gebhart/patrepeval huggingface dataset:
Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations (2016)

Human microbiome data from genomic sequencing technologies is fast accumulating, giving us insights into bacterial taxa that contribute to health and disease. Predictive modeling of such microbiota count data for classification of human infection from parasitic worms such as helminths can help in detection and management across global populations. Real-world datasets of microbiome experiments are typically sparse containing hundreds of measurements for bacterial species, of which only a few are detected in the bio-specimens that are analyzed. This feature of microbiome data produces the challenge of needing more observations for accurate predictive modeling and has been dealt with previously using different methods of feature reduction. To our knowledge, integrative methods such as transfer learning has not been explored in the microbiome domain yet, as a way to deal with data sparsity by incorporating knowledge of different but related datasets. One way of incorporating this knowledge is by using a meaningful mapping among features of these datasets. In this paper, we claim that this mapping would exist among members of each individual cluster grouped based on phylogenetic dependency among taxa and their association to the phenotype. We validate our claim by showing that models incorporating associations in such a grouped feature space result in no performance deterioration for the given classification task. In this paper, we test our hypothesis using classification models that detect helminth infection in microbiota of human fecal samples obtained from Indonesia and Liberia countries. In our experiments, we first learn binary classifiers for helminth infection detection by using Naive Bayes, Support Vector Machines, Multilayer Perceptrons, and Random Forest methods. In the next step, we add taxonomic modeling using the SMART-scan module to group the data, and learn classifiers using the same four methods, to test the validity of the achieved groupings. We observed a 6% to 23% and 7% to 26% performance improvement based on the Area Under ROC Curve (AUC) and Balanced Accuracy(Bacc) measures, respectively, over 10 runs of 10-fold cross-validation. These results show that using phylogenetic dependency for grouping our microbiota data actually results in a noticeable improvement in classification performance for helminth infection detection. These promising results from this feasibility study demonstrate that methods such as SMART-scan can be utilized in the future for knowledge transfer from different but related microbiome datasets by phylogenetically-related functional mapping, to enable novel integrative biomarker discovery.
Organometallic thermochemistry. Metal hydrocarbyl, hydride, halide, carbonyl, amide, and alkoxide bond enthalpy relationships and their implications in pentamethylcyclopentadienyl and cyclopentadienyl complexes of zirconium and hafnium (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganometallic thermochemistry. Metal hydrocarbyl, hydride, halide, carbonyl, amide, and alkoxide bond enthalpy relationships and their implications in pentamethylcyclopentadienyl and cyclopentadienyl complexes of zirconium and hafniumLaurel E. Schock and Tobin J. MarksCite this: J. Am. Chem. Soc. 1988, 110, 23, 7701–7715Publication Date (Print):November 1, 1988Publication History Published online1 May 2002Published inissue 1 November 1988https://pubs.acs.org/doi/10.1021/ja00231a020https://doi.org/10.1021/ja00231a020research-articleACS PublicationsRequest reuse permissionsArticle Views1618Altmetric-Citations255LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
AC 2007-627: NEW FACULTY, UNDERGRADUATES, AND INDUSTRY CONTRACTS: OBSERVATIONS AND LESSONS LEARNED FROM ENGINEERING PROFESSORS (2007)

Abstract Most new faculty have little experience managing contracts, and most have minimal experience advising undergraduates conducting research. Combining these two roles leads to both synergistic and antagonistic opportunities/challenges often not obvious at the outset. In this paper, relatively new (3-6 years) authors from civil, electrical, and mechanical engineering departments describe their observations on this topic based upon over 30 different contracts, specifically: • 3 types of research contracts, and the benefits and difficulties with each. • 6 tips for success in choosing and writing suitable contracts • 3 tips for success in choosing suitable students • 3 tips for success in conducting projects • examples and analysis of projects that went well • examples and analysis of projects that went poorly • things the authors wish they had known in their first year As an example, using both specific examples and inductive generalizations, the suitability of federally-funded and industry (including traditional industry, consulting firms and municipalities)-funded contract sources are analyzed. Each of these funding sources is evaluated for undergraduate research suitability with respect to typical timelines, funding agency’s criticality of success, the undergraduate’s class year, and the professor’s time before tenure review.
In Silico Prediction of hERG Inhibition (2015)

