Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Reasoning in the SIPE-2 Planner

This paper describes a project that added temporal information and constraints to SRI International’s SIPE–2 hierarchical, nonlinear planning system. The goal was to incorporate the ability to represent temporal relationships between actions within a plan, and time window constraints on individual actions, and to maintain these constraints during the planning process. The extensions described in this paper were added as a “temporal plan critic” that checks the temporal constraints at the end of each planning level. This project was the initial phase of a Technology Integration Experiment (TIE) undertaken as part of the DARPA/Rome Laboratory Planning Initiative to explore the integration of temporal reasoning into planning systems. The TIE involves researchers from SRI, GE, and Honeywell. Integrating temporal reasoning into planning systems is an important area of research, since many domains contain temporal constraints that must be represented in order for planning to be successful. The work described in this paper is a relatively small-scale effort that lays the groundwork for a more complete integration of temporal reasoning capabilities into SIPE–2. The rest of this paper is organized as follows: Section 2 describes SIPE–2 and SOCAP, the application that was used as the domain for implementation and testing. Section 3 describes the current temporal reasoning capabilities of SIPE–2. Section 4 describes the methods we implemented for representing and maintaining temporal information in SIPE–2 plans. Section 5 presents our results and the status of the TIE. Section 6 presents related work on the use of temporal reasoning in planning, and Section 7 describes open problems, future work, and conclusions.
Effects of Halothane on Left Ventricular Function and Distribution of Regional Blood Flow in Dogs and Primates

Left ventricular and regional vascular effects of halothane were assessed in dogs and primates in which coronary, mesenteric, renal, and iliac blood flows, arterial blood pressure, left ventricular diameter and pressure, dD/dt (i.e., the velocity of myocardial fiber shortening), and dP/dt were continuously measured in the control resting state, while the conscious animals were breathing O2, and during halothane-O2 anesthesia maintained at 1% or at 2% for 90 minutes (separate experimental days). Halothane caused a concentration-dependent depression of myocardial contractility: (dP/dt)/P fell 68 ± 5% during 2% halothane anesthesia and left ventricular end-diastolic diameter rose. Halothane also caused a redistribution of regional blood flows. At a concentration of 1% halothane, the most intense vasodilatation occurred in the renal bed (renal resistance fell 46 ± 5%), but mesenteric resistance rose (42 ± 15%). With 1% halothane regional vascular resistances tended to rise with time, but with 2% halothane regional blood flows rose with time. A direct vasodilating action of halothane was observed following direct intra-arterial injection of the drug. Probably this action was responsible for the renal and iliac vasodilatations and for the opposition to the metabolically induced vasoconstriction in the coronary bed. Thus, the administration of the most commonly employed potent inhalation anesthetic, halothane, substantially alters myocardial contractility and regional blood flows and resistances. These effects are, in many instances, a function of the concentration of the anesthetic and the duration of its administration.
Monitoring dynamic spatial fields using responsive geosensor networks

Information about dynamic spatial fields, such as temperature, windspeed, or the concentration of gas pollutant in the air, is important for many environmental applications. At the same time, the development of geosensor networks (wirelessly communicating, sensor-enabled, small computing devices distributed throughout a geographic environment) present new opportunities for monitoring dynamic spatial fields in much greater detail than ever before. This paper develops a new model for querying information about dynamic spatial fields using geosensor networks. In order to manage the inherent complexity of dynamic geographic phenomena, our approach is to focus on the qualitative representation of spatial entities, like regions, boundaries, and holes, and of events, like splitting, merging, appearance, and disappearance. Based on combinatorial maps, we present a qualitative model as the underlying data management paradigm for geosensor networks. This model is capable of tracking salient changes in the network in an energy-efficient way. Further, our model enables reconfiguration of the geosensor network in response to changes in the environment. We present an algorithm capable of adapting sensor network granularity according to dynamic monitoring requirements. Regions of high variability can trigger increases in the geosensor network granularity, leading to more detailed information about the dynamic field. Conversely, regions of stability can trigger a coarsening of the sensor network, leading to efficiency increases in particular with respect to power consumption and longevity of the sensor nodes. Querying of this responsive geosensor network is also considered, and the paper concludes with a review of future research directions.
Serotonin1B Receptors in the Ventral Tegmental Area Modulate Cocaine-Induced Increases in Nucleus Accumbens Dopamine Levels

