gebhart/patrepeval huggingface dataset:
Reconstructing randomized social networks (2010)

In social networks, nodes correspond to entities and edges to links between them. In most of the cases, nodes are also associated with a set of features. Noise, missing values or efforts to preserve privacy in the network may transform the original network G and its feature vectors F. This transformation can be modeled as a randomization method. Here, we address the problem of reconstructing the original network and set of features given their randomized counterparts G′ and F′ and knowledge of the randomization model. We identify the cases in which the original network G and feature vectors F can be reconstructed in polynomial time. Finally, we illustrate the efficacy of our methods using both generated and real datasets.
Cellular program controlling the recovery of adipose tissue mass: An <i>in vivo</i> imaging approach (2008)

The cellular program responsible for the restoration of adipose tissue mass after weight loss is largely uncharacterized. Leptin mRNA levels are highly correlated with adipose tissue mass, and leptin expression can thus be used as a surrogate for changes in the amount of adipose tissue. To further study the responses of adipocytes to changes in weight, we created a transgenic mouse expressing the luciferase reporter gene under the control of leptin regulatory sequences, which allows noninvasive imaging of the leptin expression of mice in vivo. We used these animals to show that weight loss induced by fasting or leptin treatment results in the retention of lipid-depleted adipocytes in adipose depots. To further study the cellular response to weight regain after leptin treatment, a leptin withdrawal protocol was used to induce a state of acute leptin deficiency in wild type mice. Acute leptin deficiency led to the transient deposition of large amounts of glycogen within pre-existing, lipid-depleted adipocytes. This was followed by rapid reaccumulation of lipid. Transcriptional profiling revealed that this cellular response was associated with induction of mRNAs for the entire pathway of enzymes necessary to convert glucose into acetyl-CoA and glycerol, key substrates for the synthesis of triglycerides.
Xstream-X264: Real-time H.264 streaming with cross-layer integration (2011)

We present Xstream-x264: a real-time cross-layer video streaming technique implemented within a well known open-source H.264 video encoder tool x264 for on-line video quality evaluation experiments. Xstream-x264 uses the transport protocol provided indication of the available data rate for corresponding adjustments in the video encoder. We discuss the design, implementation and the quality evaluation methodology utilized with our tool. We demonstrate via experimental results that the streaming video quality greatly improves with the presented cross-layer approach both in terms of lost frame count and the objective video quality metrics Peak Signal to Noise Ratio (PSNR).
Lack of correlation between expression and function of P-glycoprotein in acute myeloid leukemia cell lines. (1995)

In a panel of acute myeloblastic leukemia (AML) cell lines, representative of distinct differentiation stages, we investigated the possible correlation between drug-resistance and both expression and function of the multidrug resistance (MDR)-related P-glycoprotein (P-gp). The AML cell lines were KG1a, KG1, TF1, HEL, ML1, and two non drug-selected P-gp positive subclones originating from HL-60 (HL-60JD) and U937 (U937AQ). All these cells overexpressed the mdr1 gene (analyzed by RT-PCR) and displayed variable levels of P-gp expression. Flow cytometric semi-quantitative evaluation of P-gp with two P-gp specific monoclonal antibodies (MRK16 and UIC2) showed the following P-gp expression hierarchy: TF1 < KG1a < HEL < KG1 < HL-60JD < ML1 < U937AQ; the latter expressing 13 times more P-gp than TF1. When P-gp function was assessed by Rhodamine 123 (Rh123) efflux kinetics, we found that only KG1a and KG1 cells, which have an early (immature) CD34+ CD33- CD38- phenotype, and to a lesser extent TF1, with an intermediate (CD34+ CD33+ CD38+) phenotype, displayed significant P-gp activity which could be inhibited by both verapamil and SDZ PSC 833. In contrast, the other more mature CD33+ CD34- AML cell lines presented no Rh123 efflux capacity although they expressed higher P-gp levels. Daunorubicin (DNR) accumulation studies showed that inhibitors of P-gp increased DNR accumulation only in the immature AML cells whereas they had no impact on the mature AML cell lines. MTT drug cytotoxicity assay confirmed that the immature AML cells were 10-15-fold more resistant to DNR than the mature AML cells. Although P-gp inhibitors were able to increase the cytotoxicity of DNR in AML cells which displayed functional P-gp, they could not increase DNR cytotoxicity to levels comparable to that of the CD34- CD33+ cells, suggesting that DNR resistance of immature AML cells may not solely be related to P-gp. With drug-selection, AML subclones displayed higher levels of P-gp expression and higher extruding capacities, and therefore chemoresistance, and this independently of their initial differentiation phenotype. Finally, this study provides evidence for a lack of correlation between expression and function of P-gp in AML cells; this relationship being dependent upon leukemic cell differentiation in unselected myeloid leukemic cells.
Polo-like kinase 1 (PLK1) inhibition suppresses cell growth and enhances radiation sensitivity in medulloblastoma cells (2012)

