gebhart/patrepeval huggingface dataset:
Strong Coresets for Hard and Soft Bregman Clustering with Applications to Exponential Family Mixtures (2015)

Coresets are efficient representations of data sets such that models trained on the coreset are provably competitive with models trained on the original data set. As such, they have been successfully used to scale up clustering models such as K-Means and Gaussian mixture models to massive data sets. However, until now, the algorithms and the corresponding theory were usually specific to each clustering problem. We propose a single, practical algorithm to construct strong coresets for a large class of hard and soft clustering problems based on Bregman divergences. This class includes hard clustering with popular distortion measures such as the Squared Euclidean distance, the Mahalanobis distance, KL-divergence and Itakura-Saito distance. The corresponding soft clustering problems are directly related to popular mixture models due to a dual relationship between Bregman divergences and Exponential family distributions. Our theoretical results further imply a randomized polynomial-time approximation scheme for hard clustering. We demonstrate the practicality of the proposed algorithm in an empirical evaluation.
Use of Shigella flexneri ipaC and ipaH gene sequences for the general identification of Shigella spp. and enteroinvasive Escherichia coli (1989)

The products of the ipaB, ipaC, and ipaD genes are involved in the expression of the invasive phenotype in all species of Shigella and enteroinvasive Escherichia coli (EIEC). DNA probes derived from these genes are accurate indicators of the invasive phenotype (M. Venkatesan, J. M. Buysse, E. V. Vandendries, and D. J. Kopecko, J. Clin. Microbiol. 26:261-266, 1988); however, spontaneous loss of the invasion plasmid or selective deletion of invasion-associated genes may restrict the usefulness of such probes as general diagnostic tools. In this study, we report that laboratory-passaged strains of Shigella spp. and EIEC that were invasion and Sereny test negative were unable to hybridize to the ipaC DNA probe. However, a second DNA probe, derived from the Shigella flexneri ipaH gene, a multiple-copy element found on the chromosome and invasion plasmid that encodes a 60-kilodalton antigen, was more sensitive in its ability to detect virulent as well as avirulent shigellae and EIEC. Analysis of colony blots and stool blots from pediatric patients with diarrhea indicated that the ipaH probe was more effective in detecting shigellae and EIEC than was either the ipaC or 17-kilobase EcoRI fragment probe.
Defect generation in 3.5 nm silicon dioxide films (1994)

The generation of defects in thin 3.5 nm SiO2 films has been measured as a function of the average electron energy and total injected fluence. It is found that the generation of defects during electron injection for both positive and negative bias manifests itself as positive charge as measured from the increase in the current for a given bias. Positive charge generation is seen for electrons injected into the silicon dioxide conduction band, with the generation rate increasing with increasing electron energy. Electrons that traverse the oxide film via direct quantum-mechanical tunneling do not generate measurable defects. These results are consistent with previously published results on thicker films where the defects were attributed to positive charge found near the anode.
Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data (2012)

This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.
Utilization of GaAs Masking Layers for Formation of Patterned Porous Silicon (1996)

GaAs on a Si heteroepitaxial layer grown by metalorganic chemical vapor deposition (MOCVD) is used as the masking layer for the fabrication of porous silicon (PS) on silicon substrates. The photoluminescence (PL) of PS shows red light centered at a wavelength of around 630 nm. Of particular interest in the utilization of the GaAs masking layer is the anisotropic growth of PS (lateral/vertical growth ratio <1), the much higher resistance to anodization in HF solution than other kinds of masking layers (nitride, oxide, SiC, etc.) and lack of destruction in non-PS regions (implantation or irradiation). The nitride masking layer used to define the growth of PS is also studied. Surface and cross-sectional scanning electron microscopy (SEM) are carried out to determine which mask is better. The GaAs masking layer studied in this paper will lead to the realization of PS optoelectronic integrated circuits (OEIC).
Short Echo Time Proton MR Spectroscopic Imaging (1993)

Proton spectroscopic imaging at short TEs (20-30 ms) in human brain requires volume preselection inside the brain to suppress overwhelming lipid and water signals from surrounding tissue. In this article we discuss limitations of conventional volume preselection using stimulated echoes that lead to spectral contamination from surrounding tissue. Improved volume preselection was obtained by adding a complete outer volume suppression (presaturation). The performance of the method is illustrated on normal volunteers and on clinical cases with brain tumors and multiple sclerosis (MS) plaques. In normal human brain, we detected resonances with short T2 values and complex J-coupling, including rather broad methyl/methylene resonances in the chemical shift range between 0 and 2 ppm. Spectroscopic images obtained on patients with intracranial tumors and on one patient with several MS plaques demonstrate the possibility of detecting regional distributions of increased methyl/methylene resonances between 0 and 2 ppm in brain lesions.
In Silico Discovery of Plant-Origin Natural Product Inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL) (2018)

