Miracle-dz/UniFAR-FTUs huggingface dataset:
An Arenavirus RING (Zinc-Binding) Protein Binds the Oncoprotein Promyelocyte Leukemia Protein (PML) and Relocates PML Nuclear Bodies to the Cytoplasm

ABSTRACT The promyelocytic leukemia protein (PML) forms nuclear bodies which are altered in some disease conditions. We report that the cytoplasmic RNA virus lymphocytic choriomeningitis virus (LCMV) influences the distribution of PML bodies. In cells infected with LCMV, the Z protein and PML form large bodies primarily in the cytoplasm. Transient transfection studies indicate that Z alone is sufficient to redistribute PML to the cytoplasm and that PML and Z colocalize. Coimmunoprecipitation studies show specific interaction between PML and Z proteins. A similar result was observed with a Z protein from another arenavirus, Lassa virus, suggesting that this is a general feature of the Arenaviridae. Genetically engineered mutations in PML were used to show that the Z protein binds the N-terminal region of PML and does not need the PML RING or the nuclear localization signal to colocalize. The Z protein acts dominantly to overcome the diffuse phenotype observed in several PML mutants. The interaction between PML and Z may influence certain unique characteristics of arenavirus infection.
The Na+/HCO3− Co‐Transporter SLC4A4 Plays a Role in Growth and Migration of Colon and Breast Cancer Cells

The hypoxic and acidic tumor environment necessitates intracellular pH (pHi) regulation for tumor progression. Carbonic anhydrase IX (CA IX; hypoxia‐induced) is known to facilitate CO2 export and generate HCO3− in the extracellular tumor space. It has been proposed that HCO3− is re‐captured by the cell to maintain an alkaline pHi. A diverse range of HCO3− transporters, coupled with a lack of a clear over‐expression in cancers have limited molecular identification of this cellular process. Here, we report that hypoxia induces the Na+/HCO3− co‐transporter (NBCe1) SLC4A4 mRNA expression exclusively in the LS174 colon adenocarcinoma cell line in a HIF1α dependent manner. HCO3− dependent pHi recovery observations revealed the predominant use of an NBC mechanism suggesting that reversal of a Cl−/HCO3− exchanger is not utilized for tumor cell pHi regulation. Knockdown of SLC4A4 via shRNA reduced cell proliferation and increased mortality during external acidosis and spheroid growth. pHi recovery from acidosis was partially reduced with knockdown of SLC4A4. In MDA‐MB‐231 breast cancer cells expressing high levels of SLC4A4 compared to LS174 cells, SLC4A4 knockdown had a strong impact on cell proliferation, migration, and invasion. SLC4A4 knockdown also altered expression of other proteins including CA IX. Furthermore the Na+/HCO3− dependent pHi recovery from acidosis was reduced with SLC4A4 knockdown in MDA‐MB‐231 cells. Combined our results indicate that SLC4A4 contributes to the HCO3− transport and tumor cell phenotype. This study complements the on‐going molecular characterization of the HCO3− re‐uptake mechanism in other tumor cells for future strategies targeting these potentially important drug targets. J. Cell. Physiol. 230: 1954–1963, 2015. © 2015 Wiley Periodicals, Inc.
Black Sea thermohaline properties: Long‐term trends and variations

Abstract The current knowledge about spatial and temporal dynamics of the Black Sea's thermohaline structure is incomplete because of missing data and sparse distribution of existing measurements in space and time. This study presents 56 year continuous simulations of the Black Sea's hydrodynamics using the 3D General Estuarine Transport Model (GETM), without incorporating any relaxation toward climatological or observational data fields. This property of the model allows us to estimate independent temporal trends, in addition to resolving the spatial structure. The simulations suggest that the intermediate layer temperature is characterized by a weak positive trend (warming), whereas the surface temperature does not show a clear linear trend. Different salinity trends have been established at the surface (negative), upper (weaker negative) and main halocline (positive). Three distinct dynamic periods are identified (1960–1970, 1970–1995, 1995–2015), which exhibit pronounced changes in the Black Sea's thermohaline properties and basin circulation. Strengthening of the main cyclonic circulation, accompanied by intensification of the mesoscale anticyclonic eddy formation is found. Both events strongly affect the sea surface salinity but contribute in opposing directions. Specifically, strong composite large‐scale circulation leads to an increase in sea surface salinity, while enhanced formation of mesoscale anticyclones decreases it. Salinity evolution with time is thus the result of the competition of these two opposing yet interdependent processes.
Adaptive and Channel-Aware Detection of Selective Forwarding Attacks in Wireless Sensor Networks

