Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteriophage 2851 Is a Prototype Phage for Dissemination of the Shiga Toxin Variant Gene 2c in Escherichia coli O157:H7

ABSTRACT The production of Shiga toxin (Stx) (verocytotoxin) is a major virulence factor of Escherichia coli O157:H7 strains (Shiga toxin-producing E. coli [STEC] O157). Two types of Shiga toxins, designated Stx1 and Stx2, are produced in STEC O157. Variants of the Stx2 type (Stx2, Stx2c) are associated with high virulences of these strains for humans. A bacteriophage designated 2851 from a human STEC O157 encoding the Stx2c variant was described previously. Nucleotide sequence analysis of the phage 2851 genome revealed 75 predicted coding sequences and indicated a mosaic structure typical for lambdoid phages. Analyses of free phages and K-12 phage 2851 lysogens revealed that upon excision from the bacterial chromosome, the loss of a phage-encoded IS629 element leads to fusion of phage antA and antB genes, with the generation of a recombined antAB gene encoding a strong antirepressor. In wild-type E. coli O157 as well as in K-12 strains, phage 2851 was found to be integrated in the sbcB locus. Additionally, phage 2851 carries an open reading frame which encodes an OspB-like type III effector similar to that found in Shigella spp. Investigation of 39 stx2cE. coli O157 strains revealed that all except 1 were positive for most phage 2851-specific genes and possessed a prophage with the same border sequences integrated into the sbcB locus. Phage 2851-specific sequences were absent from most stx2c-negative E. coli O157 strains, and we suggest that phage 2851-like phages contributed significantly to the dissemination of the Stx2c variant toxin within this group of E. coli.
Adaptive Application Component Mapping for Parallel Computation Offloading in Variable Environments

Distinguished with traditional strategies which offload an application"s computation to a single server, parallel computation offloading can promote the performance by simultaneously delivering the computation to multiple computing resources around the mobile terminal. However, due to the variability of communication and computation environments, static application component multi-partitioning algorithms are difficult to maintain the optimality of their solutions in time-varying scenarios, whereas, over-frequent algorithm executions triggered by changes of environments may bring excessive algorithm costs. To this end, an adaptive application component mapping algorithm for parallel computation offloading in variable environments is proposed in this paper, which aims at minimizing computation costs and inter-resource communication costs. It can provide the terminal a suitable solution for the current environment with a low incremental algorithm cost. We represent the application component multi-partitioning problem as a graph mapping model, then convert it into a pathfinding problem. A genetic algorithm enhanced by an elite-based immigrants mechanism is designed to obtain the solution adaptively, which can dynamically adjust the precision of the solution and boost the searching speed as transmission and processing speeds change. Simulation results demonstrate that our algorithm can promote the performance efficiently, and it is superior to the traditional approaches under variable environments to a large extent.
The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths

Markov chain Monte Carlo has been the standard technique for inferring the posterior distribution of genome rearrangement scenarios under a Bayesian approach. We present here a negative result on the rate of convergence of the generally used Markov chains. We prove that the relaxation time of the Markov chains walking on the optimal reversal sorting scenarios might grow exponentially with the size of the signed permutations, namely, with the number of syntheny blocks.
Predicting Preferences: An Examination of Agent Learning

Agent decision making occurs when an individual acts as a purchasing agent for another. Effective agent decision making requires that the agent learn to predict the target's preferences. Two experimental studies demonstrate the impact of providing agents veridical feedback. The results further our understanding of interpersonal prediction and learning from experience. Agents who are given the opportunity to learn from their own successes and failures do not exhibit the false consensus effect, or projection, that has been demonstrated in previous research. Any facilitative effect of similarity in tastes on predictive accuracy disappears when feedback is provided. Information theory is used to establish the informational value of individual instances, as well as an overall distribution of feedback. The results of the studies reported in the present article indicate that agents spend significantly more time considering informative than uninformative feedback, which improves their predictive accuracy. Copyright 1996 by the University of Chicago.
Fault-tolerant distributed transactions for partitioned OLTP databases

