Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicted amino acid sequences for 100 JCV strains

DNA sequence variation between JCV genotypes is confined largely to noncoding intergenic regions and introns. Nevertheless, evidence suggests that the amino acid sequence variations among the 8 genotypes of JCV can influence the potential for neurovirulence of the virus. In the current study, the amino acid sequences for 100 JCV genomes were translated and grouped into genotype families. Subtype consensus sequences were determined and the type-specific amino acid sequence variants were identified.
Inhibition of pp125FAK in cultured fibroblasts results in apoptosis

The tyrosine kinase called pp125FAK is believed to play an important role in integrin-mediated signal transduction. pp125FAK is associated both functionally and spatially with integrins, which are the cell surface receptors for extracellular matrix components. Although the precise function of pp125FAK is not known, two possibilities have been proposed: pp125FAK may regulate the assembly of focal adhesions in spreading or migrating cells, or pp125FAK may participate in a signal transduction cascade to inform the nucleus that the cell is anchored. To test these models in living cells, a peptide representing the focal adhesion kinase (FAK)-binding site of the beta 1 tail was coupled to carrier protein and injected into cultured cells to competitively inhibit the binding of pp125FAK to endogenous integrin, thus inhibiting activation of pp125FAK on a cell-by-cell basis. In addition, an antibody directed against an epitope adjacent to the focal adhesion targeting sequence on pp125FAK was microinjected, as an alternative means of inhibiting pp125FAK activation. It was observed that when rounded cells were injected with either the integrin peptide or the anti-FAK antibody, the cells rapidly began to apoptose, within 4 h after injection. These results indicate that pp125FAK may play a critical role in suppressing apoptosis in fibroblasts.
Degrees of freedom achieved using subspace alignment chains for three-cell networks

In this paper we extend the notion of subspace alignment chains (SACs) for the three-user multiple-input multiple-output (MIMO) interference channel to three-cell MIMO cellular networks. By extending the notion of SACs to three-cell networks we show that when d ϵ Z+ DoF/user are achievable in a three-user M × N interference channel (IC) using linear beamforming, then any DoF-tuple {dij}, where dij ϵ Z+ represents the DoF of the jth user in the ith cell, that satisfies Σj=1k dij ≤ d ∀ i is achievable in a three-cell MIMO cellular network with K users per cell having M antennas per user and N antennas per base station (i.e., the (3, K, M, N) network) using linear beamforming. When restricted to symmetric DoF, this result states that whenever d DoF/user are achievable in a three-user M × N IC with d = rs, for some r, s ϵ Z+, then r DoF/user are achievable in the (3, s, M, N) network. Although the DoF achieved using SACs is not necessarily the largest possible, they are established through a constructive procedure where we show how SACs designed for the three-user interference channel can be modified to design transmit beamformers for the three-cell MIMO cellular networks. Further, we highlight the role played by redundant antennas in reducing the computational cost of designing transmit beamformers for interference alignment.
Digital MDA for enumeration of total nucleic acid contamination

Multiple displacement amplification (MDA) is an isothermal, sequence-independent method for the amplification of high molecular weight DNA that is driven by ϕ29 DNA polymerase (DNAP). Here we report digital MDA (dMDA), an ultrasensitive method for quantifying nucleic acid fragments of unknown sequence. We use the new assay to show that our custom ϕ29 DNAP preparation is free of contamination at the limit of detection of the dMDA assay (1 contaminating molecule per assay microliter). Contamination in commercially available preparations is also investigated. The results of the dMDA assay provide strong evidence that the so-called ‘template-independent’ MDA background can be attributed to high-molecular weight contaminants and is not primer-derived in the commercial kits tested. dMDA is orders of magnitude more sensitive than PCR-based techniques for detection of microbial genomic DNA fragments and opens up new possibilities for the ultrasensitive quantification of DNA fragments in a wide variety of application areas using MDA chemistry and off-the-shelf hardware developed for digital PCR.
Scale‐Free and Hierarchical Structures in Complex Networks

Networks with complex topology describe systems as diverse as the cell or the World Wide Web. The emergence of these networks is driven by self-organizing processes that are governed by simple but generic laws. In the last three years it became clear that many complex networks, such as the Internet, the cell, or the world wide web, share the same large-scale topology. Here we review recent advances in the characterization of complex networks, focusing the emergence of the scale-free and the hierarchical architecture. We also present empirical results to demonstrate that the scale-free and the hierarchical property are shared by a wide range of complex networks. Finally, we discuss the impact of the network topology on our ability to stop the spread of viruses in complex networks.
The effects of sentence context on the processing of figurative language in an adult population with normal cognition

