Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Evidence for an Interferon-Antagonistic Function of Rift Valley Fever Virus Nonstructural Protein NSs

ABSTRACT Rift Valley fever virus (RVFV), a phlebovirus of the family Bunyaviridae, is a major public health threat in Egypt and sub-Saharan Africa. The viral and host cellular factors that contribute to RVFV virulence and pathogenicity are still poorly understood. All pathogenic RVFV strains direct the synthesis of a nonstructural phosphoprotein (NSs) that is encoded by the smallest (S) segment of the tripartite genome and has an undefined accessory function. In this report, we show that MP12 and clone 13, two attenuated RVFV strains with mutations in the NSs gene, were highly virulent in IFNAR−/− mice lacking the alpha/beta interferon (IFN-α/β) receptor but remained attenuated in IFN-γ receptor-deficient mice. Both attenuated strains proved to be excellent inducers of early IFN-α/β production. In contrast, the virulent strain ZH548 failed to induce detectable amounts of IFN-α/β and replicated extensively in both IFN-competent and IFN-deficient mice. Clone 13 has a defective NSs gene with a large in-frame deletion. This defect in the NSs gene results in expression of a truncated protein which is rapidly degraded. To investigate whether the presence of the wild-type NSs gene correlated with inhibition of IFN-α/β production, we infected susceptible IFNAR−/− mice with S gene reassortant viruses. When the S segment of ZH548 was replaced by that of clone 13, the resulting reassortants became strong IFN inducers. When the defective S segment of clone 13 was exchanged with the wild-type S segment of ZH548, the reassortant virus lost the capacity to stimulate IFN-α/β production. These results demonstrate that the ability of RVFV to inhibit IFN-α/β production correlates with viral virulence and suggest that the accessory protein NSs is an IFN antagonist.
Gesture and emotion: Can basic gestural form features discriminate emotions?

The question how exactly gesture and emotion are interrelated is still sparsely covered in research, yet highly relevant for building affective artificial agents. In our study, we investigate how basic gestural form features (handedness, hand shape, palm orientation and motion direction) are related to components of emotion. We argue that material produced by actors in filmed theater stagings are particularly well suited for such analyses. Our results indicate that there may be a universal association of gesture handedness with the emotional dimensions of pleasure and arousal. We discuss this and more specific findings, and conclude with possible implications and applications of our study.
Functional N-Methyl-D-Aspartate Receptors Are Expressed in Cone-Driven Horizontal Cells in Carp Retina

Glutamate works as a major excitatory neurotransmitter in the vertebrate retina. Whole-cell recordings made from isolated carp cone horizontal cells (H1 cells) showed that N-methyl-D-aspartate (NMDA), co-applied with glycine, induced inward currents that were blocked by the NMDA receptor competitive antagonist D-2-amino-5-phosphonopentanoate (D-AP5) and 5,7-dichlorokynurenic acid (DCKA), a selective NMDA receptor antagonist acting at the glycine site on the NMDA receptor complex. Moreover, calcium imaging showed that NMDA caused a significant elevation of intracellular calcium levels ([Ca2+]i) of H1 cells, which was also blocked by D-AP5. In contrast, neither inward currents nor changes in [Ca2+]i could be induced by NMDA in rod horizontal cells (H4 cells). Intracellular recordings made from H1 cells in the isolated retina, superfused with Ringer’s containing 1 mM Mg2+, in the dark demonstrated that NMDA reduced the light-off overshoot of H1 cells. We therefore conclude that the functional NMDA receptor is expressed in carp H1 cells, from which this receptor has been thought to be absent, and this receptor may play a role in modulating cone-driven signal of horizontal cells in the dark.
Modeling PCS networks under general call holding time and cell residence time distributions

In a personal communication service (PCS) network, the call completion probability and the effective call holding times for both complete and incomplete calls are central parameters in the network cost/performance evaluation. These quantities will depend on the distributions of call holding times and cell residence times. The classical assumptions made in the past that call holding times and cell residence times are exponentially distributed are not appropriate for the emerging PCS networks. This paper presents some systematic results on the probability of call completion and the effective call holding time distributions for complete and incomplete calls with general cell residence times and call holding times distributed with various distributions such as gamma, erlang, hyperexponential, hyper-erlang, and other staged distributions. These results provide a set of alternatives for PCS network modeling, which can be chosen to accommodate the measured data from PCS field trials. The application of these results in billing rate planning is also discussed.
Omnidirectional Visual Servoing Using the Normalized Mutual Information

