Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Assembly of a Full-Length Infectious cDNA of Mouse Hepatitis Virus Strain A59

ABSTRACT A novel method was developed to assemble a full-length infectious cDNA of the group II coronavirus mouse hepatitis virus strain A59 (MHV-A59). Seven contiguous cDNA clones that spanned the 31.5-kb MHV genome were isolated. The ends of the cDNAs were engineered with unique junctions and assembled with only the adjacent cDNA subclones, resulting in an intact MHV-A59 cDNA construct of ∼31.5 kb in length. The interconnecting restriction site junctions that are located at the ends of each cDNA are systematically removed during the assembly of the complete full-length cDNA product, allowing reassembly without the introduction of nucleotide changes. RNA transcripts derived from the full-length MHV-A59 construct were infectious, although transfection frequencies were enhanced 10- to 15-fold in the presence of transcripts encoding the nucleocapsid protein N. Plaque-purified virus derived from the infectious construct replicated efficiently and displayed similar growth kinetics, plaque morphology, and cytopathology in murine cells as did wild-type MHV-A59. Molecularly cloned viruses recognized the MHV receptor (MHVR) for docking and entry, and pretreatment of cells with monoclonal antibodies against MHVR blocked virus entry and replication. Cells infected with molecularly cloned MHV-A59 virus expressed replicase (gene 1) proteins identical to those of laboratory MHV-A59. Importantly, the molecularly cloned viruses contained three marker mutations that had been derived from the engineered component clones. Full-length infectious constructs of MHV-A59 will permit genetic modifications of the entire coronavirus genome, particularly in the replicase gene. The method has the potential to be used to construct viral, microbial, or eukaryotic genomes approaching several million base pairs in length and used to insert restriction sites at any given nucleotide in a microbial genome.
Enhancement of Secretion and Extracellular Stability of Staphylokinase in Bacillus subtilis bywprA Gene Disruption

ABSTRACT Staphylokinase (SAK), a polypeptide secreted byStaphylococcus aureus, is a plasminogen activator with a therapeutic potential in thrombosis diseases. A Bacillus subtilis strain which is multiply deficient in exoproteases was transformed by an expression plasmid carrying a promoter and a signal sequence of subtilisin fused in frame with the sak open reading frame. However, the amount of SAK secretion was marginal (45 mg/liter). In contrast, disruption of the wprA gene, which encodes a subtilisin-type protease, strongly promoted the production of SAK in the stationary phase (181 mg/liter). In addition, the extracellular stability of mature SAK was dramatically enhanced. These data indicate a significant role of the wprA gene product in degrading foreign proteins, both during secretion and in the extracellular milieu.
The phenomenological interview: Exploring awareness of second language learning in the international ESL college student community

THE PHENOMENOLOGICAL INTERVIEW: EXPLORING AWARENESS OF SECOND LANGUAGE LEARNING IN THE INTERNATIONAL ESL COLLEGE STUDENT COMMUNITY SEPTEMBER 2001 LEOR ALCALAY, A.B. , HARVARD COLLEGE M.A., UNIVERSITY OF MASSACHUSETTS BOSTON (ESL) M.A., UNIVERSITY OF MASSACHUSETTS BOSTON (CCT) Ed.D, UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor John C. Carey This dissertation argues for a novel methodological approach to the investigation of phenomena of second language acquisition (SLA). The field of second language acquisition arose in a historical academic context which traditionally linked it to primarily quantitative research methodologies. Introspective verbalized articulations of learners had been devalued in favor of observational examination of behavioral characteristics, an approach which, despite massive investments of research energies, failed to yield a coherent theoretical understanding of the SLA process, especially in adults. An individually conducted, dialogically oriented, open-ended or phenomenological interview enables the exploration of the concerns, interests, experiences, and meanings developed by a second-language learner during the course of the process of secondlanguage acquisition. Approximately two dozen such interviews were carried out with international speakers of English as a Second Language (ESL) studying in a community
Planets and Infrared Excesses: Preliminary Results from a Spitzer MIPS Survey of Solar-Type Stars

