gebhart/patrepeval huggingface dataset:
Complexities and Challenges in the Use of Bayesian Belief Networks: Informing the Design of Causal Influence Models (2009)

Bayesian belief networks (BNs) are well-suited to capturing vague and uncertain knowledge. However, the capture of this knowledge and associated reasoning from human domain experts often requires specialized knowledge engineers responsible for translating the expert's communications into BN-based models. Across application domains, we have analyzed how these models are constructed, refined, and validated with domain experts. From this analysis, we have identified key user-centered complexities and challenges that we have used to drive the selection of simplifying assumptions. This led us to develop computational techniques and user interface methods that leverage these same assumptions with the goal of improving the efficiency and ease with which expert knowledge can be expressed, verified, validated, and encoded. In this paper, we present the results of our analysis of BN construction, validation, and use. We discuss how these results motivated the design of a simplified version of BNs called Causal Influence Models (CIMs). In addition, we detail how CIMs enable the design and construction of user interface mechanisms that address complexities identified in our analysis.
Progressive Prostate Cancer Associated With Use of Megestrol Acetate Administered for Control of Hot Flashes (1999)

Low doses of megestrol acetate are frequently used for treatment of hot flashes in men having androgen ablation for prostate cancer. We report a case in which megestrol acetate (20 mg bid) was administered for symptomatic control of hot flashes in a medically castrated patient with prostate cancer. The patient was subsequently noted to have a rising prostate-specific antigen (PSA) level. Megestrol acetate administration was discontinued, and the PSA level declined. These data indicate that even the low doses of megestrol acetate used for control of hot flashes can be associated with PSA increases in some patients with prostate cancer.
Abstract 2148: MM-151 elicits broad and unique inhibition of cells harboring EGFR extracellular domain mutations — results of multiscale experiments with genome-edited cell lines (2016)

Abstract Mutations in the extracellular domain (ECD) of EGFR have been reported in colorectal (CRC) patients as a mechanism of acquired resistance to the EGFR-directed antibodies cetuximab and panitumumab. Similar to EGFR intracellular domain mutations observed in patients treated with EGFR kinase inhibitors, these EGFR-ECD mutations inhibit the binding of the antibodies while maintaining EGFR signaling activity. MM-151, an investigational agent consisting of three anti-EGFR IgG1 antibodies, has been recently reported to overcome these mutations in over-expression and patient-derived cell line models. Here, we extend these studies to characterize the mechanisms of action that enable MM-151 to provide robust inhibition of EGFR-ECD mutations beyond that achievable by other monoclonal and oligoclonal EGFR antibodies. First, utilizing a cell-free binding assay with recombinant EGFR-ECD mutants, we found that MM-151, but not the Sym004 combination of two antibodies, maintained oligoclonal binding to all mutants. Second, we performed a panel of 2D and 3D in vitro experiments with over-expression and genome-edited (CRISPR-Cas9) cell lines harboring EGFR-ECD mutations to characterize target engagement, cell signaling, proliferation, and the impact of hetero- versus homozygous expression of EGFR wild type or mutant alleles. We observed that the three mechanisms of action for MM-151- antagonism of both low- and high-affinity EGFR ligands, EGFR down-regulation, and immune-effector activity— were preserved in these models. Third, we performed xenograft experiments to evaluate the behavior of MM-151 and found that MM-151 maintained inhibitory activity in an in vivo context. The results of our multiscale experiments identified the impact of combining three antibodies to overcome the high plasticity of the EGFR extracellular domain and thus reveal the potential for clinical evaluation of MM-151 in both EGFR-naïve and EGFR-refractory CRC populations. Citation Format: Hongfang Wang, Shawn P. Carey, Olga Burenkova, Jian Tang, Nastaran Gerami-Moayed, Sabrina Arena, Alberto Bardelli, Rachel Nering, Jeffrey D. Kearns. MM-151 elicits broad and unique inhibition of cells harboring EGFR extracellular domain mutations — results of multiscale experiments with genome-edited cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2148.
Two-branch diversity simulation of the effects of non-zero signal correlation on average fade duration (2003)

