Miracle-dz/UniFAR-FTUs huggingface dataset:
Ionic switch controls the DNA state in phage λ

We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. These results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.
Influence of DNA polymerases on quantitative PCR results using TaqMan probe format in the LightCycler instrument.

Real-time fluorescence polymerase chain reaction (PCR) techniques are increasingly used to quantitate target sequences for diagnostic and research purposes. Currently, the so called TaqMan probe chemistry is mostly used as fluorogenic system. This probe format is strictly dependent on the 5'-exonuclease activity of DNA polymerase as fragmentation of the probe during the reaction is essential for this assay. Based on our experience that dramatic differences in quantitative PCR results may be due to different DNA polymerases we performed a detailed comparison of 15 enzymes. We found that clear differences exist between polymerases of different manufacturers. Thus, three out of seven polymerases which were declared to possess 5'-exonuclease activity appeared to be completely unsuitable for this method while the remaining had significantly different reaction efficiencies. We conclude that different DNA polymerases may determine the entire analytical performance of TaqMan assays suggesting that DNA polymerase testing is of special importance when this probe format is used.
Distributed measurements for estimating and updating cellular system performance

We investigate the use of distributed measurements for estimating and updating the performance of a cellular system. Specifically, we discuss the number and placement of sensors in a given cell for estimating its signal coverage. Here, an "outage" is said to occur at a location if a mobile receiver there has inadequate signal-to-noise ratio (SNR -based outage) or, using another criterion, inadequate signal-to-interference ratio (SIR- based outage); and the "outage probability" is the fraction of the cell area over which outage occurs. A design goal is to improve measurement efficiency (i.e., minimizing the required number of measurement sensors) while accurately estimating the outage probability and mapping the coverage holes. The investigation uses a generic path loss model incorporating distance effects and spatially correlated shadow fading. Our emphasis is on the performance prediction accuracy of the sensor network, rather than on cellular system analysis per se. Through analysis and simulation, we assess several approaches to estimating the outage probability. Applying the principle of importance sampling to the sensor placement, we show that a cell outage probability of Po can be accurately estimated using ~ 10/Po power-measuring sensors distributed in a random uniform way over the area with base-sensor distances from 50% to 100% of the cell radius. This result applies to both SNR-based and SIR-based outage estimation for both indoor and outdoor environments.
Why lead?: Using narrative to explore the motivations of those aspiring to be principals in high needs schools

ABSTRACT Though research suggests identity construction and articulation of personal motivations regarding actions may be as, if not more, important to determine whether an individual may be successful in a school leadership role, collectively we know relatively little about aspiring principals’ motivations for becoming school leaders. Utilizing a narrative inquiry approach, this research addresses this gap directly. We find that aspiring principals in a turnaround leader preparation program (n = 9) presented three main motivations in their narratives regarding why they wished to become leaders in underperforming schools: (1) a desire to address perceived inequity, (2) a goal to catalyze educational change, and (3) a commitment to teaching and learning. Such findings allow us to consider how recruiting, developing and identifying leadership talent for high needs schools might need to be shifted to produce better outcomes for students and principals alike.
Robust access to large structured data using voice form-filling

A method for accurate and scalable form-filling by voice is presented. A form consists of a number of fields. Accurate speech recognition is achieved by applying task-specific inter-field constraints. The task constraints are specified typically by providing a database of valid form-entries, such as an employee directory containing the name, location, and telephone number. Scalability to very large vocabularies, number of fields, and the ability to accept a variety of user responses, is achieved by a two-pass recognition scheme. An index-based retrieval method is used in the first-pass to produce a shortlist of form-entries. These are rescored in the second-pass to obtain the final result. Experiments on a simple corporate directory access application are presented to demonstrate that the new approach compares favorably, in terms of computing needs, with a traditional one-pass speech recognition system. Experiments on a national street address recognition application are presented to demonstrate that the new approach scales very well to large tasks
Examining the association between parenting and psychosomatic problems: self-esteem as a mediator across ages in early adolescence

