gebhart/patrepeval huggingface dataset:
Deep Generative Models for Detecting Differential Expression in Single Cells (2019)

Abstract Detecting differentially expressed genes is important for characterizing subpopulations of cells. However, in scRNA-seq data, nuisance variation due to technical factors like sequencing depth and RNA capture efficiency obscures the underlying biological signal. First, we show that deep generative models, which combined Bayesian statistics and deep neural networks, better estimate the log-fold-change in gene expression levels between subpopulations of cells. Second, we use Bayesian decision theory to detect differentially expressed genes while controlling the false discovery rate. Our experiments on simulated and real datasets show that our approach out-performs state-of-the-art DE frameworks. Finally, we introduce a technique for improving the posterior approximation, and show that it also improves differential expression performance.
A Sensor for a Date-Rape Drug, Incorporated Into a Beverage Container (2012)

The objective of this project was to explore approaches for developing a beverage container that will act as a sensor indicating the presence of the date-rape drug gamma-hydroxybutyric acid (GHB) in the contained liquid. This research aimed to identify an indicator for GHB that gives a detectable color change when exposed to the typical dosage level, and to investigate methods to incorporate the indicator with a suitable material on the surface of the container. The indicators investigated were bromocresol purple and bromocresol green. The methods of incorporating the indicator that were explored were adsorption, embedding, and covalent attachment.
Effect of Proliferation and Invasion of Breast Cancer Cell by PP2 (2008)

Objective To study whether PP2 [4-Amino-5-(4-Chloro-Phenyl)-7-(t-Butyl) Pyrazolo Pyrimidine] could change the expression of src kinase and E-cadherin protein,and detect the proliferation and invasion of breast cancer cell.Methods After treating MDA-MB-231 with PP2,western blot was performed to determine the expression of src and E-cadherin;The proliferation was been tested by MTT assay;Boyden chamber assay was used to examine the effect of the invasion of MDAMB-231 cell.Results Western blot show if the dosage of PP2 increase,the expression of src is down-regulated and E-cadherin is up-regulated.MTT assay show that the proliferation of MDA-MB-231 have association with PP2 dosage(P0.05).Boyden chamber assay show that the invasion is down-regulated when the dosage of PP2 is enhanced(P0.05).Conclusion PP2 can strongly inhibit src and enhance the expression of the downstream protein of E-cadherin.The proliferation and invasion of MDAMB-231 cells is also inhibited by PP2.
Time Economical Total Synthesis of (−)-Oseltamivir (2016)

A time economical 60 min total synthesis of (-)-oseltamivir was accomplished in a single reaction vessel over five steps. One of the key issues is reduction in the number of steps by eliminating lengthy reaction steps with substitution of a rapid epimerization step. A catalytic system consisting of three reagents, namely, diphenylprolinol silyl ether, thiourea, and acid, was developed for a rapid asymmetric Michael reaction with excellent diastereo- and enantioselectivities. All reactions were optimized in terms of not only yield and selectivity but also reaction time.
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes (2020)

Digital data storage is a growing need for our society and finding alternative solutions than those based on silicon or magnetic tapes is a challenge in the era of "big data." The recent development of polymers that can store information at the molecular level has opened up new opportunities for ultrahigh density data storage, long-term archival, anticounterfeiting systems, and molecular cryptography. However, synthetic informational polymers are so far only deciphered by tandem mass spectrometry. In comparison, nanopore technology can be faster, cheaper, nondestructive and provide detection at the single-molecule level; moreover, it can be massively parallelized and miniaturized in portable devices. Here, we demonstrate the ability of engineered aerolysin nanopores to accurately read, with single-bit resolution, the digital information encoded in tailored informational polymers alone and in mixed samples, without compromising information density. These findings open promising possibilities to develop writing-reading technologies to process digital data using a biological-inspired platform.
Outcomes of Transcatheter and Surgical Aortic Valve Replacement in High-Risk Patients With Aortic Stenosis and Left Ventricular Dysfunction (2013)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT00530894.
Involuntary gesture recognition for predicting cerebral palsy in high-risk infants (2010)

