gebhart/patrepeval huggingface dataset:
Predictive survival markers in patients with surgically resected non-small cell lung carcinoma. (2000)

Among patients with resected non-small cell lung carcinoma, about 50% will present a tumor recurrence. Thus, it would be of major importance to be able to predict and try to prevent these relapses by an active chemotherapy and/or radiotherapy. In an attempt to answer this question, the tumors of 227 patients with a surgically resected non-small cell lung carcinoma were evaluated as follows: tumors were classified as squamous cell carcinoma (n = 132) or adenocarcinoma (n = 95), and tumor differentiation was evaluated for each type. Then, all tumors were classified in respect to their pathological TNM staging (WHO) and screened by immunohistochemistry for the detection of the expression of the following antigens: Bcl-2, A+B+H blood group antigens, c-erb-b2, p53, and Pan-Ras antigens. Furthermore, adenocarcinomas were screened for the presence of point mutations in Ki-Ras codons 1-31. Finally, the patient blood group was defined, and patient survival was analyzed using nonparametric tests and proportional hazard Cox models. Using Kaplan-Meier survival curves, disease pathological TNM staging was shown to be a strong predictive factor of survival for both squamous cell carcinoma and adenocarcinoma. Patients with squamous cell carcinoma experienced fewer relapses than those with adenocarcinoma (42% versus 63%; P = 0.0002) and had a significantly better survival. All evaluated antigens were more often present in squamous cell carcinoma than in adenocarcinoma except for Pan-Ras (three times more frequent in adenocarcinoma). In patients with squamous cell carcinoma, only tumor staging had a significant prognosis value (P = 0.01). In patients with lung adenocarcinoma, a well-differentiated tumor (P = 0.009) as well as a positive Bcl-2 staining (P = 0.009) and an A+B+H antigen tumor staining (P = 0.024) were associated with a better survival. In contrast, patients with a stage I or II disease and a p53-positive tumor staining and patients with the O blood group (P = 0.01) had a shorter survival. Interestingly, no relation with patient survival was related to c-erb-b2 and Pan-Ras staining. Finally, 12 point mutations were found out of 81 tumors (15%) evaluated for Ki-Ras codons 1-31; they involved codon 12 but also 8, 14, and 15 without any relationship to survival. In respect to lung adenocarcinoma, using Cox proportional hazard models stratified on tumor staging, the following markers were shown to be related to survival: (a) Independent markers of longer survival (ie., high histological degree of tumor differentiation and positive Bcl-2 and A+B+H blood group antigen expression by tumor cells); and (b) Independent markers of shorter survival (i.e., O blood group for all patients and p53 tumor staining in patients with stage I and II diseases). This study suggests that, in patients who undergo surgery for lung adenocarcinoma, the presence or absence of these criteria could be used to define a subset of patients who may benefit from a more specific follow-up.
[Studies on the thermostable L-lactate dehydrogenase from thermophilic bacteria]. (1991)

About 200 strains of extreme thermophilic bacteria were isolated from hot springs in Guandong province. A strain, HG25, was found to produce thermostable intracellular L-lactate dehydrogenase (EC. 1.1.1.27). It has the characteristic of Thermus sp. The cells were gram-negative, non-sporulating, nonmotile, aerobic rods containing yellow pigment. The optimum temperature for growth was between 65 degrees C to 75 degrees C, the maximum 85 degrees C, and minimum 40 degrees C. The generation time at the optimum was about 80 min. Starch was not hydrolyzed. Acid was not produced from glucose. The G+C content in DNA was 62-65 mol% (Tm). As the properties of strain HG25 is similar to those of Thermus aquaticus and T. thermophilus HB 8 belonging to the genus Thermus. The thermostable L-lactate dehydrogenase was partially purified by ammonium sulfate fractionation and DEAE-cellulose column chromatography. For pyruvate reduction, the optimum temperature of the enzyme was 60 degrees C and pH 8.0. After incubation in 0.1 mol/L phosphate buffer pH 7.4 at 70 degrees C for 10 min, the enzyme retained about 85% of its original activity. The half-live time (t1/2) at 85 degrees C was 10 min.
Novel positional encodings to enable tree-based transformers (2019)

Neural models optimized for tree-based problems are of great value in tasks like SQL query extraction and program synthesis. On sequence-structured data, transformers have been shown to learn relationships across arbitrary pairs of positions more reliably than recurrent models. Motivated by this property, we propose a method to extend transformers to tree-structured data, enabling sequence-to-tree, tree-to-sequence, and tree-to-tree mappings. Our approach abstracts the transformer's sinusoidal positional encodings, allowing us to instead use a novel positional encoding scheme to represent node positions within trees. We evaluated our model in tree-to-tree program translation and sequence-to-tree semantic parsing settings, achieving superior performance over both sequence-to-sequence transformers and state-of-the-art tree-based LSTMs on several datasets. In particular, our results include a 22% absolute increase in accuracy on a JavaScript to CoffeeScript translation dataset.
Direct Comparison of Linear and Macrocyclic Compound Libraries as a Source of Protein Ligands (2015)

