Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase.

Molecular mechanisms of RNA recombination were studied in turnip crinkle carmovirus (TCV), which has a uniquely high recombination frequency and non‐random crossover site distribution among the recombining TCV‐associated satellite RNAs. To test the previously proposed replicase‐driven template‐switching mechanism for recombination, a partially purified TCV replicase preparation (RdRp) was programed with RNAs resembling the putative in vivo recombination intermediates. Analysis of the in vitro RdRp products revealed efficient generation of 3′‐terminal extension products. Initiation of 3′‐terminal extension occurred at or close to the base of a hairpin that was a recombination hotspot in vivo. Efficient generation of the 3′‐terminal extension products depended on two factors: (i) a hairpin structure in the acceptor RNA region and (ii) a short base‐paired region formed between the acceptor RNA and the nascent RNA synthesized from the donor RNA template. The hairpin structure bound to the RdRp, and thus is probably involved in its recruitment. The probable role of the base‐paired region is to hold the 3′ terminus near the RdRp bound to the hairpin structure to facilitate 3′‐terminal extension. These regions were also required for in vivo RNA recombination between TCV‐associated sat‐RNA C and sat‐RNA D, giving crucial and direct support for a replicase‐driven template‐switching mechanism of RNA recombination.
Golgi Localization and Functionally Important Domains in the NH2 and COOH Terminus of the Yeast CLC Putative Chloride Channel Gef1p*

GEF1 encodes the single CLC putative chloride channel in yeast. Its disruption leads to a defect in iron metabolism (Greene, J. R., Brown, N. H., DiDomenico, B. J., Kaplan, J., and Eide, D. (1993) Mol. Gen. Genet. 241, 542–553). Since disruption of GEF2, a subunit of the vacuolar H+-ATPase, leads to a similar phenotype, it was previously suggested that the chloride conductance provided by Gef1p is necessary for vacuolar acidification. We now show that gef1cells indeed grow less well at less acidic pH. However, no defect in vacuolar acidification is apparent from quinacrine staining, and Gef1p co-localizes with Mnt1p in the medial Golgi. Thus, Gef1p may be important in determining Golgi pH. Systematic alanine scanning of the amino and the carboxyl terminus revealed several regions essential for Gef1p localization and function. One sequence (FVTID) in the amino terminus conforms to a class of sorting signals containing aromatic amino acids. This was further supported by point mutations. Alanine scanning of the carboxyl terminus identified a stretch of roughly 25 amino acids which coincides with the second CBS domain, a conserved protein motif recently identified. Mutations in the first CBS domain also destroyed proper function and localization. The second CBS domain can be transplanted to the amino terminus without loss of function, but could not be replaced by the corresponding domain of the homologous mammalian channel ClC-2.
A Method for Performing Secure User-Authentication Over a Hands-Free , Voice Communications Device 27-Jun-05

When authenticating over the telephone or mobile headphone, the user cannot always assure that no eavesdropper hears the authentication secret. We describe an eavesdropperresistant authentication scheme for spoken authentication. This entails the user memorizing a small number of plaintext-ciphertext pairs. At authentication, these are challenged randomly and interspersed with camouflage elements. It is shown that the response can be made to appear random so that no information on the memorized secret is available to eavesdroppers. We describe the method along with parameter value tradeoffs of security strength, authentication time, and memory effort. We also describe early results of its implementation in a hands-free communication system deployed at a hospital. This method is not restricted to spoken passwords. In general, it is a one-time password scheme that can be used, for instance, for computer login to defend against keystroke logger attacks. An advantage over other one-time schemes is that it does not require the user to carry a token or password list.
An approach to stabilizing the fast array RLS adaptive filter using homogeneous coordinates in projective geometry

The fast array RLS (FARLS) adaptive filter employs a circular and hyperbolic rotation to transform from a pre-array to a post-array. The algorithm is known to be numerically unstable for finite-precision implementations. It is believed that the difficulty lies in the numerical computation of the hyperbolic rotation. We propose the use of homogeneous coordinates in projective geometry to transform the hyperbolic rotation to a circular rotation. This rotation (being circular) is numerically stable. However, the transformation to the new circular representation in the projective coordinates is still numerically difficult. Nevertheless, this method may lead to a new approach that completely circumvents the instability.
Runtime Mechanisms for Eecient Dynamic Multithreading Running Head Runtime Mechanisms for Dynamic Multithreading