This thesis presents Dtxn, a fault-tolerant distributed transaction system designed specifically for building online transaction processing (OLTP) databases. Databases have traditionally been designed as general purpose data processing tools. By being designed only for OLTP workloads, Dtxn can be more efficient. It is designed to support very large databases by partitioning data across a cluster of commodity servers in a data center. Combining multiple servers together allows systems built with Dtxn to be cost effective, highly available, scalable, and fault-tolerant. Dtxn provides three novel features. First, it provides reusable infrastructure for building a distributed OLTP database out of single machine databases. This allows developers to take a specialized backend storage engine and use it across multiple machines, without needing to re-implement the distributed transaction infrastructure. We used Dtxn to build four different applications: a simple key/value store, a specialized TPC-C implementation, a main-memory OLTP database, and a traditional disk-based OLTP database. Second, Dtxn provides a novel concurrency control mechanism called speculative concurrency control, designed for main memory OLTP workloads that are primarily composed of transactions with a single round of communication between the application and database. Speculative concurrency control executes one transaction at a time, with no concurrency control overhead. In cases where there may be stalls due to network communication, it speculates future transactions. Our results show that this provides significantly better throughput than traditional two-phase locking, outperforming it by a factor of two on the TPC-C benchmark. Finally, Dtxn supports live migration, allowing part of the data on one server to be moved to another server while processing transactions. Our experiments show that our approach has nearly no visible impact on throughput or latency when moving data under moderate to high loads. It has significantly less impact than the best commercially available systems when the database is overloaded. The period of time where the throughput is reduced is less than half as long as failing over to another replica or using virtual machine migration.
From Inner City to Ivory Tower

The author draws on principles of critical race theory to reflect on his elementary education at a successful urban Catholic school. He contends that his education was built on the integration of two epistemological pillars: centric and conflict theories. The implementation of this matrix of theories served as the necessary ingredients to foster his movement from the inner city to the ivory tower and a career in mathematics education research. The article concludes with a discussion of the tension created by his "voice" within traditional academic discourse.
Interdependencies in IT Infrastructure Services: Analyzing Service Processes for Optimal Incentive Design

Information technology (IT) infrastructure outsourcing arrangements involve multiple services and processes that are interdependent. The interdependencies pose significant challenges in designing appropriate incentives to influence a provider's effort-allocation decisions. By integrating process modeling fundamentals with multitask agency theory, we enumerate the base set of possible interrelationships among different IT service processes and derive corresponding optimal incentives. Our results demonstrate the impacts of risk profile, random noise, value-cost ratio, and process structure on optimal incentive rates. We find that the current practice of treating IT services as essentially independent is optimal only in limited settings where both the service provider and customer are risk neutral. Interestingly, incongruent performance measures require optimal incentive rates to respond in complex ways to the strength of coupling between services and the complementarity and substitutability of services. We also analyze more complex process scenarios using different combinations of the base set. The results demonstrate that, while the findings from the base set largely hold, the value-cost ratio of the services and the performance measure congruity can pose unique challenges in determining incentive rates.
Regression/Eradication of gliomas in mice by a systemically-deliverable ATF5 dominant-negative peptide

Malignant gliomas have poor prognosis and urgently require new therapies. Activating Transcription Factor 5 (ATF5) is highly expressed in gliomas, and interference with its expression/function precipitates targeted glioma cell apoptosis in vitro and in vivo. We designed a novel deliverable truncated-dominant-negative (d/n) form of ATF5 fused to a cell-penetrating domain (Pen-d/n-ATF5-RP) that can be intraperitoneally/subcutaneously administered to mice harboring malignant gliomas generated; (1) by PDGF-B/sh-p53 retroviral transformation of endogenous neural progenitor cells; and (2) by human U87-MG xenografts. In vitro Pen-d/n-ATF5-RP entered into glioma cells and triggered massive apoptosis. In vivo, subcutaneously-administered Pen-d/n-ATF5-RP passed the blood brain barrier, entered normal brain and tumor cells, and then caused rapid selective tumor cell death. MRI verified elimination of retrovirus-induced gliomas within 8-21 days. Histopathology revealed growth-suppression of intracerebral human U87-MG cells xenografts. For endogenous PDGF-B gliomas, there was no recurrence or mortality at 6-12 months versus 66% mortality in controls at 6 months. Necropsy and liver-kidney blood enzyme analysis revealed no adverse effects on brain or other tissues. Our findings thus identify Pen-d/n-ATF5-RP as a potential therapy for malignant gliomas.
Automatic Modeling of Acoustic Perception of Breathiness in Pathological Voices