Geometrical features have been a key element of visual servoing for several years. Recently, different works have shown how using all the information within the images can lead to successful servoing tasks. In particular, works using mutual information have been proposed and tested on perspective cameras. In this paper we propose to adapt this approach to vision systems following the unified sphere model for central cameras using a normalized version of the mutual information. This will permit to apply the technique to large fields of view with a more reliable similarity function. Several experiments are performed on a cartesian robot with a fisheye camera to validate our approaches.
Computational Analysis of Protein Tyrosine Nitration

As an important covalent post-translational modification, Tyrosine nitration is closely related to the causes of various diseases. However, its mechanism is still largely unknown. Based on experimentally verified tyrosine nitration sites, we introduced a novel computational approach to analyze tyrosine nitration. Nearest Neighbor algorithm armed by maximum relevancy minimum redundancy feature selection approach was used to construct the tyrosine nitration predictor. The problem of the imbalance of dataset sizes was dealt with by dividing large dataset into several smaller ones. Analysis of the selected features shows some interesting phenomena of the tyrosine nitration, which could be helpful for further computational and experimental investigations.
[Assessment of bovine biomaterials containing bone morphogenetic proteins bound to absorbable hydroxyapatite in rabbit segmental bone defects].

PURPOSE To evaluate the osteo-regenerative capacity of two proprietary bone grafting materials, using a segmental defect model in both radial diaphyses of rabbits. METHODS The right defect was filled with pooled bone morphogenetic proteins (pBMPs) bound to absorbable ultrathin powdered hydroxyapatite (HA) mixed with inorganic and demineralized bone matrix and bone-derived collagen, derived from bovine bone (Group A). The left defect was filled with bovine demineralized bone matrix and pBMPs bound to absorbable ultrathin powdered HA (Group B). In both groups, an absorbable membrane of demineralized bovine cortical was used to retain the biomaterials in the bone defects, and to guide the tissue regeneration. The rabbits were euthanized 30, 90 and 150 days after surgery. Radiographic, tomographic and histologic evaluations were carried out on all specimens. RESULTS At 30 days, the demineralized cortical bone cover was totally resorbed in both groups. HA was totally resorbed from Group A defects, whereas HA persisted in Group B defects. A prominent foreign body reaction was evident with both products, more pronounced in sections from Group B. At 90 days, the defects in Group B exhibited more new bone than Group A. However, at 150 days after surgery, neither treatment had stimulated complete repair of the defect. CONCLUSION The partial bone healing of the segmental defect occurred with low or none performance of the biomaterials tested.
Establishing Theoretical Minimal Sets of Mutants

Mutation analysis generates tests that distinguish variations, or mutants, of an artifact from the original. Mutation analysis is widely considered to be a powerful approach to testing, and hence is often used to evaluate other test criteria in terms of mutation score, which is the fraction of mutants that are killed by a test set. But mutation analysis is also known to provide large numbers of redundant mutants, and these mutants can inflate the mutation score. While mutation approaches broadly characterized as reduced mutation try to eliminate redundant mutants, the literature lacks a theoretical result that articulates just how many mutants are needed in any given situation. Hence, there is, at present, no way to characterize the contribution of, for example, a particular approach to reduced mutation with respect to any theoretical minimal set of mutants. This paper's contribution is to provide such a theoretical foundation for mutant set minimization. The central theoretical result of the paper shows how to minimize efficiently mutant sets with respect to a set of test cases. We evaluate our method with a widely-used benchmark.
TSBM: The Temporal-Spatial Bayesian Model for Location Prediction in Social Networks