In this paper we describe a system that leverages accelerometers to recognize a particular involuntary gesture in babies that have been born preterm. These gestures, known as cramped-synchronized general movements are highly correlated with a diagnosis of Cerebral Palsy. In order to test our system we recorded data from 10 babies admitted to the newborn intensive care unit at the UCI Medical Center. We applied machine learning techniques to features based on their data and were able to obtain accuracies between 70% and 90% depending on the relative cost of false positives and false negatives. Validated video observation annotations were utilized as ground truth. Finally, we conducted an analysis to understand the basis of the algorithmic predictions.
Tribological characteristics of zirconia-yttria ceramics (1995)

This study was initiated to understand the wear phenomena of partially stabilized zirconia sliding against itself. A generic laboratory ball-on-ring (pin-on-disk) system was used for the testing of zirconia sintered balls and HIPed rings. Experimental design assessed the effect of various testing variables and material characteristics on the friction and wear resistance of zirconia. The coefficient of friction and wear of yttria-stabilized zirconia sliding against itself are sensitive to testing conditions, particularly the environment. Water induces the severest wear damage, probably because of low-temperature degradation. Testing in air produced extensive damage attributed to the material`s poor thermal shock resistance and low thermal conductivity. Although paraffin oil produces the lowest coefficient of friction and minimum wear volume as compared to air and water, those values are higher than acceptable in real life applications. The predominant mode of wear damage is abrasive for the pressureless-sintered balls and adhesive for the HIPed matting surface, with plastic deformation and cracking of the adhering material. Water promotes some tribochemical reaction and grain pullout. However, details of such damage have not been quantified. Further investigation of the tribochemical effects observed in this material is recommended when testing in water. From the limited data obtained here, processingmore » routes, which produce differences in the material`s strength and hardness (HIPing vs sintering), do not appear to produce a difference in wear resistance.« less
Modulation of the formation of adhesions during the healing of injured tendons (2000)

The formation of restrictive adhesions around the musculotendinous unit after injury is one of the most vexing processes faced by the surgeon. In flexor tendons it has been shown that the synovial tissue is the source of aggressive fibroblasts which contribute to this process. Using a rabbit model, we have examined the effects of treating the synovial sheath with the antimetabolite 5-fluorouracil (5-FU) for five minutes. Inflammatory, proliferative and molecular markers were compared in the response of the treated and control tendons to injury. Compared with a control group we found that the proliferative and inflammatory responses were significantly reduced (p < 0.001) in the treated tendons. Not only was there a reduction in the cellular and cytokine response, but there also was a significant (p < 0.001) reduction in the level of activity of the known pro-scarring agent, transforming growth factor beta 1 (TGF-β1). These pilot studies indicate that the formation of restrictive adhesions may be modulated using a simple single-touch technique in the hope of producing a better return of function.
Continuous flow method for simultaneous determination of nitrate and ammonia in water (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTContinuous flow method for simultaneous determination of nitrate and ammonia in waterToyoaki. Aoki, Satoshi. Uemura, and Makoto. MunemoriCite this: Environ. Sci. Technol. 1986, 20, 5, 515–517Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://doi.org/10.1021/es00147a012RIGHTS & PERMISSIONSArticle Views237Altmetric-Citations13LEARN 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 InReddit PDF (413 KB) Get e-Alerts Get e-Alerts
A PSK Group Modem for Satellite Communications (1987)

A PSK group modem which modulates and demodulates multiple PSK signals en bloc will play an important role in realizing a cost-effective satellite communications system based on the narrowband multicarrier PSK/FDMA technique. This paper briefly discusses its possible applications, and presents a developed PSK group modem including its algorithm, hardware design, and implementation. In the algorithm, filtering of respective PSK signals is effectively carried out by digital signal processing techniques applied to the digital transmultiplexer. Furthermore, in order to compensate for the difference between the operation timing of the PSK group modem and the symbol timing of each input/output data signal, digital signal processings based on a table-look-up method using ROM and a rate-conversion filter with adaptive weighting are proposed for the modulator and demodulator, respectively. An experimental 4-phase PSK group modem has been developed, and experiments have been conducted under various conditions. The measured performance of the developed hardware is also demonstrated.
Why We Don't Come: Patient Perceptions on No-Shows (2004)

The results of this study suggest that reducing no-show rates among patients who sometimes attend might be addressed by reviewing waiting times and participants' perspectives of personal respect.
Virtual Screening An Effective Tool for Lead Structure Discovery (2001)

