Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Interactions of the UL16 Tegument Protein with the Capsid of Herpes Simplex Virus

ABSTRACT The UL16 tegument protein of herpes simplex virus is conserved throughout the herpesvirus family. It has been reported to be capsid associated and may be involved in budding by providing an interaction with the membrane-bound UL11 protein. UL16 has been shown to be present in all the major locations that capsids are found (i.e., the nucleus, cytoplasm, and virions), but whether it is actually capsid associated in each of these has not been reported. Therefore, capsids were purified from each compartment, and it was found that UL16 was present on cytoplasmic but not nuclear capsids. In extracellular virions, the majority of UL16 (87%) was once again not capsid associated, which suggests that the interaction is transient during egress. Because herpes simplex virus (HSV) buds into the acidic compartment of the trans-Golgi network (TGN), the effect of pH on the interaction was examined. The amount of capsid-associated UL16 dramatically increased when extracellular virions were exposed to mildly acidic medium (pH 5.0 to 5.5), and this association was fully reversible. After budding into the TGN, capsid and tegument proteins also encounter an oxidizing environment, which is conducive to disulfide bond formation. UL16 contains 20 cysteines, including five that are conserved within a putative zinc finger. Any free cysteines that are involved in the capsid interaction or release mechanism of UL16 would be expected to be modified by N-ethylmaleimide, and, consistent with this, the amount of capsid-associated UL16 dramatically increased when virions were incubated with this compound. Taken together, these data suggest a transient interaction between UL16 and capsids, possibly modified in the acidic compartment of secretory vesicles and requiring a release mechanism that involves cysteines.
Comparison of single-model and multiple-model prediction-based audiovisual fusion

Prediction-based fusion is a recently proposed audiovisual fusion approach which outperforms feature-level fusion on laughter-vs-speech discrimination. One set of predictive models is trained per class which learns the audio-to-visual and visual-to-audio feature mapping together with the time evolution of audio and visual features. Classification of a new input is performed via prediction. All the class predictors produce a prediction of the expected audio / visual features and their prediction errors are combined for each class. The model which best describes the audiovisual feature relationship, i.e., results in the lowest prediction error, provides its label to the input. In all the previous works, a single set of predictors was trained on the entire training set for each class. In this work, we investigate the use of multiple sets of predictors per class. The main idea is that since models are trained on clusters of data, they will be more specialised and they will produce lower prediction errors which can in turn enhance the classification performance. We experimented with subject-based clustering and clustering based on different types of laughter, voiced and unvoiced. Results are presented on laughter-vs-speech discrimination on a cross-database experiment using the AMI and MAHNOB databases. The use of multiple sets of models results in a significant performance increase with the latter clustering approach achieving the best performance. Overall, an increase of over 4% and 10% is observed for F1 speech and laughter, respectively, for both datasets.
The Evolving Philosophers Problem: Dynamic Change Management

A model for dynamic change management which separates structural concerns from component application concerns is presented. This separation of concerns permits the formulation of general structural rules for change at the configuration level without the need to consider application state, and the specification of application component actions without prior knowledge of the actual structural changes which may be introduced. In addition, the changes can be applied in such a way so as to leave the modified system in a consistent state, and cause no disturbance to the unaffected part of the operational system. The model is applied to an example problem, 'evolving philosophers'. The principles of this model have been implemented and tested in the Conic environment for distributed systems. >
Distributed Information-Based Cooperative Strategy Adaptationin Opportunistic Mobile Networks

Cooperation among nodes is a fundamental necessity in opportunistic mobile networks (OMNs), where the messages are transferred using the store-carry-and-forward mechanism, due to sporadic inter-node wireless connectivity. While multiple works have addressed this issue, they are often constrained in their assumptions on solutions (e.g., requirement of central authority, and tracing the recipient nodes for providing reward or punishment). In this work, we address this research lacuna by taking an evolutionary theory-based approach. In evolutionary theory, the players analyze alternative strategies and select the best one to survive in a population. Inspired by this, in this work, we propose a Distributed Information-Based Cooperation Ushering Scheme (DISCUSS) to promote cooperation in message forwarding between nodes. In this scheme, the nodes maintain and exchange information with one another during contacts about the messages created and delivered in the network. Based on this, the nodes evaluate their own performance and compare that with the approximated network performance to adapt the most successful forwarding strategy. Simulation results show that the message delivery ratio in the network improves upto 31 percent, when the nodes dynamically switch their strategies, as compared to the case when they do not. Furthermore, the DISCUSS scheme fared closely to its variant with the nodes having complete knowledge about the network-wide performance.
Selecting Repertoires of Action in Environmental Movement Organizations

