Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of the Proximal Enhancer of the Major Immediate-Early Promoter in Human Cytomegalovirus Replication

ABSTRACT The human cytomegalovirus (CMV) enhancer has a distal component (positions −550 to −300) and a proximal component (−300 to −39) relative to the transcription start site (+1) of the major immediate-early (MIE) promoter. Without the distal enhancer, human CMV replicates slower and has a small-plaque phenotype. We determined the sequence requirements of the proximal enhancer by making 5′-end deletions to positions −223, −173, −116, −67, and −39. Even though recombinant virus with the proximal enhancer deleted to −39 has the minimal TATA box-containing MIE promoter element, it cannot replicate independently in human fibroblast cells. Recombinant virus with a deletion to −67 has an Sp-1 transcription factor binding site which may represent a minimal enhancer element for recombinant virus replication in human fibroblast cells. Although recombinant virus with a deletion to −223 replicates to titers at least 100-fold less than that of the wild-type virus, it replicates to titers 8-fold higher than that of recombinant virus with a deletion to −173 and 20-fold higher than that of virus with a deletion to −67. Recombinant virus with a deletion to −173 replicates more efficiently than that with a deletion to −116. There was a direct correlation between the level of infectious virus replication and time after infection, amount of MIE gene transcription, MIE and early viral protein synthesis, and viral DNA synthesis. The extent of the proximal enhancer determines the efficiency of viral replication.
A novel mutation in the NR2E3 gene associated with Goldmann-Favre syndrome and vasoproliferative tumor of the retina

Purpose Various autosomal recessive retinal dystrophies are reported to be associated with mutations in nuclear receptor subfamily 2, group E, member 3 (NR2E3, also called PNR) gene. The present study proposed to understand the clinical and genetic characteristics of the family of a patient with an ocular phenotype consistent with Goldmann-Favre syndrome (GFS) and vasoproliferative tumors of the retina (VPTRs). Methods Twelve family members of the proband from three generations underwent complete ophthalmic examination, including best-corrected visual acuity with Snellen optotypes, tonometry, biomicroscopic examination, indirect ophthalmoscopy after pupillary dilatation, computerized perimetry, optical coherence tomography, fundus photography, intravenous fluorescein angiography, and electroretinography (ERG). All the study subjects underwent genetic analysis of the entire coding region of the NR2E3 gene with the bidirectional DNA sequencing approach. Hundred healthy individuals were screened for the variant. Results The phenotype of the proband had features of GFS with VPTRs. The tumors showed complete resolution with cryotherapy and transpupillary thermotherapy (TTT). Sequencing of the entire coding region of the NR2E3 gene in the proband revealed a novel homozygous c.1117 A>G variant that led to the amino acid change from aspartic acid to glycine at position 406 (p.D406G). This change was present in the homozygous state in affected family members and in the heterozygous state in unaffected family members, and was undetectable in the control subjects. The identified novel p.D406G homozygous mutation was at an evolutionarily highly conserved region and may possibly affect the protein function (Sorting Intolerant From Tolerant [SIFT] score = 0.00). Conclusions Patients with GFS may present with retinal VPTRs that respond to therapy with cryotherapy and TTT. Molecular genetic studies helped to identify a novel p.D406G mutation in the affected members, which will aid in confirming the diagnosis, for genetic counseling of family members and potentially provide some form of therapy for the affected patients.
Story-based CALL for Japanese Kanji Characters: A Study on Student Learning Motivation

We investigated the feasibility and effectiveness of implementing a novel, story-based computerassisted language learning (CALL) system for students learning Japanese kanji characters. In contrast to traditional kanji instruction methods, which rely most heavily on rote learning, our story-based CALL system focuses on mnemonic stories (following Heisig, 1986) and allows the user to create and manage mnemonic stories. System features include a multi-modal audio/visual interface, a portable form factor, a flashcard quiz mode, hyperlink navigation among stories, and a story sharing facility. Experimental evaluation results indicate that after using our device for a two-week period, statistically significant and statistically suggestive improvements in six aspects of students' motivation and learning strategies for learning kanji increased, as measured by the Motivated Strategies for Learning Questionnaire.
Learning Web Queries for Retrieval of Relevant Information about an Entity in a Wikipedia Category

