Miracle-dz/UniFAR-FTUs huggingface dataset:
The histone variant H2A.Z is an important regulator of enhancer activity

Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). We also determine that H2A.Z does not influence the local nucleosome positioning around ERα enhancers using ChIP sequencing at nucleosomal resolution and unsupervised pattern discovery. We further highlight that H2A.Z-enriched enhancers are associated with chromatin accessibility, H3K122ac enrichment and hypomethylated DNA. Moreover, upon estrogen stimulation, the enhancers occupied by H2A.Z produce enhancer RNAs (eRNAs), and recruit RNA polymerase II as well as RAD21, a member of the cohesin complex involved in chromatin interactions between enhancers and promoters. Importantly, their recruitment and eRNAs production are abolished by H2A.Z depletion, thereby revealing a novel functional link between H2A.Z occupancy and enhancer activity. Taken together, our findings suggest that H2A.Z acts as an important player for enhancer functions by establishing and maintaining a chromatin environment required for RNA polymerase II recruitment, eRNAs transcription and enhancer-promoters interactions, all essential attributes of enhancer activity.
Complementarity of End Regions Increases the Lifetime of Small RNAs in Mammalian Cells

Two RNAs (4.5SH and 4.5SI) with unknown functions share a number of features: short length (about 100 nt), transcription by RNA polymerase III, predominately nuclear localization, the presence in various tissues, and relatively narrow taxonomic distribution (4 and 3 rodent families, respectively). It was reported that 4.5SH RNA turns over rapidly, whereas 4.5SI RNA is stable in the cell, but their lifetimes remained unknown. We showed that 4.5SH is indeed short-lived (t1/2∼18 min) and 4.5SI is long-lived (t1/2∼22 h) in Krebs ascites carcinoma cells. The RNA structures specifying rapid or slow decay of different small cellular RNAs remain unstudied. We searched for RNA structural features that determine the short lifetime of 4.5SH in comparison with the long lifetime of 4.5SI RNA. The sequences of genes of 4.5SH and 4.5SI RNAs were altered and human cells (HeLa) were transfected with these genes. The decay rate of the original and altered RNAs was measured. The complementarity of 16-nt end regions of 4.5SI RNA proved to contribute to its stability in cells, whereas the lack of such complementarity in 4.5SH RNA caused its rapid decay. Possible mechanisms of the phenomenon are discussed.
moreBugs: A New Dataset for Benchmarking Algorithms for Information Retrieval from Soft ware Repositories

This report presents moreBugs, a new publicly available dataset derived from the AspectJ and JodaTime repositories for the benchmarking of algorithms for retrieval from software repositories. As a case in point, moreBugs contains all the information required to evaluate a search-based bug localization framework — it includes a set of closed/resolved bugs mined from the bug-tracking system, and, for each bug, its patch-file list and the corresponding snapshot of the repository extracted from version history. moreBugs tracks commit-level changes made to a software repository along with its release information. In addition to the benchmarking of bug localization algorithms, the other algorithms whose benchmarking moreBugs should prove useful for include: change detection, impact analysis, software evolution, vocabulary evolution, incremental learning, and so on.
Electric Vehicle Participation in Transactive Power Systems Using Real-Time Retail Prices

Smart grids can help Plug-in Electric Vehicles (PEV) manage their load in a grid-friendly way. In this paper, we consider the case of PEVs participating in a retail double auction electricity regulation market, as in the so-called "transactive control" paradigm. Price-responsive charging of PEVs is modeled in conjunction with real-time retail price signals from the utility. PEVs can defer charging or even discharge when the retail prices are high. Buy and sell reservation prices are based on expectations of future prices and opportunity costs of sold energy, respectively. Feeder capacity constraints also affect the retail price and are allowed to rise to the point at which supply equals demand. For the most advanced charging strategies, as the price rises, demand from PEVs drops, and if the constraint causes further price increases, the PEVs can begin to supply energy. The results show that when rooftop solar energy is available transactive bid-response vehicle charging strategies significantly enhance short-term electricity demand elasticity and can reduce consumer energy costs by more than 75% in comparison to the unresponsive charge case.
The Emergence of a Learning Progression in Middle School Chemistry

