Miracle-dz/UniFAR-FTUs huggingface dataset:
Actin Cytoskeleton Is Involved in Targeting of a Viral Hsp70 Homolog to the Cell Periphery

ABSTRACT The cell-to-cell movement of plant viruses involves translocation of virus particles or nucleoproteins to and through the plasmodesmata (PDs). As we have shown previously, the movement of the Beet yellows virus requires the concerted action of five viral proteins including a homolog of cellular ∼70-kDa heat shock proteins (Hsp70h). Hsp70h is an integral component of the virus particles and is also found in PDs of the infected cells. Here we investigate subcellular distribution of Hsp70h using transient expression of Hsp70h fused to three spectrally distinct fluorescent proteins. We found that fluorophore-tagged Hsp70h forms motile granules that are associated with actin microfilaments, but not with microtubules. In addition, immobile granules were observed at the cell periphery. A pairwise appearance of these granules at the opposite sides of cell walls and their colocalization with the movement protein of Tobacco mosaic virus indicated an association of Hsp70h with PDs. Treatment with various cytoskeleton-specific drugs revealed that the intact actomyosin motility system is required for trafficking of Hsp70h in cytosol and its targeting to PDs. In contrast, none of the drugs interfered with the PD localization of Tobacco mosaic virus movement protein. Collectively, these findings suggest that Hsp70h is translocated and anchored to PDs in association with the actin cytoskeleton.
Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty

MOTIVATION Several measures have been recently proposed for quantifying the functional similarity between gene products according to well-structured controlled vocabularies where biological terms are organized in a tree or in a directed acyclic graph (DAG) structure. However, existing semantic similarity measures ignore two important facts. First, when calculating the similarity between two terms, they disregard the descendants of these terms. While this makes no difference when the ontology is a tree, we shall show that it has important consequences when the ontology is a DAG-this is the case, for example, with the Gene Ontology (GO). Second, existing similarity measures do not model the inherent uncertainty which comes from the fact that our current knowledge of the gene annotation and of the ontology structure is incomplete. Here, we propose a novel approach based on downward random walks that can be used to improve any of the existing similarity measures to exhibit these two properties. The approach is computationally efficient-random walks do not need to be simulated as we provide formulas to calculate their stationary distributions. RESULTS To show that our approach can potentially improve any semantic similarity measure, we test it on six different semantic similarity measures: three commonly used measures by Resnik (1999), Lin (1998), and Jiang and Conrath (1997); and three recently proposed measures: simUI, simGIC by Pesquita et al. (2008); GraSM by Couto et al. (2007); and Couto and Silva (2011). We applied these improved measures to the GO annotations of the yeast Saccharomyces cerevisiae, and tested how they correlate with sequence similarity, mRNA co-expression and protein-protein interaction data. Our results consistently show that the use of downward random walks leads to more reliable similarity measures.
Efficient and cost-effective techniques for browsing and indexing large video databases

We present in this paper a fully automatic content-based approach to organizing and indexing video data. Our methodology involves three steps:<ul><li>Step 1: We segment each video into shots using a Camera-Tracking technique. This process also extracts the feature vector for each shot, which consists of two statistical variances <i>Var<sup>BA</sup></i> and <i>Var<sup>OA</sup></i>. These values capture how much things are changing in the background and foreground areas of the video shot. </li><li>Step 2: For each video, We apply a fully automatic method to build a browsing hierarchy using the shots identified in Step 1. </li><li>Step 3: Using the <i>Var<sup>BA</sup></i> and <i>Var<sup>OA</sup></i> values obtained in Step 1, we build an index table to support a variance-based video similarity model. That is, video scenes/shots are retrieved based on given values of <i>Var<sup>BA</sup></i> and <i>Var<sup>OA</sup></i>. </li></ul> The above three inter-related techniques offer an integrated framework for modeling, browsing, and searching large video databases. Our experimental results indicate that they have many advantages over existing methods.
Simulating migrated and inverted seismic data by filtering a geologic model

The simulation of migrated and inverted data is hampered by the high computational cost of generating 3D synthetic data, followed by processes of migration and inversion. For example, simulating the migrated seismic signature of subtle stratigraphic traps demands the expensive exercise of 3D forward modeling, followed by 3D migration of the synthetic seismograms. This computational cost can be overcome using a strategy for simulating migrated and inverted data by filtering a geologic model with 3D spatial-resolution and angle filters, respectively. A key property of the approach is this: The geologic model that describes a target zone is decoupled from the macrovelocity model used to compute the filters. The process enables a target-orientedapproach, by which a geologically detailed earth model describing a reservoir is adjusted without having to recalculate the filters. Because a spatial-resolution filter combines the results of the modeling and migration operators, the simulated images can be compared directly to a real migration image. We decompose the spatial-resolution filter into two parts and show that applying one of those parts produces output directly comparable to 1D inverted real data. Two-dimensional synthetic examples that include seismic uncertainties demonstrate the usefulness of the approach. Results from a real data example show that horizontal smearing, which is not simulated by the 1D convolution model result, is essential to understand the seismic expression of the deformation related to sulfate dissolution and karst collapse.
Negative Correlations between Control Performance and Verbalizable Knowledge: Indicators for Implicit Learning in Process Control Tasks?