As part of a large Spitzer MIPS Guaranteed Time Observation program, we have searched for infrared excesses due to debris disks toward 26 FGK field stars known from radial velocity (RV) studies to have one or more planets. While none of these stars show excesses at 24 μm, we have detected 70 μm excesses around six stars at the 3 σ confidence level. The excesses are produced by cool material (<100 K) located beyond 10 AU, well outside the "habitable zones" of these systems and consistent with the presence of Kuiper Belt analogs with ~100 times more emitting surface area than in our own planetary system. These planet-bearing stars are, by selection for RV studies, typically older than 1 Gyr, and the stars identified here with excesses have a median age of 4 Gyr. We find a preliminary correlation of both the frequency and the magnitude of dust emission with the presence of known planets. These are the first stars outside the solar system identified as having both well-confirmed planetary systems and well-confirmed IR excesses.
Effect of Constitution on Mass of Individual Organs and Their Association with Metabolic Rate in Humans—A Detailed View on Allometric Scaling

Resting energy expenditure (REE)-power relationships result from multiple underlying factors including weight and height. In addition, detailed body composition, including fat free mass (FFM) and its components, skeletal muscle mass and internal organs with high metabolic rates (i.e. brain, heart, liver, kidneys), are major determinants of REE. Since the mass of individual organs scales to height as well as to weight (and, thus, to constitution), the variance in these associations may also add to the variance in REE. Here we address body composition (measured by magnetic resonance imaging) and REE (assessed by indirect calorimetry) in a group of 330 healthy volunteers differing with respect to age (17–78 years), sex (61% female) and BMI (15.9–47.8 kg/m2). Using three dimensional data interpolation we found that the inter-individual variance related to scaling of organ mass to height and weight and, thus, the constitution-related variances in either FFM (model 1) or kidneys, muscle, brain and liver (model 2) explained up to 43% of the inter-individual variance in REE. These data are the first evidence that constitution adds to the complexity of REE. Since organs scale differently as weight as well as height the “fit” of organ masses within constitution should be considered as a further trait.
Fast target enhancement in thermal infrared imagery

We show a real-time target enhancement model in thermal infrared imaging watching system. Using local frequency-selected theory, we only highlight the target areas, but not the whole image regions. The model helps and robustly improving the signal-to-background ratio, which make the objects be viewing and detected easily. The good performance in security and defence system proves the model is a strong supplement to traditional infrared imaging systems.
CM_ISA++: An instruction set for dynamic task scheduling units for more than 1000 cores

In this paper a dynamic task scheduling unit for many-core systems with over 1000 cores is introduced. It is called CoreManager. It dynamically schedules thousands of tasks of several applications, allocates processing elements, controls the prefetching of data transfers, and explicitly manages the on-chip memories. For many-core systems a high task throughput and a low latency are essential for its success. Therefore, the CoreManager integrates a newly developed application-specific instruction set, called CM_ISA++, for a superior scheduling performance. The design of the instruction set of the CoreManager is presented, explained and the performance of each component is analyzed. Furthermore, the CoreManager is integrated and evaluated in a many-core system with 1008 processing elements. Our CoreManager implementation outperforms a RISC-based implementation by 193x in scheduling and 419x in processing element allocation performance. Consequently, scalability of the system as well as task throughput and latency is dramatically improved compared to RISC-based scheduling approaches.
Off-line skilled forgery detection on handwritten Devanagri script