This paper revisits the modeling of acoustic perceptions of breathy voice (BV) quality for automatic assessment of perturbations in pathologic speech. Several acoustic measures related with the signal periodicity, harmonic components, and aspiration noise are studied to predict breathiness judgments performed on sustained vowel phonations. A novel comprehensive automatic measure is proposed that provides the highest correlation index (88.5%) with breathiness judgment performed by trained specialists on simulated and recorded utterances. The new measure reveals the most relevant aspects of BV quality and provides a vehicle to obtain reliable objectives judgments of such speech perturbation.
Electric vehicle and grid interface with modified PWM rectifier and DC-DC converter with power decoupling and unity power factor

In this paper, a configuration with modified single-phase H-bridge AC-DC converter for DC ripple compensation and power decoupling with a DC-DC converter for bidirectional power flow between PHEV (Plug in Hybrid Electric Vehicle) and power grid is proposed. It is well known that single-phase PWM voltage source converter (VSC) suffers from second-order ripple power and subsequent DC-link voltage pulsation. To reduce this low frequency pulsation of DC-link voltage and to obtain the sinusoidal grid current with unity power factor, a modified single-phase H-bridge PWM rectifier consisting of a conventional H-bridge PWM VSC and a pure passive auxiliary circuit is presented with a bidirectional DC-DC converter in order to ensure the bi-directional power flow management between PHEV and power grid at unity power factor and reduced ripple current. The modified H-bridge has the advantage of less number of switches and small DC link capacitor. First 230 V 50 Hz AC supply from source is converted to 400 V DC through single phase VSC and again the battery of EV or PHEV is charge in buck mode and discharge in boost mode with the help of bidirectional DC-DC buck - boost converter. In discharging mode, it delivers energy back to the grid at 230V, 50 Hz. A battery with a charging power of 3.6 kW at 120 V is used in PHEV.
Trust Research in the Transactional Context and Its Implications for Online Trust

In the context of electronic commerce (eCommerce), trust is critical to business relationship, because no transaction will take place before a buyer trusts an unknown online seller. However, little has been known about the nature of online trust. In this paper, we propose a framework to categorize the transactional contexts within which trust takes place. Based on this framework, we then review the literature and examine the special nature of online trust. The theoretical foundations are offered to explain the major antecedents of online trust. Finally the future research issues of online trust that are challenging the research community are identified.
Using simulation to evaluate global software development task allocation strategies

We describe a hybrid computer simulation model of the software development process that is specifically architected to study alternative ways to configure global software development (GSD) projects, including phase-based, module-based, and follow-the-sun allocation strategies. The model is a hybrid system dynamics and discrete-event model. In this paper, test cases have been developed for each allocation strategy, and project duration is computed for each configuration under a range of plausible assumptions for key parameters. The primary finding is that although under ideal assumptions follow-the-sun is able to produce impressive reductions in time-to-market, under more realistic assumptions the reverse is true, thus corroborating findings by other researchers. We also conducted a factorial design to examine the impact of GSD factors including distance, culture, language, trust, and time zone on project duration under different task allocation strategies. The analysis reveals that different factors affected the performance of the selected allocation strategies in unique ways. These findings show how the unique ability of our GSD model to represent detailed development processes and work artifact transfer allows researchers to address challenging questions that are critical to GSD project success. Copyright © 2007 John Wiley & Sons, Ltd.
Melanesian mtDNA Complexity

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ∼30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ∼3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.
Regular expression types for XML

We propose regular expression types as a foundation for XML processing languages. Regular expression types are a natural generalization of Document Type Definitions (DTDs), describing structures in XML documents using regular expression operators (i.e., *, ? , |, etc.) and supporting a simple but powerful notion of subtyping.The decision problem for the subtype relation is EXPTIME-hard, but it can be checked quite efficiently in many cases of practical interest. The subtyping algorithm developed here is a variant of Aiken and Murphy's set-inclusion constraint solver, to which are added several optimizations and two new properties: (1) our algorithm is provably complete, and (2) it allows a useful "subtagging" relation between nodes with different labels in XML trees.
Brazilian version of the body dysmorphic disorder examination.