Wireless sensor networks (WSNs) are vulnerable to selective forwarding attacks that can maliciously drop a subset of forwarding packets to degrade network performance and jeopardize the information integrity. Meanwhile, due to the unstable wireless channel in WSNs, the packet loss rate during the communication of sensor nodes may be high and vary from time to time. It poses a great challenge to distinguish the malicious drop and normal packet loss. In this paper, we propose a channel-aware reputation system with adaptive detection threshold (CRS-A) to detect selective forwarding attacks in WSNs. The CRS-A evaluates the data forwarding behaviors of sensor nodes, according to the deviation of the monitored packet loss and the estimated normal loss. To optimize the detection accuracy of CRS-A, we theoretically derive the optimal threshold for forwarding evaluation, which is adaptive to the time-varied channel condition and the estimated attack probabilities of compromised nodes. Furthermore, an attack-tolerant data forwarding scheme is developed to collaborate with CRS-A for stimulating the forwarding cooperation of compromised nodes and improving the data delivery ratio of the network. Extensive simulation results demonstrate that CRS-A can accurately detect selective forwarding attacks and identify the compromised sensor nodes, while the attack-tolerant data forwarding scheme can significantly improve the data delivery ratio of the network.
Interdecadal Thermocline Variability in the North Pacific for 1958–97: A GCM Simulation*

An ocean general circulation model is forced with the NCEP reanalysis wind stress for 1958‐97 to understand mechanisms of ocean subsurface variability. With relatively high horizontal (1 83 18) and vertical (41 levels) resolutions, the model produces mode waters on a range of density surfaces in the western, central, and eastern North Pacific, in qualitative agreement with observations. These mode waters appear as a thermostad or a region of weak stratification in the upper thermocline as they flow southward from their formation regions in the Kuroshio and its extension. In the model, subsurface temperature variability in the central subtropical gyre reaches a maximum within the thermostad, in contrast to what might be expected from the linear baroclinic Rossby wave theory. This variance maximum is associated with the longitudinal shift in the path of mode waters. In particular, deepened mixed layer and accelerated eastward currents in the Kuroshio Extension by wind changes in the mid-1970s act cooperatively to move the central mode waters toward the east, causing large subsurface temperature anomalies. Besides the local maximum in the central North Pacific subtropical gyre, two additional maxima of the subsurface anomaly are identified in the northwestern and southern parts of the gyre, respectively. Among these subsurface anomaly centers, the one in the northwestern North Pacific has a strong effect on the model sea surface temperature, suggesting that the Kuroshio and its extension are a key region to decadal/interdecadal ocean‐atmosphere interaction. Finally, possible effects of atmospheric thermal forcing are discussed.
The performance characteristics of groundnut (Arachis hypogea, L.) biodiesel in a diesel engine

The performance of groundnut ethyl ester blended with diesel in a compression ignition engine was experimentally determined. Groundnut oil reacted with ethanol to produce ethyl esters in a two-step transesterification process. The ethyl-esters were blended with automotive gas oil at (0 to 20%) mix with 5% increment of groundnut ethyl-esters to produce biodiesel. The performance of a 2.46 kW diesel engine was evaluated using the groundnut biodiesel at five loading conditions (0, 25, 50, 75 and 100% of full load). Automotive gas oil was used as a reference diesel fuel. The engine torque had a peak value of 8.5 Nm at full load, while the peak value of speed was 1300 rev/min at 25% full load when using 15% groundnut ester-AGO blend. The exhaust gas temperature had a peak value of 420°C at full load when using 5% groundnut ester-AGO blend. There were no significant differences (p>0.05) in average values of torque, speed and exhaust gas temperature of the engine for groundnut biodiesel and automotive gas oil. Groundnut biodiesel can be used to fuel a diesel engine. Key words: Groundnut oil, ethyl esters, biodiesel, diesel engine.
Contact Pressure Prediction in Total Knee Joint Replacements Part 1: General Elasticity Solution for Elliptical Layered Contacts

