gebhart/patrepeval huggingface dataset:
Right ventricular infarction—diagnosis and treatment (2000)

Right ventricular infarction (RVI) as assessed by various diagnostic methods accompanies inferior-posterior wall myocardial infarction (MI) in 30 to 50% of patients. Recognition of the syndrome of RVI is important as it defines a significant clinical entity, which is associated with considerable immediate morbidity and mortality and has a well-delineated set of priorities for its management. Patients may clinically present with hypotension, elevated jugular venous pulse (JVP), and occasionally shock, all in the presence of clear lung fields. The ST-segment elevation of > or = 0.1 mV in the right precordial leads V4R is a readily available electrocardiographic sign used for diagnosis of RVI. Other diagnostic approaches for assessing RVI include echocardiography, radionuclide ventriculography, technetium pyrophosphate scanning, and hemodynamic measurements. The proper management of RVI includes volume loading to maintain adequate right ventricular preload, ionotropic support, and maintenance of atrioventricular synchrony. Reperfusion therapy should be initiated at the earliest signs of right ventricular dysfunction. Finally, complete recovery over a period of weeks to months is a rule in a majority of patients, suggesting right ventricular "stunning" rather than irreversible necrosis has occurred.
Parseweb (2007)

Programmers commonly reuse existing frameworks or libraries to reduce software development efforts. One common problem in reusing the existing frameworks or libraries is that the programmers know what type of object that they need, but do not know how to get that object with a specific method sequence. To help programmers to address this issue, we have developed an approach that takes queries of the form "Source object type → Destination object type" as input, and suggests relevant method-invocation sequences that can serve as solutions that yield the destination object from the source object given in the query. Our approach interacts with a code search engine (CSE) to gather relevant code samples and performs static analysis over the gathered samples to extract required sequences. As code samples are collected on demand through CSE, our approach is not limited to queries of any specific set of frameworks or libraries. We have implemented our approach with a tool called PARSEWeb, and conducted four different evaluations to show that our approach is effective in addressing programmer's queries. We also show that PARSEWeb performs better than existing related tools: Prospector and Strathcona
Accumulation of the Vitamin D Precursor Cholecalciferol Antagonizes Hedgehog Signaling to Impair Hemogenic Endothelium Formation (2015)

Hematopoietic stem and progenitor cells (HSPCs) are born from hemogenic endothelium in the dorsal aorta. Specification of this hematopoietic niche is regulated by a signaling axis using Hedgehog (Hh) and Notch, which culminates in expression of Runx1 in the ventral wall of the artery. Here, we demonstrate that the vitamin D precursor cholecalciferol (D3) modulates HSPC production by impairing hemogenic vascular niche formation. Accumulation of D3 through exogenous treatment or inhibition of Cyp2r1, the enzyme required for D3 25-hydroxylation, results in Hh pathway antagonism marked by loss of Gli-reporter activation, defects in vascular niche identity, and reduced HSPCs. Mechanistic studies indicated the effect was specific to D3, and not active 1,25-dihydroxy vitamin D3, acting on the extracellular sterol-binding domain of Smoothened. These findings highlight a direct impact of inefficient vitamin D synthesis on cell fate commitment and maturation in Hh-regulated tissues, which may have implications beyond hemogenic endothelium specification.
Free-standing Single Crystal Silicon Nanoribbons (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTFree-standing Single Crystal Silicon NanoribbonsWensheng Shi, Hongying Peng, Ning Wang, Chi Pui Li, Lu Xu, Chun Sing Lee, Rafi Kalish, and Shuit-Tong LeeView Author Information Center Of Super-Diamond and Advanced Films (COSDAF) and the Department of Physics and Materials City University of Hong Kong, Hong Kong SAR, China Cite this: J. Am. Chem. Soc. 2001, 123, 44, 11095–11096Publication Date (Web):October 11, 2001Publication History Received28 May 2001Published online11 October 2001Published inissue 1 November 2001https://pubs.acs.org/doi/10.1021/ja0162966https://doi.org/10.1021/ja0162966rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1316Altmetric-Citations143LEARN 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 SUBJECTS:Crystallization,Oxides,Silicon,Thickness,Two dimensional materials Get e-Alerts
Overexpression of the Endoplasmic Reticulum Chaperone BiP3 Regulates XA21-Mediated Innate Immunity in Rice (2010)