CONTEXT AND OBJECTIVE Body image improvement is considered to be the main reason for undergoing plastic surgery. The objective was to translate the Body Dysmorphic Disorder Examination (BDDE) into Brazilian Portuguese and to adapt and validate this questionnaire for use in Brazil. DESIGN AND SETTING Cross-sectional survey, at the Department of Plastic Surgery of Universidade Federal de São Paulo. METHODS The BDDE was first translated into Portuguese and then back-translated into English. These translations were then discussed by healthcare professionals in order to establish the final Brazilian version. In a second stage, the validity and reliability of the BDDE were assessed. For this, patients were initially interviewed by two interviewers and subsequently, by only one of these interviewers. On the first occasion, in addition to the BDDE, the body shape questionnaire (BSQ) and the Rosenberg self-esteem scale were also applied. These questionnaires were applied to 90 patients. RESULTS Six questions were modified during the assessment of cultural equivalence. Cronbach's alpha was 0.89 and the intraclass correlation coefficients for interobserver and test-retest reliability were 0.91 and 0.87, respectively. Pearson's coefficient showed no correlation between the BDDE and the Rosenberg self-esteem scale (0.22), whereas there was a moderate correlation between the BDDE and the BSQ (0.64). CONCLUSIONS The BDDE was successfully translated and adapted, with good internal consistency, reliability and construct validity.
Collaboration through Open Superposition

Collaboration through open superposition 2 ABSTRACT This paper develops and illustrates the theory of collaboration through open superposition: the process of depositing motivationally independent layers of work on top of each other over time. The theory is developed in a study of development of community-based Free and Open Source Software (FLOSS), through a research arc of discovery (participant observation), replication (two archival case studies) and theorization. The theory explains two key findings: 1) the overwhelming majority of work is accomplished with only a single programmer working on a task, and 2) tasks that appear too large for an individual are more likely to be deferred until they are easier rather than being undertaken through structured teamwork. Moreover, the theory explains how working through open superposition can lead to the discovery of a work breakdown that results in complex, functionally interdependent work being accomplished without crippling search-costs. We identify a set of socio-technical contingencies under which collaboration through open superposition is likely to be effective, including characteristics of artifacts made from information as the objects being worked on. We demonstrate the usefulness of the theory by using it to analyze difficulties in learning from FLOSS in other domains of work and in the IS function of for-profit organizations.
Elderly Wellbeing and the Psychology of Social Comparison

ABSTRACT Twenty-two elderly retired people were interviewed for their beliefs about the sources of wellbeing in old age. Manual and Professional social class responses were compared, controlling for age, gender and health status. Respondents' free discourse was characterised by spontaneous social comparisons of the self with other people. In Social Comparison Theory, these serve as a means of self-assessment or wellbeing-enhance-ment. The comparison statements were analysed by Direction, Target, Dimension, and Wellbeing Yield. Significant class differences were apparent. Both groups compared Downward with others on the Dimensions of ageing, longevity, keeping active, security, and money. The Manual group derived less wellbeing from their Downward comparisons, many of which focused on entitlement to money benefits. The Professional group made more Upward comparisons, focusing on the younger self as Target, and yielding neutral or negative wellbeing. The predominant Upward Dimensions were perceived cognitive and physical condition. The Professionals tended to rationalise cognitive decline, but neither group showed psychological defence against physical decline, using social comparison as a means to objective self-assessment rather than self-enhancement.
Simple Two-Transistor Single-Supply Resistor–Capacitor Chaotic Oscillator

We have modified an otherwise standard one-transistor self-biasing resistor-capacitor phase shift oscillator to induce chaotic oscillations. The circuit uses only two transistors, no inductors, and is powered by a single supply voltage. As such, it is an attractive and low-cost source of chaotic oscillations for many applications. We compare experimental results to SPICE simulations, showing good agreement. We qualitatively explain the chaotic dynamics to stem from hysteretic jumps between unstable equilibria, around which growing oscillations exist.
On Objective Function, Regularizer, and Prediction Error of a Learning Algorithm for Dealing With Multiplicative Weight Noise

In this paper, an objective function for training a functional link network to tolerate multiplicative weight noise is presented. Basically, the objective function is similar in form to other regularizer-based functions that consist of a mean square training error term and a regularizer term. Our study shows that under some mild conditions the derived regularizer is essentially the same as a weight decay regularizer. This explains why applying weight decay can also improve the fault-tolerant ability of a radial basis function (RBF) with multiplicative weight noise. In accordance with the objective function, a simple learning algorithm for a functional link network with multiplicative weight noise is derived. Finally, the mean prediction error of the trained network is analyzed. Simulated experiments on two artificial data sets and a real-world application are performed to verify theoretical result.