Negative correlations between task performance in dynamic control tasks and verbalizable knowledge, as assessed by a post-task questionnaire, have been interpreted as dissociations that indicate two antagonistic modes of learning, one being “explicit”, the other “implicit”. This paper views the control tasks as finite-state automata and offers an alternative interpretation of these negative correlations. It is argued that “good controllers” observe fewer different state transitions and, consequently, can answer fewer post-task questions about system transitions than can “bad controllers”. Two experiments demonstrate the validity of the argument by showing the predicted negative relationship between control performance and the number of explored state transitions, and the predicted positive relationship between the number of explored state transitions and questionnaire scores. However, the experiments also elucidate important boundary conditions for the critical effects. We discuss the implications of these findings, and of other problems arising from the process control paradigm, for conclusions about implicit versus explicit learning processes.
A platelet alpha granule membrane protein that is associated with the plasma membrane after activation. Characterization and subcellular localization of platelet activation-dependent granule-external membrane protein.

We have identified and purified a platelet integral membrane protein (140,000 mol wt), using the KC4 monoclonal antibody specific for activated platelets, that is internal in resting platelets but exposed on activated platelets (Hsu-Lin S.-C., C.L. Berman, B.C. Furie, D. August, and B. Furie, 1984, J. Biol. Chem. 259: 9121-9126.). The expression of the protein on the platelet surface is secretion-dependent. This protein has been named platelet activation-dependent granule-external membrane (PADGEM) protein. PADGEM protein is distinct from the surface glycoproteins of resting platelets, but identical to the S12 antigen, GMP-140. Using immunofluorescent staining, resting platelets failed to stain for PADGEM protein with the KC4 antibody, but after permeabilization showed a punctate staining of the cell interior. Thrombin-stimulated intact platelets stained with a peripheral rim pattern thus demonstrating the translocation of PADGEM protein from an internal location to the cell surface. PADGEM protein expression on the platelet surface at varying thrombin concentrations correlated with alpha granule release, as measured by the secretion of platelet factor 4. Further evidence for an alpha granule localization of PADGEM protein was provided by nitrogen cavitation of resting platelets followed by metrizamide density gradient centrifugation; PADGEM protein codistributed with platelet factor 4. Using immunoelectron microscopy, the protein was localized to the alpha granule in frozen ultrathin sections of resting platelets labeled using rabbit anti-PADGEM protein antibodies, whereas in thrombin-activated platelets, the plasma membrane was labeled. These studies indicate that PADGEM protein is a component of the alpha granule membrane of resting platelets and is incorporated into the plasma membrane upon activation and secretion.
Top-down high-resolution mass spectrometry of cardiac myosin binding protein C revealed that truncation alters protein phosphorylation state

Cardiac myosin binding protein C (cMyBP-C), bound to the sarcomere's myosin thick filament, plays an important role in the regulation of muscle contraction. cMyBP-C is a large multidomain protein that interacts with myosin, titin, and possibly actin. Mutations in cMyBP-C are the most common known cause of heritable hypertrophic cardiomypathies. Phosphorylation of cMyBP-C plays an essential role in the normal cardiac function. cMyBP-C (142 kDa) has 81 serine and 73 threonine residues presenting a major challenge for unequivocal identification of specific phosphorylation sites. Top-down mass spectrometry, which directly analyzes intact proteins, is a powerful technique to universally observe and quantify protein posttranslational modifications without a priori knowledge. Here, we have extended top-down electron capture dissociation mass spectrometry to comprehensively characterize mouse cMyBP-C expressed in baculovirus. We have unambiguously identified all of the phosphorylation sites in the truncated (28–115 kDa) and full-length forms of cMyBP-C (142 kDa) and characterized the sequential phosphorylations, using a combination of top-down and middle-down (limited proteolysis) MS approach, which ensures full sequence coverage. Unit mass resolution and high mass accuracy (<5 ppm) have been achieved for a 115-kDa protein (the largest protein isotopically resolved to date). Remarkably, we discovered that truncations in recombinant proteins, even a seemingly minor one, can dramatically alter its phosphorylation state, which is significant because truncated recombinant proteins are routinely substituted for their full-length forms in crystal structure and functional studies. Our study provides direct evidence of alterations in the posttranslational state between the truncated and full-length recombinant proteins, which can lead to variations in structure and function.
Encoding Large RCC8 Scenarios Using Rectangular Pseudo-Solutions