This paper provides a simulation method that provides two Rayleigh fading signal envelopes of a desired correlation coefficient. This is based on previous work and uses an improved technique (iterative step) to achieve higher numerical accuracy between the desired and the resultant cross correlation coefficient. The average fade duration is used as a measure of the diversity scheme performance, and various diversity combining techniques (switch combining: pure selection and threshold selection-switch and stay, switch and examine) are examined. It is shown that non-zero cross correlation affects the performance of the particular combining technique differently. A model to predict the diversity performance, for a given correlation coefficient and signal level, is examined.
Biolasing from Individual Cells in a Low‐Q Resonator Enables Spectral Fingerprinting (2020)

Abstract Lasing from cells has recently been subject of thorough investigation because of the potential for sensitive and fast biosensing. Yet, lasing from individual cells has been studied in high‐quality resonators, resulting in limited dependence of the lasing properties on the cellular microenvironment. Here, lasing is triggered by cells floating in a low quality factor resonator composed of a disposable poly(methyl methacrylate) (PMMA) cell counting‐slide, hence in absence of conventional high‐reflectivity optical cavities. The exceptional spectral narrowing and the steep slope increase in the input–output energy diagram prove occurrence of laser action in presence of cells. The observed biolasing is an intrinsically dynamic signal, with large fluctuations in intensity and spectrum determined by the optical properties of the individual cell passing through the pump beam. Numerical simulations of the scattering efficiency rule out the possibility of optical feedback from either WGM (whispering gallery mode) or multiple scattering within the cell, and point to the enhanced directional scattering field as the crucial contribution of cells to the laser action. Finally, principal component analysis of lasing spectra measured from freely diffusing cells yields spectral fingerprints of cell populations, which allows discriminating cancer from healthy Rattus glial cells with high degree of confidence.
Measurement of underlying event characteristics using charged particles inppcollisions ats=900  GeVand 7 TeV with the ATLAS detector (2011)

Measurement of underlying event characteristics using charged particles in pp collisions at ffiffi ffi s p 900 GeV and 7 TeV with the ATLAS detector
Borehole-integrated anisotropic processing of converted modes (2001)

Processing multicomponent surface seismic data for converted mode imaging is geophysically demanding. The usual challenges confronting conventional P-wave processing are compounded by the problems of determining a second (shear) velocity field, asymmetric raypaths, much stronger anisotropy effects, and often increased attenuation.
Dynamic biometrics: The case for a real-time solution to the problem of access control, privacy and security (2009)

From a certain perspective, security is broken. The security authorization triangle (possession, knowledge, identity) has in some cases been reduced to a single point (knowledge) because of the limitations to possession attributable to virtualization, and because of the limitations to identity attributable to the use of static biometrics. This paper makes the case for a stronger security rights triangle-privacy, security and access control-underpinned by the resurrection of possession and identity through the use of dynamic biometrics. New technologies in mobile and cloud computing, pattern recognition and user interaction provide a potential path forward for an identity-matching ecosystem in which both privacy and security needs can be accommodated.
Assembly of Photopolymerizable Discotic Molecules on an Aligned Polyimide Layer Surface to Form a Negative Retardation Film with an Oblique Optical Axis (2003)

