Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Mutated Cyclization Sequences That Permit Efficient Replication of West Nile Virus Genomes: Use in Safer Propagation of a Novel Vaccine Candidate

ABSTRACT Existing live-attenuated flavivirus vaccines (LAV) could be improved by reducing their potential to recombine with naturally circulating viruses in the field. Since the highly conserved cyclization sequences (CS) found in the termini of flavivirus genomes must be complementary to each other to support genome replication, we set out to identify paired mutant CS that could support the efficient replication of LAV but would be unable to support replication in recombinant viruses harboring one wild-type (WT) CS. By systematic evaluation of paired mutated CS encoded in West Nile virus (WNV) replicons, we identified variants having single and double mutations in the 5′- and 3′-CS components that could support genome replication at WT levels. Replicons containing only the double-mutated CS in the 5′ or the 3′ ends of the genome were incapable of replication, indicating that mutated CS could be useful for constructing safer LAV. Despite the identity of the central portion of the CS in all mosquito-borne flaviviruses, viruses carrying complementary the double mutations in both the 5′- and the 3′-CS were indistinguishable from WT WNV in their replication in insect and mammalian cell lines. In addition to the utility of our novel CS pair in constructing safer LAV, we demonstrated that introduction of these mutated CS into one component of a recently described two-component genome system (A. V. Shustov, P. W. Mason, and I. Frolov, J. Virol. 81:11737-11748, 2007) enabled us to engineer a safer single-cycle WNV vaccine candidate with reduced potential for recombination during its propagation.
Variable Input Delay CMOS Logic for Low Power Design

We propose a new complementary metal-oxide semiconductor (CMOS) gate design that has different delays along various input to output paths within the gate. The delays are accomplished by inserting selectively sized ldquopermanently onrdquo series transistors at the inputs of a logic gate. We demonstrate the use of the variable input delay CMOS gates for a totally glitch-free minimum dynamic power implementations of digital circuits. Applying a linear programming method to the c7552 benchmark circuit and using the gates described in this paper, we obtained a power saving of 58% over an unoptimized design. This power consumption was 18% lower than that for an alternative low power design using conventional CMOS gates. The optimized circuits had the same critical path delays as their original unoptimized versions. Since the overall delay was not allowed to increase, the glitch elimination with conventional gates required insertion of delay buffers on noncritical paths. The use of the variable input delay gates drastically reduced the required number of delay buffers.
On a Hybrid Rule Based Recommender System

Compared with relative recently-reported counterparts, a novel recommender system prototype is implemented. Its efforts focus on the three essential issues as a whole that recommender systems have to handle: data source, data modeling and recommendation strategy. It is based on a common data format and introduces a hybrid-rule model with a strategy of one-round table scanning. Laboratory experiment results show that this recommender system produces a better outcome
Secure Public Instant Messaging: A Survey †

We provide a survey on security features and threats to exist ing Instant Messaging (IM) networks and discuss how currently available systems fail to provide adequate security in ligh t of existing threats. Our discussion and analysis provide a starting point from which to advance academic research in the area of secure IM systems, enabling security improvement in the longer term.
Using Rewarding Mechanisms for Improving Branching Heuristics

The variable branching heuristics used in the most recent and most effective SAT solvers, including zChaff and BerkMin, can be viewed as consisting of a simple mechanism for rewarding the variables participating in conflicts during the search process. In this paper we propose to extend the simple rewarding mechanism used in zChaff and BerkMin, and develop different rewarding mechanisms based on information provided by the search algorithm, namely the size of learned clauses and the size of the backjumps in the search tree. The results show that very significant gains can be obtained for real-world problem instances of SAT.
The kinesin-like protein KLP61F is essential for mitosis in Drosophila