In social networks, predicting a user's locations through those of his or her friends mainly relies on the selection method of the most influential friends of the user, which most of the existing location prediction methods fail to attach importance to. In this paper, we firstly present an analytical procedure in regard to the calculation of the theoretical maximum accuracy for location prediction by virtue of friends' locations. We further compare the theoretical maximum accuracy with the accuracy obtained by the current state-of-the-art methods, and propose an influential friend selection strategy, hoping to narrow the gap between them. More precisely, we define several features to measure the friends' influence on a user's locations, based on which we put forth a sequential random walk with restart procedure to rank the friends in terms of their influence. By dynamically selecting the top N influential friends of the user per time slice, we propose a temporal-spatial Bayesian model to characterize the dynamics of friends' influence for location prediction. Experiments on real data sets prove the effectiveness of our location prediction framework.
The Interaction of Akt with APPL1 Is Required for Insulin-stimulated Glut4 Translocation*

APPL1 (adaptor protein containing PH domain, PTB domain, and leucine zipper motif 1) is an Akt/protein kinase B-binding protein involved in signal transduction and membrane trafficking pathways for various receptors, including receptor tyrosine kinases. Here, we establish a role for APPL1 in insulin signaling in which we demonstrate its interaction with Akt2 by co-immunoprecipitation and pulldown assays. In primary rat adipocytes and skeletal muscle, APPL1 and Akt2 formed a complex that was dissociated upon insulin stimulation in both tissues. To investigate possible APPL1 function in adipocytes, we analyzed Akt phosphorylation, 2-deoxyglucose uptake, and Glut4 translocation by immunofluorescence following APPL1 knockdown by small interfering and short hairpin RNAs. We show that APPL1 knockdown suppressed Akt phosphorylation, glucose uptake, and Glut4 translocation. We also tested the effect in 3T3-L1 adipocytes of expressing full-length APPL1 or an N- or a C-terminal APPL1 construct. Interestingly, expression of full-length APPL1 and its N terminus suppressed insulin-stimulated 2-deoxyglucose uptake and Glut4 translocation to roughly the same extent (40-60%). We confirmed by cellular fractionation that Glut4 translocation was substantially blocked in 3T3-L1 adipocytes transfected with full-length APPL1. By cellular fractionation, APPL1 was localized mainly in the cytosol, and it showed a small degree of re-localization to the light microsomes and nucleus in response to insulin. By immunofluorescence, we also show that APPL1 partially co-localized with Glut4. These data suggest that APPL1 plays an important role in insulin-stimulated Glut4 translocation in muscle and adipose tissues and that its N-terminal portion may be critical for APPL1 function.
Assessor disagreement and text classifier accuracy

Text classifiers are frequently used for high-yield retrieval from large corpora, such as in e-discovery. The classifier is trained by annotating example documents for relevance. These examples may, however, be assessed by people other than those whose conception of relevance is authoritative. In this paper, we examine the impact that disagreement between actual and authoritative assessor has upon classifier effectiveness, when evaluated against the authoritative conception. We find that using alternative assessors leads to a significant decrease in binary classification quality, though less so ranking quality. A ranking consumer would have to go on average 25% deeper in the ranking produced by alternative-assessor training to achieve the same yield as for authoritative-assessor training.
A Wide-Bandwidth 2.4 GHz ISM Band Fractional-$N$ PLL With Adaptive Phase Noise Cancellation

A fast-settling adaptive calibration technique is presented that makes phase noise cancelling DeltaSigma fractional-N PLLs practical for the low reference frequencies commonly used in wireless communication systems. The technique is demonstrated as an enabling component of a 2.4 GHz ISM band CMOS PLL IC with a 730 kHz bandwidth, a 12 MHz reference, and an on-chip loop filter. In addition to the adaptive calibration technique, the IC incorporates a dynamic charge pump biasing technique to reduce power dissipation. The worst-case phase noise of the IC is -101 dBc/Hz and -124 dBc/Hz at 100 kHz and 3 MHz offsets, respectively, and the adaptive phase noise cancellation technique has a worst-case settling time of 35 mus . The IC is implemented in 0.18 CMOS technology. It measures 2.2 x 22 mm2 and its core circuitry consumes 20.9 mA from a 1.8 V supply.
Sustained Release Formulation of Primaquine for Prevention of Relapse of Plasmodium vivax Malaria: A Randomized, Double-Blind, Comparative, Multicentric Study