Previous work has demonstrated that peripheral serotonin1B (5-HT1B) receptor agonist administration facilitates the behavioral and neurochemical effects of cocaine. This study used dual probe microdialysis to investigate whether activation of serotonin1B (5-HT1B) receptors in the ventral tegmental area (VTA) alters the ability of peripherally administered cocaine to elevate dopamine (DA) levels in the ipsilateral nucleus accumbens (NAcc) of drug-naive Wistar rats. Intra-VTA administration of the selective 5-HT1B agonist 1,4-dihydro-3-(1,2,3,6-tetrahydro-4-pyridinyl)-5H-pyrrolo [3,2-b]pyridin-5-one dihydrochloride (CP 93,129) by reverse dialysis produced a dose-dependent (30 and 100 μM) potentiation of cocaine-induced (10 mg/kg i.p.) increases in NAcc DA efflux and concurrent cocaine-induced decreases in VTA GABA efflux. There was no effect of either local CP 93,129 or peripheral cocaine on VTA glutamate efflux. Intra-VTA administration of the 5-HT1A/7 receptor agonist 8-hydroxy-2-dipropylaminotetralin (8-OH-DPAT; 100 μM) did not alter cocaine-induced alterations in NAcc DA or VTA GABA, suggesting that the effects of CP 93,129 were not mediated through 5-HT1A receptors. Moreover, the effects of intra-VTA CP 93,129 (100 μM) on both cocaine-induced increases in NAcc DA levels and cocaine-induced decreases in VTA GABA levels were reversed by coadministration of the selective 5-HT1B receptor antagonist 3-[3-(dimethylamine)propyl]-4-hydroxy-N-[4-(4-pyridinyl] phenyl] benzamide dihydrochloride (GR 55562; 300 μM). In the absence of cocaine, intra-VTA CP 93,139 produced an increase in NAcc DA and decrease in VTA GABA levels. However, intra-VTA GR 55562 alone had no effect on any of our neurochemical measures. These findings indicate that activation of VTA 5-HT1B receptors potentiates cocaine-induced increases in NAcc DA levels by enhancing the ability of cocaine to decrease VTA GABA efflux.
Supramolecular stacking of doxorubicin on carbon nanotubes for in vivo cancer therapy.

Doxorubicin (DOX) is a member of the anthracycline class of chemotherapeutic agents that are used for the treatment of many common human cancers, including aggressive non-Hodgkin’s lymphoma. [1,2] However, DOX is highly toxic in humans and can result in severe suppression of hematopoiesis, gastrointestinal toxicity,[3] and cardiac toxicity. [4] To date, several approaches, including delivery using liposomes (DOXIL),[5] have been developed to reduce the toxicity and enhance the clinical utility of this highly active antineoplastic agent.
Proteomic Analysis of Differentially Expressed Chlamydia pneumoniae Genes during Persistent Infection of HEp-2 Cells