In this paper, we present a novel method to obtain a set of most appropriate queries for retrieval of relevant information about an entity from the Web. Using the body text of existing articles in a Wikipedia category, we generate a set of queries capable of fetching the most relevant content for any entity belonging to that category. We find the common topics discussed in the articles of a category using Latent Semantic Analysis (LSA) and use them to formulate the queries. Using Long Short-Term Memory (LSTM) neural network, we reduce the number of queries by removing the less sensible ones and then select the best ones out of them. The experimental results show that the proposed method outperforms the baselines. Existing approaches are performing better in generation of the relevant section title queries by extraction from the headings of the Wikipedia articles as compared to the generation of queries by extraction from the body text of the articles. Whereas, the experimental results show that the proposed approach can perform equally well and even better in extraction of the relevant queries from the body text of the Wikipedia articles.
Distributed Power-Management Techniques for Wireless Network Video Systems

Wireless sensor networks operating on limited energy resources need to be power efficient to extend the system lifetime. This is especially challenging for video sensor networks due to the large volumes of data they need to process in short periods of time. Towards this end, this paper proposes two coordinated power management policies for video sensor networks. These policies are scalable as the system grows and flexible to video parameters and network characteristics. In addition to simulation results, the prototype demonstrates the feasibility of implementing these policies. Finally, the analytical framework we provide gives an upper bound for the achievable sleep fraction and insight into how adjusting select parameters will affect the performance of the power management policies
The Generation and Evolution of Lump Solitary Waves in Surface-Tension-Dominated Flows

Three-dimensional solitary waves or lump solitons are known to be solutions to the Kadomtsev-Petviashvili I equation, which models small-amplitude shallow-water waves when the Bond number is greater than 1 . Recently, Pego and Quintero presented a proof of the existence of such waves for the Benney-Luke equation with surface tension. Here we establish an explicit connection between the lump solitons of these two equations and numerically compute the Benney- Luke lump solitons and their speed-amplitude relation. Furthermore, we numerically collide two Benney-Luke lump solitons to illustrate their soliton wave character. Finally, we study the flow over an obstacle near the linear shallow-water speed and show that three-dimensional lump solitons are periodically generated.
DSP Based Real Time Implementation of ac-DC-ac Converter Using SPWM Technique

In most of the drives applications, variable speed concept is achieved by using a back-to-back two level frequency converters. Firstly the open loop system model of ac-dc-ac converter is designed, simulated and realized in SIMULINK. TMS 320F28335 is used for pulse generation by SPWM technique. The problem of controlling the induction motors driven through ac-dc-ac converters is considered. The control objective is restricted to forcing the motor speed to track reference signal and is done with D-Q voltage control technique. The simulation is carried out in MATLAB/SIMULINK and results of both simulation and actual model are compared.
General Virtual Hosting with Softwarepot

Present-day computers provide sufficient resources to share them between hosting services for multiple Internet sites. This kind of resource sharing is called virtual hosting. However, continuous increase in the amount of network attacks force us to focus on security. In order to realize safe virtual hosting, resources for hosted services need to be isolated. Virtual machine managers (VMMs) are commonly utilized for this purpose, however they require a significant amount of extra work for setting up and resources for running them. OS specific solutions such as FreeBSD jail provide more efficient execution, but still require the preparation of a full basic operating system for each virtual host. This paper proposes a general method for virtual hosting of arbitrary services based on the SoftwarePot Secure Execution System and describes how the virtual hosting facility was implemented. Our approach allows reducing the work required for setting up the virtual hosting system, while maintaining a relatively low runtime overhead.
Automatic Parallelization of Non-uniform Dependences