Abstract Ultraviolet (UV) polymerizable discotic liquid‐crystalline (DLC) molecules (2,3,6,7,10,11‐hexakis(4′‐acryloy‐ m ‐alkyloxybenzoyoxy)triphenylene [HAHBT‐ m , where m was the number of methylene units, and here m = 6 (HAHBT‐6)]) were assembled to form a negative retardation film with an oblique optical axis on a specifically designed rubbing‐aligned polyimide layer surface [6FDA‐11CBBP (where 11 is the number of methylene units in the side chains)]. The side chains of this polyimide were terminated by cyanobiphenyl groups. Surface‐enhanced Raman scattering (SERS) and optical second harmonic generation results showed that rubbing caused a surface structural re‐arrangement in the alignment layer resulting in a negative pre‐tilt angle (θ s ) of –8.5° (which was in the direction opposite to the rubbing direction). The molecular topology at the rubbed surface was governed by a stable fold‐like bent structure of the cyanobiphenyl side chains, in which the CN groups preferentially pointed down towards the surface. When the DLC molecules were deposited onto the alignment surface and polymerized via UV irradiation to generate a new optical film, an oblique optical axis with an average tilt angle of –18.6° with respect to the film normal was detected using ellipsometric measurements. This tilted optical axis was developed by the DLC molecules being wedged on top of the cyanobiphenyl groups when in the bent conformation. Furthermore, the tilt angle difference between the θ s at the alignment surface and at the air interface of the DLC molecules was attributed to a splay deformation of the DLC molecules along the film surface normal. Optical modeling has also confirmed our experimental observations.
Dynamically re-configurable communication protocols using key identifiers (2005)

In this paper we present a novel concept and methodology for generating tailored communication protocols specific to an application's requirements and the operating environment for a mobile node roaming among different access networks within the global Internet. Since the scheme that we present employs a universal technique, it can be also deployed in small-scale independent networks such as sensor networks to generate application-specific lightweight transport protocols as is appropriate to its energy-constrained operating environments. We present preliminary experimental and analytical results that confirm and justify the feasibility of our method based on a practical example applicable to the sensor network environment.
Defect in Glucose Removal in Nonketotlc Diabetic Patients with Fasting Hyperglycemia (1978)

The present experiments were performed to determine the ability of insulin to stimulate glucose uptake in normal subjects as compared with nonobese patients with fasting hyperglycemia at similar steady state plasma glucose and insulin concentrations. The studies were carried out at two different steady state plasma glucose levels (approximately 250 and 350 mg/100ml), and, in both instances, patients with fasting hyperglycemia removed approximately one-half as much glucose from the plasma as did normal subjects. Since the plasma insulin levels were comparable in the two groups (approximately 100 μU/ml), these results demonstrate that patients with fasting hyperglycemia are more insulin resistant than are normal subjects. Furthermore, the differences in glucose removal were observed under conditions in which the plasma glucose levels in the normal and the diabetic groups were similar; therefore, the insulin resistance of patients with fasting hyperglycemia is independent of differences in plasma glucose pool size. Finally, glucose removal increased proportionately in both experimental.groups at the higher plasma glucose levels, suggesting that saturation of the glucose transport system does hot occur at these plasma glucose concentrations. These results further document the fact that nonobese patients with significant fasting hyperglycemia are less responsive than normal subjects to the acute action of insulin that stimulates glucose removal from plasma.
Ultrafast charge separation in supramolecular tetrapyrrole–graphene hybrids (2012)

Supramolecular donor-acceptor hybrids composed of few-layer graphene as an electron acceptor and phthalocyanine or porphyrin bearing four pyrene entities as photosensitizer donors have been synthesized, and occurrence of ultrafast charge separation in the order of 10(11)-10(12) s(-1) due to close proximity of the donor and acceptor entities is demonstrated.
Moving The Par Reduction Criterion Into The Line Driver (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Interaction of sulfonylurea‐conjugated polymer with insulinoma cell line of MIN6 and its effect on insulin secretion (2001)