Environmental movement organizations (EMOs) that have similar goals frequently rely on different tactics and strategies to advance their agendas. This article uses an interpretive perspective to examine the factors influencing EMO selection of a repertoire of action. Building on concepts from organization and social movement theories, and relying on interview and archival data from Friends of the Earth and Greenpeace, this study suggests that experience, core values and beliefs, environmental philosophy, and political ideology work together to create distinct organizational interpretations of the political environment, efficacy of action, acceptability of tactics, significance of an issue, and source of the problem. These interpretations combine to shape EMO determinations of what types of action will be most appropriate and effective. Although structural factors influence the decisions that are made within EMOs, organizations also rely on interpretive processes in their selection of a repertoire of action.
DHT-based localized service discovery in wireless mesh networks

Wireless mesh networks (WMNs) provide high-bandwidth wireless network access to mobile clients in extensible, robust multi-hop networks. WMNs support distributed service provision and data storage, catering to the advanced capabilities of current mobile devices. Services and data discovery using undirected broadcast or multicast messages, as in traditional discovery protocols, significantly harms network performance due to interference and collisions. In contrast, distributed hash tables (DHTs) offer consistent mapping of service and data identifiers to the providing devices and therefore allow a directed unicast discovery and access. However, traditional DHTs place identifiers at arbitrary distant devices in the network, resulting in frequent use of long multi-hop routing paths. Such multi-hop transmissions suffer from performance loss at each hop and also degrade the overall network performance. We propose DLSD, a DHT-based localized index structure that establishes a hierarchy of locally bounded address spaces ranging from a few nearby devices to the whole network. Iterating through this hierarchy bottom-up allows devices to find the most local provider of the requested item, thereby minimizing multi-hop transmissions while ensuring global reachability. Through this reduction of routing hops, we maintain high transmission performance and minimize interference in the network. We evaluate the feasibility of our approach and show that it significantly reduces routing overhead and outperforms traditional service discovery and DHT approaches.
Targeting of the cytosolic poly(A) binding protein PABPC1 to mitochondria causes mitochondrial translation inhibition

Mammalian mitochondria contain their own genome that is almost fully transcribed from both strands, generating polycistronic RNA units that are processed and matured. The mitochondrial mRNA is modified by oligo- or polyadenylation at the 3′ termini, but the exact function of this post-transcriptional addition is unclear. Current debate focuses on the role of polyadenylation in transcript stability. An equally likely function that has received little attention is that, as in the cytosol of eukaryotes, polyadenylation facilitates translation in the mitochondrion. To address this issue, we have targeted cytosolic proteins to the mitochondrion, a poly(A) specific 3′ exoribonuclease, mtPARN, and a poly(A)binding protein, mtPABP1. Removal of the 3′ adenylyl extensions had a variable effect on mt-mRNA steady-state levels, increasing (MTND1, 2, 5) or decreasing (MTCO1, 2, RNA14) certain species with minimal effect on others (RNA7, MTND3). Translation was markedly affected, but interpretation of this was complicated by the concomitant 3′ truncation of the open reading frame in most cases. Coating of the poly(A) tail by mtPABP1, however, did not lead to transcript decay but caused a marked inhibition of mitochondrial translation. These data are consistent with endogenous RNA-binding factor(s) interacting with the poly(A) to optimize mitochondrial protein synthesis.
The bromodomain: a conserved sequence found in human, Drosophila and yeast proteins.

Identification of conserved domains or motifs in proteins may aid in the localization and analysis of important structural and functional regions. We report here a protein sequence motif, called the bromodomain (1), that has been found in six genes from humans (CCG1 and RING3), Drosophila (fsh and brm), and yeast (SPT7 and SNF2). The fsh and brm genes are required maternally for proper expression of certain homeotic genes (1,2). The SPT7 and SNF2 genes of Saccharomyces cerevisiae encode transcriptional activators (3,4). The SNF2 and brm proteins have extensive sequence homology (1). It is not clear whether the two human genes are involved in processes. CCG1 is a DNA-binding protein that complements temperature sensitive mutations that cause cell cycle arrest in Gl (5). The RING3 gene is a newly identified human gene of unknown function, mapping to the class II region of the human major histocompatibility locus, that has substantial homology to the fsh gene (6). Each of these proteins has one or two copies of the 61 —63 amino acid bromodomain (Figure 1). The sequence identity is highest (~ 80%) between the corresponding fsh and RING3 repeats. More typically, any two motifs show 25-40% identity, with 50-60% identity between two repeats within the same protein. There are seven invariant residues, four of which are aromatic amino acids, and numerous conservative substitutions. The location of the motif(s) within the individual proteins is variable, and two motifs may be present in tandem or separated by sequences unrelated to the motif. Secondary structure prediction methods were applied to the bromodomain and revealed two strongly predicted amphipathic a helices followed by reverse turns. Four of the invariant residues are located within the turns, and the other three are located among four highly conserved proline residues at the N terminus. The functional significance of the bromodomain is unknown, and experiments with the two yeast proteins indicate that it may be dispensable in some cases (6; P.Tan and F.W., unpublished data). However, the widespread conservation of the bromodomain suggests that it is important for some aspects of protein function. We speculate that the hydrophobic surfaces of the helices and the invariant hydrophobic residues could serve as sites of intramolecular or intermolecular protein-protein interaction. Such interactions could influence the assembly or activity of multicomponent complexes involved in transcription activation or other cellular processes.
Prenatal estrogens and the development of homosexual orientation.