This report summarizes our current experiences with Automatic Program Parallelization tools for converting sequential Fortran code for use on a multiprocessor computer. A number of such tools were evaluated, including Parafrase, Adaptor, PAT, Petit and the SUIF compiler package. We evaluated the suitability of such tools for parallelizing Computational Fluid Dynamics code supplied by the Army Research Laboratory, Aberdeen Proving Grounds. SUIF was found to be most suitable by carrying out extensive tests on a suite of test programs and a matrix multiplication program. As a result of these experiments we suggest some modiications to the existing SUIF toolkit for eecient parallelization of the CFD code. Although SUIF does eecient loop partitioning for uniform dependences, it cannot handle nested loops with irregular dependencies eeciently. Unlike the case of nested loops with uniform dependencies these will have a complicated dependence pattern which forms a non-uniform dependence vector set. We propose to incorporate additional passes in SUIF based on results from our previous research, to generate code which will handle applications with non-uniform dependences.
Wind measurement analysis for deployment urban small scale wind turbine

The wind energy usage is an attractive promise for the energy conscious people. This paper introduces and evaluates a small scale urban wind turbine application. Although the turbine works by its original characteristics, the output power/energy falls far away the expectations. The wind we feel daily in the cities may be too much for the human abstention but it is few for the nominal operation of the turbines that requires more than 40 km/h wind speed. We show also a calculation method where based on short-term local wind measurements we define the relation to other, long-term metering. The yearly production can be estimated on base of the decade long wind data.
Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine

The cytosine analogues 5‐azacytosine (azacytidine) and 2′‐deoxy‐5‐azacytidine (decitabine) are the currently most advanced drugs for epigenetic cancer therapies. These compounds function as DNA methyltransferase inhibitors and have shown substantial potency in reactivating epigenetically silenced tumor suppressor genes in vitro. However, it has been difficult to define the mode of action of these drugs in patients and it appears that clinical responses are influenced both by epigenetic alterations and by apoptosis induction. To maximize the clinical efficacy of azacytidine and decitabine it will be important to understand the molecular changes induced by these drugs. In this review, we examine the pharmacological properties of azanucleosides and their interactions with various cellular pathways. Because azacytidine and decitabine are prodrugs, an understanding of the cellular mechanisms mediating transmembrane transport and metabolic activation will be critically important for optimizing patient responses. We also discuss the mechanism of DNA methyltransferase inhibition and emphasize the need for the identification of predictive biomarkers for the further advancement of epigenetic therapies. © 2008 Wiley‐Liss, Inc.
125I brachytherapy of locally advanced non-small-cell lung cancer after one cycle of first-line chemotherapy: a comparison with best supportive care

Objectives The objective of this study was to assess the efficacy of computed tomography (CT)-guided 125I brachytherapy alone in improving the survival and quality of life of patients with unresectable locally advanced non-small-cell lung cancer (NSCLC) after one cycle of first-line chemotherapy. Patients and methods Sixteen patients with locally advanced NSCLC were treated with CT-guided 125I brachytherapy after one cycle of first-line chemotherapy (group A). Sixteen patients who received only best supportive care (group B) were matched up with the patients in group A. Primary end point included survival, and secondary end point included assessment of safety, effectiveness of CT-guided 125I brachytherapy, and improvement in the quality of life. Results The two groups were well balanced in terms of age, disease histology, tumor stage, tumor location, and performance status (P>0.05). The median follow-up time was 16 months (range, 3–30). The total tumor response rate was 75.0% in group A, which was significantly higher than that in group B (0.0%) (P<0.01). The median progression-free survival time was 4.80 months for patients in group A and 1.35 months for patients in group B (P<0.001). Kaplan–Meier survival analysis showed that the median survival time of group A was 9.4±0.3 months versus 8.4±0.1 months in group B (P=0.013). Tumor-related symptoms of patients were significantly relieved, and the quality of life was markedly improved in group A than in group B. Conclusion CT-guided 125I brachytherapy improved the survival of patients with locally advanced NSCLC and quality of life after one cycle of first-line chemotherapy compared with best supportive care.
KWISC — Dependency visualization for understanding context