Abstract Supportive parenting is known to protect against psychosomatic manifestations of distress, yet the mechanisms through which this association operates are less clear. The present study evaluates children’s self-esteem as a mediator, partially explaining the association between parent–child relationship quality and psychosomatic problems from late childhood to mid-adolescence. Results from a large, nationally-representative Canadian sample indicated that self-esteem partially mediated these associations, and self-esteem accounted for more shared variance between parent–child relationship quality and psychosomatic problems among younger children. Among older children, shared variance with self-esteem explained a smaller portion of this association, but the remaining direct effect of parent–child relationship on psychosomatic problems was larger. These findings suggest that supportive parents protect against psychosomatic problems, and that they do so by promoting self-esteem for younger children and through other mechanisms as children age. Results are discussed in the context of attachment theory and age-related trends in self-esteem development.
Function Composition in Physical Chaining Applications

We introduce the notion of function composition, an interaction technique employed in several graphical user interfaces (GUIs), for use in physical chaining applications. Allowing the user to perform function composition in systems utilizing tangible user interfaces (TUIs) for input allows for more efficient use of the interactive workspace and the physical icons. In addition, it allows the user to customize the mapping of a physical icon to a function through end-user physical macro programming. In this paper we discuss the design of function composition in physical applications, as well as lessons learned from implementing function composition in one sample application, an image manipulation application.
Product Accumulate Codes on Fading Channels

Product accumulate codes are a special case of differentially coded low density parity check (LDPC) codes. This work analyzes the noncoherent performance of PA codes and general differentially-coded LDPC codes on flat Rayleigh fading channels using extrinsic information transfer charts, and proposes a convergence-constraint method to design good LDPC ensembles matched to differential coding.
DTI abnormalities in adults with past history of attention deficit hyperactivity disorder: a tract-based spatial statistics study

Background Diffusion tensor imaging (DTI) is a magnetic resonance imaging (MRI) technique enabling visualization and measurement of white matter tracts. Attention deficit hyperactivity disorder (ADHD) has been studied with DTI earlier with variable results, yet there is little research on remitted ADHD. Purpose To compare the brain white matter between ADHD drug naïve subjects whose ADHD symptoms have mostly subsided and healthy controls. Material and Methods Tract-based spatial statistics (TBSS) was used to compare 30 subjects with adolescent ADHD with control subjects at the age of 22–23 years. The study population was derived from a population-based Northern Finland Birth Cohort 1986. Fractional anisotropy (FA), mean diffusivity (MD), and measures of diffusion direction (λ1–3) were calculated. Permutation testing was used to test for differences in mean values of FA, MD, and λ1–3 between the groups. The results were corrected for multiple comparisons across the whole white matter skeleton. Results The ADHD group showed increased FA related to decreased radial diffusivity in the left forceps minor (P < 0.05). In the vicinity along the same tract, axial diffusion was significantly decreased without any significant effect on FA. No between-group difference in MD was observed. Regressor analysis revealed no gender-, IQ- or GAF-related changes. After removal of left handed subjects the statistical significance was only barely lost. Conclusion In a setting with remitted ADHD, the results may represent a compensatory mechanism in the left forceps minor.
Community-Based Literacy Learning Spaces as Counterhegemonic Figured Worlds for African American Readers

Community-based literacy learning spaces are crucial to the enduring African American pursuit of literacy. This article reports findings from a study exploring the impact of a community-based literacy tutoring program for African American readers in grades 3-5. Findings also report on ways the community literacy site was similar to historic African American figured communities. Mixed methods analysis revealed significant improvements in decoding, and counternarratives that existed with the figured community cultivated by community volunteers. Taken together, both highlight the powerful role communities’ can play in promoting African American student success. Recommendations for community organizations, teacher educators, and literacy researchers are included.
Acetylation and activation of STAT3 mediated by nuclear translocation of CD44

Expression of the type I transmembrane glycoprotein CD44 has recently been recognized as a signature for cancer stem cells. In this study, we demonstrate that CD44, once engaged, is internalized and translocated to the nucleus, where it binds to various promoters, including that of cyclin D1, leading to cell fate change through transcriptional reprogramming. In regulating cyclin D1 expression, the internalized CD44 forms a complex with STAT3 and p300 (acetyltransferase), eliciting STAT3 acetylation at lysine 685 and dimer formation in a cytokine- and growth factor–independent manner. A bipartite nuclear localization signal (NLS) was mapped to the cytoplasmic tail of CD44, which mediates its nuclear translocation. Expression of CD44(NLS) mutant sequesters STAT3 in cytosol. In the nucleus, the acetylated STAT3 dimer remains associated with CD44 and binds to the cyclin D1 promoter, leading to increased cyclin D1 expression and cell proliferation. This study describes a novel function for CD44 in transcriptional modulation through nuclear translocation of the internalized CD44 and complex formation with transcription factors.
Spectroscopic and hyperspectral evaluation of possible hydrocarbon occurrences in estuarine sediments, North Charleston, South Carolina, USA

