Miracle-dz/UniFAR-FTUs huggingface dataset:
Neutral Endopeptidase Protein Expression and Prognosis in Localized Prostate Cancer

Purpose: Neutral endopeptidase (NEP) is a cell-surface peptidase that inactivates neuropeptide growth factors implicated in prostate cancer progression. The clinical significance of decreased NEP expression observed in prostate cancer is unclear. We investigated whether decreased NEP expression in localized prostate cancers is associated with prostate-specific antigen (PSA) relapse after radical prostatectomy. Experimental Design: NEP expression patterns were examined by immunohistochemistry in 223 men, who underwent radical prostatectomy between 1990 and 2000 at the Veterans Administration Medical Center (New York, NY) with available representative tissues and adequate follow up. We also examined whether hypermethylation of the NEP promoter contributes to down-regulation of NEP protein expression in a subset of patients that showed decreased NEP expression (n = 22). Results: Three patterns of NEP expression were observed: (a) membranous expression similar to benign prostate epithelium (n = 82; 37%); (b) complete loss of NEP expression in prostate cancer compared with adjacent benign prostate glands (n = 105; 47%); and (c) heterogeneous NEP expression (n = 36; 16%). In a multivariate analysis, complete loss of NEP expression was associated with PSA relapse after controlling for grade, stage, pretreatment PSA, and race simultaneously (hazard ratio, 1.99; 95% confidence interval, 1.13–3.52; two-sided χ2 P = 0.017). In addition, DNA hypermethylation of the NEP promoter was frequently (73%) identified in a subset of 22 of cases that showed decreased NEP expression. Conclusion: Our data suggest that decreased NEP expression might contribute to progression of localized prostate cancer after surgery. Data also suggest that methylation is an important mechanism of NEP protein silencing. Larger prospective studies are required for confirmation.
Cell Wall Chitosan Is Necessary for Virulence in the Opportunistic Pathogen Cryptococcus neoformans

ABSTRACT Cryptococcus neoformans is an opportunistic fungal pathogen that causes meningoencephalitis. Its cell wall is composed of glucans, proteins, chitin, and chitosan. Multiple genetic approaches have defined a chitosan-deficient syndrome that includes slow growth and decreased cell integrity. Here we demonstrate chitosan is necessary for virulence and persistence in the mammalian host.
A Cortico-Spinal Model of Reaching and Proprioception under Multiple Task Constraints

A model of cortico-spinal trajectory generation for voluntary reaching movements is developed to functionally interpret a broad range of behavioral, physiological, and anatomical data. The model simulates how arm movements achieve their remarkable efficiency and accuracy in response to widely varying positional, speed, and force constraints. A key issue in arm movement control is how the brain copes with such a wide range of movement contexts. The model suggests how the brain may set automatic and volitional gating mechanisms to vary the balance of static and dynamic feedback information to guide the movement command and to compensate for external forces. For example, with increasing movement speed, the system shifts from a feedback position controller to a feedforward trajectory generator with superimposed dynamics compensation. Simulations of the model illustrate how it reproduces the effects of elastic loads on fast movements, endpoint errors in Coriolis fields, and several effects of muscle tendon vibration, including tonic and antagonist vibration reflexes, position and movement illusions, effects of obstructing the tonic vibration reflex, and reaching undershoots caused by antagonist vibration.
Chronic inhibition of endothelial nitric oxide synthase activity in nucleus tractus solitarii enhances baroreceptor reflex in conscious rats