ABSTRACT Recent data have shown that the respiratory pathogen Chlamydia pneumoniae expresses an altered gene transcription profile during gamma interferon (IFN-γ)-induced persistent infection in vitro. In the present study, we examined, by proteomics, expression of C. pneumoniae proteins labeled intracellularly with [35S]methionine/cysteine under normal conditions or IFN-γ-mediated persistence. The identity of differentially expressed proteins during persistent infection was determined by matching spots to those of proteins identified in C. pneumoniae elementary bodies by matrix-assisted laser desorption ionization mass spectrometry. Upon treatment with 50 U of IFN-γ per ml, a marked upregulation of major outer membrane protein (MOMP), heat shock protein 60 (Hsp-60/GroEL), and proteins with functions in DNA replication (GyrA), transcription (RpoA, PnP), translation (Rrf), glycolysis (PgK, GlgP), and type III secretion (SctN) was observed at 24 h of infection. In contrast, no significant decreases in bacterial protein expression were found in C. pneumoniae-infected cells due to IFN-γ treatment. Upregulation of C. pneumoniae proteins involved in diverse functions during persistent infection may allow the organism to resist the inhibitory effects of IFN-γ while retaining basic functions. Future studies should examine the differential expression of chlamydial proteins during the developmental cycle under IFN-γ pressure to obtain a finer representation of the gene products involved in establishing persistence.
Open Access Research Article Comparison of Scores for Bimodality of Gene Expression Distributions and Genome-wide Evaluation of the Prognostic Relevance of High-scoring Genes

Background: A major goal of the analysis of high-dimensional RNA expression data from tumor tissue is to identify prognostic signatures for discriminating patient subgroups. For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and low expression groups is easier compared to genes with unimodal expression distributions. Recently, several methods for the identification of genes with bimodal distributions have been introduced. A straightforward approach is to cluster the expression values and score the distance between the two distributions. Other scores directly measure properties of the distribution. The kurtosis, e.g., measures divergence from a normal distribution. An alternative is the outlier-sum statistic that identifies genes with extremely high or low expression values in a subset of the samples. Results: We compare and discuss scores for bimodality for expression data. For the genome-wide identification of bimodal genes we apply all scores to expression data from 194 patients with node-negative breast cancer. Further, we present the first comprehensive genome-wide evaluation of the prognostic relevance of bimodal genes. We first rank genes according to bimodality scores and define two patient subgroups based on expression values. Then we assess the prognostic significance of the top ranking bimodal genes by comparing the survival functions of the two patient subgroups. We also evaluate the global association between the bimodal shape of expression distributions and survival times with an enrichment type analysis. Various cluster-based methods lead to a significant overrepresentation of prognostic genes. A striking result is obtained with the outlier-sum statistic (p < 10-12). Many genes with heavy tails generate subgroups of patients with different prognosis. Conclusions: Genes with high bimodality scores are promising candidates for defining prognostic patient subgroups from expression data. We discuss advantages and disadvantages of the different scores for prognostic purposes. The outlier-sum statistic may be particularly valuable for the identification of genes to be included in prognostic signatures. Among the genes identified as bimodal in the breast cancer data set several have not yet previously been recognized to be prognostic and bimodally expressed in breast cancer. Background Genome-wide RNA expression analysis with microarrays has become a standard technology for screening for genes that are differentially expressed between different entities of tissues. In the clinical context, a frequent goal is the
A Novel Antibacterial Modification Treatment of Titanium Capable to Improve Osseointegration

Background Among the different causes of orthopedic and dental implant failure, infection remains the most serious and devastating complication associated with biomaterial devices. Purpose The aim of this study was to develop an innovative osteointegrative and antibacterial biomimetic coating on titanium and to perform a chemical-physical and in vitro biological characterization of the coating using the SAOS-2 cell line. We also studied the antibacterial properties of the coating against both Gram-positive and Gram-negative bacteria strains. Methods An electrochemical solution containing silicon, calcium, phosphorous, sodium, and silver nanoparticles was used to obtain the antibacterial by Anodic Spark Deposition (ASD) treatment. Surface morphology was characterized using SEM and laser profilometry A qualitative analysis of the chemical composition of the coating was assessed by EDS. The adhesion properties of the coating to the titanium bulk were performed with a 3-point bending test. SAOS-2 osteoblastic cell line spreading and morphology and viability were investigated. The bacterial adhesion and the antibacterial properties were investigated after 3 h and 24 h of incubation with Streptococcus mutans, Streptococcus epidermidis, and Escherichia coli bacterial strains. Results The proposed anodization treatment created a chemically and morphologically modified, adherent titanium oxide layer, characterized by a microporous morphology enriched by calcium, silicon, phosphorous, and silver. The preliminary biological characterization showed optimal SAOS-2 cell adhesion and proliferation as well as a strong antibacterial effect. Conclusions Based on the results of this study, we believe that this novel biomimetic and antibacterial treatment hold promise for enhancing osteointegration while conferring strong antibacterial properties to titanium.
Ge/Si Nanostructures with Quantum Dots Grown by Ion-Beam-Assisted Heteroepitaxy