Our data suggest that targeting PLK1 with small molecule inhibitors, in combination with radiation therapy, is a novel strategy in the treatment of medulloblastoma that warrants further investigation.
Assessment of tropical forest degradation by selective logging and fire using Landsat imagery (2010)

article Many studies have assessed the process of forest degradation in the Brazilian Amazon using remote sensing approaches to estimate the extent and impact by selective logging and forest fires on tropical rain forest. However, only a few have estimated the combined impacts of those anthropogenic activities. We conducted a detailed analysis of selective logging and forest fire impacts on natural forests in the southern Brazilian Amazon state of Mato Grosso, one of the key logging centers in the country. To achieve this goal a 13-year series of annual Landsat images (1992-2004) was used to test different remote sensing techniques for measuring the extent of selective logging and forest fires, and to estimate their impact and interaction with other land use types occurring in the study region. Forest canopy regeneration following these disturbances was also assessed. Field measurements and visual observations were conducted to validate remote sensing techniques. Our results indicated that the Modified Soil Adjusted Vegetation Index aerosol free (MSAVIaf )i s a reliable estimator of fractional coverage under both clear sky and under smoky conditions in this study region. During the period of analysis, selective logging was responsible for disturbing the largest proportion (31%) of natural forest in the study area, immediately followed by deforestation (29%). Altogether, forest disturbances by selective logging and forest fires affected approximately 40% of the study site area. Once disturbed by selective logging activities, forests became more susceptible to fire in the study site. However, our results showed that fires may also occur in undisturbed forests. This indicates that there are further factors that may increase forest fire susceptibility in the study area. Those factors need to be better understood. Although selective logging affected the largest amount of natural forest in the study period, 35% and 28% of the observed losses of forest canopy cover were due to forest fire and selective logging combined and to forest fire only, respectively. Moreover, forest areas degraded by selective logging and forest fire is an addition to outright deforestation estimates and has yet to be accounted for by land use and land cover change assessments in tropical regions. Assuming that this observed trend of land use and land cover conversion continues, we predict that there will be no undisturbed forests remaining by 2011 in this study site. Finally, we estimated that 70% of the total forest area disturbed by logging and fire had sufficiently
Abnormal Surface Distribution of the Human Asialoglycoprotein Receptor in Cirrhosis (1992)

Serum concentrations of asialoglycoproteins are increased in cirrhosis. We hypothesized that this increase results from abnormalities in the asialoglycoprotein receptor, which is located on the sinusoidal and lateral membrane of hepatocytes. Therefore we searched for morphological alterations in the distribution of the asialoglycoprotein receptor in human liver, using a light microscopic immunoperoxidase method in autopsy livers. In 24 of 25 (96%) of patients without liver disease, the asialoglycoprotein receptor was located on the sinusoidal and, less prominently, the lateral surface of hepatocytes but not the canalicular surface. In contrast, in 12 of 18 (67%) patients with cirrhosis of various causes, the receptor also was localized strikingly along the canalicular surface, with a corresponding decrease on the sinusoidal and lateral surfaces. We conclude that an abnormal cell-surface distribution of the asialoglycoprotein receptor commonly occurs in cirrhosis. This abnormality might result in impaired clearance of desialylated glycoproteins from plasma.
Quantitative Molecular Analysis of Sentinel Lymph Node May Be Predictive of Axillary Node Status in Breast Cancer Classified by Molecular Subtypes (2013)