In acute experiments, we demonstrated previously that nitric oxide (NO) donors exogenously applied to the nucleus tractus solitarii (NTS) depressed the baroreceptor cardiac reflex. In this study, we determined a role for endogenous endothelial nitric oxide synthase (eNOS) activity in the NTS for chronically regulating baroreceptor reflex function in conscious rats. A recombinant adenoviral vector directing expression of a truncated form of eNOS was microinjected bilaterally into the NTS to inhibit endogenous eNOS activity. Arterial pressure was monitored continuously using radio‐telemetry in freely moving animals and spontaneous baroreceptor reflex gain (sBRG) determined by a time‐series method. sBRG showed a gradual increase from day 7 to 21 after gene transfer and the value at day 21 (1.68 ± 0.20 ms mmHg−1, n= 6) was significantly higher than that before gene transfer (1.13 ± 0.09 ms mmHg−1, P < 0.001). This value was also significantly higher than that in rats in which enhanced green fluorescent protein (eGFP) was expressed in the NTS (1.04 ± 0.21 ms mmHg−1; n= 6, P < 0.01) and saline‐treated groups (1.12 ± 0.15 ms mmHg−1; n= 4, P < 0.05), which did not change from control levels. In addition, heart rate decreased from 336 ± 6 to 318 ± 8 b.p.m. (P < 0.05) 21 days after gene transfer. This value was also significantly lower than that in control groups (eGFP: 348 ± 9 b.p.m., n= 6, P < 0.01; saline: 347 ± 5 b.p.m., n= 4, P < 0.05). Gene transfer did not affect arterial pressure. These findings suggest that in the conscious rat eNOS is constitutively active within the NTS and is a factor regulating baroreceptor reflex gain and heart rate.
2015 Ieee International Conference on Big Data (big Data) Maritime Situation Analysis Framework Vessel Interaction Classification and Anomaly Detection

—Maritime domain awareness is critical for protecting sea lanes, ports, harbors, offshore structures like oil and gas rigs and other types of critical infrastructure against common threats and illegal activities. Typical examples range from smuggling of drugs and weapons, human trafficking and piracy all the way to terror attacks. Limited surveillance resources constrain maritime domain awareness and compromise full security coverage at all times. This situation calls for innovative intelligent systems for interactive situation analysis to assist marine authorities and security personal in their routine surveillance operations. In this article, we propose a novel situation analysis approach to analyze marine traffic data and differentiate various scenarios of vessel engagement for the purpose of detecting anomalies of interest for marine vessels that operate over some period of time in relative proximity to each other. We consider such scenarios as probabilistic processes and analyze complex vessel trajectories using machine learning to model common patterns. Specifically, we represent patterns as left-to-right Hidden Markov Models and classify them using Support Vector Machines. To differentiate suspicious activities from unobjectionable behavior, we explore fusion of data and information, including kinematic features, geospatial features, contextual information and maritime domain knowledge. Our experimental evaluation shows the effectiveness of the proposed approach using comprehensive real-world vessel tracking data from coastal waters of North America.
Tl+-induced μs Gating of Current Indicates Instability of the MaxiK Selectivity Filter as Caused by Ion/Pore Interaction

Patch clamp experiments on single MaxiK channels expressed in HEK293 cells were performed at high temporal resolution (50-kHz filter) in asymmetrical solutions containing 0, 25, 50, or 150 mM Tl+ on the luminal or cytosolic side with [K+] + [Tl+] = 150 mM and 150 mM K+ on the other side. Outward current in the presence of cytosolic Tl+ did not show fast gating behavior that was significantly different from that in the absence of Tl+. With luminal Tl+ and at membrane potentials more negative than −40 mV, the single-channel current showed a negative slope resistance concomitantly with a flickery block, resulting in an artificially reduced apparent single-channel current Iapp. The analysis of the amplitude histograms by β distributions enabled the estimation of the true single-channel current and the determination of the rate constants of a simple two-state O-C Markov model for the gating in the bursts. The voltage dependence of the gating ratio R = Itrue/Iapp = (kCO + kOC)/kCO could be described by exponential functions with different characteristic voltages above or below 50 mM Tl+. The true single-channel current Itrue decreased with Tl+ concentrations up to 50 mM and stayed constant thereafter. Different models were considered. The most likely ones related the exponential increase of the gating ratio to ion depletion at the luminal side of the selectivity filter, whereas the influence of [Tl+] on the characteristic voltage of these exponential functions and of the value of Itrue were determined by [Tl+] at the inner side of the selectivity filter or in the cavity.
Sensitivity of Traffic Matrix Estimation Techniques to Their Underlying Assumptions