The purpose of this study was to investigate how contextual information, prior to an idiomatic expression, affects the automatic processing of idiomatic expressions in an adult population with normal cognition. An on-line wordmonitoring reaction-time task was used in which subjects were required to identify target words in spoken passages. The target words were final words from six idiomatic expressions. The idiomatic expressions were embedded in contexts biasing them to either a figurative interpretation, a literal interpretation, or an ambiguous context in which neither a figurative or a literal interpretation could be predicted from the contextual information preceding the idiomatic phrase. A filler condition was also presented in which target words were presented without the idiomatic expressions. It was found that subjects responded faster to target words in the idiomatic, literal, and ambiguous context conditions than to target words in the filler condition. Reaction times to target words in the literal context condition were faster than target words in the ambiguous context condition. Reaction times to target words in idiomatic context conditions were faster than ambiguous context conditions and slower than literal context conditions; however, this difference was not significant. These results support the Key Word Hypothesis which assumes that idiomatic expressions are processed literally until the key word is encountered. When the key word is encountered, the figurative interpretation is triggered.
Principal stream surfaces

The use of stream surfaces and streamlines is well established in vector visualization. However, the proper placement of starting points is critical for these constructs to clearly illustrate the flow topology. In this paper, we present the principal stream surface algorithm, which automatically generates stream surfaces that properly depict the topology of an irrotational flow. For each velocity point in the fluid field, we construct the normal to the principal stream surface through the point. The set of all such normal vectors is used to construct the principal stream function, which is a scalar field describing the direction of velocity in the fluid field. Volume rendering can then be used to visualize the principal stream function, which is directly related to the flow topology. Thus, topology in a fluid field can be easily modeled and rendered.
Neutral Competition for Drosophila Follicle and Cyst Stem Cell Niches Requires Vesicle Trafficking Genes

Stem cell niche competition a common but poorly understood process. One impediment to understanding is a lack of useful niche competition alleles. In. The process of selecting for cellular fitness through competition plays a critical role in both development and disease. The germarium, a structure at the tip of the ovariole of a Drosophila ovary, contains two follicle stem cells (FSCs) that undergo neutral competition for the stem cell niche. Using the FSCs as a model, we performed a genetic screen through a collection of 126 mutants in essential genes on the X chromosome to identify candidates that increase or decrease competition for the FSC niche. We identified ∼55 and 6% of the mutations screened as putative FSC hypo- or hyper-competitors, respectively. We found that a large majority of mutations in vesicle trafficking genes (11 out of the 13 in the collection of mutants) are candidate hypo-competition alleles, and we confirmed the hypo-competition phenotype for four of these alleles. We also show that Sec16 and another COPII vesicle trafficking component, Sar1, are required for follicle cell differentiation. Lastly, we demonstrate that, although some components of vesicle trafficking are also required for neutral competition in the cyst stem cells of the testis, there are important tissue-specific differences. Our results demonstrate a critical role for vesicle trafficking in stem cell niche competition and differentiation, and we identify a number of putative candidates for further exploration.
An Optimized Switching Strategy for Quick Dynamic Torque Control in DTC-Hysteresis-Based Induction Machines

A dynamic overmodulation strategy for fast dynamic torque control in direct torque control (DTC)-hysteresis-based induction machine is proposed. The fastest dynamic torque response with a six-step mode can be achieved in the proposed method by switching only the most optimized voltage vector that produces the largest tangential component to the circular flux locus. This paper also discusses the performance of dynamic torque control in basic DTC in order to justify on how the proposed selected voltage vector results in excellent dynamic torque performance. The main benefit of the proposed method is its simplicity, since it only requires a minor modification to the conventional DTC-hysteresis-based structure and does not require a space vector modulator. To verify the feasibility of the proposed dynamic overmodulation strategy, simulation and experimentation, as well as comparison with the conventional DTC scheme, are carried out. Results showed a significant improvement in the dynamic torque response when compared to the conventional DTC-hysteresis-based method.
Bandwidth Reservation as a Coexistence Strategy in Opportunistic Spectrum Access Environments

We consider a scenario in which a licensed wireless operator or primary network (PN) coexists with an ad-hoc, cognitive, secondary network. To minimize harmful interference on the primary users (PUs), secondary users (SUs) sense the PU activity on the licensed spectrum band before transmitting in spectrum opportunities. We study a bandwidth reservation (BR) scheme by which the PN keeps a set of adjacent channels free of PU transmissions. These reserved channels only accommodate PU traffic when all the non-reserved channels are used, and the SUs only occupy available channels within the reserved spectrum. Intuitively, this strategy reduces collision probability and simplifies the design of opportunistic spectrum access (OSA) mechanisms. However, from the point of view of the PN, BR entails a tradeoff between the benefits of an improved coexistence with SUs, and the capacity reduction associated to having fewer options for PU channel allocation. The main objective of this paper is to determine when BR improves the overall PN performance under SU activity. The SUs are characterized by a hardware limited radio, imperfect spectrum sensing, bayesian estimation of PU activity and multichannel access. Because PU capacity is the central issue, we assume a PN capable of exploiting all the available bandwidth at every moment. By means of a Markov-reward model, we compute the expected PU capacity with and without BR, considering propagation effects, interference and random locations. The results show that, in a non-congested PN with SU activity, the interference reduction capability of BR increases the overall capacity of the PN compared to not using BR.
Time to choose – DSM-5, ICD-11 or both?