Previously, a small scale, interview-based, 3-year longitudinal study (ages 11–14) in one school had suggested a learning progression related to the concept of a substance. This article presents the results of a large-scale, cross-sectional study which used Rasch modeling to test the hypothesis of the learning progression. Data were collected from 4,450 students, aged 11–14, across 30 secondary schools in England using a computer-based assessment instrument. The construction of the items was informed by the research literature on students' understanding in chemistry. One hundred seventy-six fixed response items, in three formats, involving the use of video and animation were developed. Scored dichotomously, overall, the data show a good fit to the Rasch model. Item difficulties have a high degree of invariance across ability, schools, gender, and year group. Conceptually, when items are placed in order of difficulty, a coherent progression of ideas emerges which matches the expectations from the longitudinal study. The learning progression is presented. Independent, nationally standardized data allow tentative projection of student performance to the wider population in England. Implications for research and curriculum design are discussed. © 2011 Wiley Periodicals, Inc. J Res Sci Teach 48: 849–877, 2011
Täuschungsstrategien bei der Schilderung von Sexualstraftaten

Zusammenfassung: Eine wesentliche Basis fur die Anwendung der merkmalsorientierten Inhaltsanalyse (Steller & Kohnken, 1989) zur Beurteilung der Glaubhaftigkeit von Zeugenaussagen bildet die Annahme, dass Falschaussagende bestimmte Inhalte meiden, weil diese einer positiven Selbstprasentation zuwiderlaufen. Ergebnisse neuerer Untersuchungen zu Tauschungsstrategien von Kindern und Erwachsenen stutzten diese Annahme weitgehend, fuhrten hinsichtlich einzelner motivationsbezogener Merkmale (Selbstbelastungen, Inschutznahme des Beschuldigten) jedoch zu Ergebnissen, die im Widerspruch zu aussagepsychologischen Annahmen standen. In bisherigen Studien wurden Szenarien verwendet, deren Ubertragbarkeit auf spezifisch rechtspsychologische Inhalte wie Sexualstraftaten als begrenzt zu betrachten war. Ziel der vorliegenden Untersuchung war es, Aussagen uber die Bedeutung spezifischer inhaltlicher Merkmale im Zusammenhang mit berichteten sexuellen Ubergriffen treffen zu konnen. Eine nicht-studentische Stichprobe von Frau.
Boundary Organizations in Environmental Policy and Science: An Introduction

Scholarship in the social studies of science has argued convincingly that what demarcates science from nonscience is not some set of essential or transcendent characteristics or methods but rather an array of contingent circumstances and strategic behavior known as "boundary work" (Gieryn 1995, 1999). Although initially formulated to explain how scientists maintain the boundaries of their community against threats to its cognitive authority from within (e.g., fraud and pseudo-science), boundary work has found useful, policy-relevant applications-for example, in studying the strategic demarcation between political and scientific tasks in the advisory relationship between scientists and regulatory agencies (Jasanoff 1990). This work finds that the blurring of boundaries between science and politics, rather than the intentional separation often advocated and practiced, can lead to more productive policy making. If it is the case, however, that the robustness of scientific concepts such as causation and representation are important components of liberal-democratic thought and practice (Ezrahi 1990), one can imagine how the flexibility of boundary work might lead to confusion or even dangerous instabilities between science and nonscience. These risks could be conceived, perhaps, as the politicization of science or the reciprocal scientification of politics. Neither risk should here be understood to mean the importation to one enterprise from the other elements that are entirely foreign; that is, science is not devoid of values prior to some politicization, nor politics of rationality, prior to any scientification. Rather, both should be understood to mean the rendering of norms and practices in one enterprise in a way that unreflexively mimics norms and practices in the other. These concerns have been central to the socalled science wars, and to the extent that they are implicated in public discussions of such policy issues as health and safety regulation, climate change, or genetically modified organisms, they are real problems for policy makers and publics alike. '
Cloning and Characterization of TRAIL-R3, a Novel Member of the Emerging TRAIL Receptor Family