In this paper we study the traffic matrix estimation problem. Based on the nature of additional information that is used to make the problem solvable, we identify two major groups among the estimation methods proposed in literature: The gravity model based methods and the second moment methods. All methods make some assumptions in order to deploy the extra information in the estimation process. We study the sensitivity of the estimation accuracy to these underlying assumptions. The gravity model methods are found to be more accurate when the assumptions hold, but on the other hand their accuracy declines faster than that of the second moment methods when the assumption is not exactly true. In addition, we propose a novel estimation technique which incorporates both sources of extra information. This method is shown in many cases to outperform the current estimation methods relying only on one or the other.
The Federal Budget: Issues for FY2011, FY2012, and Beyond

The federal budget is central to Congress's ability to exercise its "power of the purse. " Over the last several fiscal years the imbalance between spending and revenues has grown as a result of the economic downturn and policies enacted in response to financial turmoil. In FY2010, the last completed fiscal year, the U.S. government spent $3,456 billion (23.8% of GDP) and collected $2,162 billion in revenue (14.9% of GDP), resulting in a budget deficit of $1,294 billion (8.9% of GDP).
A 3 H : Fifth International Workshop on Authoring of Adaptive and Adaptable Hypermedia

Authoring ITS domain models is a difficult task re quiring many skills. We explored whether modeling Ontology reduces the problem, by g ivin the students of an e-learning summer school the task of developing the model for a simpl e domain in under sixty minutes using ontology. Some students also used our tool to develop a compl ete tutor in around eight hours, which is much faster than they could be expected to author the sy stem without the tool. The results suggest this style of authoring can lead to very rapid ITS devel opment.
Information Trustworthiness AAAI 2013 Tutorial

Decision makers and citizens are heavily influenced these days by information they obtain from online resources – from news portals, online encyclopedias, blogs and forums, product websites and reviews, etc. However, the lack of control over what gets published online can often lead to dissemination of unreliable and misleading information. In such a scenario, how can one verify if a claim is true or determine which sources are trustworthy? In this tutorial, the instructors systematically consider various approaches that address this problem. This tutorial is aimed at AI researchers who are interested in future research on trustworthiness of information. The goal of the tutorial is to present the audience with an exhaustive survey of relevant research on this topic and to outline future directions of research that may interest the AI community. No specific background knowledge is assumed of the audience.
Optimization of Therapeutic proteins to Delete T-Cell epitopes while Maintaining Beneficial Residue Interactions

Exogenous enzymes, signaling peptides, and other classes of nonhuman proteins represent a potentially massive but largely untapped pool of biotherapeutic agents. Adapting a foreign protein for therapeutic use poses numerous design challenges. We focus here on one significant problem: modifying the protein to mitigate the immune response mounted against "non-self" proteins, while not adversely affecting the protein's stability or therapeutic activity. In order to propose such variants suitable for experimental evaluation, this paper develops a computational method to select sets of mutations predicted to delete immunogenic T-cell epitopes, as evaluated by a 9-mer potential, while simultaneously maintaining important residues and residue interactions, as evaluated by one- and two-body potentials. While this design problem is NP-hard, we develop an integer programming approach that works very well in practice. We demonstrate the effectiveness of our approach by developing plans for biotherapeutic proteins that, in previous studies, have been partially deimmunized via extensive experimental characterization and modification of limited segments. In contrast, our global optimization technique considers an entire protein and accounts for all residues, residue interactions, and epitopes in proposing candidates worth subjecting to experimental evaluation.
Building a Cloud-Based Mobile Application Testbed

A proliferation of mobile smartphone platforms, including Android devices, has triggered a rise in mobile application development for a diverse set of situations. Testing of these smartphone applications can be exceptionally difficult, due to the challenges of orchestrating production-scale quantities of smartphones such as difficulty in managing thousands of sensory inputs to each individual smartphone device. This work presents the Android Tactical Application Assessment and Knowledge (ATAACK) Cloud, which utilizes a cloud computing environment to allow smartphone-based security, sensing, and social networking researchers to rapidly use model-based tools to provision experiments with a combination of 1,000+ emulated smartphone instances and tens of actual devices. The ATAACK Cloud provides a large-scale smartphone application research testbed.
The eta ganglion cell type of cat retina

