gebhart/patrepeval huggingface dataset:
Supplementary Protocol SP1 from Novel Paired Normal Prostate and Prostate Cancer Model Cell Systems Derived from African American Patients (2023)

&lt;p&gt;Material and methods of cell culture and CRC protocol&lt;/p&gt;
Mobile-phase solute mass transfer in supercritical fluid chromatography (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMobile-phase solute mass transfer in supercritical fluid chromatographyStephen R. Springston and Milos. NovotnyCite this: Anal. Chem. 1984, 56, 11, 1762–1766Publication Date (Print):August 1, 1984Publication History Published online1 May 2002Published inissue 1 August 1984https://doi.org/10.1021/ac00275a002RIGHTS & PERMISSIONSArticle Views89Altmetric-Citations32LEARN 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 (2 MB) Get e-Alerts Get e-Alerts
Synthesis of Phthalocyanine Fused with Bicyclo[2.2.2]octadienes and Thermal Conversion into Naphthalocyanine (2007)

Mg complex of phthalocyanine fused with bicyclo[2.2.2]octadiene (BCOD) units is prepared by the reaction of BCOD-fused phthalonitrile with Mg(OPr) 2 in PrOH at 100 ºC overnight in 42% yield.Subsequent heating the product at 250 ºC results in clean formation naphthalocyanine via the retro Diels-Alder reaction.An attempt to the synthesis of BCOD-fused tetraazaporphyrin by the similar cyclization of the Diels-Alder adduct of dicyanoacetylene with 1,3-cyclohexadiene was unsuccessful.
Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability (2017)

Genomic instability is a hallmark of human cancer, and results in widespread somatic copy number alterations. We used a genome-scale shRNA viability screen in human cancer cell lines to systematically identify genes that are essential in the context of particular copy-number alterations (copy-number associated gene dependencies). The most enriched class of copy-number associated gene dependencies was CYCLOPS (Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS) genes, and spliceosome components were the most prevalent. One of these, the pre-mRNA splicing factor <i>SF3B1</i>, is also frequently mutated in cancer. We validated <i>SF3B1</i> as a CYCLOPS gene and found that human cancer cells harboring partial <i>SF3B1</i> copy-loss lack a reservoir of SF3b complex that protects cells with normal <i>SF3B1</i> copy number from cell death upon partial <i>SF3B1</i> suppression. These data provide a catalog of copy-number associated gene dependencies and identify partial copy-loss of wild-type <i>SF3B1</i> as a novel, non-driver cancer gene dependency.
Supplementary Methods, Legends from Nuclear–Cytoplasmic Transport Is a Therapeutic Target in Myelofibrosis (2023)

&lt;p&gt;Supplementary Methods, Legends&lt;/p&gt;
Use of a Conformational Radical Clock for Evaluating Alkyllithium-Mediated Cyclization Reactions (2001)

The reductive lithiation of nitrile 9 led to the cyclic product 11 as a single diastereomer in 42% ee. The intermediate radical is a conformational radical clock. The radical lifetime can be determined from the optical purity of the product 11. We show that the lifetime of the intermediate radical is too brief to allow a radical cyclization, and thus the cyclization proceeds through an alkyllithium intermediate.
Conformational Transitions of an Unmodified tRNA:  Implications for RNA Folding (1998)

Unmodified tRNAs are powerful systems to study the effects of posttranscriptional modifications and site-directed mutations on both the structure and function of these ribonucleic acids. To define the general limitations of synthetic constructs as models for native tRNAs, it is necessary to elucidate the conformational states of unmodified tRNAs as a function of solution conditions. Here we report the conformational properties of unmodified yeast tRNAPhe as a function of ionic strength, [Mg2+], and temperature using a combination of spectroscopic measurements along with chemical and enzymatic probes. We find that in low [Na+] buffer at low temperature, native yeast tRNAPhe adopts tertiary structure in the absence of Mg2+. By contrast, tertiary folding of unmodified yeast tRNAPhe has an absolute requirement for Mg2+. Below the melting temperature of the cloverleaf, unmodified yeast tRNAPhe exists in a Mg2+-dependent equilibrium between secondary and tertiary structure. Taken together, our findings suggest that although the tertiary structures of tRNAs are broadly comparable, the intrinsic stability of the tertiary fold, the conformational properties of intermediate states, and the stability of intermediate states can differ significantly between tRNA sequences. Thus, the use of unmodified tRNAs as models for native constructs can have significant limitations. Broad conclusions regarding "tRNA folding" as a whole must be viewed cautiously, particularly in cases where structural changes occur, such as during protein synthesis.
Diagnostic Performance of Magnetic Resonance Elastography for the Staging of Liver Fibrosis: A Systematic Review and Collaborative Individual Participant Data Meta-Analysis (2014)