TRAIL-R3, a new member of the TRAIL receptor family, has been cloned and characterized. TRAIL-R3 encodes a 299 amino acid protein with 58 and 54% overall identity to TRAIL-R1 and -R2, respectively. Transient expression and quantitative binding studies show TRAIL-R3 to be a plasma membrane–bound protein capable of high affinity interaction with the TRAIL ligand. The TRAIL-R3 gene maps to human chromosome 8p22-21, clustered with the genes encoding two other TRAIL receptors. In contrast to TRAIL-R1 and -R2, this receptor shows restricted expression, with transcripts detectable only in peripheral blood lymphocytes and spleen. The structure of TRAIL-R3 is unique when compared to the other TRAIL receptors in that it lacks a cytoplasmic domain and appears to be glycosyl-phosphatidylinositol–linked. Moreover, unlike TRAIL-R1 and -R2, in a transient overexpression system TRAIL-R3 does not induce apoptosis.
A Study of Patients with "Interface Respiratory Failure" Due to Chronic Obstructive Pulmonary Diseases.

OBJECTIVE To explain a definition of "interface respiratory failure" as arterial blood gas assay with arterial oxygen partial pressure in the range of 60-75 mmHg. SUBJECTS AND METHODS We compared arterial blood gases (ABGs), resting respiratory drive and its derivatives, mechanics of respiratory muscles, resistance and compliance of the respiratory tract and some important cytokines (interleukin-4 and interferon-γ) of stable chronic obstructive pulmonary disease (COPD) subgroups (total 50 cases) and control group (25 cases). RESULTS The patients attaining the "interface respiratory failure" stage developed great changes in respiratory mechanics parameters and inflammatory mediator, which might cause the exacerbation of COPD and the inclination to generate "real respiratory failure" and COPD progression. CONCLUSIONS The definition of interface respiratory failure is scientific, direct and its width is appropriate. We should intervene appropriately and positively to avoid progression from "interface respiratory failure" to the "real respiratory failure" stage, and this avoidance means a higher survival rate and a lower medical expense. Interventions should focus on oxygen therapy, bronchodilators, improving respiratory compliance, cytokines and anti-infective agents, respectively.
Trust-Preserving Overlays for Fast Reputation Aggregation in Peer-to-Peer Grid Systems ∗

In recent years, Peer-to-Peer (P2P) systems and computational Grids are evolving into a new distributed computing model, called P2P Grid. This paper presents a new approach to solving the trust and security problems in a P2P Grid. Establishing trust in P2P Grids is essential to build lasting working relationships among the peers joining collective Grid applications. A P2P reputation system is thus needed to collect peer trust scores and aggregates them to yield a global reputation in both P2P and Grid systems. We use a new trust-preserving overlay network (TON) to model the trust relationships among the peers. Examining the eBay transaction trace data, we discover a power-law distribution in user feedbacks, which is proven applicable to any dynamic P2P system or any P2P Grid system. We develop a new P2P reputation system, PowerTrust, to leverage on power-law feedback characteristics. Our system is built with locality-preserving hash functions and a lookahead random walk strategy. Dynamic P2P system reconfiguration is enabled by using power nodes with well-established reputations. This power-node approach significantly reduces the global aggregation overhead. Through P2P simulation experiments on distributed file sharing and Grid parameter-sweeping applications (PSA) applications, we demonstrate the advantages of fast reputation convergence and accurate ranking of peer reputations. Simulated P2P Grid performance results are reported with enhanced query success rate, shortened job makespan, increased job success rate, and the alleviation of ill effects of malicious peers, after trust binding in either P2P systems or in P2P Grids. Keyword: Peer-to-Peer systems, Grid computing, overlay network, trust management, distributed hash table, reputation system, distributed file sharing, parameter sweeping applications (PSA, and network security. ∗ Manuscript submitted to IEEE-TPDS, Nov. 5, 2005. This work was supported by NSF Grant ITR0325409 at the University of Southern California. Corresponding author is Kai Hwang at Email: kaihwang@usc.edu, Tel. 213 740 4470, and Fax: 213 740 4418.
Lessons from the Practice of Household Surveys[1]