Reflectance spectroscopy is becoming an important tool in remote identification and mapping of surface hydrocarbons, which may be very useful in determining past and present introduction of hydrocarbons into the environment. Using surface sediment samples in a complex urban/estuarine setting of North Charleston, SC it is possible to define the natural background of the area. By introducing common hydrocarbon pollutants (e.g. crude, motor oil, diesel) into typical background, a spectral library of background spectra, affected by a particular pollutant can be produced. Using the lab-derived hydrocarbon pollutant spectra as an input, it is possible to carry out classification of airborne hyperspectral data as a response to past events and baselining or current response and mapping of a potential spill. The results show that introduction of hydrocarbons produces observable effects, which can be used to delineate presence of affected areas. Relatively simple spectral-similarity algorithms (SAM, Spectral Unmixing) can be successfully used to extract the similar spectral matches in the hyperspectral image data on the basis of the library spectra produced.
The Language Acquisition Approaches and the Development of Literacy Skills in Children

The purpose of this study is to examine the language acquisition approaches whose conceptions of language acquisitions are transferred to learning environments through adjustments made on the basis of application methods. The paper also discussed their similarities and differences. Different approaches to language acquisition in various disciplines, different views, and perceptions of it have been developed. There are some approaches completely distinct from others, while there are some others affected by different perspectives. In addition to the language acquisition approaches mentioned above, the paper delineated what literacy skills are and what kind of hierarchical order is followed by the development of these skills. The study, on one hand, deliberated children’s innate abilities and their acquired skills. by examining the reading and writing methods and from which approach they have been affected. The study, on the other hand, summarized the views of Vygotsky, whose contributions to learning in general and language acquisition in particular are better understood today. In brief, this paper discusses and explains the language acquisition approaches and the development process of children’s literacy skills.
Using a genetic algorithm to model broadband regional waveforms for crustal structure in the western United States

In this study, we analyze regional seismograms to obtain the crustal structure in the eastern Great Basin and western Colorado plateau. Adopting a forward-modeling approach, we develop a genetic algorithm (GA) based parameter search technique to constrain the one-dimensional crustal structure in these regions. The data are broadband three-component seismograms recorded at the 1994-95 IRIS PASSCAL Colorado Plateau to Great Basin experiment (CPGB) stations and supplemented by data from U.S. National Seismic Network (USNSN) stations in Utah and Nevada. We use the southwestern Wyoming mine collapse event (Mb = 5.2) that occurred on 3 February 1995 as the seismic source. We model the regional seismograms using a four-layer crustal model with constant layer parameters. Timing of teleseismic receiver functions at CPGB stations are added as an additional constraint in the modeling. GA allows us to efficiently search the model space. A carefully chosen fitness function and a windowing scheme are added to the algorithm to prevent search stagnation. The technique is tested with synthetic data, both with and without random Gaussian noise added to it. Several separate model searches are carried out to estimate the variability of the model parameters. The average Colorado plateau crustal structure is characterized by a 40-km-thick crust with velocity increases at depths of about 10 and 25 km and a fast lower crust while the Great Basin has approximately 35-km-thick crust and a 2.9-km-thick sedimentary layer.
TCR and IL-7 Signaling Are Altered in the Absence of Functional GTPase of the Immune Associated Nucleotide Binding Protein 5 (GIMAP5)

GTPase of the immune associated nucleotide binding protein (GIMAP) family of proteins are expressed essentially in cells of the hematopoietic system. Mutation in the founding member of this gene family, Gimap5, results in the lymphopenic phenotype in Bio-Breeding diabetes prone rats. In mice, deletion of functional Gimap5 gene affects the survival and renewal of hematopoietic stem cells in addition to the defects observed in T cells. Here we show that T cells from OTII TCR-transgenic Gimap5sph/sph mice do not proliferate in response to its cognate antigen. Furthermore, T cells from Gimap5 mutant rats and mice show decreased phosphorylation of STAT5 following stimulation with IL-7. Our results suggest that functional Gimap5 is required for optimal signaling through TCR and IL-7R in T cells.
Diffusion and Impacts of the Internet and E-Commerce in Japan