To determine the performance of intraoperative one-step nucleic acid amplification (OSNA) assay in detecting sentinel lymph node metastases compared to postoperative histology taking into account breast cancer molecular classification and to evaluate whether the level of cytokeratin 19 mRNA copy number may be useful in predicting the likelihood of a positive axillary lymph node dissection. OSNA assay was performed in a prospective series of 903 consecutive sentinel lymph nodes from 709 breast cancer patients using 2 alternate slices of each sentinel lymph node. The remaining 2 slices were investigated by histology. Cytokeratin 19 mRNA copy number, which distinguishes negative cases (<250 copies), micrometastases (+, ≥250≤5000 copies) and macrometastases (++, >5000 copies), was compared to axillary lymph node dissection status and to the biological tumor profile. Concordance between OSNA and histopathology was 95%, specificity 95% and sensitivity 93%. Multiple Corresponce Analysis and logistic regression evidenced that positive axillary lymph node dissection was significantly associated with a higher cytokeratin 19 mRNA copy number (>5000; p<0.0001), HER2 subtype (p = 0.007) and lymphovascular invasion (p<0.0001). Conversely, breast cancer patients with cytokeratin 19 mRNA copy number <2000 mostly presented a luminal subtype and a negative axillary lymph node dissection. We confirmed that OSNA assay can provide standardized and reproducible results and that it represents a fast and quantitative tool for intraoperative evaluation of sentinel lymph node. Omission of axillary lymph node dissection could be proposed in patients presenting a sentinel lymph node with a cytokeratin 19 mRNA copy number <2000 and a Luminal tumor phenotype.
Numerical simulation of breakup of a viscous drop in simple shear flow through a volume-of-fluid method (2000)

A spherical drop, placed in a second liquid of the same density, is subjected to shearing between parallel plates. The subsequent flow is investigated numerically with a volume-of-fluid (VOF) method. The scheme incorporates a semi-implicit Stokes solver to enable computations at low Reynolds number. Our simulations compare well with previous theoretical, numerical, and experimental results. For capillary numbers greater than the critical value, the drop deforms to a dumbbell shape and daughter drops detach via an end-pinching mechanism. The number of daughter drops increases with the capillary number. The breakup can also be initiated by increasing the Reynolds number.
Large hierarchical object recognition using libraries of parameterized model sub-parts (2003)

A description is given of the development of a model-based vision system that utilizes hierarchies of both object structure and object scale. The focus of the research is to use these hierarchies to achieve robust recognition based on effective organization and indexing schemes for model libraries. The goal of the system is to recognize parameterized instances of nonrigid model objects contained in a large knowledge base, despite the presence of noise and occlusion. The approach presented is to develop an object shape representation that incorporates a component subpart hierarchy, to allow for efficient and correct indexing into an automatically generated model library as well as for relative parametrization among subparts, and a scale hierarchy, to allow for a general to specific recognition procedure. The implemented system uses a representation based on significant contour curvature changes and recognition engine based on geometric constraints of feature properties. Examples of the system's performance are given, followed by an analysis of the results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Selective Blockade of Interferon-α and -β Reveals Their Non-Redundant Functions in a Mouse Model of West Nile Virus Infection (2015)