DSM-5 was published in May 2013, and ICD 11 is not due to be published until the end of 2015 at the earliest. Nevertheless, it is possible to make a comparison at this early stage as much of the main decisions have been made with both classifications. DSM-5 aimed to make a paradigm shift by providing objective, independent measures of classification, but in this respect it clearly failed. It did respond to previous criticisms that there were too many diagnoses in the classification and that eliminated some conditions in favour of larger groupings (eg, autism spectrum disorder), but it has still come in for heavy criticism. ICD 11 deviates from DSM-5 in radically different classifications of personality and stress disorders and in general has pursued a different pathway, concentrating on clinical utility as the main guide to the classification. It is up to practitioners to choose which they prefer, but ICD 11 will be in a much stronger position than ICD 10 was when it was published in 1992.
Seasonal variation in hypothalamic content of gonadotropin-releasing hormone (GnRH), pituitary receptors for GnRH, and pituitary content of luteinizing hormone and follicle-stimulating hormone in the mare.

Seasonal changes in the hypothalamic-hypophyseal axis were investigated using tissue from 49 light-horse mares, of mixed breeding. Hypothalamic and pituitary tissues were collected at 5 intervals throughout the years 1981 and 1982, representing midbreeding season (July, n = 10), transition out of the breeding season (October, n = 11), midanestrus (December, n = 8), transition into the breeding season (March, n = 10), and again in the following midbreeding season (July, n = 10). The hypothalamic region was dissected into preoptic area, body and median eminence. Gonadotropin-releasing hormone (GnRH) was extracted from hypothalamic samples with methanol-formic acid and quantified by radioimmunoassay. The anterior pituitary was homogenized and receptors for GnRH were quantified in a crude membrane fraction. Concentrations of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) were measured in the resulting supernatant. Content of GnRH in each of the 3 hypothalamic areas varied with season (P less than 0.01) and was lowest during midanestrus (P less than 0.05). There was no effect of season (P greater than 0.01) on either concentration or total number of receptors for GnRH, or concentration of FSH in the anterior pituitary. Concentrations of LH in the anterior pituitary varied with season (P less than 0.001). Means (+/- SEM) for the 5 collection times were 15.5 +/- 2.7, 9.7 +/- 2.4, 2.3 +/- 0.5, 2.7 +/- 0.4 and 11.7 +/- 1.5 microgram LH/mg anterior pituitary, respectively. (ABSTRACT TRUNCATED AT 250 WORDS)
A radix-4 soft-output Viterbi architecture

A new radix-4 soft-output Viterbi architecture is presented, which achieves higher data rates than prior radix-2 SOVA designs. The proposed architecture is also more hardware-efficient than a previously reported radix-4 SOVA architecture. New circuits are presented for the generation of path metric differences, the path comparison unit, and reliability update unit. The presented architecture is suitable for highspeed applications such as magnetic recording, where data rates are currently approaching 3 Gb/s.
Refactoring test code

Two key aspects of extreme programming (XP) are unit testing and merciless refactoring. Given the fact that the ideal test code / production code ratio approaches 1:1, it is not surprising that unit tests are being refactored. We found that refactoring test code is different from refactoring production code in two ways: (1) there is a distinct set of bad smells involved, and (2) improving test code involves additional test-specific refactorings. To share our experiences with other XP practitioners, we describe a set of bad smells that indicate trouble in test code, and a collection of test refactorings to remove these smells.
Deferred Action: Theoretical model of process architecture design for emergent business processes

E-Business modelling and ebusiness systems development assumes fixed company resources, structures, and business processes. Empirical and theoretical evidence suggests that company resources and structures are emergent rather than fixed. Planning business activity in emergent contexts requires flexible ebusiness models based on better management theories and models . This paper builds and proposes a theoretical model of ebusiness systems capable of catering for emergent factors that affect business processes. Drawing on development of theories of the ‘action and design’class the Theory of Deferred Action is invoked as the base theory for the theoretical model. A theoretical model of flexible process architecture is presented by identifying its core components and their relationships, and then illustrated with exemplar flexible process architectures capable of responding to emergent factors. Managerial implications of the model are considered and the model’s generic applicability is discussed.
Public health implications of sleep loss: the community burden