We report here that disruption of a recently discovered kinesin-like protein in Drosophila melanogaster, KLP61F, results in a mitotic mutation lethal to the organism. We show that in the absence of KLP61F function, spindle poles fail to separate, resulting in the formation of monopolar mitotic spindles. The resulting phenotype of metaphase arrest with polyploid cells is reminiscent of that seen in the fungal bimC and cut7 mutations, where it has also been shown that spindle pole bodies are not segregated. KLP61F is specifically expressed in proliferating tissues during embryonic and larval development, consistent with a primary role in cell division. The structural and functional homology of the KLP61F, bimC, cut7, and Eg5 kinesin-like proteins demonstrates the existence of a conserved family of kinesin-like molecules important for spindle pole separation and mitotic spindle dynamics.
Science teaching methods: a rationale for practices

This article is a version of the talk given by Jonathan Osborne as the Association for Science Education (ASE) invited lecturer at the National Science Teachers' Association Annual Convention in San Francisco, USA, in April 2011. The article provides an explanatory justification for teaching about the practices of science in school science that form a core element of the Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas published in July 2011 by the National Research Council of the US National Academies.
Surgical Automation for Multilateral Multi-Throw Suturing

Surgical Automation for Multilateral Multi-Throw Suturing by Siddarth Sen Master of Science in Electrical Engineering and Computer Science University of California, Berkeley Professor Ken Goldberg, Chair For supervised automation of multi-throw suturing in Robot-Assisted Minimally Invasive Surgery, we present a novel mechanical needle guide and a framework for optimizing needle size, trajectory, and control parameters using sequential convex programming. The Suture Needle Angular Positioner (SNAP) results in a 3x error reduction in the needle pose estimate in comparison with the standard actuator. We evaluate the algorithm and SNAP on a da Vinci Research Kit using tissue phantoms and compare completion time with that of humans from the JIGSAWS dataset [6]. Initial results suggest that the dVRK can perform suturing at 30% of human speed while completing 86% suture throws attempted.
Coronary artery disease detection using photoplethysmography

This paper presents a technique for coronary artery disease (CAD) detection through photoplethysmography (PPG). This work is aimed at developing a non-invasive, inexpensive screening technique suitable for home monitoring. Time domain analysis of PPG signal and its second derivative has been carried out to extract distinguishing features. Support Vector Machine based classifier has been used to classify CAD patients. ICU patient data from MIMIC-II dataset has been used for performance evaluation. Sensitivity of 85% and specificity of 78% has been achieved for the analysed data.
Dyslipidaemia and Medical Outcome (Health Related Quality of Life) in Patients with Schizophrenia Taking Antipsychotics in Enugu, Nigeria

Aim. Determine association between use (and type) of antipsychotics and dyslipidaemia in newly diagnosed schizophrenia patients attending Federal Neuropsychiatric Hospital, Enugu. Methods. From sixty antipsychotic naive patients with schizophrenia and sixty first-degree relatives matched for gender and age, fasting blood lipid profiles were measured at baseline and after twelve weeks. Medical Outcome Study Short Form General Health Survey was administered to patients on both occasions. Fasting lipid profile changes of both groups were compared. Results. Mean endpoint of total cholesterol (TC), low density lipoprotein (LD), and triglycerides (TG) in mmol/l for cases was significantly higher than initial values (TC 4.5 versus 4.3, t = 4.3, p < 0.0001), (LDL 2.8 versus 2.6, t = 14.3, p < 0.0001), and (TG 1.3 versus 1.0, t = 12.1, p < 0.0001). Mean endpoint of high density lipoprotein (HDL) in mmol/l for cases was significantly lower than initial values (1.1 versus 1.2, t = 12.1, p < 0.0001). Prevalence of dyslipidaemia for cases was 13%. Mean endpoint of TC, LDL, TG, and HDL in mmol/l for controls was not significantly different from initial values (TC 4.30 versus 4.27, t = 1.09, p = 0.279), (LDL 2.49 versus 2.46, t = 1.28, p = 0.205), (TG 0.96 versus 0.94, t = 1.27, p = 0.207), and (HDL 1.37 versus 1.38, t = 1.61, p = 0.113). Subjects on atypical antipsychotics had higher risk for dyslipidaemia. Conclusion. Use of antipsychotics was significantly associated with dyslipidaemia.
Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques

MOTIVATION With the increase in submission of sequences to public databases, the curators of these are not able to cope with the amount of information. The motivation of this work is to generate a system for automated annotation of data we are particularly interested in, namely proteins related to the Mycoplasmataceae family. Following previous works on automatic annotation using symbolic machine learning techniques, the present work proposes a method of automatic annotation of keywords (a part of the SWISS-PROT annotation procedure), and the validation, by an expert, of the annotation rules generated. The aim of this procedure is twofold: to complete the annotation of keywords of those proteins which is far from adequate, and to produce a prototype of the validation environment, which is aimed at an expert who does not have a deep knowledge of the structure of the current databases containing the necessary information s/he needs. RESULTS As for the first objective, a rate of correct keywords annotation of 60% is reported in the literature. Our preliminary results show that with a slightly different method, applied this method to data related to Mycoplasmataceae only, we are able to increase that rate of correct annotation.
N‐methylmesoporphyrin IX fluorescence as a reporter of strand orientation in guanine quadruplexes

Guanine quadruplexes (GQ) are four‐stranded DNA structures formed by guanine‐rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs in vivo has proven difficult, in part because of their structural diversity. The development of GQ‐selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N‐methylmesoporphyrin IX (NMM) interacts selectively with parallel‐stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60‐fold in the presence of parallel‐stranded GQs and by about 40‐fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10‐fold increases in NMM fluorescence. Single‐stranded DNA, duplex, or i‐motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a ‘turn‐on’ fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation.
A new subclass of nucleoporins that functionally interact with nuclear pore protein NSP1.

NSP1 is a nuclear pore protein (nucleoporin) essential for cell growth. To identify the components that functionally interact with NSP1 in the living cell, we developed a genetic screen for mutants that are lethal in a genetic background of mutated, but not wild type NSP1. Fourteen synthetic lethal mutants were obtained, belonging to at least four different complementation groups. The genes of two complementation groups, NSP116 and NSP49, were cloned. Like the previously described nucleoporins, these genes encode proteins with many repeat sequences. NSP116 and NSP49, however, contain a new repetitive sequence motif ‘GLFG’, which classifies them as a subclass of nucleoporins. NSP116 and NSP49, tagged with the IgG binding domain of protein A and expressed in yeast, are located at the nuclear envelope. These data provide in vivo evidence that distinct subclasses of nucleoporins physically interact or share overlapping function in nuclear pore complexes.
Replacing dietary fish oil by vegetable oils has little effect on lipogenesis, lipid transport and tissue lipid uptake in rainbow trout (Oncorhynchus mykiss)

In order to investigate the effects of dietary lipid sources on mechanisms involved in lipid deposition, two groups of rainbow trout were fed from first-feeding to the commercial size of 1kg (for 62 weeks) with two diets differing only by lipid source: 100% fish oil or 100% blend of vegetable oils (55% rapeseed oil, 30% palm oil, 15% linseed oil). The activities and levels of gene expression of lipogenic enzymes (fatty acid synthetase, glucose-6-phosphate dehydrogenase and malic enzyme) in liver and of lipoprotein lipase in perivisceral adipose tissue, white muscle and liver were determined. Transport of lipid was studied by determining lipid composition of plasma and lipoprotein classes. We also examined the clearance of LDL by assaying the level of LDL receptor gene expression in several tissues. Total replacement of dietary fish oil by the blend of vegetable oils did not affect growth of rainbow trout and did not modify muscle lipid content. Hepatic lipogenesis and lipid uptake in perivisceral adipose tissue, white muscle and liver were also not modified by dietary treatments. Diets containing the blend of vegetable oils induced a decrease in plasma cholesterol and LDL. In trout fed the vegetable oils diet, expression of LDL receptor gene in the liver was down-regulated.
Inter-vehicle information-fusion with shared perception information