Different methods of virtual screening as a tool for lead structure discovery are described. They range from structure based docking procedures to ligand based methods such as the chemical features based pharmacophore hypothesis approach. A review on several successful applications of virtual screening is given. Different approaches have been described to derive pharmacophore models, which were subsequently used for 3D database searching. The studies so far published cover a wide range of pharmacological applications. The results hereby obtained clearly indicate that focused assessment of corporate databases by virtual screening using well validated pharmacophore models yield to a significant improvement in lead structure determination compared to high throughput screening.
ANUARIO DE LETRAS CELEBRA CINCO D‚CADAS DE EXISTENCIA (2011)

EDICION PRECURSORA EN MEXICO DEL ANALISIS DEL ESPANOL EN TODAS SUS VERTIENTES, DESDE LINGISTICA HASTA LITERATURA, EL ANUARIO DE LETRAS, PUBLICADO POR EL CENTRO DE LINGISTICA HISP NICA JUAN M. LOPE BLANCH, DEL INSTITUTO DE INVESTIGACIONES FILOLOGICAS (IIFL), CELEBRO 50 ANOS DE EXISTENCIA. CON ARTICULOS ORIGINALES QUE TRATAN TEMAS DE GRAM TICA, MORFOLOGIA, FON‚TICA, EVOLUCION DEL ESPANOL Y SUS VARIEDADES DISPERSAS EN DIFERENTES PAISES Y ESPACIOS SOCIALES, REVISTA SE COMPLEMENTA CON TEXTOS QUE DESENTRANAN LITERATURA HISP NICA ANTIGUA Y CONTEMPOR NEA, CREADA TANTO EN ESPANA COMO EN AM‚RICA, SENALARON INVESTIGADORES VINCULADOS CON ESE PROYECTO, REUNIDOS EN UN COLOQUIO PARA CELEBRAR DICHO ANIVERSARIO. AURELIA VARGAS VALENCIA, DIRECTORA DEL INSTITUTO, FELICITO A QUIENES LABORAN EN PUBLICACION, FUNDADA EN 1961 POR EL PROFESOR JUAN MIGUEL LOPE BLANCH. ANUARIO DE LETRAS, DESTACO, CONSERVA EN SUS P GINAS EL RIGOR ACADEMICO Y VARIEDAD, CON AUTORES MEXICANOS Y EXTRANJEROS. ELIZABETH LUNA TRAILL, DIRECTORA DE REVISTA, INTEGRANTE DE JUNTA DE GOBIERNO DE UNAM E INVESTIGADORA DEL CENTRO DE LINGISTICA HISP NICA, DIJO QUE, DESDE SUS INICIOS, ‚STA GANO GRAN PRESTIGIO ENTRE COMUNIDAD INTERNACIONAL. EN EL AULA MAGNA DE FILOLOGICAS, JOS‚ G. MORENO DE ALBA, INVESTIGADOR EMERITO DEL IIFL, RECORDO QUE EN FECHA DE FUNDACION, LOPE BLANCH SE UBICO COMO EDITOR, Y EL PRIMER DIRECTOR FUE FRANCISCO LARROYO; ANOS MAS TARDE, LOPE ASUMIO DIRECCION Y EDICION, QUE DEJO CERCA DE SU FALLECIMIENTO, EN 2002; ENTONCES SE HIZO CARGO SU DISCIPULA, ELIZABETH LUNA TRAILL. AMBOS HAN TRABAJADO EN FORTALECER PRESENCIA Y MANTENER UN EQUILIBRIO ENTRE LINGISTICA Y LITERATURA, DOS CARAS DE MISMA MONEDA, APUNTO. MARGIT FRENK, PROFESORA EM‚RITA DE FFL Y DOCTORA HONORIS CAUSA POR ESTA CASA DE ESTUDIOS, CONSIDERO QUE RIQUEZA DEL ANUARIO DE LETRAS ES QUE SIDO Y ES UNA ENORME CONTRIBUCION A CULTURA HUMANISTICA DE ESTE PAIS Y DE OTROS DE HABLA HISPANA. ENTRE LOS TEMAS LITERARIOS, HA PRESENTADO CON MAYOR FRECUENCIA ANALISIS SOBRE EL SIGLO DE ORO ESPANOL, LITERATURA MEDIEVAL, POESIA POPULAR Y LITERATURA MODERNA ESPANOLA E HISPANOAMERICANA. NO OBSTANTE, LA LINGISTICA ES AUN EL PLATO FUERTE, CON TEMAS DE FON‚TICA, MORFOLOGIA Y LEXICOLOGIA, ENTRE OTROS. POR SU PARTE, EDITORA MARIA DEL REFUGIO CAMPOS ADELANTO QUE ACTUALMENTE SE DISENA UNA NUEVA ‚POCA, PARA MODERNIZARLA, INCORPORAR SOPORTES TECNOLOGICOS Y RECUPERAR CONTINUIDAD, AUNQUE YA SE PREPARA EL VOLUMEN 46. ADEMAS, PUBLICACION EST  EN PROCESO DE DIGITALIZACION. EN EL EVENTO PARTICIPARON TAMBI‚N LOS INVESTIGADORES DE FILOLOGICAS ARMANDO PEREIRA Y FERNANDO RODRIGUEZ; EL FILOLOGO CUBANO HUMBERTO LOPEZ MORALES, SECRETARIO GENERAL DE ASOCIACION DE ACADEMIAS DE LENGUA ESPANOLA, Y EL ACADEMICO ESPANOL PEDRO MARTIN BUTRAGUENO, DE EL COLEGIO DE MEXICO.
Performance Optimization of Virtual Keyboards (2002)