High performance on distributed memory machines for programming models with dynamic thread creation and multithreading requires eecient thread management and communication. Traditional mul-tithreading runtimes, consisting of few general-purpose, bundled mechanisms that assume minimal compiler and hardware support, are suitable for computations involving coarse-grained threads but provide low eeciency in the presence of small granularity threads and irregular communication behavior. We describe two mechanisms of the Illinois Concert runtime system which address this shortcoming. The rst, hybrid stack-heap execution, exploits close coupling with the compiler to dynamically form coarse-grained execution units; threads are lazily created as required by runtime situations. The second, pull messaging, exploits hardware support to implement a distributed message queue with receiver-initiated data transfer, delivering robust performance across a wide range of dynamic communication characteristics. We measure their performance impact based on a Cray T3D implementation of the Concert system. Individually, the mechanisms increase absolute execution eeciency by up to 50%. Together, they increase the feasible space of eecient computations, enabling compute granularities an order of magnitude smaller. Performance results for two large irregular applications demonstrate that expressing programs using dynamic multithreading need not compromise on performance.
EFFECT OF REWARD MANAGEMENT PRACTICES ON ORGANIZATIONAL COMMITMENT IN STATE CORPORATIONS IN KENYA: A CASE STUDY OF KEFRI

Studies indicate that when employees are committed to organizations they work for they produce better outcomes for such organizations. Rewards are considered as one of the tools for enhancing organizational commitment. The pertinent issues of reward management practices that KEFRI could be facing are similar to what other research institutions are facing. This study therefore sought to investigate the effect of reward management practices on organizational commitment in KEFRI. In this regard, the study was guided by two specific objectives: to establish the effect of benefits administration and to find out what employees perceived as the base for rewards. This study adopted a case study research design using stratified sampling since data was gathered from a single source. The population was divided into sets or strata and which were mutually exclusive. The unit of analysis was the entire population of KEFRI employees, 1012 in number from which a sample of 100 was derived at from top management, middle and lower level staff. The study used questionnaires and interviews as the data collection instruments. The research carried out a pilot study to pretest and validate the instruments. Quantitative data collected were analyzed using SPSS (Version 22). Content analysis was used to test data that was qualitative in nature or aspect of the data collected from the open ended questions. The information was presented using tables, charts and in prose form. Key Words: Benefits of Administration, Base for Rewards, Rewards Management Practices, Organizational Commitment, KEFRI
Flexible 3D Object Recognition Framework Using 2D Views via a Similarity-Based Aspect-Graph Approach

This work presents a flexible framework for recognizing 3D objects from 2D views. Similarity-based aspect-graph, which contains a set of aspects and prototypes for these aspects, is employed to represent the database of 3D objects. An incremental database construction method that maximizes the similarity of views in the same aspect and minimizes the similarity of prototypes is proposed as the core of the framework to build and update the aspect-graph using 2D views randomly sampled from a viewing sphere. The proposed framework is evaluated on various object recognition problems, including 3D object recognition, human posture recognition and scene recognition. Shape and color features are employed in different applications with the proposed framework and the top three matching rates show the efficiency of the proposed method.
African immigrant women’s experience in western host societies: a scoping review

Abstract There is a dearth of literature on new African immigrant populations in Canada, especially women from Sub-Saharan Africa. Much of the sparse literature focuses on men’s experiences. We analyzed the sparse literature on African immigrant women in western host countries with a focus on previous and emerging trends in the discourse, gaps in literature, important areas for consideration in future research as well as potentially viable theoretically and methodological directions that scholars could follow. We also briefly shared the results of a set of focus group discussions with African women in Canada that followed our scoping review. The findings of our scoping review of literature, largely reinforced in the focus group discussions, underscore the need for more studies on Sub-Saharan African immigrant women’s experiences within and outside the family. Active community engagement as well as the mobilization of women's agency and cultural knowledge, resonate as crucial factors that enhance the transition and integration of Africans into Western host societies.
Association of Eleven Common, Low-Penetrance Colorectal Cancer Susceptibility Genetic Variants at Six Risk Loci with Clinical Outcome

Background Low-penetrance genetic variants have been increasingly recognized to influence the risk of tumor development. Risk variants for colorectal cancer (CRC) have been mapped to chromosome positions 8q23.3, 8q24, 9p24.1, 10p14, 11q23, 14q22.2, 15q13, 16q22.1, 18q21, 19q13.1 and 20p12.3. In particular, the 8q24 single nucleotide polymorphism (SNP), rs6983267, has reproducibly been associated with the risk of developing CRC. As the CRC risk SNPs may also influence disease outcome, thus in this study, we evaluated whether they influence patient survival. Methodology/Principal Findings DNA samples from 583 CRC patients enrolled in the prospective, North Carolina Cancer Care Outcomes Research and Surveillance Consortium Study (NC CanCORS) were genotyped for 11 CRC susceptibility SNPs at 6 CRC risk loci. Relationships between genotypes and patient survival were examined using Cox regression analysis. In multivariate analysis, patients homozygous for the CRC risk allele of rs7013278 or rs7014346 (both at 8 q24) were only nominally significant for poorer overall survival compared to patients homozygous for the protective allele (hazard ratio = 2.20 and 1.96, respectively; P<0.05). None of these associations, however, remained statistically significant after correction for multiple testing. The other nine susceptibility SNPs tested were not significantly associated with survival. Conclusions/Significance We did not find evidence of association of CRC risk variants with patient survival.
Self-organization, Learning and Language