A carboxylated derivative of sulfonylurea (SU), an insulinotropic agent, was synthesized and grafted onto a water-soluble polymer as a biospecific and stimulating polymer for insulin secretion. To evaluate the effect of the SU-conjugated polymer on insulin secretion, its solution in dimethyl sulfoxide was added to the culture of insulinoma cell line of MIN6 cells to make 10 nM of SU units in the medium and incubated for 3 h at 37°C. The culture medium was conditioned with glucose concentration of 3.3 or 25 mM. To verify the specific interaction between the SU (K+ channel closer)-conjugated polymer and MIN6 cells, the cells were pretreated with diazoxide, an agonist of adenosine triphosphate–sensitive K+ channel (K+ channel opener), before adding the SU-conjugated polymer to the cell culture medium. This treatment suppressed the action of SUs on MIN6 cells. Fluorescence-labeled polymer with rodamine-B isothiocyanate was used to visualize the interactions, and we found that the labeled polymer strongly absorbed to MIN6 cells, probably owing to its specific interaction mediated by SU receptors on the cell membrane. The fluorescence intensity on the cells significantly increased with an increase in incubation time and polymer concentration. A confocal laser microscopic study further confirmed this interaction. The results from this study provided evidence that SU-conjugated copolymer stimulates insulin secretion by specific interactions of SU moieties in the polymer with MIN6 cells. © 2001 John Wiley & Sons, Inc. J Biomed Mater Res 55: 72–78, 2001
Selective Expression of Type I IFN Genes in Human Dendritic Cells Infected with Mycobacterium tuberculosis (2002)

Type I IFN regulates different aspects of the immune response, inducing a cell-mediated immunity. We have recently shown that the infection of dendritic cells (DC) with Mycobacterium tuberculosis (Mtb) induces IFN-alpha. In this work we have monitored a rapid induction of IFN-beta followed by the delayed production of the IFN-alpha1 and/or -alpha13 subtypes. The Mtb infection rapidly activates the NF-kappaB complex and stimulates the phosphorylation of IFN regulatory factor (IRF)-3, events known to induce IFN-beta expression in viral infection. In turn, the autocrine production of IFN-beta induces the IFN-stimulated genes that contain binding sites for activated STATs in their promoters. Among the IFN-stimulated genes induced in DC through STAT activation are IRF-1 and IRF-7. The expression of IRF-1 appears to be dependent on the sequential activation of NF-kappaB and STAT-1. Once expressed, IRF-1 may further stimulate the transcription of IFN-beta. Induction of IRF-7 is also regulated at the transcriptional level through the binding of phosphorylated STAT-1 and STAT-2, forming the IFN-stimulated gene factor-3 complex. In turn, the IRF-1 and IRF-7 expression appears to be required for the delayed induction of the IFN-alpha1/13 genes. Although correlative, our results strongly support the existence of a cascade of molecular events in Mtb-infected DC. Upon infection, constitutively expressed NF-kappaB and IRF-3 are activated and likely contribute to the rapid IFN-beta expression. In turn, IFN-beta-induced IRF-1 and IRF-7 may cooperate toward induction of IFN-alpha1/13 if infection persists and these factors are activated.
T cell leukemia control via Ras-Raf pathway inhibition with peptides. (2018)

Our study demonstrated an improvement in survival curves in mice model affected by spontaneous T lymphoid leukemia when peptides WO2015001045 A2 were used. These peptides might be a valid option to become part of the therapeutic armory for malignant lymphoproliferative diseases control.
The Yeast KRE5 Gene Encodes a Probable Endoplasmic Reticulum Protein Required for (1→6)-β-D-Glucan Synthesis and Normal Cell Growth (1990)

Yeast kre mutants define a pathway of cell wall (1----6)-beta-D-glucan synthesis, and mutants in genes KRE5 and KRE6 appear to interact early in such a pathway. We have cloned KRE5, and the sequence predicts the product to be a large, hydrophilic, secretory glycoprotein which contains the COOH-terminal endoplasmic reticulum retention signal, HDEL. Deletion of the KRE5 gene resulted in cells with aberrant morphology and extremely compromised growth. Suppressors to the KRE5 deletions arose at a frequency of 1 in 10(7) to 1 in 10(8) and permitted an analysis of deletions which were found to contain no alkali-insoluble (1----6)-beta-D-glucan. These results indicate a role for (1----6)-beta-D-glucan in normal cell growth and suggest a model for sequential assembly of (1----6)-beta-D-glucan in the yeast secretory pathway.
Rational value of information estimation for measurement selection (2012)