In psychobiological research on sexual orientation, the prenatal hormone theory has a central posi tion. This article examines the hypothesis that prenatal estrogens contribute to the development of human sexual orientation. Several groups of women with a history of prenatal exposure to diethyl stilbestrol (DES), a nonsteroidal synthetic estrogen, were compared with several samples of control women in the context of a comprehensive study of the psychiatric and psychologic effects of prenatal DES. Various aspects of sexual orientation were assessed by systematic interview. Consistently across samples, more DES-exposed women than controls were rated as bisexual or homosexual (scores 2-6 on Kinsey-format scales ranging from 0 to 6). The data are compatible with the hypothesis that prenatal estrogens may play a role in the development of human sexual orientation
Studies on the mechanism of resistance to rapamycin in human cancer cells.

Rapamycin is a potent cytostatic agent that arrests cells in the G1 phase of the cell cycle. The relationships between cellular sensitivity to rapamycin, drug accumulation, expression of mammalian target of rapamycin (mTOR), and inhibition of growth factor activation of ribosomal p70S6 kinase (p70(S6k)) and dephosphorylation of pH acid stable protein I (eukaryotic initiation factor 4E binding protein) were examined. We show that some cell lines derived from childhood tumors are highly sensitive to growth inhibition by rapamycin, whereas others have high intrinsic resistance (>1000-fold). Accumulation and retention of [14C]rapamycin were similar in sensitive and resistant cells, with all cells examined demonstrating a stable tight binding component. Western analysis showed levels of mTOR were similar in each cell line (<2-fold variation). The activity of p70(S6k), activated downstream of mTOR, was similar in four cell lines (range, 11.75-41. 8 pmol/2 x 10(6) cells/30 min), but activity was equally inhibited in cells that were highly resistant to rapamycin-induced growth arrest. Rapamycin equally inhibited serum-induced phosphorylation of pH acid stable protein I in Rh1 (intrinsically resistant) and sensitive Rh30 cells. In serum-fasted Rh30 and Rh1 cells, the addition of serum rapidly induced c-MYC (protein) levels. Rapamycin blocked induction in Rh30 cells but not in Rh1 cells. Serum-fasted Rh30/rapa10K cells, selected for high level acquired resistance to rapamycin, showed >/=10-fold increased c-MYC compared with Rh30. These results suggest that the ability of rapamycin to inhibit c-MYC induction correlates with intrinsic sensitivity, whereas failure of rapamycin to inhibit induction or overexpression of c-MYC correlates with intrinsic and acquired resistance, respectively.
The cost-effectiveness of elective Cesarean delivery to prevent hepatitis C transmission in HIV-coinfected women

Objectives: To determine the net health consequences, costs, and cost-effectiveness of elective Cesarean delivery (C-section) to prevent perinatal transmission of hepatitis C virus (HCV) in HIV/HCV-coinfected women with suppressed HIV RNA but detectable HCV RNA. Design: Cost-effectiveness analysis using a probabilistic decision model. Methods: The model compared two strategies: (i) C-section for all coinfected women with suppressed HIV RNA but detectable HCV RNA; (ii) C-section only when indicated based on fetal status. Outcomes included vertical transmission of HCV, maternal mortality, quality-adjusted life expectancy, delivery and HCV treatment costs, and incremental cost-effectiveness ratios. Data were obtained from the literature and national databases. Delivery cost data were from a hospital consortium database. Probability distributions were derived from published confidence intervals or estimated ranges, or calculated using reported sample sizes. Results: Elective C-section in coinfected women with suppressed HIV RNA but detectable HCV RNA would avoid 45 vertical HCV transmissions per 1000 deliveries and increase maternal mortality by one death per 100 000 deliveries. The incremental cost-effectiveness ratio of a recommendation for C-section versus current practice was $3900–6100 per quality-adjusted life year for the mother–child pair. Results are sensitive to the efficacy of C-section in preventing transmission, the probability of vaginal delivery without a recommendation, and rates of maternal acceptance of the recommendation. Conclusions: Assuming 2000 births/year among HIV/HCV-coinfected women in the United States, a recommendation for elective C-section in these women could avoid an additional 90 perinatal HCV transmissions per year with a risk of one maternal death in 50 years.
Social Self-perception Accuracy: Variations as a Function of Child Age and Gender