This paper is aimed at exploring the potential of using discriminatory primitives containing words for the task of detecting skilled forgeries. We consider handwritten Devanagri documents for this work. We have obtained experimental handwriting data from subjects who have contributed handwriting samples in their natural handwriting. Other authors are asked to imitate the writing style of the subjects to produce a skilled forgery sample. Most of the literature dealing with writer recognition focus on signatures and very few reports have addressed the problem of detecting forgeries for handwritten Indian scripts. We also use multiple words based classification for the targeted task of forgery detection. Our experiments show encouraging results.
Microtubules and Lis-1/NudE/Dynein Regulate Invasive Cell-on-Cell Migration in Drosophila

The environment through which cells migrate in vivo differs considerably from the in vitro environment where cell migration is often studied. In vivo many cells migrate in crowded and complex 3-dimensional tissues and may use other cells as the substratum on which they move. This includes neurons, glia and their progenitors in the brain. Here we use a Drosophila model of invasive, collective migration in a cellular environment to investigate the roles of microtubules and microtubule regulators in this type of cell movement. Border cells are of epithelial origin and have no visible microtubule organizing center (MTOC). Interestingly, microtubule plus-end growth was biased away from the leading edge. General perturbation of the microtubule cytoskeleton and analysis by live imaging showed that microtubules in both the migrating cells and the substrate cells affect movement. Also, whole-tissue and cell autonomous deletion of the microtubule regulator Stathmin had distinct effects. A screen of 67 genes encoding microtubule interacting proteins uncovered cell autonomous requirements for Lis-1, NudE and Dynein in border cell migration. Net cluster migration was decreased, with initiation of migration and formation of dominant front cell protrusion being most dramatically affected. Organization of cells within the cluster and localization of cell-cell adhesion molecules were also abnormal. Given the established role of Lis-1 in migrating neurons, this could indicate a general role of Lis-1/NudE, Dynein and microtubules, in cell-on-cell migration. Spatial regulation of cell-cell adhesion may be a common theme, consistent with observing both cell autonomous and non-autonomous requirements in both systems.
Stock or Print? Impact of 3D Printing on Spare Parts Logistics

We present a general framework to study the design of spare parts logistics in the presence of three-dimensional (3-D) printing technology. We consider multiple parts facing stochastic demands and adopt procure/manufacture-to-stock versus print-on-demand to highlight the main difference of production modes featured in traditional manufacturing and 3-D printing. To minimize long-run average system cost, our model determines which parts to stock and which to print. We find that the optimal 3-D printer’s utilization increases as the additional unit cost of printing declines and the printing speed improves. The rate of increase, however, decays, demonstrating the well-known diminishing returns effect. We also find the optimal utilization to increase in part variety and decrease in part criticality, suggesting the value of 3-D technology in tolerating large part variety and the value of inventory for critical parts. By examining the percentage cost savings enabled by 3-D printing, we find that, although the reduction in printing cost continuously adds to the value of 3-D printing in a linear fashion, the impact of the improvement of printing speed exhibits S-shaped growth. We also derive various structural properties of the problem and devise an efficient algorithm to obtain near optimal solutions. Finally, our numerical study shows that the 3-D printer is, in general, lightly used under realistic parameter settings but results in significant cost savings, suggesting complementarity between stock and print in cost minimization. This paper was accepted by Victor Martínez-de-Albéniz, operations management.
An intelligent video categorization engine

Purpose – We describe an intelligent video categorization engine (IVCE) that uses the learning capability of artificial neural networks (ANNs) to classify suitably preprocessed video segments into a predefined number of semantically meaningful events (categories). Design/methodology/approach – We provide a survey of existing techniques that have been proposed, either directly or indirectly, towards achieving intelligent video categorization. We also compare the performance of two popular ANNs: Kohonen's self‐organizing map (SOM) and fuzzy adaptive resonance theory (Fuzzy ART). In particular, the ANNs are trained offline to form the necessary knowledge base prior to online categorization.Findings – Experimental results show that accurate categorization can be achieved near instantaneously.Research limitations – The main limitation of this research is the need for a finite set of predefined categories. Further research should focus on generalization of such techniques.Originality/value – Machine understandin.
A Model-Based Framework for Legal Policy Simulation and Legal Compliance Checking