There has been much discussion of the potential desirability of macrocyclic molecules for the development of tool compounds and drug leads. But there is little experimental data comparing otherwise equivalent macrocyclic and linear compound libraries as a source of protein ligands. In this Letter, we probe this point in the context of peptoid libraries. Bead-displayed libraries of macrocyclic and linear peptoids containing four variable positions and 0-2 fixed residues, to vary the ring size, were screened against streptavidin and the affinity of every hit for the target was measured. The data show that macrocyclization is advantageous, but only when the ring contains 17 atoms, not 20 or 23 atoms. This technology will be useful for conducting direct comparisons between many different types of chemical libraries to determine their relative utility as a source of protein ligands.
Activation of Liver X Receptors Promotes Neuroprotection and Reduces Brain Inflammation in Experimental Stroke (2008)

This work highlights the transcriptional action of LXR as a protective pathway in brain injury and the potential use of LXR agonists as therapeutic agents in stroke.
Persistence of Use of Lipid-Lowering Medications (1998)

Context.—Although clinical trials have demonstrated the benefits of lipid-lowering therapy, little is known about how these drugs are prescribed or used in the general population.Objective.—To estimate predictors of persistence with therapy for lipid-lowering drug regimens in typical populations of patients in the United States and Canada.Design.—A cohort study defining all prescriptions filled for lipid-lowering drugs during 1 year, as well as patients' demographic and clinical characteristics.Setting.—New Jersey's Medicaid and Pharmacy Assistance for the Aged and Disabled programs and Quebec's provincial medical care program.Patients.—All continuously enrolled patients older than 65 years who filled 1 or more prescriptions for lipid-lowering drugs (N=5611 in the US programs, and N = 1676 drawn from a 10% sample in Quebec).Main Outcome Measures.—Proportion of days during the study year for which patients had filled prescriptions for lipid-lowering drugs; predictors of good vs poor persistence with therapy.Results.—In both populations, patients failed to fill prescriptions for lipid-lowering drugs for about 40% of the study year. Persistence rates with 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors were significantly higher than those seen with cholestyramine (64.3% vs 36.6% of days with drug available, respectively). Patients with hypertension, diabetes, or coronary artery disease had significantly higher rates of persistence with lipid-lowering regimens. In New Jersey, multivariable analysis indicated that the poorest patients (those enrolled in Medicaid) had lower rates of drug use than less indigent patients (those enrolled in Pharmacy Assistance for the Aged and Disabled) after adjusting for possible confounders, despite virtually complete drug coverage in both programs. When rates of use were measured in the US population for the 5 years following the study year, only 52% of surviving patients who were initially prescribed lipid-lowering drugs were still filling prescriptions for this drug class.Conclusion.—In all populations studied, patients who were prescribed lipid-lowering drug regimens remained without filled prescriptions for over a third of the study year on average. Rates of persistence varied substantially with choice of agent prescribed, comorbidity, and socioeconomic status, despite universal coverage of prescription drug costs. After 5 years, about half of the surviving original cohort in the United States had stopped using lipid-lowering therapy altogether.
Numerical and Experimental Investigation of a Novel Thermal Management System Test Bench (2016)

Increasing power requirements of military armored vehicles and space constrains of powertrain cabin result in some thermal parts, over heat load and more parasitic losses. Therefore, more intelligent Thermal Management Systems (TMS) are implemented, which with more than one cooling loops. A alternative Thermal Management System Test Bench (TMSTB) which with two cooling loops and three independent heat sources, was presented in this work utilized to investigate these problems. Numerical model is built and validated with experimental tests excellently. Computational results are used to investigate/research the system level characteristics of each loops and their relationship and relative influence of various parameters. In particular, fan speed has a great effect on the temperature of both cooling circuits. However the pump speed and fan speed should math with each other well to improve the heat dissipation ability of the system. Furthermore, some parameters, such as fan speed, pump speed, working fluid and the relationship between different loops have a considerable effect on the heat dissipation ability and controlled performance.
Performance analyses of plasmonic lithography (2017)

We analyzed the field contrast, aspect ratio, pattern uniformity as well as the line-edge roughness (LER) of the patterns fabricated in plasmonic lithography. Deep subwavelength patterns with high aspect-ratio and large-area uniformity were achieved by coupling the evanescent waves into an optical waveguide as well as the selection of a single high spatial frequency mode. In addition, the impacts of defects on photomasks and the surface roughness on thin films are studied in two exemplary plasmonic lithography systems: superlens and hyperbolic metamaterials (HMM). Superlens is capable of replicating arbitrary patterns, which also inherently make it vulnerable to roughness of the thin film and imperfections on the mask; while HMM system is more immune to such imperfections due to its spatial frequency selection function property.
Hypothesis testing framework for active object detection (2013)