Scanning tunneling microscopy (STM) experiments were performed to study growth modes induced by hyperthermal Ge ion action during molecular-beam epitaxy (MBE) of Ge on Si(100). Continuous and pulsed ion-beams were used. STM studies have shown that ion-beam action during heteroepitaxy leads to decrease in critical film thickness for transition from two-dimensional (2D) to three-dimensional (3D) growth modes, enhancement of 3D island density and narrowing of size distribution, as compared with conventional MBE experiments. The crystal perfection of Ge/Si structures with Ge islands embedded in Si was analyzed by the Rutherford backscattering/channeling technique (RBS) and transmission electron microscopy (TEM). The studies of Si/Ge/Si(100) structures indicated defect-free Ge dots and Si layers for the initial stage of heteroepitaxy (5 monolayers of Ge) in pulsed ion beam action growth mode at 350°C. Continuous ion-beam irradiation was found to induce dislocations around Ge dots. The results of kinetic Monte Carlo (KMC) simulations have shown that two mechanisms of ion-beam action can be responsible for stimulation of 2D-3D transition: (i) surface defect generation by ion impacts, and (ii) the enhancement of surface diffusion.
A Stochastic Multiple Players Multi-Issues Bargaining Model for the Piave River Basin

The objective of this paper is to investigate the usefulness of non-cooperative bargaining theory for the analysis of negotiations on water allocation and management. We explore the impacts of different economic incentives, a stochastic environment and varying individual preferences on players’ strategies and equilibrium outcomes through numerical simulations of a multilateral, multiple issues, non-cooperative bargaining model of water allocation in the Piave River Basin, in the North East of Italy. Players negotiate in an alternating-offer manner over the sharing of water resources (quantity and quality). Exogenous uncertainty over the size of the negotiated amount of water is introduced to capture the fact that water availability is not known with certainty to negotiating players. We construct the players’ objective function with their direct input. We then test the applicability of our multiple players, multi-issues, stochastic framework to a specific water allocation problem and conduct comparative static analyses to assess sources of bargaining power. Finally, we explore the implications of different attitudes and beliefs over water availability.
Silencing of USP18 potentiates the antiviral activity of interferon against hepatitis C virus infection.

BACKGROUND & AIMS Modulation of the host innate immune response is an attractive means of inhibiting hepatitis C virus (HCV) replication. Having previously determined that expression of the interferon-sensitive gene (ISG)15 protease USP18 is increased in the liver biopsy specimens of patients who do not respond to interferon (IFN)-alfa therapy, we hypothesized that USP18 might hinder the ability of IFN to inhibit HCV replication. METHODS The role of USP18 in IFN antiviral activity was examined using an in vitro model of HCV replication that reproduces the full viral life cycle. USP18 was silenced specifically using small inhibitory RNAs (siRNAs), and the dose response of HCV replication and infectious virus production to IFN-alfa was measured. RESULTS The siRNA knockdown of USP18 in human cells consistently potentiated the ability of IFN to inhibit HCV-RNA replication and infectious virus particle production by a factor of 1-2 log(10). USP18 knockdown also resulted in a number of cellular changes consistent with increased sensitivity to IFN. Decreasing USP18 expression led to increased cellular protein ISGylation in response to exogenous IFN-alfa, prolonged tyrosine phosphorylation of signal transducer and activation of transcription (STAT1), and a general enhancement of IFN-stimulated gene expression. CONCLUSIONS These data suggest that USP18 modulates the anti-HCV type I IFN response, and is a possible therapeutic target for the treatment of HCV infection.
Structural bioinformatics iFoldRNA : three-dimensional RNA structure prediction and folding