Background. Primaquine is used to eradicate latent Plasmodium vivax parasite from liver, with administration of standard dose daily up to 14 days. We studied efficacy, safety, and tolerability of sustained release (SR) formulation of primaquine in comparison with conventional primaquine in preventing relapse of P. vivax malaria. Methods. Microscopically confirmed cases of P. vivax malaria received chloroquine therapy for three days. Aparasitemic and asymptomatic patients were then randomized to receive either conventional primaquine 15 mg for 14 days or primaquine SR 15 mg for 14 days, or primaquine SR 30 mg for seven days. Results. Of the 360 patients, who received chloroquine therapy, 358 patients were randomized. Two-hundred eighty-eight patients completed six-month follow-up and four patients (three: conventional primaquine 15 mg (2.86%), one: primaquine SR 30 mg (0.93%)) showed relapse confirmed by PCR genotyping. Drug compliance was significantly better in primaquine SR 30 mg group (95.57%, p = 0.039) without any serious adverse events. Conclusion. Primaquine SR 15 mg and primaquine SR 30 mg could be an effective alternative to conventional primaquine 15 mg due to their comparable cure rates and safety profile. Shorter treatment duration with primaquine SR 30 mg may increase patient compliance and may further reduce relapse rates. Clinical Trial Registration. This trial is registered with CTRI/2010/091/000245.
Oxygen uptake during early cardiogenesis of the chick.

Oxidative metabolism of the isolated embryonic heart of the chick has been determined using a spectrophotometric technique allowing global as well as localized micromeasurements of the O2 uptake. Entire hearts, excised from embryos of 10 somites (primordia fused, stage 10 HH) and 40 somites (S shaped, stage 20 HH) were placed in a special chamber under controlled metabolic conditions where they continued to beat spontaneously and regularly. During the 32 h of development, the O2 consumption of the whole heart increased from 0.9 +/- 0.1 to 5.3 +/- 0.8 nmol O2/h. These values corrected for protein content were, however, comparable (0.45 nmol O2.h-1.micrograms-1). At stage 10-12, the O2 uptake varied along the cardiac tube (from 0.74 to 1.0 nmol O2.h-1.mm-2). From stage 10 to 20, the O2 uptake per unit area of ventricle wall increased from 0.7 +/- 0.2 to 1.8 +/- 0.2 nmol O2.h-1.mm-2, and the O2 uptake per myocardial volume during one cardiac cycle varied from 7 to 2.5 nmol O2/cm3. These results indicate that, despite an intense morphogenesis, the cardiac tissue has a rather low and stable oxidative metabolism, although the O2 requirement of the whole heart increases significantly. Moreover, the normalized suprabasal aerobic energy expenditure decreases throughout early cardiogenesis. The functional integrity of the isolated embryonic heart combined with the experimental possibilities of the microtechnique make the preparation appropriate for studying the changes in cardiac metabolism during development.
A new feature selection method for sentiment analysis of Turkish reviews

Sentiment analysis identifies people's opinions, sentiments about a product, a service, an organization, or an event. Because of huge review documents, researchers explore different feature selection methods that aim to eliminate non valuable features. However, not much work has been done on feature selection methods for sentiment analysis of Turkish reviews. In this study, we propose a new feature selection method called Query Expansion Ranking that is based on query expansion term weighting methods, which are used in Information Retrieval domain to determine the most valuable terms for query expansion. We compare Query Expansion Ranking with Chi Square method, which is a well-known and successful feature selector, and Document Frequency Difference which is a feature selection method proposed for sentiment analysis of English reviews. Experiments are conducted on four Turkish product review datasets that are book, DVDs, electronics, and kitchen appliances reviews by using a supervised machine learning classification method, namely Naïve Bayes Multinomial classifier. We show that our new proposed method improves sentiment analysis performance in terms of classification accuracy and time. In the experimental evaluation, we also show that our new feature selector improves classification accuracy better than Chi Square, and Document Frequency Difference methods.
Improved clustering protocol for energy efficiency algorithms in wireless sensor networks