One of the central problems in computer vision is the detection of semantically important objects and the estimation of their pose. Most of the work in object detection has been based on single image processing and its performance is limited by occlusions and ambiguity in appearance and geometry. This paper proposes an active approach to object detection by controlling the point of view of a mobile depth camera. When an initial static detection phase identifies an object of interest, several hypotheses are made about its class and orientation. The sensor then plans a sequence of viewpoints, which balances the amount of energy used to move with the chance of identifying the correct hypothesis. We formulate an active M-ary hypothesis testing problem, which includes sensor mobility, and solve it using a point-based approximate POMDP algorithm. The validity of our approach is verified through simulation and experiments with real scenes captured by a kinect sensor. The results suggest a significant improvement over static object detection.
Technical innovation and perceived usability outperform NPS in correlation to financial performance in US publicly traded companies (2020)

Since its creation, Net Promoter Score (NPS) has become a standard measurement of customer loyalty and business growth. However, independent research results have challenged that status yet without budging corporate beliefs. The blind eye to inconsistent outcomes is due in part NPS’ simplicity and uneven but hopeful measures of positive business impact, even as companies are in the dark about the factors that impact their score. Therefore, measuring 1605 US-based customers of US publicly traded companies, this study has found that NPS was positively and significantly correlated with financial performance. However, two other dimensions of customer experience, technical innovation (TI) and perceived usability (PU) outperformed NPS with stronger correlations demonstrating both the value of NPS but also perhaps the need to look beyond. In addition, TI and PU were also strongly correlated with NPS, offering insights into aspects of the customer experience, customer loyalty and business performance that companies can use to impact their NPS score, which they would otherwise not know.
The Effect of Emergency Department Treatment Time on Outcomes in Acute Stroke Patients (2010)

BACKGROUNDStroke is a disease that leads to a long period of disability and death. Accordingly, the initial treatment is so influential on the prognosis of a patient that shortening the time to initial treatment after hospital admission has a very important role in the entire treatment regimen. This study aimed to demonstrate the effect of the Emergency Department treatment time at Bundang CHA Hospital for acute stroke patients to improve the treatment regimen through six sigma activities.METHODSThe outcomes for 246 patients with suspected acute strokes who were admitted to the Emergency Department of Bundang CHA Hospital, the flow of the emergency department process divided into 11 phases, and the duration of each phase were determined. Patients were classified as before and after six sigma activities and compared.RESULTSThe five phases statistically demonstrated the effect of meaningful improvement in the duration of visit-receiving CT prescriptions, visit-receiving lab prescriptions, consult request-arriving to the emergency department, visit-CT angiography results, and visit-the issue of hospital admissions. In the next 2 phases, the sigma level also improved by 0.71sigma and 0.06sigma. However, the total emergency department stay time was not statistically meaningful. The time required time was increased and the sigma level was decreased by 0.19sigma.CONCLUSIONSThe result of six sigma activities showed the effect of the treatment system improvement with a partial decrease in the duration of each phase, but the total emergency department stay time was not improved owing to environmental factors. For better results, continuous improvement of the treatment system and expansion of hospital facilities will be required.
An Autonomous System for the Evaluation of a Robot Tool Center Point using Computer Vision (2015)

The main purpose of this thesis is to study a method for finding the geometric relationship between the TCP (tool center point) of a tool attached to the robot flange (the last axis) and the robot itself using a camera. From a theoretical point of view the TCP computed is not an approximation. The proposed method computes the TCP performing two rotations from the initial flange pose around two different rotation axis. There is no constraints about the rotation angle
Involvement of matrix metalloproteinase-2 activity in invasion and metastasis of pancreatic carcinoma (1998)

The results of the current study indicate that MMP-2 activation plays a significant role in tumor invasion and metastasis in pancreatic carcinoma.
Fundamentals of Polarimetric Remote Sensing (2009)

Introduction Review of Radiometry Wave Nature of EM Energy and Introduction of the Polarization Ellipse Ways to Represent the Polarimetric State of a Beam Polarimetric Interactions: Reflection and Transmission Polarimetric Bidirectional Reflectance Distribution Functions (BRDF) Polarized Form of the Governing Equation Including Atmospheric Scattering Terms Sensors for Measuring the Polarized State of a Beam Processing and Display Algorithms Measurements and Modeling of the pBRDF of Materials Longwave Infrared pBRDF Principles LWIR pBRDF Measurements and Modeling.
Eugenol prevents amyloid formation of proteins and inhibits amyloid-induced hemolysis (2017)