Several issues related to learning process are discussed from the viewpoint of self-organization in this paper. Though Hebbian rule and BCM rule are widely used in learning process, there may be a more general mechanism behind the rules and J structure with specific attractors may be such kind of mechanism. Chinese character learning is good example of learning process. A neural network based on Hebbian rule is developed to learn Chinese grapheme. The results show that the Chinese character can be learned with appropriate parameters and integration method. Two properties in Chinese learning at behavioral level are discussed. However, at the level of neurons and neuron groups, a small network with dynamic synapse was put forward by Berger and the complex cognitive activities such as sound recognition can be achieved by such simple neural network. The supposition the that there should be basic mechanism to govern cognitive activities is partly validated. Furthermore, information is involved in any learning process. How information changes is the core problem of learning process and still open. Some discussion on this problem is also given in this paper
Small Nuclear Ribonucleoprotein Remodeling During Catalytic Activation of the Spliceosome

Major structural changes occur in the spliceosome during its activation just before catalyzing the splicing of pre–messenger RNAs (pre-mRNAs). Whereas changes in small nuclear RNA (snRNA) conformation are well documented, little is known about remodeling of small nuclear ribonucleoprotein (snRNP) structures during spliceosome activation. Here, human 45S activated spliceosomes and a previously unknown 35S U5 snRNP were isolated by immunoaffinity selection and were characterized by mass spectrometry. Comparison of their protein components with those of other snRNP and spliceosomal complexes revealed a major change in protein composition during spliceosome activation. Our data also suggest that the U5 snRNP is dramatically remodeled at this stage, with the Prp19 complex and other factors tightly associating, possibly in exchange for other U5 proteins, and suggest that after catalysis the remodeled U5 is eventually released from the postsplicing complex as a 35S snRNP particle.
Myth busters: Microprocessor clocking is from Mars, ASICs clocking is from Venus

This paper compares and contrasts two common clock distribution styles: clock grids, the preferred microprocessor distribution style, and clock trees, the preferred ASICs distribution style. After a high level description of the routing methodologies for clock grids and clock trees, a case study is presented to compare the performance and cost trade-off of grids and trees. Our results show that clock grids consume more power and wiring resources but only to achieve aggressive clock targets. In this example a clock tree style uses 28% less wiring than a full clock grid style but suffers 12 ps more skew. However, compared to a sparse grid style, a clock tree solution uses only 4% less wiring and suffers 9.6 ps higher skew. The key message is that the cost in extra wiring and power consumption across different clock distribution styles is mainly driven by performance targets as opposed to being fundamentally dictated by the grid vs. tree decision.
Cd30 Expression in Peripheral T-cell Lymphoma Early Release Paper

Haematologica 2013 [Epub ahead of print] Publisher's Disclaimer. E-publishing ahead of print is increasingly important for the rapid dissemination of science. Haematologica is, therefore, E-publishing PDF files of an early version of manuscripts that have completed a regular peer review and have been accepted for publication. E-publishing of this PDF file has been approved by the authors. After having E-published Ahead of Print, manuscripts will then undergo technical and English editing, typesetting, proof correction and be presented for the authors' final approval; the final version of the manuscript will then appear in print on a regular issue of the journal. All legal disclaimers that apply to the journal also pertain to this production process. www.haemato-logica.org) publishes peer-reviewed papers across all areas of experimental and clinical hematology. The journal is owned by the Ferrata Storti Foundation, a non-profit organization , and serves the scientific community with strict adherence to the principles of open access publishing (www.doaj.org). In addition, the journal makes every paper published immediately available in PubMed Central (PMC), the US National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature. Support Haematologica and Open Access Publishing by becoming a member of the European Hematology Association (EHA) and enjoying the benefits of this membership, which include free participation in the online CME program
The role of unlearning in metamorphosis and strategic resilience