There is an increasing tendency to use questionnaire surveys in the research of Chinese organization and management. For 2005 alone, a web search generates several hundreds of Chinese language reports and articles based on current and past surveys of various organizations. Many of these surveys, however, lack documentation to show how they were implemented. Following a more careful reading of the materials from three well-known survey series of enterprises', one still has concerns about survey quality, namely the validity and reliability of survey instruments, sample representativeness, and response biases as influenced by internal and external factors of the survey contexts. In this essay, I do not evaluate the quality of organizational surveys, since my limited experience with two such surveys offers no systematic understanding of them. I have, instead, conducted many more household surveys, whose problems and analyses might give hints on how to obtain and improve the quality of organizational surveys. Although households and organizations are two different kinds of units of analysis, survey problems may commonly be associated with (1) sampling, (2) survey implementation, and (3) quality control of interviews. ^ To elaborate on each of these three components of the household survey, I will base my discussion on the Chinese General Social Survey (CGSS), an annual household survey of the country that my sociology colleagues and I have conducted since 2003. At the end of this essay, I will draw from our household survey experiences a few lessons for organizational survey researchers.
Model Driven Development with Interactive Use Cases and UML Models

Large scale enterprise software systems are inherently complex and hard to maintain. To deal with this complexity, current mainstream software engineering practices aim at raising the level of abstraction to visual models described in OMG’s UML modeling language. Current UML tools, however, produce static design diagrams for documentation which quickly become out-ofsync with the software. To address this issue, modeldriven development approaches focus on software automation with generators that translate models into code. Unfortunately, automated code generation tends to emphasize “replacement” rather than “evolution”, and as a result, don’t integrate well with existing legacy code. This research investigates an alternative approach to model driven development using dynamic models developed interactively with existing code. We believe that such an approach provides better support for maintaining and evolving software by keeping models more in sync with code and focusing on code integration with models rather than model driven code generation.
The Structure of Psychopathology in Adolescence

This study aimed to replicate a study by Caspi and colleagues, which proposed that the structure of psychopathology is characterized by a general psychopathology factor, in addition to smaller internalizing and externalizing factors. Our study expanded the approach of the original by using continuous adolescent data and testing additional models, including both self- and parent-reported data, to bolster the robustness of the findings. Our findings indicate that the structure of psychopathology is best characterized by a model including a general factor, in addition to smaller internalizing and externalizing factors. These results emphasize the importance of this model for understanding the structure of psychopathology. Given the increasing emphasis on the importance of, and need for, replication, the overall evidence of a general factor seems rather robust.
Evaluation of PERSIANN-CCS rainfall measurement using the NAME event rain gauge network

Abstract Robust validation of the space–time structure of remotely sensed precipitation estimates is critical to improving their quality and confident application in water cycle–related research. In this work, the performance of the Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks-Cloud Classification System (PERSIANN-CCS) precipitation product is evaluated against warm season precipitation observations from the North American Monsoon Experiment (NAME) Event Rain Gauge Network (NERN) in the complex terrain region of northwestern Mexico. Analyses of hourly and daily precipitation estimates show that the PERSIANN-CCS captures well active and break periods in the early and mature phases of the monsoon season. While the PERSIANN-CCS generally captures the spatial distribution and timing of diurnal convective rainfall, elevation-dependent biases exist, which are characterized by an underestimate in the occurrence of light precipitation at high elevations and an overest.
T-cell receptor early signalling complex activation in response to interferon-α receptor stimulation