We define a morphologic type of ganglion cell in cat retina by using intracellular staining in vitro. The eta cell has a small soma, slender axon, and delicate, highly branched dendritic arbor. Dendritic fields are intermediate in size among cat ganglion cells, with diameters typically two to three times those of beta cells. Fields increase in size as a function of distance from the area centralis, ranging in diameter from 90 μm to 200 μm centrally to a maximum of 600 μm in the periphery. This increase is unusually radially symmetric. By contrast with other cat ganglion cell types, eta cells do not have markedly smaller dendritic fields within the visual streak than above or below it nor much smaller fields nasally than temporally. Dendrites ramify broadly throughout sublamina a (OFF sublayer) of the inner plexiform layer. They arborize most densely in S2, where they costratify with dendrites of OFF alpha cells. There is apparently no matching ON variety of eta cell. Experiments combining retrograde labeling with intracellular staining indicate that eta cells project to the superior colliculus and to two components of the dorsal lateral geniculate nucleus (the C laminae and medial interlaminar nucleus). Eta cells apparently project contralaterally from the nasal retina and ipsilaterally from the temporal retina. The morphology and projection patterns of the eta cell suggest that its physiologic counterpart is a type of sluggish or W‐cell with an OFF center, an ON surround, and possibly a transient light response. J. Comp. Neurol. 408:204–219, 1999. © 1999 Wiley‐Liss, Inc.
Kv4.3-Mediated A-Type K+ Currents Underlie Rhythmic Activity in Hippocampal Interneurons

Hippocampal-dependent learning and memory processes are associated with theta frequency rhythmic activity. Interneuron and pyramidal cell network interactions underlie this activity, but contributions of interneuron voltage-gated membrane conductances remain unclear. We show that interneurons at the CA1 lacunosum-moleculare (LM) and radiatum (RAD) junction (LM/RAD) display voltage-dependent subthreshold membrane potential oscillations (MPOs) generated by voltage-gated tetrodotoxin-sensitive Na+ and 4-aminopyridine (4-AP)-sensitive K+ currents. They also exhibit prominent 4-AP-sensitive A-type K+ currents, with gating properties showing activation at subthreshold membrane potentials. We found that LM/RAD cells are part of specific interneuron subpopulations expressing the K+ channel subunit Kv4.3 and their transfection with Kv4.3 small interfering RNA selectively impaired A-type K+ currents and MPOs. Thus, our findings reveal a novel function of Kv4.3-mediated A-type K+ currents in the generation of intrinsic MPOs in specific subpopulations of interneurons that may participate in hippocampal theta-related rhythmic activity.
Effect of Temporal Organization of the Visuo-Locomotor Coupling on the Predictive Steering

Studies on the direction of a driver’s gaze while taking a bend show that the individual looks toward the tangent-point of the inside curve. Mathematically, the direction of this point in relation to the car enables the driver to predict the curvature of the road. In the same way, when a person walking in the street turns a corner, his/her gaze anticipates the rotation of the body. A current explanation for the visuo-motor anticipation over the locomotion would be that the brain, involved in a steering behavior, executes an internal model of the trajectory that anticipates the completion of the path, and not the contrary. This paper proposes to test this hypothesis by studying the effect of an artificial manipulation of the visuo-locomotor coupling on the trajectory prediction. In this experiment, subjects remotely control a mobile robot with a pan-tilt camera. This experimental paradigm is chosen to manipulate in an easy and precise way the temporal organization of the visuo-locomotor coupling. The results show that only the visuo-locomotor coupling organized from the visual sensor to the locomotor organs enables (i) a significant smoothness of the trajectory and (ii) a velocity-curvature relationship that follows the “2/3 Power Law. ” These findings are consistent with the theory of an anticipatory construction of an internal model of the trajectory. This mental representation used by the brain as a forward prediction of the formation of the path seems conditioned by the motor program. The overall results are discussed in terms of the sensorimotor scheme bases of the predictive coding.
Are stress hormone levels a good proxy of foraging success? An experiment with King Penguins, Aptenodytes patagonicus