A general elasticity contact theory has been developed, to predict the contact area and the contact pressure in total knee joint replacements with elliptical contacts where the thickness of ultra high molecular weight polyethylene (UHMWPE) is similar or less than the contact half width. The interfacial boundary condition between the UHMWPE component and the underlying metal substrate has been considered to be either perfectly bonded or perfectly unbonded in the model. Poisson's ratio for UHMWPE has been assumed to be 0.3 or 0.4. The effect of the thickness of the UHMWPE layer on the contact area and the contact pressure has been examined. The predictions of the maximum contact pressure and the contact area have been presented in non-dimensional forms and can readily be applied for typical design configurations of current total knee joint replacements. Furthermore, the present results can readily be applied to design considerations for total knee joint replacements to reduce contact stresses within the UHMWPE component.
Developmental Shifts in Children's Sensitivity to Visual Speech: a New Multimodal Picture–word Task

Keywords: Picture–word task Audiovisual speech perception U-shaped developmental function Phonological processing Picture word interference Picture naming Multimodal speech processing Dynamic systems theory a b s t r a c t This research developed a multimodal picture–word task for assessing the influence of visual speech on phonological processing by 100 children between 4 and 14 years of age. We assessed how manipulation of seemingly to-be-ignored auditory (A) and audiovisual (AV) phonological distractors affected picture naming without participants consciously trying to respond to the manipulation. Results varied in complex ways as a function of age and type and modality of distractors. Results for congruent AV distractors yielded an inverted U-shaped function with a significant influence of visual speech in 4-year-olds and 10-to 14-year-olds but not in 5-to 9-year-olds. In concert with dynamic systems theory, we proposed that the temporary loss of sensitivity to visual speech was reflecting reorganization of relevant knowledge and processing subsystems, particularly phonology. We speculated that reorganization may be associated with (a) formal literacy instruction and (b) developmental changes in multimodal processing and auditory perceptual, linguistic, and cognitive skills. Introduction Speech communication by adults is naturally a multimodal event with auditory and visual speech integrated mandatorily. This basic property of mature speech perception is illustrated dramatically by 0022-0965/$-see front matter Ó 2008 Elsevier Inc. All rights reserved.
Role of Endoplasmic Reticulum Aminopeptidases in Health and Disease: from Infection to Cancer

Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are essential for the maturation of a wide spectrum of proteins involved in various biological processes. In the ER, these enzymes work in concert to trim peptides for presentation on MHC class I molecules. Loss of ERAPs function substantially alters the repertoire of peptides presented by MHC class I molecules, critically affecting recognition of both NK and CD8+ T cells. In addition, these enzymes are involved in the modulation of inflammatory responses by promoting the shedding of several cytokine receptors, and in the regulation of both blood pressure and angiogenesis. Recent genome-wide association studies have identified common variants of ERAP1 and ERAP2 linked to several human diseases, ranging from viral infections to autoimmunity and cancer. More recently, inhibition of ER peptide trimming has been shown to play a key role in stimulating innate and adaptive anti-tumor immune responses, suggesting that inhibition of ERAPs might be exploited for the establishment of innovative therapeutic approaches against cancer. This review summarizes data currently available for ERAP enzymes in ER peptide trimming and in other immunological and non-immunological functions, paying attention to the emerging role played by these enzymes in human diseases.
Automatic detection of children's engagement using non-verbal features and ordinal learning