The voltage-gated potassium channel encoded by hERG carries a delayed rectifying potassium current (IKr) underlying repolarization of the cardiac action potential. Pharmacological blockade of the hERG channel results in slowed repolarization and therefore prolongation of action potential duration and an increase in the QT interval as measured on an electrocardiogram. Those are possible to cause sudden death, leading to the withdrawals of many drugs, which is the reason for hERG screening. Computational in silico prediction models provide a rapid, economic way to screen compounds during early drug discovery. In this review, hERG prediction models are classified as 2D and 3D quantitative structure-activity relationship models, pharmacophore models, classification models, and structure based models (using homology models of hERG).
Supplemental Experimental Procedures from <i>JAK3</i> Variant, Immune Signatures, DNA Methylation, and Social Determinants Linked to Survival Racial Disparities in Head and Neck Cancer Patients (2023)

&lt;p&gt;Supplemental Methods, Figures and Tables&lt;/p&gt;
Tolerância política no Brasil (2019)

Resumo Entendendo a tolerância política como uma das dimensões de uma cultura política democrática, o artigo utiliza um conjunto de dados inéditos produzidos pelo Latin American Public Project para compor, de forma exploratória, um quadro geral sobre essa atitude no contexto nacional. Por meio de técnicas de análise descritivas e multivariadas, identificamos os principais grupos que são alvo de antipatia dos brasileiros e o grau de tolerância em relação a eles, bem como as suas bases demográficas e atitudinais. Os resultados indicam que a manifestação da tolerância é função de atributos tanto sociais (como a geração) quanto atitudinais (como adesão à democracia e interesse por política) e apontam para uma ampla agenda de investigações futuras sobre o tema.
[Therapy of rhinophyma]. (1989)

The formation of rhinophyma is due to hyperplasia and hypertrophia of the sebaceous glands of the nose and represents the final stage of rosacea. The associated fibrosis can only be reduced by surgical procedures. Thus the therapy of choise is surgical excision completed by dermabrasion. From 1977 to 1985, 23 patients with rhinophyma were treated in this way at our clinic.
Nonlinear Optics of Chiral Media (1997)

Chiral media interact differently with left- and right-hand circularly-polarized light. In linear optics this gives rise to optical activity effects like circular dichroism, optical rotation and optical rotatory dispersion. Optical activity effects also occur in nonlinear optics. For example, second-harmonic generation from chiral surfaces is different for left- and right-hand circularly-polarized fundamental excitation.[1,2]
Figures S7-S9 from Extracellular-Regulated Protein Kinase 5-Mediated Control of p21 Expression Promotes Macrophage Proliferation Associated with Tumor Growth and Metastasis (2023)

&lt;p&gt;These supplementary figures show the in vitro cell culture strategies utilized in this study to demonstrate the requirement of ERK5 signaling for mediating tumor macrophage proliferation.&lt;/p&gt;
Presenting to local and remote audiences (2000)

The current generation of desktop computers and networks are bringing streaming audio and video into widespread use. A small investment allows presentations or lectures to be multicast, enabling passive viewing from offices or rooms. We surveyed experienced viewers of multicast presentations and designed a lightweight system that creates greater awareness in the presentation room of remote viewers and allows remote viewers to interact with each other and the speaker. We report on the design, use, and modification of the system, and discuss design tradeoffs.
Radio Resource Allocation for OFDM-Based Dynamic Spectrum Sharing: Duality Gap and Time Averaging (2014)

This paper considers radio resource allocation (RRA) in the downlink of an orthogonal frequency division multiple access (OFDM)-based spectrum-sharing network. The objective of RRA is to maximize the average achievable throughput subject to the primary service interference threshold and the secondary service transmit power constraint. RRA is usually implemented based on a time window T over which system parameters are averaged and checked against resource constraints. We use short-term ( T=1 time slot) and long-term ( T ≫ 1 slots) averaging as approximations to instantaneous and average constraints, respectively. RRA is also investigated for this system with long-term interference threshold and short-term interference threshold constraints. RRA optimization is a nonconvex optimization problem in which the duality principle is adopted to obtain approximate solutions. The duality gap indicates the degree of approximation in the thus-obtained solution. We prove that the duality gap corresponding to each resource allocation asymptotically decays at least with an exponential rate of T. We further show that OFDMA is, asymptotically, the optimal subcarrier assignment. We also propose a practically implementable online power and subcarrier allocation with on-the-fly channel state information measurement. An extensive simulation study has been conducted to verify the theoretically predicted duality gap behavior and to investigate the impact of different system parameters on the secondary service performance. The developed algorithms are also validated to be robust in practical settings and converge fast to theoretical bounds, and thus practically implementable.
Object Recognition based on Depth Aspect Image Matching (2000)