Text entry has been a bottleneck of nontraditional computing devices. One of the promising methods is the virtual keyboard for touch screens. Correcting previous estimates on virtual keyboard efficiency in the literature, we estimated the potential performance of the existing QWERTY, FITALY, and OPTI designs of virtual keyboards to be in the neighborhood of 28, 36, and 38 words per minute (wpm), respectively. This article presents 2 quantitative design techniques to search for virtual keyboard layouts. The first technique simulated the dynamics of a keyboard with digraph springs between keys, which produced a Hooke keyboard with 41.6 wpm movement efficiency. The second technique used a Metropolis random walk algorithm guided by a “Fitts-digraph energy” objective function that quantifies the movement efficiency of a virtual keyboard. This method produced various Metropolis keyboards with different Shumin Zhai is a human–computer interaction researcher with an interest in inventing and analyzing interaction methods and devices based on human performance insights and experimentation; he is a Research Staff Member in the
Genome Sequence of Enterobacter sp. Strain SP1, an Endophytic Nitrogen-Fixing Bacterium Isolated from Sugarcane (2012)

Enterobacter sp. strain SP1 is an endophytic nitrogen-fixing bacterium isolated from a sugarcane stem and can promote plant growth. The draft genome sequence of strain SP1 presented here will promote comparative genomic studies to determine the genetic background of interactions between endophytic enterobacteria and plants.
<title>Enhanced visualization of MR angiogram with modified MIP and 3D image fusion</title> (1997)

We have developed a 3D image processing and display technique that include image resampling, modification of MIP, volume rendering, and fusion of MIP image with volumetric rendered image. This technique facilitates the visualization of the 3D spatial relationship between vasculature and surrounding organs by overlapping the MIP image on the volumetric rendered image of the organ. We applied this technique to a MR brain image data to produce an MRI angiogram that is overlapped with 3D volume rendered image of brain. MIP technique was used to visualize the vasculature of brain, and volume rendering was used to visualize the other structures of brain. The two images are fused after adjustment of contrast and brightness levels of each image in such a way that both the vasculature and brain structure are well visualized either by selecting the maximum value of each image or by assigning different color table to each image. The resultant image with this technique visualizes both the brain structure and vasculature simultaneously, allowing the physicians to inspect their relationship more easily. The presented technique will be useful for surgical planning for neurosurgery.
Two New Cleistanthane Diterpenes and a New Isocoumarine from Cultures of the Basidiomycete Albatrellus confluens (2009)