In this paper proposes a novel clustering algorithm for energy efficient routing based on a cluster head selection. To extend the lifetime of networks and it improves node energy efficiency, balances energy consumption of all sensor nodes, increases dependability of data transmission and remits network lifetime in comparison of existing clustering protocol. Furthermore, the protocol increases the balance of energy dissipation, quantifiability and dependability of WSN.
Asymmetric Information and Overinvestment in Quality

In a standard adverse selection world, asymmetric information about product quality leads to quality deterioration in the market. Suppose that a higher investment level makes the realization of high quality more likely. Then, if consumers observe the investment (but not the realization of product quality) before purchase, they can infer the probability distribution of high and low quality that may be put on the market. We uncover two effects that may lead the firm to overinvest in quality compared to a market with full information: first, an adverse selection effect according to which a sufficiently large investment can avoid adverse selection and, second, an efficiency effect according to which a larger investment reduces the probability of having in the market low quality products that are not socially valuable.
The Queue-Read Queue-Write PRAM Model: Accounting for Contention in Parallel Algorithms

This paper introduces the queue-read queue-write ({\sc qrqw}) parallel random access machine ({\sc pram}) model, which permits concurrent reading and writing to shared-memory locations, but at a cost proportional to the number of readers/writers to any one memory location in a given step. Prior to this work there were no formal complexity models that accounted for the contention to memory locations, despite its large impact on the performance of parallel programs. The {\sc qrqw pram} model reflects the contention properties of most commercially available parallel machines more accurately than either the well-studied {\sc crcw pram} or {\sc erew pram} models: the {\sc crcw} model does not adequately penalize algorithms with high contention to shared-memory locations, while the {\sc erew} model is too strict in its insistence on zero contention at each step. The {\sc qrqw pram} is strictly more powerful than the {\sc erew pram}. This paper shows a separation of $\sqrt{\log n}$ between the two models, and presents faster and more efficient {\sc qrqw} algorithms for several basic problems, such as linear compaction, leader election, and processor allocation. Furthermore, we present a work-preserving emulation of the {\sc qrqw pram} with only logarithmic slowdown on Valiant's {\sc bsp} model, and hence on hypercube-type noncombining networks, even when latency, synchronization, and memory granularity overheads are taken into account. This matches the best-known emulation result for the {\sc erew pram}, and considerably improves upon the best-known efficient emulation for the {\sc crcw pram} on such networks. Finally, the paper presents several lower bound results for this model, including lower bounds on the time required for broadcasting and for leader election.
A Generic, Flexible Protocol for Preimplantation Human Leukocyte Antigen Typing Alone or in Combination with a Monogenic Disease, for Rapid Case Work-up and Application

Abstract Human leukocyte antigen (HLA) typing of in vitro fertilization (IVF) embryos, aims to establish a pregnancy that is HLA compatible with an affected sibling who requires hematopoietic stem cell transplantation (HSCT). It can be performed with or without preimplantation genetic diagnosis (PGD) for exclusion of a single-gene disorder (SGD) and it is a multistep, technically challenging procedure at every stage. Our purpose was to address the difficulties of genetic analysis by developing a fast, reliable and accurate PGD-HLA protocol, to simplify patient work-up and PGD application, while providing high flexibility for combination with any SGD. Requests included PGD-HLA for β-thalassemia (β-thal)/sickle cell disease (most common request), Diamond-Blackfan anemia (DBA), chronic granulomatous disease (CGD) and preimplantation-HLA typing only. For HLA haplotyping, we selected a panel of 26 short tandem repeats (STRs) distributed across the entire HLA locus, following PGD guidelines. When required, mutation detection was performed by both a direct and indirect approach. To support concurrent SGD exclusion and HLA typing, a one-step, single-tube, multiplex fluorescent touchdown-polymerase chain reaction (PCR) was optimized. The described touchdown-PCR was successfully applied for all PGD-HLA protocols. Eight clinical cycles were performed with a diagnosis achieved for 94.7% of amplified biopsied blastomeres. Embryo transfer took place in six cycles, with two pregnancies achieved and two healthy female infants (from a twin pregnancy) born so far. Our protocol enables HLA typing in a single PCR, reducing the risk of contamination and the cost, and providing faster results. It requires minimum optimization before clinical application, irrespective of the SGD involved, decreasing the waiting time from referral to treatment for all PGD-HLA cases.