Developing concepts for cooperative awareness was subject of several international research programs in the past years 2. The main concept for cooperative awareness is the communication of localization information enriched by situation specific content by meanwhile standardized messages like the Cooperative Awareness Message (CAM) in Europe or the Basic Safety Message (BSM) in the US. The concept of cooperative perception extends the state of the art concept of cooperative awareness by integrating perception information from infrastructure perception systems (IPS)3 and vehicle perception systems (VPS) in the ego-vehicles environment model. In this paper three variants of the Covariance Intersection (CI) method used for state fusion in an Inter-Vehicle Information-Fusion (IV-IF) System are compared. The goal is to figure out which CI method out of the selection is the best choice for an active road safety application described in a recent publication, which was developed within the research project Ko-PER (cooperative perception).
A Common Dataset for Genomic Analysis of Livestock Populations

Although common datasets are an important resource for the scientific community and can be used to address important questions, genomic datasets of a meaningful size have not generally been available in livestock species. We describe a pig dataset that PIC (a Genus company) has made available for comparing genomic prediction methods. We also describe genomic evaluation of the data using methods that PIC considers best practice for predicting and validating genomic breeding values, and we discuss the impact of data structure on accuracy. The dataset contains 3534 individuals with high-density genotypes, phenotypes, and estimated breeding values for five traits. Genomic breeding values were calculated using BayesB, with phenotypes and de-regressed breeding values, and using a single-step genomic BLUP approach that combines information from genotyped and un-genotyped animals. The genomic breeding value accuracy increased with increased trait heritability and with increased relationship between training and validation. In nearly all cases, BayesB using de-regressed breeding values outperformed the other approaches, but the single-step evaluation performed only slightly worse. This dataset was useful for comparing methods for genomic prediction using real data. Our results indicate that validation approaches accounting for relatedness between populations can correct for potential overestimation of genomic breeding value accuracies, with implications for genotyping strategies to carry out genomic selection programs.
Body area nanonetworks with molecular communications in nanomedicine

Recent developments in nano and biotechnology enable promising therapeutic nanomachines (NMs) that operate on inter- or intracellular area of human body. The networks of such therapeutic NMs, body area nanonetworks (BAN2s), also empower sophisticated nanomedicine applications. In these applications, therapeutic NMs share information to perform computation and logic operations, and make decisions to treat complex diseases. Hence, one of the most challenging subjects for these sophisticated applications is the realization of BAN2 through a nanoscale communication paradigm. In this article, we introduce the concept of a BAN2 with molecular communication, where messenger molecules are used as communication carrier from a sender to a receiver NM. The current state of the art of molecular communication and BAN2 in nanomedicine applications is first presented. Then communication theoretical efforts are reviewed, and open research issues are given. The objective of this work is to introduce this novel and interdisciplinary research field and highlight major barriers toward its realization from the viewpoint of communication theory.
More Effective Transfer of Competitor and Customer Intelligence - Mediating Roles of Common Knowledge Sharing and Source Credibility

This research study examines the antecedents of competitor and customer intelligence transfer process between front-line and support personnel. Using structural equation analysis, the authors analyzed relationships among seven constructs—ties, motivation, supportive corporate culture, inter-departmental relationship, perception of common knowledge sharing, source credibility, and a transfer of competitor and customer intelligence. Hypotheses were tested among business executives and managers in four organizations in Thailand. The findings support the partially mediating effects of perception of common knowledge sharing and source credibility on a relationship between the antecedents and a transfer of competitor and customer intelligence.
Pharmacological characterization of rat paw edema induced by Cerastes gasperettii (cerastes) venom