Purpose This paper aims to conceptualize what it means to be resilient in the face of our current reality of indisputable turbulence and uncertainty, suggest that continual metamorphosis is key to resilience, demonstrate the role of unlearning in that metamorphosis and suggest that problem formulation is a key deliberate mechanism of driving continual cycles of learning and unlearning. Design/methodology/approach The paper entails a conceptual analysis. Findings It is found that both the unlearning and resilience literature streams are stuck in a paradigm whereby organizational behavior entails adaptation to the external environment and reaction to crisis. This paper suggests that, given a world of turbulence and uncertainty, a more useful paradigm is one where organizations take action before action is desperately needed, and that they proactively contribute to enacting their environment via their own continual metamorphosis. Research limitations/implications Future research should explore further the factors that can facilitate sensing the early warning signs, and facilitate the cyclical learning–unlearning process of metamorphosis. Practical implications The primary practical implication is that to ensure strategic resilience, managers must be able to identify early warning signs and initiate metamorphosis. This means understanding the processes needed to support unlearning, namely, problem formulation. Originality/value The originality and value of the present paper lies in that it suggests a shift in paradigm from adaptation and reaction, to action and enactment. Further, it proposes a cyclical process of learning and unlearning that together define periods of metamorphosis, and suggests problem formulation, whereby the mission statement is assessed and revised, as a mechanism in that endeavor.
Set-theoretical Properties of Extreme Combinatorial Problems

Concepts of constructive combinatorial problem and, in particular, of extreme combinatorial problem (ECP) are deened. It is announced a sequential principle of construction of the constructive combinatorial problems' solution. This principle leads to necessity to consider ECP as system of independence with weighted elements. Auxiliary sets, which are connected to the solution of optimization problem, are deened. Concept of a normal form of the ECP is introduced. It is established that representation of a problem in normal form in some cases permits essentially to simplify an initial problem. It is introduced concepts of dual and self-dual problems. Two classes of combinatorial optimization problems, which are discerned by method of search of the admissible solution, are considered. Concept of the canonical form the ECP is introduced. It is shown that the problem in canonical form { new problem which is equivalent to initial, i.e. all optimum solutions of a problem in canonical form are the optimum solutions of an initial problem as well. The fulllled researches in some cases simplify the search of the optimization problem solution. 1 Statement of the problem In combinatorics concept of sample is deened 6]. (m) , called ordered or disorder sample respectively. If W (1) = W (2) = = W (m) = W, it is said to be an sample of elements from the set W. One of main problems of combinatorics is construction of such sample from elements of initial n-set W which satisses to given restrictions. Any combinatorial problem on construction of sample we'll call constructive.
A New Dynamic-Bias Measurement Setup for Nonlinear Transistor Model Identification

In this paper, we present a new dynamic-bias measurement setup and its application to the extraction of a nonlinear model for microwave field-effect transistors. The dynamic-bias technique has been recently proposed and relies on the use of low-frequency (LF) and high-frequency (HF) vector-calibrated measurements acquired, for instance, by means of a large-signal network analyzer. In this paper, we propose a new and alternative technique to perform the dynamic-bias measurements, based on relatively low-cost instrumentation commonly available in microwave laboratories. The new acquisition system is composed of a four-channel vector LF receiver (e.g., an oscilloscope) and a one-channel HF scalar receiver (e.g., a spectrum analyzer), which replace the eight-channel vector receiver. Moreover, the proposed architecture greatly simplifies the measurement setup and the calibration procedure. As a case study, a 0.25- $\mu \text{m}$ GaN HEMT is considered. Dynamic-bias measurements, carried out by means of the proposed measurement setup, are used for the identification of a nonlinear model of this device. Finally, the model is fully validated through comparison with time-domain harmonic load–pull measurements carried out at 5 GHz.
Protein Crystallography in Vaccine Research and Development

The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines.
Is the Optically Unidentified Radio Source FIRST J121839.7+295325 a Dark Lens?

We present evidence that the optically unidentified radio source FIRST J121839.7+295325 may be strongly lensing a background galaxy. We estimate the redshift of the assumed gravitational arc, discovered in parallel imaging with HST, from MMT-Blue Channel spectroscopy to be zarc = 2.48−0.05+0.14. We present lens models with an Einstein radius of RE = 1.3′′ which contains a mass of Mdyn = 1012 ± 0.5 M☉, where the uncertainty reflects the range of possible lens redshifts. The putative lens is not detected to Jlim = 22.0 mag and Hlim = 20.7 mag in our MMT-SWIRC imaging. Using the flux limits from WFPC2 and SWIRC, we estimate that the dynamical mass-to-light ratio of J121839.7+295325 is Mdyn/LB ≳ 10 M☉ L☉−1 for AV = 1 mag, and this lower limit could be as high as 30 M☉ L☉−1 for AV = 0 mag. Since the radio source is optically unidentified (Vlim = 25.5 mag) and has a radio flux of S1.4 GHz = 33 mJy, it is likely a massive early-type galaxy which hosts a radio-loud AGN at 0.8 ≲ zradio ≲ 1.5. However, the present data cannot uniquely determine the mass-to-light ratio of the lensing galaxy, and hence the possibility that this system may be a reasonably dark lens is not ruled out.