Recognition of pathogen-associated molecular patterns by pattern recognition receptors (PRRs) activates the innate immune response. Although PRR-mediated signaling events are critical to the survival of plants and animals, secretion and localization of PRRs have not yet been clearly elucidated. Here we report the in vivo interaction of the endoplasmic reticulum (ER) chaperone BiP3 with the rice XA21 PRR, which confers resistance to the Gram negative bacterium, Xanthomonas oryzae pv. oryzae (Xoo). We show that XA21 is glycosylated and is primarily localized to the ER and also to the plasma membrane (PM). In BiP3-overexpressing rice plants, XA21-mediated immunity is compromised, XA21 stability is significantly decreased, and XA21 proteolytic cleavage is inhibited. BiP3 overexpression does not affect the general rice defense response, cell death or brassinolide-induced responses. These results indicate that BiP3 regulates XA21 protein stability and processing and that this regulation is critical for resistance to Xoo.
Dual multiresolution HyperSlice for multivariate data visualization (2002)

We present a new multiresolution visualization design which allows a user to control the physical data resolution as well as the logical display resolution of multivariate data. A system prototype is described which uses the HyperSlice representation. The notion of space projection in multivariate data is introduced. This process is coupled with wavelets to form a powerful tool for very large data visualization.
Sclerotherapy with or without Octreotide for Acute Variceal Bleeding (1995)

In patients with cirrhosis, the combination of sclerotherapy and octreotide is more effective than sclerotherapy alone in controlling acute variceal bleeding, but there is no difference between the overall mortality rates associated with the two approaches to treatment.
Thin-film growth dynamics with shadowing and re-emission effects (2011)

Growth dynamics of thin-films involves both shadowing and re-emission effects. Shadowing can originate from obliquely incident atoms being preferentially deposited on hills of the surface, which leads to a long range geometrical effect, as well as from an atomic shadowing process that can occur even during normal angle deposition. Re-emission effect is a result of nonsticking atoms, which can bounce off from hills and deposit on valleys of the surface. In the case of an energetic incident flux, re-emission can also originate from a resputtering process that includes a surface atom being knocked off by an incident ion/atom followed by redeposition to another surface point. Due to their long-range nonlocal nature, both the shadowing effect (which tries to roughen the surface) and re-emission effect (which has a smoothening effect) have been shown to be more dominant over local effects such as surface diffusion, and have been proven to be critical processes in accurately determining the dynamic evolution of surface roughness. Recent Monte Carlo simulation methods that involve shadowing, re-emission, surface diffusion, and noise effects successfully predicted many experimentally relevant surface roughness evolution results reported in the literature. For example, root-mean-square surface roughness (ω) of Monte Carlo simulated thin-films have evolved with time t according to a power law behavior ω ∼ tβ, with β values ranging from about 0 to 1 for a growth with strong re-emission effects (i.e., low sticking coefficients) and a growth with dominant shadowing effects (i.e., with high sticking coefficients), respectively. Potential future thin-film growth modeling studies are also discussed.These include advanced simulation approaches that can incorporate atomistic details of physical and chemical processes and a recently developed network growth model that can potentially capture some universal aspects of thin-film growth dynamics independent of the details of growth process.
Tetrahydrobiopterin therapy of atypical phenylketonuria due to defective dihydrobiopterin biosynthesis. (1978)