A method for three dimensional object recognition based on depth image information is proposed. A depth aspect image is defined as an orientation standardized appearance from the original depth data of the object, which is transformed by the rigid transformation drawn by each possible basis pair of every three feature points of the object depth data. They are made from the original depth images of models and then learned in the system as the database for retrieval of any instances on the models. Matching between an object aspect and the ones from models can be performed by two-dimensional image comparison, which is based on the least quantile of residuals and is robust against occlusion possibly occurred in cluttered scene. The paper includes a formalization of the proposed method and some experimental results with real objects. fine resolution of partial shapes of models[8] A novel matching scheme is also presented, which is based on a robust statistic and hence model instances with occluded part can be searched in the real scene. Depth aspect images are fundamental in the method and they are made through relative coordinates by the feature points on the model surfaces, enabling position and posture estimation of the models in the scene. The proposed method is suitable for hardware realization and so fast and real time processing. The paper consists as follows: In Section 2, an outline of the method is given together with definition of depth aspect images and the algorithm for generating them. In Section 3, a robust recognition algorithm using image-based matching is given for handling complex scenes with multiple objects. In Section 4, experiments with real scenes are pre sented, and then we conclude the paper with some remarks in Section 5. 1 Introduction 2 Depth
Study of Development Technology of Brake Caliper Which Balances Preventing Squeal with Weight Reduction (2015)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;It is well known that improving NV performance and weight saving are reciprocity. Brake squeal free is one of the top priority issues during development of brake system. To date, complex eigenvalue analysis has been utilized for prediction of brake squeal. It solves the structural instability problems by modal coupling which is the phenomenon that natural frequencies of normal modes are quite consistent. The positive real parts of complex eigenvalues are identified as instable vibration which causes brake squeal. On the other hand, the needs for light-weight brake system are higher than before due to recent trends of economizing fuel consumption and high driving performance. In order to obtain coexistence of brake squeal free with weight saving, shape optimization technique has been proposed for complex eigenvalue analysis. In this study, the real parts of eigenvalues are shifted to stable side analytically by optimization algorithm using response curved surface with minimizing mass of a brake assembly. For simplified FEM model consisting of a rotor and a pad, thickness of backplate of brake pad is set as design parameter, mass minimization as objective function, and real parts of the eigenvalues are lower than zero as a constraint condition. Shape optimization technology, as mentioned above, achieves the lightweight construction with brake squeal free analytically.&lt;/div&gt;&lt;/div&gt;
Imaging of uterine carcinoma by carbon-11-methionine and PET. (1994)

Uterine carcinoma accumulated [11C]methionine more than the normal endometrium. However, the physiological accumulations of [11C]methionine in the pelvis may confuse the interpreter of the PET image; thus, morphological imaging also needs to be performed as a reference to localize the tumor accurately. We conclude that human uterine carcinoma can be effectively imaged with [11C]methionine and PET.
Catalyseurs Zieger‐Natta supportés sur MgCl2 pour la polymérisation stéréorégulée du propène. II. Système catalytique simple: Solide binaire MgCl2‐TiCl4 et solution cocatalytique triéthylaluminium, benzoate d'ethyle (1984)

Abstract The kinetics of propene polymerization in heptane slurry at 1–4 bars was studied with a catalytic system that consisted of a solid catalyst prepared by adsorption of TiCI 4 on pure porous MgCl 2 (by dehydrating MgCl 2 , 6 H 2 O with thionyl chloride) and a cocatalytic, heptanic solution of ethylbenzoate (BE) and triethylaluminium (TEA). At a temperature approaching 60°C/polymerization began immediately after the introduction of the monomer. The polymerization rate decreased continuously during the reaction. The loss in activity, however, was not due to a diffusional effect (e.g., blocking of the catalyst by the growing polymer). Studies of the ageing of the catalytic system showed a deactivation of the catalytic system itself as a function of the time of contact between the catalyst and the cocatalyst. The product of the thermal decomposition of the complex 1:2 formed by the reaction of BE with TEA was not associated with the deactivation process or stereospecific control, which depend on the BE/AI ratio and the presence of the complex.
Comparison of scatter correction methods for CBCT (2006)