In collaborative play, young children can exhibit different types of engagement. Some children are engaged with other children in the play activity while others are just looking. In this study, we investigated methods to automatically detect the children's levels of engagement in play settings using non-verbal vocal features. Rather than labelling the level of engagement in an absolute manner, as has frequently been done in previous related studies, we designed an annotation scheme that takes the order of children's engagement levels into account. Taking full advantage of the ordinal annotations, we explored the use of SVM-based ordinal learning, i.e. ordinal regression and ranking, and compared these to a rule-based ranking and a classification method. We found promising performances for the ordinal methods. Particularly, the ranking method demonstrated the most robust performance against the large variation of children and their interactions.
Effects of feedback and peer pressure on contributions to enterprise social media

Increasingly, large organizations are experimenting with internal social media (e.g., blogs, forums) as a platform for widespread distributed collaboration. Contributions to their counterparts outside the organization's firewall are driven by attention from strangers, in addition to sharing among friends. However, employees in a workplace under time pressures may be reluctant to participate and the audience for their contributions is comparatively smaller. Participation rates also vary widely from group to group. So what influences people to contribute in this environment? In this paper, we present the results of a year-long empirical study of internal social media participation at a large technology company, and analyze the impact attention, feedback, and managers' and coworkers' participation have on employees' behavior. We find feedback in the form of posted comments is highly correlated with a user's subsequent participation. Recent manager and coworker activity relate to users initiating or resuming participation in social media. These findings extend, to an aggregate level, the results from prior interviews about blogging at the company and offer design and policy implications for organizations seeking to encourage social media adoption.
AtLSG1-2 Regulates Leaf Growth by Affecting Cell Proliferation and the Onset of Endoreduplication and Synergistically Interacts with AtNMD3 during Cell Proliferation Process

AtLSG1-2 is a circularly permuted GTPase required for ribosome biogenesis and recently shown to be involved in early leaf development, although it was unclear how AtLSG1-2 affects leaf growth. Here, we found that atlsg1-2 mutants had reduced leaf size as a result of decreased cell size and cell number. Leaf kinematic analysis and CYCB1;1::GUS expression pattern in atlsg1-2 mutant indicated that loss of function of AtLSG1-2 delays the transition from cell division to cell expansion. Decreases in ploidy levels and trichome branch number suggest that AtLSG1-2 deficiency suppresses endoreduplication. Real-time PCR analysis showed that genes specifically expressed in the proliferation stage were highly expressed and those involved in endoreduplication were differentially regulated. LSG1 is known to mediate the recruitment of nucleocytoplasmic shuttling protein NMD3 back to the nucleus in yeast, yet their relationship was unclear in plants. Our genetic analysis revealed that the atlsg1 atnmd3 double mutant displayed enhanced phenotypes as compared with the respective single mutant and that AtLSG1-2 and AtNMD3 synergistically affect the cell proliferation process.
A hedonic model for effective web marketing: an empirical examination

Purpose – To identify the relative effects of three features of response toward web interface (RWI) on their advertising promotion effectiveness as measured by the number of accesses to various web pages.Design/methodology/approach – A factorial design experiment was conducted on the internet to empirically test the hedonic stimulation web interface model developed by the authors.Findings – The results reveal that there are three main effects and two two‐variable interactions which are found to be significant. In respect to our hedonic stimulation web interface design model (HSWIDM). No three variables of the hedonic salience interact simultaneously.Research limitations/implications – Among the potential limitations of this research is the main effect of colour in the design of the experiment. The other potential limitation is related to the broad assumption of subjects selected.Practical implications – In operational terms, the major finding regarding the key aim of this research is that all three hedoni.
LCM: An Efficient Algorithm for Enumerating Frequent Closed Item Sets

In this paper, we propose three algorithms LCMfreq, LCM, and LCMmax for mining all frequent sets, frequent closed item sets, and maximal frequent sets, respectively, from transaction databases. The main theoretical contribution is that we construct treeshaped transversal routes composed of only frequent closed item sets, which is induced by a parent-child relationship defined on frequent closed item sets. By traversing the route in a depth-first manner, LCM finds all frequent closed item sets in polynomial time per item set, without storing previously obtained closed item sets in memory. Moreover, we introduce several algorithmic techniques using the sparse and dense structures of input data. Algorithms for enumerating all frequent item sets and maximal frequent item sets are obtained from LCM as its variants. By computational experiments on real world and synthetic databases to compare their performance to the previous algorithms, we found that our algorithms are fast on large real world datasets with natural distributions such as KDD-cup2000 datasets, and many other synthetic databases.
Modeling and Rendering Architecture from Photographs