Analyzing legal policies for many laws, such as taxes and social benefits, is a common way for governments to identify risks, e.g., risk of legal policies not achieving expected revenue. A typical analysis includes validation of policies and the verification of the systems implementing them. One efficient way to validate policies is simulation, e.g., by simulating whether a proposed law reform would realize target objectives. Once validated, policies are implemented into public administration procedures and eGovernment applications. Systems implementing legal policies also need to be analyzed and verified, e.g., through testing, to ensure that they are compliant with the underlying policies. Currently, legal policy analysis is conducted using a combination of spreadsheets and software code. Such strategy suffers mainly from being hard to use by legal experts due to the lack of adequate background. This is partly rooted in the fact that available techniques to formalize legal policies are based on complex logical expressions and code. The main goal of this research project, that this paper describes, is to narrow the aforementioned expertise gap by proposing convenient, systematic and automated techniques to support analysis of legal polices from their design to their implementation.
The implications of intensive singing training on the vocal health and development of boy choristers in an English cathedral choir

Boy choristers who sing in UK cathedrals and major chapels perform to a professional standard on a daily basis, with linked rehearsals, whilst also following a full school curriculum. This research will investigate the impact of this intensive schedule in relation to current vocal health and future development. This research reports the findings of a longitudinal chorister study, based in one of London's cathedrals. Singing and vocal behaviour have been profiled on a six-monthly basis across three years using data from a specially designed perceptual and acoustic assessment protocol. The speaking and singing voice data have been analysed using a selection of techniques in current usage in both laboratory and clinical settings. Evaluation and comparison of these methods has enabled a range of effective assessment protocols to be suggested. The behaviour of the voice at the onset of adolescent voice change has been observed using electroglottogram data. The boarding choristers numbered thirty-four in total, eleven of whom were selected for longitudinal analysis. Similar acoustic data have also been collected from three other groups of boys, a total of ninety individuals, for comparative purposes. It has been possible to quantify the possible influence of both school environment and vocal activity on overall vocal health. Significant differences have been noted between the vocal health of the boys in the chorister group and the non-choristers; the boarding choristers, although having the highest vocal loading, have the lowest incidence of voice disorder. This would in itself suggest that either the voice is being athletically conditioned to support such activity, or that the chorister group employs some self-regulation with regard to overusing the voice. The comparison with various other groups of boys implicates the cultural and social influences of peer groups in voice use. The longitudinal observations of the choristers illustrate the development of vocal skills and the impact of increased choral responsibility on the vocal health of the individuals. It has also provided insights into the vocal behaviour during the onset of adolescent voice change with particular information about the vocal skills employed in the upper pitch range; the nature of phonation in the upper pitch range of trained boy singers entering voice change
Multicenter evaluation of a self-expanding carotid stent system with distal protection in the treatment of carotid stenosis.

PURPOSE Carotid artery stent placement may be limited by the embolization of atheromatous material. We evaluated the safety and feasibility of the Medtronic Self-Expanding Carotid Stent (Exponent) in combination with the Medtronic Interceptor Carotid Filter System for the treatment of carotid stenosis among patients at high risk for carotid endarterectomy. METHODS Patients at high risk for carotid endarterectomy but amenable to percutaneous treatment with stent placement were enrolled. Clinical follow-up was performed at 30 days and 6 and 12 months postprocedure. The National Institutes of Health Stroke Scale was assessed before and within 3 days postprocedure and at 30 days and 6 months postprocedure. Angiography was performed pre- and postprocedure, and carotid duplex scans were performed at baseline and at 30 days and 6 months. RESULTS Fifty-two carotid procedures were performed in 51 patients (mean age, 69 years; 84% of patients were men). The major adverse event (MAE) rate (death, stroke, and myocardial infarction [MI]) at 30 days was 5.9%: 2 strokes and a single death from periprocedural MI. MAE rates after 6 and 12 months were 5.9% and 11.8%, respectively. The delivery success rate was 94.2% (49/52) for the Interceptor Filter System and 95.9% (47/49) for the Exponent Stent. The mean diameter stenosis of the target lesion was reduced from 62.4% preprocedure to 21.2% postprocedure. CONCLUSION High delivery success rates were achieved with a low rate of MAE (death, stroke, or MI) in a high-risk population. Treatment of carotid artery disease with the Exponent Carotid Stent combined with distal protection from the Interceptor Filter System is effective and safe.
Generating test data for branch coverage