Significant theoretical and research efforts have addressed children's self-perceptions. However, questions remain about the factors that affect variability in self-perceptions both between children and across development. The present study examined social self-perceptions and self-perception accuracy as defined by concordance between self and peer report of positive and negative social behaviors. Accuracy was examined as a function of grade level (grades 2–8) and gender within a broad sample (n = 1883). Younger children reported more positive self-perceptions, but concordance with peers was stronger at higher grade levels. Although boys and girls differed in their self-perceptions, concordance did not vary as a function of gender or whether the peer reference group was composed of same- or opposite-gender peers.
Neighbourhood distribution interacts with orthographic priming in the lexical decision task

Lexical decision tasks (LDTs) were used with a masked priming procedure to test whether neighbourhood distribution interacts with orthographic priming. Word targets had either ‘single’ neighbours when their two higher frequency orthographic neighbours were spread over letter positions (e.g., neighbours of LOBE: robe-loge) or ‘twin’ neighbours when they were concentrated on a single letter position (e.g., neighbours of FARD: lard-tard). All word targets were preceded by their highest frequency orthographic neighbour or by a control prime. An inhibitory priming effect was found for words with single neighbours, but not for words with twin neighbours, in both a yes/no LDT (Experiment 1a) and a go/no-go LDT (Experiment 1b). This interaction was replicated in a go/no-go LDT when the position of the letter yielding the neighbour prime was controlled (Experiment 2). Simulations run on the word materials revealed that the interactive activation model captures the inhibitory priming effect in the single-neighbour condition but fails to capture the loss of priming in the twin-neighbour condition.
Comparison of cooperative spectrum sensing strategies in distributed cognitive radio networks

Cooperative spectrum sensing has been proposed to significantly improve spectrum sensing accuracy by taking advantage of the cooperation among secondary users (SUs), but also this incurs some sensing cost. In this paper, we present a cooperative spectrum sensing model with consideration to spectrum sensing cost in distributed cognitive radio networks where each SU aims to maximize its utility. Under the scenario with selfish SUs, we formulate cooperative spectrum sensing as a non-cooperative game and obtain the mixed strategy Nash equilibrium of the formulated spectrum sensing game by deriving the sensing probabilities of SUs. Under the scenario with limited collaboration of SUs, we formulate cooperative spectrum sensing as a nonlinear optimization problem and derive the optimal sensing strategy of SUs by using our proposed Newton-Raphson based algorithm. Numerical results demonstrate that SUs with limited collaboration are able to achieve much better performance than the outcome of the Nash equilibrium and by choosing the optimal sensing strategy SUs are able to maximize their utility, which is an effective tradeoff between SU throughput and sensing cost.
WaterlooClarke: TREC 2015 Total Recall Track

The total recall track in TREC 2015 seeks an enhanced model to accelerate the autonomous technology-assisted review process. This paper introduces several noval ideas such as clustering based seed selection method, extended n-grams features and continuous query expansion learned from the relevant documents derived from each iteration. These methods can retrieve more relevant documents from each iteration thereby achieving high recall while requiring less review e↵ort.
Design of a high capacity Electro Permanent Magnetic adhesion for climbing robots

The interest for robotic solutions to perform inspection and maintenance of steel structures is realised with reduced costs, improved safety and improved efficiency. However current robotic solutions are limited by the required adhesion to support the robot and payload device. The design of an Electro Permanent Magnetic device is studied to yield a high capacity adhesion method for use with industrial climbing robots. The adhesion device must provide a lightweight, low power and a failsafe solution for ferromagnetic surfaces. The design process to achieve maximum holding force for Electro Permanent Magnets is presented.
Oscillations in H+ and Ca2+ Ion Fluxes around the Elongation Region of Corn Roots and Effects of External pH

Net fluxes of H+ and Ca2+ around the elongation region of low-salt corn (Zea mays L.) roots were measured using the microelectrode ion flux estimation (MIFE) technique. At pH 5.2 two oscillatory components were found. Fast, 7-min oscillations in H+ flux were superimposed on slow oscillations of about 1.5 h. Fast oscillations in Ca2+ flux showed a strong dependence on the H+ oscillations and were normally leading in phase by about 1 to 1.5 min. Both oscillatory components were strongly affected by external pH values. Preincubation for 20 h in buffered pH 4.0 solution suppressed the slow oscillatory component and caused huge H+ influxes in the elongation region. The fast oscillations were 8 times larger in amplitude and were slightly lengthened. Preincubation at pH 6.0 did not suppress the rhythmic character of the ion fluxes but it shifted the average H+ flux to greater efflux. The fast and slow oscillatory components of H+ flux seem to relate to biophysical and biochemical mechanisms of intracellular pH homeostasis, respectively. The origin of the Ca2+ flux oscillations is discussed in terms of the “weak acid Donnan Manning” model of cell wall ion exchanges.