Diffusion and Impacts of the Internet and E-Commerce in Japan 1 February 2004 DENNIS TACHIKI Faculty of Business Administration Tamagawa University tachiki@bus.tamagawa. ac.jp SATOSHI HAMAYA Economic Research Center Fujitsu Research Institute hamayas@fri.fujitsu. com KOH YUKAWA Economic Research Center Fujitsu Research Institute yukawak@fri.fujitsu. com This research is part of the Globalization and E-Commerce project of the Center for Research on Information Technology and Organizations (CRITO) at the University of California, Irvine. The material is based upon work supported by a grant to CRITO from the National Science Foundation (CISE/IIS/DST, Grant No. 0085852). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Center for Research on Information Technology and Organizations University of California, Irvine | www.crito. uci.edu
Hyperion: High Volume Stream Archival for Retrospective Querying

Network monitoring systems that support data archiving and after-the-fact (retrospective) queries are useful for a multitude of purposes, such as anomaly detection and network and security forensics. Data archiving for such systems, however, is complicated by (a) data arrival rates, which may be hundreds of thousands of packets per second on a single link, and (b) the need for online indexing of this data to support retrospective queries. At these data rates, both common database index structures and general-purpose file systems perform poorly. This paper describes Hyperion, a system for archiving, indexing, and on-line retrieval of high-volume data streams. We employ a write-optimized stream file system for high-speed storage of simultaneous data streams, and a novel use of signature file indexes in a distributed multi-level index. We implement Hyperion on commodity hardware and conduct a detailed evaluation using synthetic data and real network traces. Our streaming file system, StreamFS, is shown to be fast enough to archive traces at over a million packets per second. The index allows queries over hours of data to complete in as little as 10-20 seconds, and the entire system is able to index and archive over 200,000 packets/sec while processing simultaneous on-line queries.
Viscous pump for highly backdrivable Electro-Hydrostatic Actuator

It is widely acknowledged that the actuator's intrinsic backdrivability is important in realizing a force sensitive behavior. It is desirable to realize such actuator with electric motor that is advantageous from power-to-weight ratio and controllability point of view. Electro-Hydrostatic Actuator is a type of hydraulic actuators that can realize high backdrivability by reducing transmission friction and by providing dynamics decoupling with an implicit serial damper. To farther enhance the backdrivability of a EHA, a pump with minimum static and Coulomb friction is necessary. In this paper, we introduce an EHA with viscous screw pump that minimizes static and Coulomb friction by eliminating the mechanical contact between pump components. Viscous screw pumps also have the advantage that there is no pulsation in pressure due to the continuity of the force transmission from the rotor to the fluid. The property of the actuator, including pulsation performance and impedance control performance were evaluated on a prototype of EHA with a viscous screw pump.
COMPOSITION, COORDINATION AND SIMULATION OF REACTIVE FUZZY BEHAVIORS FOR AN MOBILE AGRICULTURAL ROBOT

The work presents the development of a complex navigational behavior combining some simple fuzzy behaviors for a mobile agricultural robot (MAR). Fuzzy rules are used to compose and coordinate the simple behaviors and an experimental robotic platform based on Khepera mini-robot is proposed to simulate and support the researches on behavior based architecture for agricultural robots. The mini-robot is used for testing of the navigational controller with an integrated perceptual circuit based on light dependent resistors (LDR) to facilitate a path following behavior. Experiments have been performed to evaluate the implemented behaviors and the ability of the platform to operate on a simulated agricultural environment. The results show the feasibility of the approach on the platform and the behaviors that could be used to improve behavior based architectures for MAR’s.
Linked data as enabler for mobile applications for complex tasks in industrial settings

Nowadays, apps provide support for various simple tasks. They are easy to use and highly usable. However, future apps should support more complex workflows especially when trying to enter the professional business world. They need to provide higher reusability and composability in order to make them suitable for complex and alterable workflows that are common in industry. The concept of App Orchestration allows supporting complex tasks with aid of an ensemble of adapted and managed apps. Therefore, the apps raise several demands on the underlying information backend. This article describes these requirements and presents the Linked Data approach, which is a possible methodology for an integrated, semantically described information space for this purpose. It describes possible uses and benefits for the concept of App Orchestration and shows them in a use case of mobile maintenance. It further discusses the current status of the approach and provides future research challenges.