Poor sleep imparts a significant personal and societal burden. Therefore, it is important to have accurate estimates of its causes, prevalence and costs to inform health policy. A recent evaluation of the sleep habits of Australians demonstrates that frequent (daily or near daily) sleep difficulties (initiating and maintaining sleep, and experiencing inadequate sleep), daytime fatigue, sleepiness and irritability are highly prevalent (20%–35%). These difficulties are generally more prevalent among females, with the exception of snoring and related difficulties. While about half of these problems are likely to be attributable to specific sleep disorders, the balance appears attributable to poor sleep habits or choices to limit sleep opportunity. Study of the economic impact of sleep disorders demonstrates financial costs to Australia of $5.1 billion per year. This comprises $270 million for health care costs for the conditions themselves, $540 million for care of associated medical conditions attributable to sleep disorders, and about $4.3 billion largely attributable to associated productivity losses and non‐medical costs resulting from sleep loss‐related accidents. Loss of life quality added a substantial further non‐financial cost. While large, these costs were for sleep disorders alone. Additional costs relating to inadequate sleep from poor sleep habits in people without sleep disorders were not considered. Based on the high prevalence of such problems and the known impacts of sleep loss in all its forms on health, productivity and safety, it is likely that these poor sleep habits would add substantially to the costs from sleep disorders alone.
Method to study cell migration under uniaxial compression

A method is described for imposing mechanical compression on individual cells while monitoring their morphology and migratory phenotype. A compression of the order of 500 Pa flattens the cells by up to 50% and triggers a transition in the mode of migration. This approach is convenient for studying mechanotransduction in confined environments.
1.5 billion words Arabic Corpus

This study is an attempt to build a contemporary linguistic corpus for Arabic language. The corpus produced, is a text corpus includes more than five million newspaper articles. It contains over a billion and a half words in total, out of which, there is about three million unique words. The data were collected from newspaper articles in ten major news sources from eight Arabic countries, over a period of fourteen years. The corpus was encoded with two types of encoding, namely: UTF-8, and Windows CP-1256. Also it was marked with two mark-up languages, namely: SGML, and XML.
Effects of Parental Interpersonal Power/Prestige and Acceptance on the Psychological Adjustment of Spanish Youth

This article analyzed the moderator role of perceived interpersonal power and prestige in the relation between perceived parental acceptance and children’s psychological adjustment. The sample consisted of 187 children (43% boys) ranging in age from 9 through 12 years (M = 10.58). The measures used were the child versions of the Parental Acceptance–Rejection Questionnaire, the youth version of the Parental Power–Prestige Questionnaire, and the child version of the Personality Assessment Questionnaire. Results indicate that perceived maternal acceptance and perceived paternal acceptance were significantly related to children’s psychological adjustment. Paternal acceptance was also significantly related to both interpersonal power and prestige. Results of hierarchical regression analyses revealed that perceived parental acceptance and interpersonal prestige made significant independent contributions to children’s (both boys’ and girls’) psychological adjustment. Analyses of the interactions between these variables revealed a moderating role of both perceived interpersonal power and prestige in the relationship between perceived paternal acceptance and children’s psychological adjustment.
Register write specialization register read specialization: a path to complexity-effective wide-issue superscalar processors

With the continuous shrinking of transistor size, processor designers are facing new difficulties to achieve high clock frequency. The register file read time, the wake up and selection logic traversal delay and the bypass network transit delay with also their respective power consumptions constitute major difficulties for the design of wide issue superscalar processors. In this paper, we show that transgressing a rule, that has so far been applied in the design of all the superscalar processors, allows to reduce these difficulties. Currently used general-purpose ISAs feature a single logical register file (and generally a floating-point register file). Up to now all superscalar processors have allowed any general-purpose functional unit to read and write any physical general purpose register. First, we propose Register Write Specialization, i.e, forcing distinct groups of functional units to write only in distinct subsets of the physical register file, thus limiting the number of write ports on each individual register. Register Write Specialization significantly reduces the access time, the power consumption and the silicon area of the register file without impairing performance. Second, we propose to combine Register Write Specialization with Register Read Specialization for clustered superscalar processors. This limits the number of read ports on each individual register and simplifies both the wakeup logic and the bypass network. With a 8-way 4-cluster WSRS architecture, the complexities of the wake-up logic entry and bypass point are equivalent to the ones found with a conventional 4-way issue processor. More physical registers are needed in WSRS architectures. Nevertheless, using WSRS architecture allows a dramatic reduction of the total silicon area devoted to the physical register file (by a factor four to six). Its power consumption is more than halved and its read access time is shortened by one third. Some extra hardware and/or a few extra pipeline stages are needed for register renaming. WSRS architecture induces constraints on the policy for allocating instructions to clusters. However, performance of a 8-way 4-cluster WSRS architecture stands the comparison with the one of a conventional 8-way 4-cluster conventional superscalar processor.