Eugenol has attracted considerable attention because of its potential for many pharmaceutical applications including anti-inflammatory, anti-tumorigenic and anti-oxidant properties. Here, we have investigated the effect of eugenol on amyloid formation of selected globular proteins. We find that both spontaneous and seed-induced aggregation processes of insulin and serum albumin (BSA) are significantly suppressed in the presence of eugenol. Isothermal titration calorimetric data predict a single binding site for eugenol-insulin complex confirming the affinity of eugenol for native soluble insulin species. We also find that eugenol suppresses amyloid-induced hemolysis. Our findings reveal the inherent ability of eugenol to stabilize native proteins and to delay the conversion of protein species of native conformation into β-sheet assembled mature fibrils, which seems to be crucial for its inhibitory effect.
Numerical simulation of elasto-plastic electro-osmosis consolidation at large strain (2015)

In this paper, a numerical solution for the electro-osmosis consolidation of clay in multi-dimensional domains at large strains is presented, with the coupling of the soil mechanical behaviour, pore water transport and electrical fields being considered. In particular, the Modified Cam Clay model is employed to describe the elasto-plastic behaviour of clay, and some empirical expressions are used to consider the nonlinear variation of the hydraulic and electrical conductivities of the soil mass during the consolidation processes. The implementation of the theoretical model in a finite element code allows for analysis of the evolution of the transient response of the clay subjected to electro-osmosis treatment. The proposed model is verified via comparison with data from a large strain electro-osmosis laboratory test, to demonstrate its accuracy and effectiveness. Various numerical examples are also investigated to study the deformation characteristics and time-dependent evolution of the excess pore pressure. Finally, a well-documented field application of electro-osmosis is simulated to provide further verification. The results show that the numerical solution is effective in predicting the nonlinear behaviour of clay during electro-osmosis consolidation.
Potential impact of acid precipitation on arsenic and selenium (2020)

The potential impact of acidic precipitation on the environmental mobility of the metalloids arsenic (As) and selenium (Se) has not been given much attention and is poorly understood. As with other elements, the interest here is the potential effect of environmental acidification on environmental behavior in ways that are relevant to human exposure to these metalloids. Available information on acid precipitation and the environmental behavior of these metalloids do, however, permit some preliminary conclusions to be drawn. Both As and Se appear to be mobilized from household plumbing into tap water by the corrosive action of soft, mildly acidic water, while surface water catchment systems in areas impacted by acidic deposition may contain elevated soluble As levels. Acidification of aquatic ecosystems that are drinking water sources may pose the prospect of enhanced release of As from sediment to water as well as reduction in water levels of Se. Acidification of ground waters, where As appears to be especially mobile, is of particular concern in this regard. The potential impact of acidic deposition on As and Se in soils cannot readily be assessed with respect to human exposure, but it would appear that the behavior of these metalloids in poorly buffered, poorly immobilizing soils, e.g., sandy soils of low metal hydrous oxide content, would be most affected. The effect is opposite for the two elements; lowered pH would appear to enhance As mobility and to reduce Se availability. Altered acidity of both soil and aquatic systems poses a risk for altered biotransformation processes involving both As and Se, thereby affecting the relative amounts of different chemical forms varying in their toxicity to humans as well as influencing biogeochemical cycling.
Deep learning interpretation of echocardiograms (2020)

Echocardiography uses ultrasound technology to capture high temporal and spatial resolution images of the heart and surrounding structures, and is the most common imaging modality in cardiovascular medicine. Using convolutional neural networks on a large new dataset, we show that deep learning applied to echocardiography can identify local cardiac structures, estimate cardiac function, and predict systemic phenotypes that modify cardiovascular risk but not readily identifiable to human interpretation. Our deep learning model, EchoNet, accurately identified the presence of pacemaker leads (AUC = 0.89), enlarged left atrium (AUC = 0.86), left ventricular hypertrophy (AUC = 0.75), left ventricular end systolic and diastolic volumes ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:math> = 0.74 and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:math> = 0.70), and ejection fraction ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:math> = 0.50), as well as predicted systemic phenotypes of age ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:math> = 0.46), sex (AUC = 0.88), weight ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:math> = 0.56), and height ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup><mml:mrow><mml:mi>R</mml:mi></mml:mrow> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msup> </mml:math> = 0.33). Interpretation analysis validates that EchoNet shows appropriate attention to key cardiac structures when performing human-explainable tasks and highlights hypothesis-generating regions of interest when predicting systemic phenotypes difficult for human interpretation. Machine learning on echocardiography images can streamline repetitive tasks in the clinical workflow, provide preliminary interpretation in areas with insufficient qualified cardiologists, and predict phenotypes challenging for human evaluation.