Computing value of information (VOI) is a crucial task in various aspects of decision-making under uncertainty, such as in meta-reasoning for search; in selecting measurements to make, prior to choosing a course of action; and in managing the explora
Level Set Method for Tracking the Penetration Front of a Fracturing Fluid in Heterogeneous Reservoirs (2014)

Abstract Shale permeability is low enough to require unconventional stimulation treatment, such as hydraulic fracturing. Hydraulic fracturing is now widely used to achieve a larger stimulated reservoir volume by connecting intrakerogen pores, which are otherwise isolated from one another. It is important to monitor and predict the migration of fracturing fluid. The authors studied fracturing fluid injection in a granite rock in the laboratory and observed a sharp penetration front, implying the motion of the penetration front is advection-dominated. Based on this, they developed a numerical model using the level set method to track the penetration front of fracturing fluid. In the model, auto-correlated Gaussian random fields are generated to represent heterogeneous permeability distributions. Reservoir heterogeneity is measured using the coefficient of variation, which is defined as the ratio between standard deviation of permeability and mean permeability. The correlation length in the horizontal direction is much larger than in the vertical direction, implying a horizontal layered structure. The authors investigated the effect of heterogeneity on penetration front motion. Using the same statistical parameters, numerous realizations of the permeability field are generated. A finite difference reservoir simulator equipped with the weighted Jacobi iteration method was then used to solve for the Darcy flow fields, and the level set simulation was repeated to study the collective behavior of the system. In all simulations, the authors observed linear relationships between time and the first- and second-order spatial moments of the penetration fronts. The time derivatives of the first- and second-order spatial moments were the velocity and dispersion coefficient, respectively. With increasing reservoir heterogeneity, velocity decreased linearly, while the dispersion coefficient increased linearly. These observations imply there is a strong coupling between penetration front motion and reservoir heterogeneity. Therefore, to accurately predict the movement of fracturing fluids, it is necessary to effectively characterize heterogeneity of the host formation. This study is the first to systematically investigate the correlation between fracturing fluid penetration and reservoir heterogeneity using the level set method. It has important applications with respect to optimization of fracturing fluid injection.
Figure S1-3, Table S1-4 from Large-scale Circulating microRNA Profiling for the Liquid Biopsy of Prostate Cancer (2023)

&lt;p&gt;Figure S1-3, Table S1-4&lt;/p&gt;
Development of a digital reactivity meter and reactor physics data processor (1986)

Reactor physics tests at initial startup and after refueling are performed to verify the nuclear design and to assure safe operations thereafter. Analogue computers and instruments have been widely used for the acquisition of data and those data have been reduced by hand. These conventional procedures, however, require much time and labor. On the other hand, the development of digital computers and devices has made great progress. Under these circumstances the authors have digitalized the procedures mentioned. As described in the paper, the digitalized reactivity meter and data processor system proved to function satisfactorily as intended at the design stage.
Preparation of Three Dimensionally Ordered Macroporous Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> Electrode (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
On Point Sampling versus Space Sampling for Dimensionality Reduction (2007)

In recent years, random projection has been used as a valuable tool for performing dimensionality reduction of high dimensional data. Starting with the seminal work of Johnson and Lindenstrauss [8], a number of interesting implementations of the random projection techniques have been proposed for dimensionality reduction. These techniques are mostly space symmetric random projections in which random hyperplanes are sampled in order to construct the projection. While these methods can provide effective reductions with worst-case bounds, they are not sensitive to the fact that the underlying data may have much lower implicit dimensionality than the full dimensionality. This may often be the case in many real applications. In this work, we analyze the theoretical effectiveness of point sampled random projections, in which the sampled hyperplanes are defined in terms of points sampled from the data. We show that point sampled random projections can be significantly more effective in most data sets, since the implicit dimensionality is usually significantly lower than the full dimensionality. In pathological cases, where space sampled random projections are better, it is possible to use a mixture of the two methods to design a random projection method with excellent average case behavior, while retaining the worst case behavior of space sampled random projections.