Summary: Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input RNA sequences. Starting from simplified linearchain conformations, RNA molecules (<50 nt) fold to native-like structures within half an hour of simulation, facilitating rapid RNA structure prediction. All-atom reconstruction of energetically stable conformations generates iFoldRNA predicted RNA structures. The predicted RNA structures are within 2–5 Å root mean squre deviations (RMSDs) from corresponding experimentally derived structures. RNA folding parameters including specific heat, contact maps, simulation trajectories, gyration radii, RMSDs from native state, fraction of native-like contacts are accessible from iFoldRNA. We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses. Availability: http://iFoldRNA.dokhlab. org. Contact: dokh@med.unc. edu Supplementary information: Supplementary data are available at Bioinformatics online.
Pedestrian detection: A benchmark

Pedestrian detection is a key problem in computer vision, with several applications including robotics, surveillance and automotive safety. Much of the progress of the past few years has been driven by the availability of challenging public datasets. To continue the rapid rate of innovation, we introduce the Caltech Pedestrian Dataset, which is two orders of magnitude larger than existing datasets. The dataset contains richly annotated video, recorded from a moving vehicle, with challenging images of low resolution and frequently occluded people. We propose improved evaluation metrics, demonstrating that commonly used per-window measures are flawed and can fail to predict performance on full images. We also benchmark several promising detection systems, providing an overview of state-of-the-art performance and a direct, unbiased comparison of existing methods. Finally, by analyzing common failure cases, we help identify future research directions for the field.
Mental health disorders influence admission rates for pain in children with sickle cell disease

Patients with sickle cell disease (SCD) experience a broad range of mental health disorders placing them at risk for more complicated hospitalizations for pain. The current study examined the impact of mental health disorders on admission rates and hospital length of stay (LOS) for vaso‐occlusive pain events (VOE) in pediatric patients with SCD.
Erasure of the paternal transcription program during spermiogenesis: The first step in the reprogramming of sperm chromatin for zygotic development

Male germ cells possess a unique epigenetic program and express a male‐specific transcription profile. However, when its chromatin is passed onto the zygote, it expresses an transcription/epigenetic program characteristic of the zygote. The mechanism underlying this reprogramming process is not understood at present. In this study, we show that an extensive range of chromatin factors (CFs), including essential transcription factors and regulators, remodeling factors, histone deacetylases, heterochromatin‐binding proteins, and topoisomerases, were removed from chromatin during spermiogenesis. This process will erase the paternal epigenetic program to generate a relatively naive chromatin, which is likely to be essential for installation of the zygotic developmental program after fertilization. We have also showed that transcription termination in male germ cells was temporally correlated with CF dissociation. A genome‐wide CF dissociation will inevitably disassemble the transcription apparatus and regulatory mechanism and lead to transcription silence. Based on data presented in this and previous studies (Sun et al., Cell Research [ 2007 ] 17:117–134), we propose that paternal‐zygotic transcription reprogramming begins with a genome‐wide CF dissociation to erase the existing transcription program in later stages of spermatogenesis. This will be followed by assembling of the zygotic equivalent after fertilization. The transcription/epigenetic program of the male germ cell is transformed into a zygotic one using an erase‐and‐rebuild strategy similar to that used in the maternal‐zygotic transition. It is also noted that transcription is terminated long after meiosis is completed and before chromatin becomes highly condensed during spermatogenesis. The temporal order of these events suggests that transcription silence does not have to be coupled to meiosis or chromatin condensation. Developmental Dynamics 237:1463‐1476, 2008. © 2008 Wiley‐Liss, Inc.