A patient with atypical phenylketonuria (defective BH2 synthesis), detected at age 6 months because of severe muscle hypotonia and serum phenylalanine of 20 mg/100 ml, had normal activities of phenylalanine-4-hydroxylase and DHPR in liver biopsy, but only 2% activity in the phenylalanine-4-hyroxylase in vivo test using deuterated phenylalanine. After IV administration of 2.5 mg/kg chemically pure tetrahydrobiopterin bishydrochloride (BH4 . 2HCl), serum phenylalanine decreased from 20.4 to 2.1 mg/100 ml within 3 hours. Administration of 25 mg BH4 . HCl and 100 mg ascorbic acid through a gastric tube decrease; serum phenylalanine from 13.7 to less than 1.6 mg/100 ml within 3 hours and it remained less than 2 mg/100 ml for 2 days.
A HISTORY OF PHOTODYNAMIC THERAPY (1991)

The origins of light as a therapy in medicine and surgery are traced from antiquity to the modern day. Phototherapy began in ancient Greece, Egypt and India but disappeared for many centuries, only being rediscovered by Western civilization at the beginning of the twentieth century through the Dane, Niels Finsen, and the Germans Oscar Raab and Herman von Tappeiner. The discovery of the tumour-localizing ability of haematoporphyrin, together with its phototoxic effect on tumour cells led to the development of photodynamic therapy, a promising tool in modern cancer treatment.
Microfabrication and microcharacterization techniques for laser fusion targets (1980)

A review is presented of some recent accomplishments in the fabrication and characterization of laser fusion targets. These targets are used in a research program at the University of Rochester’s Laboratory for Laser Energetics whose goal is to demonstrate the scientific feasibility of laser fusion. Exploding pusher targets, consisting of deuterium–tritium filled glass microballoons, are discussed. Techniques are described for selecting high quality shells, filling them with D–T fuel by permeation, and characterizing their fuel content by nondestructive beta counting. More advanced targets have been employed in experiments designed to produce higher compressions using the six beam laser system ZETA. These consist of argon filled glass shells coated with plastic. A novel method is described for filling the shells with argon, which involves laser drilling a submicron hole in the balloon wall and sealing the gas with a meltable plug. Three methods are discussed for applying smooth and uniform plastic coatings to these targets. The thermal pyrolysis of di-paraxylene, plasma polymerization of organic monomers (e.g. p-xylene) and colloidal coatings of polyacrylates have all yielded excellent hydrocarbon coatings on glass microballons. Targets for upcoming experiments on the 24 beam laser system OMEGA involve multishell configurations. A new microfabrication molding and replication technique is being implemented to produce spherical and identical hemispherical shells used in the assembly of OMEGA targets. Details of this technique are provided, along with some preliminary examples of plastic and copper hemishells. A versatile physical vapor deposition system is also described which has the capability of coating levitated microballoons with metals and other materials amenable to sputtering. Finally, a unique method of examining opaque targets using contact microradiography is discussed. The x-ray source is generated by the focussed beam of a scanning electron microscope. Readout of the developed radiographic image is also performed in the SEM, using backscattered electrons from the silver grains in the emulsion. Edge resolution of 0.25 μm has been demonstrated in this radiography system. The characterization of localized defects and geometrical defects such as decentrations are possible with superior resolution in this system.
Expression of human apolipoprotein A-I in transgenic mice results in reduced plasma levels of murine apolipoprotein A-I and the appearance of two new high density lipoprotein size subclasses. (1991)