Most approaches in the field of qualitative spatial reasoning (QSR) use constraint networks to encode spatial scenarios. The size of these networks is quadratic in the number of variables, which has severely limited the real-world application of QSR. In this paper, we propose another representation of spatial scenarios, in which each variable is associated with one or more rectangles. Instead of requiring these rectangles to define a solution of the corresponding constraint network, we construct sequences of rectangles that define partial solutions to progressively weaker constraint networks. We present experimental results that illustrate the effectiveness of this strategy.
Frequency-Dependent Glycinergic Inhibition Modulates Plasticity in Hippocampus

Previous studies have demonstrated the presence of functional glycine receptors (GlyRs) in hippocampus. In this work, we examine the baseline activity and activity-dependent modulation of GlyRs in region CA1. We find that strychnine-sensitive GlyRs are open in the resting CA1 pyramidal cell, creating a state of tonic inhibition that “shunts” the magnitude of EPSPs evoked by electrical stimulation of the Schaffer collateral inputs. This GlyR-mediated shunting conductance is independent of the presynaptic stimulation rate; however, pairs of presynaptic and postsynaptic action potentials, repeated at frequencies above 5 Hz, reduce the GlyR-mediated conductance and increase peak EPSP magnitudes to levels at least 20% larger than those seen with presynaptic stimulation alone. We refer to this phenomenon as rate-dependent efficacy (RDE). Exogenous GlyR agonists (glycine, taurine) block RDE by preventing the closure of postsynaptic GlyRs. The GlyR antagonist strychnine blocks postsynaptic GlyRs under all conditions, occluding RDE. During RDE, GlyRs are less responsive to local glycine application, suggesting that a reduction in the number or sensitivity of membrane-inserted GlyRs underlies RDE. By extending the RDE induction protocol to include 500 paired presynaptic and postsynaptic spikes, we can induce long-term synaptic depression (LTD). Manipulations that lead to reduced functionality of GlyRs, either pharmacologically or through RDE, also lead to increased LTD. This result suggests that RDE contributes to long-term synaptic plasticity in the hippocampus.
An architecture-level approach for mitigating the impact of process variations on extensible processors

In this paper, we present an architecture-level approach to mitigate the impact of process variations on extended instruction set architectures (ISAs). The proposed architecture adds one extra cycle to execute custom instructions (CIs) that violate the maximum allowed propagation delay due to the process variations. Using this method, the parametric yield of manufactured chips will greatly improve. The cost is an increase in the cycle latency of some of the CIs, and hence, a slight performance degradation for the extensible processor architectures. To minimize the performance penalty of the proposed approach, we introduce a new merit function for selecting the CIs during the selection phase of the ISA extension design flow. To evaluate the efficacy of the new selection method, we compare the extended ISAs obtained by this method with those selected based on the worst-case delay. Simulation results reveal that a speedup improvement of about 18% may be obtained by the proposed selection method. Also, by using the proposed merit function, the proposed architecture can improve the speedup about 20.7%.
Soft Frequency Reuse in the Uplink of an OFDMA Network

The challenges with deploying a cellular wireless communication network with static frequency reuse in an interference limited environment is that for highly loaded cells, significant regions of coverage will experience high interference levels, resulting in unserviceable low signal-to-interference values. Therefore, interference mitigation approaches as adaptive fractional frequency reuse are considered to tackle the problem. In this paper, different strategies for user and resource allocation are evaluated along with fractional frequency reuse schemes. In contrast to downlink scenarios, we investigate the performance of the OFDMA uplink. It is shown that soft frequency reuse is well-performing in the uplink although it is easy to deploy since it does not rely on resource coordination.
Psychedelic therapy utilizing LSD in the treatment of the alcoholic patient: a preliminary report.

The rationale of psychedelic therapy with alcoholic patients is focused on the alienation-breaking potential of "peak" or psychedelic experiences induced with the aid of LSD. An exemplary LSD session report and MMPI data on 69 pilot patients are presented for illustration. While all present results indicate that psychedelic therapy does add significantly to presently available alcoholic rehabilitation resources, it is emphasized that safe and effective use of LSD requires specialized training.
Loss of Smad Signaling in Human Colorectal Cancer Is Associated with Advanced Disease and Poor Prognosis