An <i>in silico</i> drug discovery pipeline for the virtual screening of plant-origin natural products (NPs) was developed to explore new direct inhibitors of TNF and its close relative receptor activator of nuclear factor kappa-B ligand (RANKL), both representing attractive therapeutic targets for many chronic inflammatory conditions. Direct TNF inhibition through identification of potent small molecules is a highly desired goal; however, it is often hampered by severe limitations. Our approach yielded a priority list of 15 NPs as potential direct TNF inhibitors that were subsequently tested <i>in vitro</i> against TNF and RANKL. We thus identified two potent direct inhibitors of TNF function with low micromolar IC<sub>50</sub> values and minimal toxicity even at high concentrations. Most importantly, one of them (A11) was proved to be a dual inhibitor of both TNF and RANKL. Extended molecular dynamics simulations with the fully automated EnalosMD suite rationalized the mode of action of the compounds at the molecular level. To our knowledge, these compounds constitute the first NP TNF inhibitors, one of which being the first NP small-molecule dual inhibitor of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.
Mechanism of reductive activation of cobalamin-dependent methionine synthase: an electron paramagnetic resonance spectroelectrochemical study (1990)

The mechanism of reductive methylation of cobalamin-dependent methionine synthase (5-methyltetrahydrofolate:homocysteine methyltransferase, EC 2.1.1.13) has been investigated by electron paramagnetic resonance (EPR) spectroelectrochemistry. The enzyme as isolated is inactive, and its UV/visible absorbance and EPR spectra are characteristic of cob(II)alamin. There is an absolute requirement for catalytic amounts of AdoMet and a reducing system for the formation and maintenance of active enzyme during in vitro turnover. The midpoint potentials of the enzyme-bound cob(II)alamin/cob(I)alamin and cob(III)alamin/cob(II)alamin couples have been determined to be -526 +/- 5 and +273 +/- 4 mV (versus the standard hydrogen electrode), respectively. The presence of either CH3-H4folate or AdoMet shifts the equilibrium distribution of cobalamin species observed during reduction by converting cob(I)alamin to methylcobalamin. The magnitude of these shifts is however vastly different, with AdoMet lowering the concentration of cob(II)alamin at equilibrium by a factor of at least 3 X 10(7), while CH3-H4folate lowers it by a factor of 19. These studies of coupled reduction/methylation reactions elucidate the absolute requirement for AdoMet in the in vitro assay system, in which the ambient potential is approximately -350 mV versus the standard hydrogen electrode. At this potential, the equilibrium distribution of cobalamin in the presence of CH3-H4folate would be greatly in favor of the cob(II)alamin species, whereas in the presence of AdoMet the equilibrium favors methylated enzyme. In these studies, a base-on form of cob(II)alamin in which the dimethylbenzimidazole substituent of the corrin ring is the lower axial ligand for the cobalt has been observed for the first time on methionine synthase.(ABSTRACT TRUNCATED AT 250 WORDS)
The influence of the pH and osmotic pressure upon tracheal ciliary beat frequency as determined with a new photo-electric registration device. (1980)

A method for measurement of tracheal ciliary beat frequency in vitro is described. Light transmitted through the cilia is detected by a phototransistor mounted in a microscope, while the frequency is measured instantaneously and the waveform is displayed by an oscilloscope, connected to a transient recorder. Due to the magnification and the method of illumination, the movement of approximately 30 cilia is projected on the phototransistor. In Locke-Ringer solution the waveform shows a very constant amplitude. Interference arises after a noxious influence and is dependent on the frequency of the ciliary movement. The effect of pH and osmotic pressure on chicken embryo and rat tracheal ciliary beat frequency is assessed. The frequency is not influenced between pH = 7 and pH = 10, but higher and lower pH values decrease the frequency. Hypertonic NaCl solutions decrease the frequency of chicken embryo cilia as much as hypotonic NaCl solutions. Rat cilia turned out to be less sensitive for hypotonic NaCl solutions.
Metal-Catalyzed Hydrostannations (2000)