In Western societies high density lipoprotein (HDL) levels correlate inversely with the risk for coronary heart disease. The primary protein component of both human and mouse HDL is apolipoprotein A-I (apoAI), which comprises greater than 70% of HDL protein and 30% of HDL mass. Human HDLs include particles of several distinct size subpopulations, whereas HDLs from inbred C57BL/6 mice contain a single population of particles. To study the regulation of apoAI expression and its role in HDL assembly, we created transgenic C57BL/6 mice containing the human apoAI gene. Two independent lines of transgenic mice with approximately twice the normal plasma levels of total apoAI were studied. The level of mouse apoAI is reduced greater than 4-fold in both transgenic lines, comprising only 4% of total plasma apoAI levels in one transgenic line and 13% in the other. We demonstrate that the mechanism responsible for the decrease in mouse apoAI is posttranscriptional. Parallel to the replacement of mouse with human apoAI, the single HDL species normally present in the plasma of C57BL/6 is replaced by two HDL subclasses similar in size to human HDL2b and HDL3a. The changes in murine apolipoprotein levels and HDL subclass size are inherited by all transgenic offspring of the two founder animals. These results suggest a dominant role of apoAI in determining the HDL particle size distribution and a mechanism involving expression of human apoAI transgenes that alters the plasma levels of mouse apoAI.
Systematic characterization of genome editing in primary T cells reveals proximal genomic insertions and enables machine learning prediction of CRISPR-Cas9 DNA repair outcomes (2018)

Abstract The Streptococcus pyogenes Cas9 (SpCas9) nuclease has become a ubiquitous genome editing tool due to its ability to target almost any location in DNA and create a double-stranded break 1,2 . After DNA cleavage, the break is fixed with endogenous DNA repair machinery, either by non-templated mechanisms (e.g. non-homologous end joining (NHEJ) or microhomology-mediated end joining (MMEJ)), or homology directed repair (HDR) using a complementary template sequence 3,4 . Previous work has shown that the distribution of repair outcomes within a cell population is non-random and dependent on the targeted sequence, and only recent efforts have begun to investigate this further 5–11 . However, no systematic work to date has been validated in primary human cells 5,7 . Here, we report DNA repair outcomes from 1,521 unique genomic locations edited with SpCas9 ribonucleoprotein complexes (RNPs) in primary human CD4+ T cells isolated from multiple healthy blood donors. We used targeted deep sequencing to measure the frequency distribution of repair outcomes for each guide RNA and discovered distinct features that drive individual repair outcomes after SpCas9 cleavage. Predictive features were combined into a new machine learning model, CRI SP R R epair OUT come (SPROUT), that predicts the length and probability of nucleotide insertions and deletions with R 2 greater than 0.5. Surprisingly, we also observed large insertions at more than 90% of targeted loci, albeit at a low frequency. The inserted sequences aligned to diverse regions in the genome, and are enriched for sequences that are physically proximal to the break site due to chromatin interactions. This suggests a new mechanism where sequences from three-dimensionally neighboring regions of the genome can be inserted during DNA repair after Cas9-induced DNA breaks. Together, these findings provide powerful new predictive tools for Cas9-dependent genome editing and reveal new outcomes that can result from genome editing in primary T cells.
Human Infection with the Virus of Vesicular Stomatitis during an Epizootic (1967)

IN the summer of 1965 an epizootic of vesicular stomatitis, primarily in cattle, occurred in northwest New Mexico and southwest Colorado. The disease was confirmed as the Indiana type by serologic examination of affected cattle and by isolation of the virus from vesicular lesions of cattle by Dr. E. Jenney, of the National Animal Disease Laboratory, Ames, Iowa.According to preliminary reports obtained from the Animal Health Division, United States Department of Agriculture, the epizootic began in early July in the contiguous counties of Rio Arriba (New Mexico) and La Plata (Colorado) (Fig. 1). The disease spread in an erratic . . .
Electrochemical Detection for Paper-Based Microfluidics (2009)