Signalling through the IFNαR (interferon-α receptor) and TCR (T-cell receptor) in Jurkat T lymphocytes results in distinct immune responses. Despite this both receptors elicit ERK (extracellular-signal-regulated kinase)/MAPK (mitogen-activated protein kinase) phosphorylation. Vav and Slp76 are shown to be required for IFNα (interferon-α)-stimulated ERK activity. These form a subset of proteins which behave identically on stimulation of both receptors. TCR deletion abrogates IFNαR-stimulated MAPK activity, whereas the canonical JAK/STAT (Janus kinase/signal transducer and activator of transcription) pathway is unaffected. Thus recruitment of the intact TCR ESC (early signalling complex) is necessary for this downstream MAPK response. Despite using a common ESC, stimulation of the IFNαR does not produce the transcriptional response associated with TCR. Up-regulation of the MAPK pathway by IFNαR might be important to ensure that the cell responds to only one stimulant.
Scare stories. Or some arguments for providing journalism with a licence to think

Journalists are often blamed for producing scare stories. It seems to have been forgotten that many, perhaps most, modern scare stories are based on scientific risk calculations, and that journalists are not trained in scaring the wits out of people in that particular way. A more precise accusation might be that journalists are eager, unthinking and unquestioning conveyors of results from scientific risk calculations. Calculation of risk has become an important research product; a product fitting nicely into conventional journalistic storytelling, but the concept of risk tends to dilute value disagreement and conflict of interests into seemingly purely factual issues, leaving little room for political debate. Moreover, the cargo attitude of journalism is in conflict with the journalistic ideal of critical investigation and analysis on behalf of the public to stimulate common deliberation in the public sphere. Apparently, the production of scientific knowledge is excluded from the public sphere. Regarding discussions on science and technology, journalists will have to enquire into aspects of facts, values and social interests to live up to the ideal of investigation on behalf of the public. Several obstacles along this path can be identified, one of them being the commercialization of journalism in the media-industry and of scientific research in the knowledge-industry. Universities, in the search for a meaning of life, might consider providing a home for independent, reflexive journalism on science in a social context.
An Examination of the I ndependent and Joint Contributions of Organizational Commitment and Job Satisfaction on Employee Intentions to Quit

Based on an argument that organizational commitment and job-facet satis faction represented different constructs, the present study explored the independent and joint effects of these variables on employees' intentions to quit their jobs. Consistent with prior findings, the present investigation indicated that commitment bears a significant and relatively strong relation ship to withdrawal intentions and is more closely related to such intentions than is job satisfaction. Moreover, the present data indicate that satisfaction, above and beyond commitment itself, tends to have independent and interactive effects on the criterion measure. These results are discussed with regard to understanding employee withdrawal processes.
Jordanian Arabic Final Geminates: An Experimental Clinical Phonetic Study

Jordanian Arabic Final Geminates: An Experimental Clinical Phonetic Study An experimental study was carried out to investigate word-final geminates in Jordanian Arabic. Monosyllabic singleton and geminate minimal pairs (CVC and CVCC) were considered to answer the three main questions of the study: Does gemination occur word-finally in Jordanian Arabic? Is there a temporal compensatory relationship between the vowels preceding geminate/singleton consonants? Are these differences contrastive? Eighteen participants produced 324 tokens with Ira. , n, 1 and m:, n:, 1:/ occurring word-finally Spectrographic and videofluoroscopic analyses show that final geminates are permissible in Jordanian Arabic. The temporal compensation maintained with the preceding vowel and the tension in articulating the geminates enhance perceptuality boundaries and maintain phonemicity.
A Path Analysis of a Model of the Antecedents and Consequences of Organizational Commitment

An attitudinal model of organizational commitment was tested using a sample of 367 managerial employees. Several aspects of the organization: perceived structure, process, and climate, as well as job satisfaction were found to be predictive of commitment. Job satisfaction and commitment were found to be equally predictive of voluntary turnover. Commitment was found to be predictive of individual motivation and objective job performance, but not of supervisors' ratings of job performance.