ADVERTISEMENT RETURN TO ISSUEPREVArticleMetal-Catalyzed HydrostannationsNicholas D. Smith, John Mancuso, and Mark LautensView Author Information Merck Research Laboratories, 505 Coast Boulevard, South, Suite 300, La Jolla, California 92037, and Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, M5S 3H6, Canada Cite this: Chem. Rev. 2000, 100, 8, 3257–3282Publication Date (Web):July 18, 2000Publication History Received26 April 2000Published online18 July 2000Published inissue 1 August 2000https://pubs.acs.org/doi/10.1021/cr9902695https://doi.org/10.1021/cr9902695research-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views4949Altmetric-Citations190LEARN 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-Alertsclose SUBJECTS:Allenes,Catalysts,Group 14 compounds,Hydrocarbons,Selectivity Get e-Alerts
A wide dynamic range receiver channel for a pulsed time-of-flight laser radar (2001)

An integrated receiver channel for a pulsed time-of-flight (TOF) laser rangefinder has been designed and tested. The bandwidth of the receiver channel is 170 MHz, the transimpedance can be controlled in the range from 1.1 k/spl Omega/ to 260 k/spl Omega/, and the input-referred noise is /spl sim/6 pA//spl radic/Hz. The distance measurement accuracy is /spl plusmn/4.7 mm (average of 10000 measurements), taking into account walk error (input signal amplitude varies in the range 1:624) and jitter. A considerable increase in the input dynamic range of the receiver has been achieved by placing an integrated current buffer with variable attenuation between the external photodetector and the transimpedance preamplifier. Integrated electronic gain control structures together with the small size and low power consumption achieved by the use of full custom integrated technology considerably simplifies rangefinding devices for many applications. The circuit was implemented in an 0.8-/spl mu/m BiCMOS process.
POLYMERIC CO-ORDINATION COMPOUNDS (1961)

CONTENTS I. Introduction 499 II. Classification of inorganic polymers 500 III. Co-ordination polymers of low molecular weight 500 IV. Co-ordination polymers of high molecular weight 504 V. Electron-deficient polymers 511 VI. Polymeric chelate compounds 513 VII. Formation of co-ordination polymers in solution 515 VIII. Prospects and outstanding problems 520
Structure and Regulation of the Type VI Secretion System (2010)

The type VI secretion system (T6SS) is a complex and widespread gram-negative bacterial export pathway with the capacity to translocate protein effectors into a diversity of target cell types. Current structural models of the T6SS indicate that the apparatus is composed of at least two complexes, a dynamic bacteriophage-like structure and a cell-envelope-spanning membrane-associated assembly. How these complexes interact to promote effector secretion and cell targeting remains a major question in the field. As a contact-dependent pathway with specific cellular targets, the T6SS is subject to tight regulation. Thus, the identification of regulatory elements that control T6S expression continues to shape our understanding of the environmental circumstances relevant to its function. This review discusses recent progress toward characterizing T6S structure and regulation.
A modular device for large area integrated photoelectrochemical water-splitting as a versatile tool to evaluate photoabsorbers and catalysts (2017)

We present a stand-alone integrated solar water-splitting device with an active area of 64 cm<sup>2</sup> and a long-term stable operation. The modular setup of the device provides a versatile tool to integrate and evaluate various combinations of photoelectrodes and catalysts.
Application of a low cost array-based technique — TAB-Array — for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells (2014)

5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals at base resolution. Implementing this approach, termed "TAB-array", we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular progenitors and neural precursor cells. With the ability to discriminate 5mC and 5hmC, we identified a large number of novel dynamically methylated genomic regions that are implicated in the development of these lineages. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease.
Inverse scattering solutions using low-coherence light (2014)

We present a new wave-vector-space approach for solving inverse scattering problems. In our formulation, the theories for diffraction tomography and coherence gating are combined to explain 3D reconstruction with low-coherence light. Specifically, we apply this method to solve the scattering problem with broadband fields for transmission and reflection measurements. Our results can be applied to any interferometric measurements with low-coherence light, including optical coherence tomography, angle-resolved low-coherence interferometry, and white-light diffraction tomography.
Pilot Contamination Reduction by Shifted Frame Structure in Massive MIMO TDD Wireless System (2015)