We report the first demonstration of electrochemical detection for paper-based microfluidic devices. Photolithography was used to make microfluidic channels on filter paper, and screen-printing technology was used to fabricate electrodes on the paper-based microfluidic devices. Screen-printed electrodes on paper were characterized using cyclic voltammetry to demonstrate the basic electrochemical performance of the system. The utility of our devices was then demonstrated with the determination of glucose, lactate, and uric acid in biological samples using oxidase enzyme (glucose oxidase, lactate oxidase, and uricase, respectively) reactions. Oxidase enzyme reactions produce H2O2 while decomposing their respective substrates, and therefore a single electrode type is needed for detection of multiple species. Selectivity of the working electrode for H2O2 was improved using Prussian Blue as a redox mediator. The determination of glucose, lactate, and uric acid in control serum samples was performed using chronoamperometry at the optimal detection potential for H2O2 (0 V versus the on-chip Ag/AgCl reference electrode). Levels of glucose and lactate in control serum samples measured using the paper devices were 4.9 +/- 0.6 and 1.2 +/- 0.2 mM (level I control sample), and 16.3 +/- 0.7 and 3.2 +/- 0.3 mM (level II control sample), respectively, and were within error of the values measured using traditional tests. This study shows the successful integration of paper-based microfluidics and electrochemical detection as an easy-to-use, inexpensive, and portable alternative for point of care monitoring.
The dopamine D2 receptor locus as a modifying gene in neuropsychiatric disorders (1991)

--The A1 allele of the Taq I polymorphism of the dopamine D2 receptor (DRD2) gene has been earlier reported to occur in 69% of alcoholics, compared with 20% of controls. Other research has reported no significant difference in the prevalence of the A1 allele in alcoholics vs controls and no evidence that the DRD2 gene was linked to alcoholism. We hypothesized that these seemingly conflicting results might be because increases in the prevalence of the A1 allele may not be specific to alcoholism. Thus, we examined other disorders frequently associated with alcoholism or those believed to involve defects in dopaminergic neurotransmission.--Case comparison study. To minimize the effect of racial differences in gene frequencies, the study was restricted to non-Hispanic whites.--Ambulatory and hospitalized patients.--Among all known controls (n = 314), 77 (24.5%) carried the A1 allele. Of the 69 controls known not to be alcoholics, 10 (14.5%) carried the A1 allele. The prevalence of the A1 allele was significantly increased in patients with Tourette's syndrome (44.9%, n = 147), attention deficit hyperactivity disorder (46.2%, n = 104), autism (54.5%, n = 33), alcoholism (42.3%, n = 104), and posttraumatic stress disorder (45.7%, n = 35). After correction for multiple comparisons (requiring P less than .0009 for significance), all remained significant except posttraumatic stress disorder. The prevalence of the A1 allele was not significantly increased in patients with depression, panic attacks, Parkinson's disease, or obesity. The prevalence of the A1 allele in drug addiction and schizophrenia was only significant when compared with that of controls who were not alcoholics, and no correction was made for multiple comparisons.--These results suggest the A1 allele of the DRD2 gene is associated with a number of behavior disorders in which it may act as a modifying gene rather than as the primary etiological agent.
Control of ColE1 DNA replication: the rop gene product negatively affects transcription from the replication primer promoter. (1982)

A 600-base-pair region essential for ColE1 and pMBl plasmid replication contains two promoters responsible for the synthesis of two RNA molecules central to copy number control. One promoter directs synthesis of the primer RNA precursor. The second promoter directs the synthesis of a small RNA molecule, RNAl, which acts in trans to inhibit processing of the RNA primer precursor. We have fused each promoter to the beta-galactosidase structural gene contained in a lambda phage. Expression of the RNAl promoter in lysogens is not influenced by the presence of wild-type pMBl or ColEl plasmids residing in the cell. Transcription from the RNA primer promoter, however, is repressed by the product of a trans-acting plasmid gene product, which we have designated rop (for repressor of primer). The rop gene maps downstream from the replication origin in a region that encodes a polypeptide of 63 amino acids whose sequence is completely conserved in pMBl and ColE1. We propose that this polypeptide is the rop gene product and that it regulates plasmid DNA replication by modulating the initiation of transcription of the primer RNA precursor.
The Function and Mechanism of Promoters of Carcinogenesis (1973)

(1973). The Function and Mechanism of Promoters of Carcinogenesis. CRC Critical Reviews in Toxicology: Vol. 2, No. 4, pp. 419-444.