Although type I interferons (IFNs) were first described almost 60 years ago, the ability to monitor and modulate the functional activities of the individual IFN subtypes that comprise this family has been hindered by a lack of reagents. The major type I IFNs, IFN-β and the multiple subtypes of IFN-α, are expressed widely and induce their effects on cells by interacting with a shared heterodimeric receptor (IFNAR). In the mouse, the physiologic actions of IFN-α and IFN-β have been defined using polyclonal anti-type I IFN sera, by targeting IFNAR using monoclonal antibodies or knockout mice, or using Ifnb-/- mice. However, the corresponding analysis of IFN-α has been difficult because of its polygenic nature. Herein, we describe two monoclonal antibodies (mAbs) that differentially neutralize murine IFN-β or multiple subtypes of murine IFN-α. Using these mAbs, we distinguish specific contributions of IFN-β versus IFN-α in restricting viral pathogenesis and identify IFN-α as the key mediator of the antiviral response in mice infected with West Nile virus. This study thus suggests the utility of these new reagents in dissecting the antiviral and immunomodulatory roles of IFN-β versus IFN-α in murine models of infection, immunity, and autoimmunity.
Impact of Dispersion Fluctuations on Dual-Pump Fiber-Optic Parametric Amplifiers (2004)

Effects of zero-dispersion wavelength (ZDWL) fluctuations on dual-pump fiber-optic parametric amplifiers are investigated analytically and numerically. It is found that the signal gain varies considerably from fiber to fiber even though each fiber may have the same ZDWL on average. Moreover, the gain spectrum becomes highly nonuniform for a given fiber because of such dispersion fluctuations. Numerical simulations show that this problem can be solved to a large extent by reducing wavelength separation between the two pumps, but only at the expense of a reduced amplifier bandwidth.
Signal transducers and activators of transcription 3 (STAT3) inhibits transcription of the inducible nitric oxide synthase gene by interacting with nuclear factor κB (2002)

Prolific generation of NO by inducible nitric oxide synthase (iNOS) can cause unintended injury to host cells during glomerulonephritis and other inflammatory diseases. While much is known about the mechanisms of iNOS induction, few transcriptional repressors have been found. We explored the role of signal transducers and activators of transcription 3 (STAT3) proteins in interleukin (IL)-1beta- and lipopolysaccharide (LPS)+interferon (IFN)-gamma-mediated iNOS induction in murine mesangial cells. Both stimuli induced rapid phosphorylation of STAT3 and sequence-specific STAT3 DNA-binding activity. Supershift assays with a STAT3 element probe demonstrated that nuclear factor kappaB (NF-kappaB) p65 and p50 complexed with STAT3 in the DNA-protein complex. The direct interaction of STAT3 and NF-kappaB p65 was verified in vivo by co-immunoprecipitation and in vitro by pull-down assays with glutathione S-transferase-NF-kappaB p65 fusion protein and in vitro -translated STAT3alpha. Overexpression of STAT3 dramatically inhibited IL-1beta- or LPS+IFN-gamma-mediated induction of iNOS promoter-luciferase constructs that contained the wild-type iNOS promoter or ones harbouring mutated STAT-binding elements. In tests of indirect inhibitory effects of STAT3, overexpression of STAT3 dramatically inhibited the activity of an NF-kappaB-dependent promoter devoid of STAT-binding elements without affecting NF-kappaB DNA-binding activity. Thus STAT3, via direct interactions with NF-kappaB p65, serves as a dominant-negative inhibitor of NF-kappaB activity to suppress indirectly cytokine induction of the iNOS promoter in mesangial cells. These results provide a new model for the termination of NO production by activated iNOS following exposure to pro-inflammatory stimuli.
Concentration-controlled phase selection of silicide formation during reactive deposition (1999)

Slow (low-rate) reactive deposition of a metal onto a Si substrate can result in direct formation of a metal disilicide, thereby skipping the metal-rich phases in the formation sequence. These observations have been explained thermodynamically by using the effective heat of formation model. As a result of this concentration-controlled phase selection, it is possible to form disilicides, such as CoSi2, NiSi2, or β-FeSi2 at much lower growth temperatures than possible in conventional solid-phase reaction of a metal layer deposited onto Si at room temperature (i.e., lower than the nucleation temperature). Moreover, epitaxial growth of CoSi2/Si(100), which is not possible by solid-phase reaction, becomes achievable when depositing Co atoms sufficiently slowly onto a heated Si substrate.
Cyber attack simulation and information fusion process refinement optimization models for cyber security (2006)