Inflammatory response induced by the venom of the Arabian sand viper Cerastes gasperettii was studied by measuring rat hind-paw edema. Cerastes gasperettii venom (CgV, 3.75-240 µg/paw), heated for 30s at 97°C, caused a marked dose and time-dependent edema in rat paw. Response was maximal 2h after venom administration and ceased within 24h. Heated CgV was routinely used in our experiments at the dose of 120 µg/paw. Among all the drugs and antivenoms tested, cyproheptadine and 5-nitroindazole were the most effective in inhibiting edema formation. Aprotinin, mepyramine, dexamethasone, diclofenac, dipyridamole, Nw-nitro-L-arginine, quinacrine, and nordihydroguaiaretic acid showed statistically (p<0.001) significant inhibitory effect, but with variations in their inhibition degree. Equine polyspecific and rabbit monospecific antivenoms significantly (p<0.001) reduced edema when locally administered (subplantar) but were ineffective when intravenously injected. We can conclude that the principal inflammatory mediators were serotonin, histamine, adenosine transport factors, phosphodiesterase (PDE), cyclooxygenase, lipoxygenase and phospholipase A2 (PLA2), in addition to other prostaglandins and cytokines.
Efficacy of Orally Administered Low Dose N-methanocarbathymidine against Lethal Herpes Simplex Virus Type-2 Infections of Mice

Background: N-methanocarbathymidine (N-MCT) has previously been shown to be effective against lethal orthopoxvirus and herpes simplex virus type-1 infections in mice. In this investigation, the antiviral activity of N-MCT was assessed against herpes simplex virus type-2 (HSV-2) in BALB/c mice. Methods: BALB/c mice were infected intranasally with a lethal challenge dose of HSV-2. N-MCT was administered orally twice daily to mice using doses of 0.01 to 100 mg/kg to determine effects on survival and on viral replication in organ and central nervous system (CNS) samples. Results: N-MCT provided significant protection from mortality even when treatments were delayed until 3 days after viral infection. Viral replication in organ and CNS samples from N-MCT-treated mice was reduced below the limit of detection after 4 days of treatment. Conclusions: These results indicated that low dose N-MCT treatment was more effective than acyclovir therapy. N-MCT may be effective against HSV disease in humans and is currently undergoing preclinical evaluation. In particular, its potential use as a combination therapy for HSV, with its differing metabolism from acyclovir, make it a promising compound to develop for human use.
Presence of tumour-infiltrating FOXP3+ lymphocytes correlates with immature tumour angiogenesis in renal cell carcinomas.

BACKGROUND FOXP3+ regulatory T cells (Tregs) inhibit effector T cell functions and are implicated in tumour progression. However, together with microvessel density (MVD) they remain controversial prognostic predictors for renal cell carcinoma (RCC), and potential associations have yet to be determined. The objective of this study was to determine the prognostic significance of Tregs and MVD and their potential relationship in RCCs. DESIGN Paraffin-embedded tissues from 62 RCC patients were analysed using immunohistochemistry to detect FOXP3+ lymphocytes, and double immunohistochemistry to detect different microvessel types in the tumour interior, rim and normal kidney tissue, and their correlation with clinicopathological characteristics. Survival analysis was also performed. RESULTS The presence of FOXP3+ cells in the tumour interior or the rim showed no correlation with death from RCC and other pathological characteristics. Negative correlations were noted between the immature MVD in the tumour interior or the rim and tumour size, tumour stage and overall survival; however, there was no correlation with the nuclear grade or pathological type. A positive correlation between FOXP3+ Tregs and immature MVD (r=0.363, P=0.014) and mature MVD (r=0.383, P=0.009) was confirmed in the tumour interior. However, there was no correlation between FOXP3+ Tregs and mature MVD (r=0.281, P=0.076) or immature MVD (r=0.064, P=0.692) in the tumour rim. CONCLUSIONS In this study, a positive correlation between the presence of FOXP3+ Tregs and immature and mature MVD in RCC was confirmed, which suggests a link between suppression of immunity, tumour angiogenesis and poor prognosis.