Two new cleistanthane-type diterpenes, 3alpha,5alpha,8beta-trihydroxycleistanth-13(17),15-dien-18-oic acid (1) and 8beta-hydroxy-18-norcleistanth-4(5),13(17),15-trien-3-one (2), a new isocoumarine, 3R-(2R-hydroxypropyl)-8-hydroxyl-7-methyl-3,4-dihydroisocoumarine (3), along with three known aurovertins, aurovertins B (4), C (5) and E (6), four known polyesters, orbuticin (7), BK223A (8), BK223B (9) and 15G256alpha-2-me (10), and a known isocoumarine, 3R-6-hydroxymellein (11), were isolated from cultures of the basidiomycete Albatrellus confluens. The structures of these compounds were established on the basis of spectroscopic and chemical methods.
General approach leading to the development of imidazoquinoline and imidazopyrimidine benzodiazepine receptor ligands (1991)

Abstract The observation that the imidazoquinoxaline ethyl ester RU32180 possessed an affinity of 175 nM for benzodiazepine (BDZ) receptors led to the discovery of several series of potent receptor ligands such as esters ofimidazoquinolines and imidazobenzothiazoles. The lack of oral activity shown by these esters was rectified in the benzoyl imidazoquinolne RU31719, which possessed nearly all the properties of a classical BDZ agonist but with reduced muscle relaxant activity. Structure‐activity studies led to the benzoyl imidazoquinazoline RU32514 and from there to the imidazopyrimidine RU32698, which has robust anxiolytic activity, but induces little sedation and no muscle relaxation in a range of animal models. Further studies yielded the oxadiazolyl imidazopyrimidines such as RU33203, a potent partial agonist, and the thiazolyl imidazopyrimidine RU33356, the first member of the series to possess antagonist/inverse agonist properties.
Analgetic activity and in vitro binding constants of some N-alkyl-3-benzazocines (1975)

A homologous series of 3-alkyl-1,2,3,4,5,6-hexahydro-8-hydroxy-6-methyl-3-benzazocines (2) has been synthesized. Analgetic activity and binding constants for the opiate receptor for 2 and for an analogous series of benzomorphans (1 and 3) are reported. In 1, hot-plate analgesic activity is lost on increase of the N-alkyl chain length from ethyl through butyl (lc-e) and regained with amyl (lf) and hexyl (lg). Compounds lc-e show that antagonist properties and binding constants are similar throughout the series. With 2, where there has been loss of steric constraints through removal of the 2,6-methano bridge of 1 and 3, greatly diminished analgetic activity and receptor affinity and no antagonist properties were observed. Like 1, however, greatest agonist activity was shown by the N-methyl (2c), amyl (2g), hexyl (2h), and heptyl (2i) homologs and there is a parallel of in vitro binding strength and analgetic activity.
Total Variation Deconvolution using Split Bregman (2012)

Deblurring is the inverse problem of restoring an image that has been blurred and possibly corrupted with noise. Deconvolution refers to the case where the blur to be removed is linear and shift-invariant so it may be expressed as a convolution of the image with a point spread function. Convolution corresponds in the Fourier domain to multiplication, and deconvolution is essentially Fourier division. The challenge is that since the multipliers are often small for high frequencies, direct division is unstable and plagued by noise present in the input image. Effective deconvolution requires a balance between frequency recovery and noise suppression. Total variation (TV) regularization is a successful technique for achieving this balance in deblurring problems. It was originally developed for image denoising by Rudin, Osher, and Fatemi and then applied to deconvolution by Rudin and Osher. In this article, we discuss TV-regularized deconvolution with Gaussian noise and its efficient solution using the split Bregman algorithm of Goldstein and Osher. We show a straightforward extension for Laplace or Poisson noise and develop empirical estimates for the optimal value of the regularization parameter λ.
Optical Study of PbZr<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>and NaNb<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Single Crystals (1955)

The twinning of the antiferroelectric crystals PbZr${\mathrm{O}}_{3}$ and NaNb${\mathrm{O}}_{3}$ has been studied. Essential differences between this twinning and the domain structure of ferroelectric BaTi${\mathrm{O}}_{3}$ have been observed. It is shown that both orthorhombic PbZr${\mathrm{O}}_{3}$ and NaNb${\mathrm{O}}_{3}$ are optically negative and the refractive index is smallest along the $a$ axis, along which axis the main antiparallel ion shifts have been reported. The birefringence of the crystals has been measured as a function of the temperature up to the transition points, and compared with the temperature dependence of the spontaneous strain.