We propose a dependency visualization method for understanding context, KWISC. KWISC displays dependency between bunsetsus in Japanese sentences. In particular, it splits sentences into bunsetsus and displays them hierarchically according to the depth of dependency, to understand context. In addition, KWISC is able to align two keywords respectively, while KWIC aligns one keyword. This helps to find collocations among words. Furthermore, KWISC is able to expand and collapse bunsetsus. It can shorten distances of collocating words since it shows only the main structure of sentences by collapsing the bunsetsus. Therefore, collocating words are easy to fit on the screen, and horizontal eye movement is decreased when we look for collocations. As an evaluation experiment, we have collected pairs consisting of a bunsetsu that includes a keyword and another bunsetsu on which it depends from 207,802 sentences in the EDR corpus, and have measured the distances between them in KWISC. As a result, it is confirmed that KWISC makes the distances shorter than the conventional methods, and we have shown that KWISC makes it easy to find collocations.
Sadness bright as glass: the acceptance of emotionally sensitive radical innovation

Abstract The existing literature acknowledges the importance of emotions in consumer decision-making and the challenges of radical innovation adoption; however, the literature seldom combines these two streams. The purpose of this study was to analyse potential adopters’ considerations concerning an innovation that is targeted at intense negative emotions. Choosing a case-study strategy enabled us to focus on extremely negative emotions (related to death) and the acceptance of a radical innovation (a memorial stone made of glass). In this study, we applied a longitudinal mixed-methods approach. Data were collected via interviews with consumers (357 respondents), the entrepreneur and her employee. Findings show that an emotionally sensitive radical innovation evokes more intense emotions and emotional ambivalence among consumers. Its acceptance also seems to depend on the age and gender of the customers and requires cultural change. A lengthy adoption process seems to be characteristic of emotionally intensive innovation. This study has implications for managers facing the challenge of creating new markets for a radical innovation that involves extreme emotions on the part of consumers. Theoretically, the study contributes to both innovation adoption and consumer decision-making literature.
Surgically Induced Interpregnancy Weight Loss and Prevalence of Overweight and Obesity in Offspring

Introduction According to the fetal overnutrition hypothesis, obesity in pregnancy predisposes the offspring to obesity. Previous studies have suggested that after biliopancreatic surgery for obesity, the offspring is less likely to be obese. This study aims to further compare the BMI development of children born before and after maternal surgical weight loss. Method Women with at least one child born before and one child born after bariatric surgery were identified by record-linkage. Information about maternal BMI was extracted from medical records, as was information about the children's BMI from birth to 10 years of age. We retrieved BMI data at four years of age for 340 children, born to 223 women (164 children born before surgery (BS), 176 children born after surgery (AS)). We evaluated prevalence of overweight/obesity and mean BMI in children born BS and AS at the ages of four, six and ten using GEE regression models. For 71 families, where we had complete data on mother and both children, we used a fixed-effects regression model to explore the association between differences in maternal BMI in w10 of the pre- and post-operative pregnancies with siblings' BMI differences at age four. Results In no age group did we see a significantly reduced prevalence of overweight/obesity AS. For 10-year-old girls, the AS group had significantly higher rates of obesity. There was no association between differences in maternal BMI in early pregnancy and differences in siblings' BMI at four years of age (β = −0.01, CI 95% = −0.11; 0.09). Conclusions We have been unable to demonstrate any effect of bariatric surgery on weight development in offspring. It seems unlikely that restrictive bariatric surgery conveys a protective effect in offspring with regards to obesity.
Therapeutic Target Achievement in Type 2 Diabetic Patients after Hyperglycemia, Hypertension, Dyslipidemia Management