PURPOSEBased largely on in vitro inve stigations and animal studies, investigators believe that disruptions of transforming growth factor-β (TGF-β) signaling contribute to the development and progression of human colorectal cancer. The purpose of this study was to directly assess the status of the TGF-β signaling pathway in colorectal cancer and determine the effects of its disruption on clinical behavior and outcome. MATERIALS AND METHODSSmad proteins are the principal intracellular components of the TGF-β signaling pathway. We conducted a high-throughput analysis of the expression patterns of Smad2, phosphorylated (activated) Smad2 (pSmad2), and Smad4 in more than 600 human colorectal cancer specimens assembled in tissue microarrays. RESULTSThe vast majority (93.8%; 95% Cl: 92%–96%) of colorectal cancers expressed phosphorylated Smad2, indicating the ability of the tumors to survive and proliferate within a microenvironment that contains bioactive TGF-β. Twelve of 633 (1.9%; 95% Cl: 1%–3%) cases failed to express Smad2, and 15 of 641 (2.3%; 95% Cl: 1%–4%) cases failed to express Smad4. Moreover, 29 of 615 (4.7%; 95% Cl: 3%–7%) of cases expressed Smad2 but not its activated form (pSmad2), suggesting the presence of a TGF-β receptor defect. Based on an analysis of 577 cases for which clinical outcome information was available, failure to express Smad2, pSmad2, or Smad4 was associated with advanced stage disease, the presence of lymph node metastases, and a significantly shorter overall survival (median survival: 35 vs 58 months). DISCUSSIONLoss of Smad activation and/or expression occurs in approximately 10% of colorectal cancers. This subset has a poor prognosis because of its association with advanced disease and the presence of lymph node metastases at diagnosis.
Mixed Epithelial and Stromal Tumor of the Kidney: Preliminary Immunohistochemical and Electron Microscopic Studies of the Epithelial Component

Mixed epithelial and stromal tumor of the kidney is a rare biphasic tumor composed of cysts and tubules embedded in the spindle cell stroma. Although the histogenesis of this tumor is unknown, it has been proposed that both components of the tumor, i.e., stromal and epithelial, are neoplastic. The authors report preliminary immunohistochemical and electron microscopic studies of the epithelial component from one case of a typical, benign, mixed epithelial, and stromal tumor of the kidney. In this study, some tubules showed positivity for proximal, while others showed positivity for distal, nephron immunomarkers. By electron microscopy, some tubules had features of proximal tubular epithelium, while other tubules had features of the loop of Henle (thin segments). The authors believe that in a benign tumor such morphologic heterogeneity is inconsistent with neoplastic proliferation. Therefore, they postulate that in mixed epithelial and stromal tumor of the kidney the tubules are entrapped rather than neoplastic. Additional studies are needed to address this issue and electron microscopy should play a significant role in this process.
Spatial-Temporal Opportunity Detection for Spectrum-Heterogeneous Cognitive Radio Networks: Two-Dimensional Sensing

This paper investigates the issue of spatial-temporal opportunity detection for spectrum-heterogeneous cognitive radio networks, where at a given time secondary users (SUs) at different locations may experience different spectrum access opportunities. Most prior studies address either spatial or temporal sensing in isolation and explicitly or implicitly assume that all SUs share the same spectrum opportunity. However, this assumption is not realistic and the traditional non-cooperative sensing (NCS) and cooperative sensing (CS) schemes are not very effective in a more realistic setting considering the heterogeneous spectrum availability among SUs. We define new performance metrics to guide the spatial-temporal opportunity detection and propose a two-dimensional sensing (TDS) framework to improve the opportunity detection performance, which exploits correlations in time and space simultaneously by effectively fusing sensing results in a spatial-temporal sensing window. Furthermore, in terms of maximum interference constrained transmission power (MICTP), we classify the spatial opportunities for SUs into three groups: black, grey, and white, and propose a TDS-based distributed power control scheme to further improve the spectrum utilization by exploiting both grey and white spectrum opportunities. The effectiveness of the proposed scheme is demonstrated through in-depth numerical simulations under a variety of scenarios.
Ensemble averaging stress–strain fields in polycrystalline aggregates with a constrained surface microstructure – Part 2: crystal plasticity

The effect of three-dimensional (3D) grain morphology on the deformation at a free surface in polycrystalline aggregates is investigated by means of a large-scale finite element and statistical approach. For a given two-dimensional surface at z = 0 containing 39 grains with given crystal orientations, eight 3D random polycrystalline aggregates are constructed having different 3D grain shapes and orientations except at z = 0, based on an original 3D image analysis procedure. They are subjected to overall tensile loading conditions. The continuum crystal plasticity framework is adopted and the resulting plastic strain fields at the free surface z = 0 are analyzed. Ensemble average and variance maps of the plastic strain field at the observed free surface are computed. In the case of elastoplastic copper grains, fluctuations ranging between 2% and 80% are found in the equivalent plastic slip level at a given material point of the observed surface from one realization of the microstructure to another. The obtained fields are compared to the prediction based on the associated columnar grain microstructure, often used in the literature.