Branch coverage is an important criteria used during the structural testing of programs. We present a new program execution based approach to generate input data that exercises a selected branch in a program. The test data generation is initiated with an arbitrarily chosen input from the input domain of the program. A new input is derived from the initial input in an attempt to force execution through any of the paths through the selected branch. The method dynamically switches among the paths that reach the branch by refining the input. Using a numerical iterative technique that attempts to generate an input to exercise the branch, it dynamically selects a path that offers less resistance. We have implemented the technique and present experimental results of its performance for some programs. Our results show that our method is feasible and practical.
Underachieving to Protect Self-Worth: Theory, Research and Interventions

Part 1 Description and differentiation: introduction nature of self-worth protection long-term costs alternative accounts of failure kindred concepts. Part 2 Mediating variables and development: aspects of personality situational variables development of self-worth protection. Part 3 Implications and intervention: organizing classroom learning the role of teachers teacher training counselling implications addtitional components.
Towards Automatic Intoxication Detection from Speech in Real-Life Acoustic Environments

In-car intoxication detection from speech is a highly promising non-intrusive method to reduce the accident risk associated with drunk driving. However, in-car noise significantly influences the recognition performance and needs to be addressed in practical applications. In this paper, we investigate how seriously the intrinsic in-car noise and background music affect the accuracy of intoxication recognition. In extensive test runs using the official speech corpus of the INTERSPEECH 2011 Intoxication Challenge, realistic car noise and original popular music we conclude that stationary driving noise as well as music introduce a significant downgrade when acoustic models are trained on clean speech only, which can partly be alleviated by multi-condition training. Besides, exploiting cumulative evidence over time by late decision fusion appears to be a promising way to further enhance performance in noisy conditions.
Acquisition of polychlorinated biphenyls (PCBs) by pacific chinook salmon: An exploration of various exposure scenarios

In 2011, as part of an update to its state water quality standards (WQS) for protection of human health, the State of Oregon adopted a fish consumption rate of 175 g/day for freshwater and estuarine finfish and shellfish, including anadromous species. WQS for the protection of human health whose derivation is based in part on anadromous fish, create the expectation that implementation of these WQS will lead to lower contaminant levels in returning adult fish. Whether this expectation can be met is likely a function of where and when such fish are exposed. Various exposure scenarios have been advanced to explain acquisition of bioaccumulative contaminants by Pacific salmonids. This study examined 16 different scenarios with bioenergetics and toxicokinetic models to identify those where WQS might be effective in reducing polychlorinated biphenyls (PCBs)—a representative bioaccumulative contaminant—in returning adult Fall chinook salmon, a representative salmonid. Model estimates of tissue concentrations and body burdens in juveniles and adults were corroborated with observations reported in the literature. Model results suggest that WQS may effect limited (< approximately 2 ×) reductions in PCB levels in adults who were resident in a confined marine water body or who transited a highly contaminated estuary as out‐migrating juveniles. In all other scenarios examined, WQS would have little effect on PCB levels in returning adults. Although the results of any modeling study must be interpreted with caution and are not necessarily applicable to all salmonid species, they do suggest that the ability of WQS to meet the expectation of reducing contaminant loadings in anadromous species is limited. Integr Environ Assess Manag 2012; 8: 553–562. © 2012 SETAC