Background Our study group established "3H care" in 2002. The meaning of "3H care" attain and maintain adequate controls over hypertension, hyperlipidemia, and hyperglycemia in type 2 diabetic patients. This study evaluated the achievement of target goals after one year or more of "3H care" by specialists in our diabetic clinic. Methods This was a retrospective study of 200 type 2 diabetic patients who received "3H care" for one year or more in our diabetic clinic. We evaluated achievement of target goals for metabolic controls as suggested by the American Diabetes Association. Results Overall, 200 type 2 diabetes patients were enrolled, of whom 106 were males (53%) and 94 were females (47%). After one year of "3H care," the mean HbA1c was 7.2±1.5% and the percentage of patients achieving glycemic control (HbA1c <7%) was 51.8%. However only 32.2% of hypertensive patients achieved the recommended target. After one year of "3H care," the percentages of those who achieved the target value for dyslipidemia were 80.0% for total cholesterol, 66.3% for low density lipoprotein cholesterol, 57.9% for triglyceride, and 51.8% for high density lipoprotein cholesterol. The percentage that achieved all three targets level was only 4.4% after one year and 14.8% after two years. Conclusion The results of this study demonstrate that only a minor proportion of patients with type 2 diabetes achieved the recommended goals despite the implementation of "3H care. " It is our suggestion that better treatment strategies and methods should be used to control hypertension, hyperlipidemia and hyperglycemia.
Structural Diversity and Initial Oligomerization of PrP106–126 Studied by Replica-Exchange and Conventional Molecular Dynamics Simulations

Prion diseases are marked by cerebral accumulation of the abnormal isoform of the prion protein. A fragment of prion protein composed of residues 106–126 (PrP106–126) exhibits similar properties to full length prion and plays a key role in the conformational conversion from cellular prion to its pathogenic pattern. Soluble oligomers of PrP106–126 have been proposed to be responsible for neurotoxicity. However, the monomeric conformational space and initial oligomerization of PrP106–126 are still obscure, which are very important for understanding the conformational conversion of PrP106–126. In this study, replica exchange molecular dynamics simulations were performed to investigate monomeric and dimeric states of PrP106–126 in implicit solvent. The structural diversity of PrP106–126 was observed and this peptide did not acquire stable structure. The dimeric PrP106–126 also displayed structural diversity and hydrophobic interaction drove the dimerization. To further study initial oligomerization of PrP106–126, 1 µs conventional molecular dynamics simulations of trimer and tetramer formation were carried out in implicit solvent. We have observed the spontaneous formation of several basic oligomers and stable oligomers with high β-sheet contents were sampled in the simulations of trimer and tetramer formation. The β-hairpin formed in hydrophobic tail of PrP106–126 with residues 118–120 in turn may stabilize these oligomers and seed the formation oligomers. This study can provide insight into the detailed information about the structure of PrP106–126 and the dynamics of aggregation of monomeric PrP106–126 into oligomers in atomic level.
On failure of the pruning technique in “Error repair in shift-reduce parsers”

A previous article presented a technique to compute the least-cost error repair by incrementally generating configurations that result from inserting and deleting tokens a syntactically incorrect input. An additional mechanism to improve the run-time efficiency of this algorithm by pruning some of the configurations was discussed as well. In this communication we show that the pruning mechanism may lead to suboptimal repairs or may block all repairs. Certain grammatical errors in a common construct of the Java programming language also lead to the above kind of failure.
VEAP: Global optimization based efficient algorithm for VLSI placement

In this paper we present a very simple, efficient while effective placement algorithm for Row-based VLSIs. This algorithm is based on strict mathematical analysis, and provably can find the global optima. From our experiments, this algorithm is one of the fastest algorithms, especially for very large scale circuits. Another point desired to point out is that our algorithm can be run in both wirelength and timing-driven modes.