SUMMARY In seabirds, variations in stress hormone (corticosterone; henceforth CORT) levels have been shown to reflect changing marine conditions and, especially, changes in food availability. However, it remains unclear how CORT levels can be mechanistically affected by these changes at the individual level. Specifically, the influence of food acquisition and foraging success on CORT secretion is poorly understood. In this study, we tested whether food acquisition can reduce baseline CORT levels (`the food intake hypothesis') by experimentally reducing foraging success of King Penguins (Aptenodytes patagonicus). Although CORT levels overall decreased during a foraging trip, CORT levels did not differ between experimental birds and controls. These results demonstrate that mass gain at sea is not involved in changes in baseline CORT levels in this species. The overall decrease in CORT levels during a foraging trip could result from CORT-mediated energy regulation (`the energy utilisation hypothesis'). Along with other evidence, we suggest that the influence of foraging success and food intake on CORT levels is complex and that the ecological meaning of baseline CORT levels can definitely vary between species and ecological contexts. Therefore, further studies are needed to better understand (1) how baseline CORT levels are functionally regulated according to energetic status and energetic demands and (2) to what extent CORT can be used to aid in the conservation of seabird populations.
Bayesian models for functional magnetic resonance imaging data analysis

Functional magnetic resonance imaging (fMRI), a noninvasive neuroimaging method that provides an indirect measure of neuronal activity by detecting blood flow changes, has experienced an explosive growth in the past years. Statistical methods play a crucial role in understanding and analyzing fMRI data. Bayesian approaches, in particular, have shown great promise in applications. A remarkable feature of fully Bayesian approaches is that they allow a flexible modeling of spatial and temporal correlations in the data. This article provides a review of the most relevant models developed in recent years. We divide methods according to the objective of the analysis. We start from spatiotemporal models for fMRI data that detect task‐related activation patterns. We then address the very important problem of estimating brain connectivity. We also touch upon methods that focus on making predictions of an individual's brain activity or a clinical or behavioral response. We conclude with a discussion of recent integrative models that aim at combining fMRI data with other imaging modalities, such as electroencephalography/magnetoencephalography (EEG/MEG) and diffusion tensor imaging (DTI) data, measured on the same subjects. We also briefly discuss the emerging field of imaging genetics. WIREs Comput Stat 2015, 7:21–41. doi: 10.1002/wics.1339
Modeling Semantic Emotion Space Using a 3D Hypercube-Projection: An Innovative Analytical Approach for the Psychology of Emotions

The widely accepted two-dimensional circumplex model of emotions posits that most instances of human emotional experience can be understood within the two general dimensions of valence and activation. Currently, this model is facing some criticism, because complex emotions in particular are hard to define within only these two general dimensions. The present theory-driven study introduces an innovative analytical approach working in a way other than the conventional, two-dimensional paradigm. The main goal was to map and project semantic emotion space in terms of mutual positions of various emotion prototypical categories. Participants (N = 187; 54.5% females) judged 16 discrete emotions in terms of valence, intensity, controllability and utility. The results revealed that these four dimensional input measures were uncorrelated. This implies that valence, intensity, controllability and utility represented clearly different qualities of discrete emotions in the judgments of the participants. Based on this data, we constructed a 3D hypercube-projection and compared it with various two-dimensional projections. This contrasting enabled us to detect several sources of bias when working with the traditional, two-dimensional analytical approach. Contrasting two-dimensional and three-dimensional projections revealed that the 2D models provided biased insights about how emotions are conceptually related to one another along multiple dimensions. The results of the present study point out the reductionist nature of the two-dimensional paradigm in the psychological theory of emotions and challenge the widely accepted circumplex model.