The creation of three-dimensional models of existing architectural scenes with the aid of the computer has been commonplace for some time, and the resulting models have been both entertaining virtual environments as well as valuable visualization tools. Large-scale efforts have pushed the campuses of Iowa State University, California State University – Chico, and swaths of downtown Los Angeles [23] through the graphics pipeline. Unfortunately, the modeling methods employed in such projects are very labor-intensive. They typically involve surveying the site, locating and digitizingarchitectural plans (if available), and converting existing CAD data (if available). Moreover, the renderings of such models are noticeably computer-generated; even those that employ large number of texture-maps generally fail to resemble real photographs.
Evaluation of the Role of the Vaccinia Virus Uracil DNA Glycosylase and A20 Proteins as Intrinsic Components of the DNA Polymerase Holoenzyme*

The vaccinia virus DNA polymerase is inherently distributive but acquires processivity by associating with a heterodimeric processivity factor comprised of the viral A20 and D4 proteins. D4 is also an enzymatically active uracil DNA glycosylase (UDG). The presence of an active repair protein as an essential component of the polymerase holoenzyme is a unique feature of the replication machinery. We have shown previously that the A20-UDG complex has a stoichiometry of ∼1:1, and our data suggest that A20 serves as a bridge between polymerase and UDG. Here we show that conserved hydrophobic residues in the N′ terminus of A20 are important for its binding to UDG. Our data argue against the assembly of D4 into higher order multimers, suggesting that the processivity factor does not form a toroidal ring around the DNA. Instead, we hypothesize that the intrinsic, processive DNA scanning activity of UDG tethers the holoenzyme to the DNA template. The inclusion of UDG as an essential holoenzyme component suggests that replication and base excision repair may be coupled. Here we show that the DNA polymerase can utilize dUTP as a substrate in vitro. Moreover, uracil moieties incorporated into the nascent strand during holoenzyme-mediated DNA synthesis can be excised by the viral UDG present within this holoenzyme, leaving abasic sites. Finally, we show that the polymerase stalls upon encountering an abasic site in the template strand, indicating that, like many replicative polymerases, the poxviral holoenzyme cannot perform translesion synthesis across an abasic site.
Calprotectin (a major leucocyte protein) is strongly and independently correlated with joint inflammation and damage in rheumatoid arthritis

Objective: Calprotectin is a major leucocyte protein, shown to correlate well with laboratory and clinical assessments in several inflammatory rheumatic diseases, and large concentrations of calprotectin have been found in synovial fluid from patients with rheumatoid arthritis (RA). The objective of the present study was to examine correlations between calprotectin and joint damage. Methods: 145 patients with RA were analysed cross sectionally with laboratory (calprotectin, C reactive protein (CRP), and erythrocyte sedimentation rate (ESR)), clinical (28 joint counts (tender, swollen), physician global VAS, DAS28 and RA Articular Damage score (RAAD)), and radiographic (plain hand radiographs; modified Sharp’s method) measurements, on the same day. Results: Calprotectin showed a highly significant correlation with measures of joint damage; modified Sharp score r = 0.43 (p<0.001) and RAAD r = 0.40 (p<0.001). The association with modified Sharp score and RAAD score was maintained after adjustment for CRP, ESR, rheumatoid factor, DAS28, sex, and age in a multiple regression analysis (p = 0.018 and p = 0.04, respectively), while neither CRP nor ESR showed any independent associations. Highly significant correlations (p<0.001) were also found between calprotectin and both laboratory and clinical markers of inflammation. Conclusion: Calprotectin was found to significantly and independently explain the variation in the radiological and clinical assessments of joint damage. Longitudinal studies are required to examine whether calprotectin may predict the progression of joint damage in RA.