations of ATP caused the receptor to become sensitive to activation by CTP and ADP. The results show that ATP binding to the first of the three binding sites causes a conformational change to an intermediate closed state that shows increased effectiveness of pyrimidine and diphosphate nucleotide analogs.
A Novel Security Infrastructure for Mobile Code 1 Yougang

Mobile code secur ity has developed into a significant research area as users are increasingly relying on networked information. Traditional methods for mobile code secur ity can be costly, inefficient and er ror prone. In this paper , we introduce a novel security infrastructure called Rico. Rico leverages the Inline Reference Monitor (IRM) binary rewriting technique and interposes itself between a client that downloads mobile code and the server providing the code, enabling the system administrator to secure untrusted code by rewriting it. Rico either works separately or together with a proxy server. I t isolates end users from security concerns and supports the following features: (1) A security policy editor that simplifies policy wr iting with frame wizards, syntax reminders and error checking. (2) Third-party policy incorporation enabling reuse of secur ity policies created by trusted third par ties. (3) Policy composition, the capability of combining multiple secur ity policies into one logical policy that can be applied to a mobile program. (4) Efficient security management supported by a graphical inter face and a self-training database.
Attitudes of able-bodied young adults towards disabled people

This mixed method study examined the attitudes of able-bodied young adults towards disabled people. It also examined which factors were predictors of Yuker, Block and Young’s (1970) Attitudes Toward Disabled Persons (ATDP) scores. Two questionnaires and semi-structured interviews, using photographic images of disabled people, were employed. The questionnaire section involved an opportunity sample of 81 undergraduates from the University of Cumbria who completed two questionnaires, one of which was the ATDP Form A (Yuker, Block & Young, 1970) and the other was designed by the researcher. Eight undergraduates from the University of Cumbria participated in the qualitative section and the data was analysed using Braun and Clarke’s (2006) guidelines to thematic analysis. It was found that able-bodied young adults have positive attitudes towards disabled people and the regression analyses indicated that ‘Own Attitudes’ was a strong positive predictor of ATDP score (β = .46, t = 4.44, p < .001). The interviews revealed that whilst participant’s attitudes were positive towards disabled people they still held stereotypical views of an older person, in a wheelchair. Furthermore, respect and inspirational feelings were evoked when viewing a picture of a disabled person who was considered to have strength of character and intelligence.
Monitoring Internet of Things Application Ecosystems for Failure

For Internet of Things (IoT) application ecosystems to excel, end-to-end components including the cloud, network, and edge devices must be highly dependable and resilient. This dependability must be verifiable by continuously monitoring the constituent components for conformance to defined behavior in terms of functional and nonfunctional requirements. However, the authors contend that current techniques and frameworks for monitoring the performance of hardware and application resources in distributed systems are not capable of monitoring and detecting root causes of failure and performance degradation for entire end-to-end IoT ecosystems. Motivated by this finding, they discuss their vision of future research into developing formal approaches for monitoring end-to-end IoT ecosystems.
A New Model for Inductive Inference (extended Abstract)

We introduce a new model for inductive inference, by combining a Bayesian approach for representing the current state of knowledge with a simple model for the computational cost of making predictions from theories. We investigate the optimization problem: how should a scientist divide his time between doing experiments and deducing predictions for promising theories. We propose an answer to this question, as a function of the relative costs of making predictions versus performing experiments. We believe our model captures many of the qualitative characteristics of "real" science. We believe that this model makes two important contributions. First, it allows us to study how a scientist might go about acquiring knowledge in a world where (as in real life) there are costs associated with both performing experiments and with computing the predictions of various theories. This model also lays the groundwork for a rigorous treatment of a machine-implementable notion of "subjective probability". Subjective probability is at the heart of probability theory [5]. Previous treatments have not been able to handle the difficulty that subjective probabilities can change as the result of "pure thinking"; our model captures this (and other effects) in a realistic manner. In addition, we begin to provide an answer to the question of how to trade-off "thinking" versus "doing"-a question that is fundamental for computers that must exist in the world and learn from their experience.
15-Site Randomized Trial of Coordinated Care in Medicare FFS

Medicare beneficiaries in fee-for-service (FFS) who had chronic illnesses and volunteered to participate in 15 care coordination programs were randomized to treatment or control status. Nurses provided patient education (mostly by telephone) to improve adherence and ability to communicate with physicians. Patients were contacted an average of two times per month. The findings after 2 years are not encouraging. Few programs improved patient behaviors, health, or quality of care. The treatment group had significantly fewer hospitalizations in only one program; no program reduced gross or net expenditures. However, effects may be observed when 4 years of followup are available and sample sizes increase.
Cardiovascular responses induced during high‐intensity eccentric and concentric isokinetic muscle contraction in healthy young adults

The purpose of this study was to determine the differences in cardiovascular response between high‐intensity eccentric (ECC) and concentric (CON) contractions, and to obtain the basic data applicable to resistance training in middle‐aged and elderly individuals. The subjects who participated in this study were nine healthy men (age 24·1 ± 1·3 years). ECC and CON were randomly selected, as each test consisted of a high‐intensity (80% of peak torque) bout of 60 s of ECC and CON isokinetic contractions of the flexor carpi radialis. Systolic pressure (SBP), diastolic pressure (DBP) and heart rate (HR) during ECC and CON were measured using a Finometer. Mean arterial pressure (MAP) was calculated by SBP and DBP. Rate‐pressure product (RPP) was calculated by SBP and HR. SBP, DBP, MAP and RPP during ECC were significantly smaller compared with CON. It is clear that cardiovascular response by high‐intensity contraction is smaller in ECC than in CON. High‐intensity ECC has been suggested to exert only small stress to the cardiovascular system. Thus, being a contraction mode it may be applicable to resistance training.
Effects of Nanoparticle Doping on Electrical Properties of ${\rm MgB}_{2}$ Bulks and Wires Obtained by Reactive Mg Liquid Infiltration Technique

The effect of SiC nanoparticle and colloidal C additions on the electric transport properties of MgB2 samples, bulks and wires, was investigated at different applied magnetic fields. The samples were obtained by the Reactive Mg Liquid Infiltration (RLI) in boron powder preforms, technique with the advantages of good mechanical characteristics of the products with an easy manufacturing. It was found that SiC nanoparticle additions produce an improvement of both the irreversibility field and the upper critical field as well as the enhancement of the n-exponent in the power law voltage-current curves and of the pinning energy. In particular the analysis of the pinning energy dependence on the current density turned out that the SiC doping-induced pinning centers are of similar nature than the pristine ones. Moreover only a slight decrease of the critical temperature was measured as a consequence of the SiC doping. Higher pinning-capability enhancement was found for the C doped wires which exhibit a sharper irreversibility field enhancement at the external field increase. This issue together with a stronger critical temperature decrease (0.7 K) points towards a higher amount of C substitution for B in the MgB2 lattice than in the SiC-doped bulk samples.