Cyber crime is an increasingly prominent threat to all aspects of society including businesses, government, banks, transportation, and individuals. The security of computer networks is dependent on the ability to recognize and defend against malicious cyber attacks. The goal of this thesis is to utilize operation research techniques to create tools that will significantly contribute to cyber security. A simulation framework and template is developed to efficiently represent computer networks and cyber security intrusion detection systems. The simulation is capable of generating complex cyber attacks based on the computer network configuration and the capabilities of the attacker. The simulation results in alert messages corresponding to attack actions and ordinary network behavior which are typically used by situational awareness tools or systems administrators to identify and take action against the attack. Through verification, validation, and an experimental performance evaluation, the simulation model is shown to be an effective tool to enable testing of situational awareness tools and for determining network vulnerabilities. In addition, this thesis extends the highly effective information fusion methods of situational awareness and threat assessment by introducing a method of adaptive process refinement for cyber security. The adaptive process refinement model utilizes integer programming optimization to improve the success of cyber attack detection, tracking, and identification. The process refinement model is designed to dynamically provide recommendations for optimal allocation of network detection resources subject to processing capacity, current attack activity, and network vulnerabilities. The cyber attack simulation methodology is utilized to create a set of attack scenarios on computer networks that are used conduct an experimental performance evaluation of the adaptive process refinement model to determine its capabilities and limitations. The simulation and process refinement methods provide operations research tools that will help to advance the field of cyber security.
Congestion pricing. Paying your way in communication networks (2001)

Network congestion is a fundamental problem facing Internet users today. A network where users are selfish, and thus reluctant to defer to other users, may result in the famous "tragedy of the commons", where, in the absence of controls, a shared resource is overconsumed by individuals who consider only their personal costs and not the cost to society as a whole. In terms of the Internet, the "tragedy" could be viewed as congestive collapse, resulting from overconsumption of the shared network resource. It is important to distinguish congestion pricing from other forms of network pricing. Charging network users for the congestion they cause can lead to more efficient network utilization by forcing them to take social costs into account. In a congestion-pricing framework, the congestion charge would replace usage and QoS charges. Users would pay their ISPs a subscription charge to cover fixed costs and a congestion charge only when appropriate. This pricing scheme is feasible because, in the absence of congestion, the marginal cost of a network link is practically zero. Congestion pricing can also benefit network operators. By indicating the level of congestion and the user tolerance of it in their networks, congestion pricing can inform operators about when to re-provision and increase network capacity.
<title>Electromagnetic tracking for catheter localization</title> (1999)

A low frequency AC electromagnetic tracking system is presented that is capable of determining the position and orientation of a catheter tip. Advantages of using magnetic tracking for this application is that magnetic fields are non-ionizing and pass through the human body with minimal attenuation. Low frequency fields are used to mitigate the effects of eddy currents induced in conductive materials found in the environment. There are two significant differences between this and other magnetic tracking technologies, these being (1) the use of a single magnetic sensing coil for position and orientation determination and (2) the eliminating of range restrictions between the sensing antenna and the magnetic field generators. This paper will discuss the general theory of electromagnetic tracking, why it is that researchers have an intense interest for internal tracking and a comparison of the new and old tracking technologies. Some applications of this tracking technology will also be presented.
Probabilistic Risk Metrics for Navigating Occluded Intersections (2019)

Among traffic accidents in the USA, 23% of fatal and 32% of non-fatal incidents occurred at intersections. For driver assistance systems, intersection navigation remains a difficult problem that is critically important to increasing driver safety. In this letter, we examine how to navigate an unsignalized intersection safely under occlusions and faulty perception. We propose a realtime, probabilistic, risk assessment for parallel autonomy control applications for occluded intersection scenarios. The algorithms are implemented on real hardware and are deployed in a variety of turning and merging topologies. We show phenomena that establish go/no-go decisions, augment acceleration through an intersection and encourage nudging behaviors toward intersections.