飞行员污染限制表演巨大多重输入多重产量(MIMO ) 系统严重地由于降级的隧道评价。及时解决这个问题的一个有效方法分割双(TDD ) 无线系统及时正在转移飞行员的地点框架在附近的房间使用了。然而，转移框架结构仅仅与独立、相等分布式的理想(i.i.d ) 在 MIMO 系统被学习了隧道系数。在这份报纸，转移框架结构为使统计褪色的隧道的某个班与很多天线在一条测量隧道被学习。为了处理高内部房间的干扰，处于如此的一个测量隧道条件由转移框架结构引起了，我们与一个帮助协变性的隧道评估者建议一种情形。这种情形证明飞行员污染能被解决，高内部房间的干扰能被做与天线的数字 asymptotically 消失。干扰拒绝的钥匙在第二顺序统计上正在获得精确条件为需要并且干扰信号。第二顺序统计的最重要的信息来自二部分，一个人在基础车站(BS ) 之中是隧道状态信息(CSI ) ，其它来自 BS 交换的估计的信息，它描绘在 BS 和用户之间的隧道。模拟给干扰拒绝和可完成的率提升的强大的结果。
A framework for virtual channel onto virtual path multiplexing in ATM-ABR (2002)

This paper proposes an algorithm for aggregating virtual channel connections (VCCs) onto virtual path connections (VPSs) in asynchronous transfer mode (ATM) networks. We focus on the interesting problem of multiplexing onto an available bit rate (ABR) VPC. ABR VPCs are particularly useful for connecting enterprise sites over the Internet, providing a virtual private network (VPN). The VPC/VCC hierarchy is also important for supporting Internet differentiated services over ATM. The coupling between the flow control mechanisms for VCCs and VPCs is not standardized. We propose fairness definitions for VPC bandwidth allocation, and describe an algorithm for allocating the VPC capacity to the multiplexed VCCs. Preliminary simulation results indicate that the algorithm achieves the required fair allocations, while controlling queue sizes.
Raman Spectroscopy-Based Creatinine Measurement in Urine Samples from a Multipatient Population (2003)

Spectroscopic methods of urinalysis offer several advantages over chemical methods, including less sample contact and higher information content. In particular, urine creatinine has been the subject of several spectroscopic studies. We report the first use of Raman spectroscopy to measure creatinine concentrations in unaltered urine samples from a multipatient population. Using near-infrared excitation and a hybrid linear analysis calibration method, a root mean squared error of cross-validation (RMSECV) of 4.9 mg/dL was obtained. The error in the reference chemical method was 1.1 mg/dL. This result shows that the Raman spectroscopy can measure creatinine at clinical levels even in the presence of patient-to-patient variations. Because most assays in urine require creatinine concentration in order to correct for fluctuations in water content, measurement of creatinine is the first step towards more extensive Raman-based urinalysis.
A phase 1b study of ONT-380, an oral HER2-specific inhibitor, combined with ado-trastuzumab emtansine (T-DM1), in HER2+ metastatic breast cancer (MBC). (2014)

TPS662 Background: ONT-380 is a selective small molecule inhibitor of HER2 kinase with nanomolar potency. Unlike dual HER2/EGFR agents, it does not inhibit EGFR at clinically relevant concentrations, decreasing the potential for EGFR-related toxicities. In preclinical studies, ONT-380 demonstrated greater than additive activity with trastuzumab, and was active in models of CNS metastases. In a single-agent phase 1 study in 50 patients (pts) with metastatic HER2+ cancer, the MTD was 600 mg BID, with DLT consisting of reversible Grade 3 ALT/AST in 2 of 4 pts treated at 800 mg. In 22 HER2+ breast cancer pts treated at doses ≥ 600 mg BID, the clinical benefit rate (partial response [n = 3] plus stable disease for at least 6 months [n = 3]) was 27%. Based on data supporting dual blockade of HER2, ONT-380 is now being evaluated in combination with T-DM1. Methods: The study objectives are to determine the safety, MTD/Phase 2 dose, and preliminary anti-tumor activity of ONT-380 given in combination with T-DM1 in pts with or without CNS metastases. Potential biomarkers of response and pharmacokinetics will also be assessed. A 3+3 design will evaluate up to four dose levels of ONT-380 (starting at 300 mg PO BID) given with T-DM1 (3.6 mg/kg IV once every 21 days). The study population includes up to 48 adult pts with HER2+ MBC who have received prior trastuzumab and a taxane, but not T-DM1, for metastatic disease. Pts with either treated CNS metastases or asymptomatic untreated CNS metastases are also eligible. Two expansion cohorts are planned, including an MTD/Phase 2 dose expansion cohort, and a cohort of pts with CNS disease, including either untreated, asymptomatic CNS metastases or CNS metastases that have progressed after local therapy. Systemic disease response will be evaluated using RECIST 1.1. CNS response will be evaluated by RECIST 1.1, modified RECIST 1.1, and volumetric criteria. Potential biomarkers of response include the presence of p95 HER2 and HER2 mutations in archived tumor biopsies. Treatment will continue until unacceptable toxicity, disease progression, or withdrawal of consent. Clinical trial information: NCT01983501.