In contrast to the narrow fan of clinical Computed Tomography (CT) scanners, Cone Beam scanners irradiate a much larger proportion of the object, which causes additional X-ray scattering. The most obvious scatter artefact is that the middle area of the object becomes darker than the outer area, as the density in the middle of the object is underestimated (cupping). Methods for estimating scatter were investigated that can be applied to each single projection without requiring a preliminary reconstruction. Scatter reduction by the Uniform Scatter Fraction method was implemented in the Varian CBCT software version 2.0. This scatter correction method is recommended for full fan scans using air norm. However, this method did not sufficiently correct artefacts in half fan scans and was not sufficiently robust if used in combination with a Single Norm. Therefore, a physical scatter model was developed that estimates scatter for each projection using the attenuation profile of the object. This model relied on laboratory experiments in which scatter kernels were measured for Plexiglas plates of varying thicknesses. Preliminary results suggest that this kernel model may solve the shortcomings of the Uniform Scatter Fraction model.
fault: A Python Embedded Domain-Specific Language For Metaprogramming\n Portable Hardware Verification Components (2020)

While hardware generators have drastically improved design productivity, they\nhave introduced new challenges for the task of verification. To effectively\ncover the functionality of a sophisticated generator, verification engineers\nrequire tools that provide the flexibility of metaprogramming. However,\nflexibility alone is not enough; components must also be portable in order to\nencourage the proliferation of verification libraries as well as enable new\nmethodologies. This paper introduces fault, a Python embedded hardware\nverification language that aims to empower design teams to realize the full\npotential of generators.\n
Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data (2006)

Optimal designs of dose levels in order to estimate parameters from a model for binary response data have a long and rich history. These designs are based on parametric models. Here we consider fully nonparametric models with interest focused on estimation of smooth functionals using plug-in estimators based on the nonparametric maximum likelihood estimator. An important application of the results is the derivation of the optimal choice of the monitoring time distribution function for current status observation of a survival distribution. The optimal choice depends in a simple way on the dose-response function and the form of the functional. The results can be extended to allow dependence of the monitoring mechanism on covariates.
Aerodynamic Performance Assessment of Part-Span Connector of Last Stage Bucket of Low Pressure Steam Turbine (2011)

Modern steam turbines often utilize very long last stage buckets (LSB’s) in their low-pressure sections to improve efficiency. Some of these LSB’s can range in the order of 5 feet long. These long buckets (aka “blades”) are typically supported at their tip by a tip-shroud and near the mid span by a part span shroud or part span connector (PSC). The PSC is a structural element that connects all the rotor blades, generally at the mid span. It is primarily designed to address various structural issues, often with little attention to its aerodynamic effects. The objective of the current work is to quantify the impact of PSC on aerodynamic performance of the last stage of a LP steam turbine by using detailed CFD analyses. A commercial CFD solver, ANSYS CFX™, is used to solve the last stage domain by setting steam as the working fluid with linear variation of specific heat ratio with temperature. A tetrahedral grid with prismatic layers near the solid walls is generated using ANSYS WORKBENCH™. The results show a cylindrical PSC reduces the efficiency of the last stage by 0.32 pts, of which 0.20 pts is due to the fillet attaching the PSC to the blade. The results also show insignificant interaction of the PSC with the bucket tip aerodynamics. The work presents a detailed flow field analysis and shows the impact of PSC geometry on the aerodynamic performance of last stage of steam turbine. Present work is useful to turbine designer for trade-off studies of performance and reliability of LSB design with or without PSC.
All-optical multi-wavelength conversion using absorption modulation of an injection-locked FP-LD (2007)

An all-optical multi-wavelength converter using absorption modulation of an injection-locked Fabry-Perot laser diode (FP-LD) is demonstrated at 2.5Gb/s. The multi-wavelength converter can simultaneously provide 1 to 4 channel outputs and support both inverted and non-inverted conversion. By optimizing the wavelength of pump signal and polarization states of pump, probes, and the FP-LD, all converted outputs show high extinction ratio and negligible crosstalk power penalty. The results guarantee to increase the number of output channels. The proposed scheme can be applied to multicasting functions as well as 1xN wavelength conversion in an all-optical wavelength division multiplexed network.
The Challenges of Studying the Anaerobic Microbial World (2014)

Studies on strictly anaerobic microorganisms represent one of the most challenging areas of research, because anaerobic conditions (oxygen-free) need to be reconstructed to understand microbial activities and to obtain enrichments and pure culture. It is well-known that the micro/macro anaerobic environments are present everywhere on the Earth, and anaerobes comprise complex communities that play an important role in the carbon, nitrogen, and sulfur cycles on earth (49). Microbial community studies using 16S rRNA gene, as well as various functional genes, have offered new insights into anaerobic microbial ecology. Furthermore, numerous new lines of evidence offered by recent omics-driven and high-throughput sequencing studies provide a new vision of the anaerobic microbial world.