Introduction: Magnetic resonance elastography (MRE) is a non-invasive tool for staging liver fibrosis. We conducted a collaborative individual participant data (IPD) meta-analysis on the diagnostic accuracy of MRE in patients with chronic liver diseases (CLD). Methods: Through a systematic literature search of bibliographic databases and conference proceedings up to September 2013, we identified studies on diagnostic performance of MRE for staging liver fibrosis in patients with CLD, using liver biopsy as gold standard. We then contacted study authors for IPD on age, sex, body mass index, liver stiffness (using MRE), fibrosis stage, staging system used, degree of inflammation, etiology of CLD, and interval between MRE and biopsy. Through pooled analysis, we calculated the cluster-adjusted area under receiver-operating curve (AUROC), sensitivity and specificity of MRE for any (≥F1), significant (≥F2) and advanced fibrosis (≥F3), and cirrhosis (F4). Results: We included 15 studies reporting on 787 patients (mean age, 55±13y; 60.4% males; mean BMI, 27.1±6.6 kg/m2; interval between MRE and biopsy <1 year, 92.6%; hepatitis C in 42.5%). Fibrosis stage distribution (F0/1/2/3/4) was 19.9%, 20.4%, 17.3%, 15.7%, and 26.7%, respectively. Mean AUROC (and 95% confidence intervals) for diagnosis of any (≥F1), significant (≥F2) or advanced fibrosis (≥F3) and cirrhosis was 0.82 (0.75-0.89), 0.86 (0.81-0.89), 0.93 (0.90-0.95), and 0.93 (0.91-0.94), respectively. Similar diagnostic performance was observed in stratified analysis based on sex (AUROC ≥F3, males vs. females: 0.93 vs. 0.92), obesity (AUROC ≥F3, obese vs. non-obese: 0.92 vs. 0.94), degree of inflammation (AUROC ≥F3, none-mild vs. moderate-severe inflammation: 0.94 vs. 0.90), and etiology of CLD (AUROC ≥F3, HCV: 0.93, HBV: 0.97; NAFLD: 0.94; alcoholic liver disease: 0.93). When we restricted analysis to patients in whom the interval between MRE and liver biopsy was <1 year (to minimize the risk of disease progression bias), MRE continued to have excellent discriminative ability for detection of advanced fibrosis (AUROC, 0.92).Table 1: Pooled Analysis of Diagnostic Performance of MREConclusion: Based on pooled IPD analysis, MRE has high accuracy for diagnosis of significant or advanced fibrosis and cirrhosis, independent of BMI, degree of inflammation, and etiology of CLD. Disclosure - The Mayo Clinic and Dr. Ehman - intellectual property rights and a Financial Conflict of Interest related to technology used in this study. This research has been conducted in compliance with oversight by the Mayo Clinic Conflict of Interest review board.
Topology Formation in Degree-Constrained Directional Antenna Networks (2007)

In a network with sophisticated directional antennas, the antenna pattern can approach an ideal where the beam width and side lobe intensity both approach zero. Assuming transmission power remains constant, the effective range of such an antenna approaches infinity and the probability of co-channel interference approaches zero. In such a network, any two nodes can have a direct link with each other, regardless of the physical distance between them. However, such a system implies both a time-division scheme that constrains the number of links each node may form, and a relatively slow in-band neighbor discovery process. In this paper, we first study a simple scheme that forms a link with every node it discovers until the node is saturated. Under certain node arrival assumptions, this creates network distances (in terms of hops) far higher than a centralized algorithm would optimally produce. A simple heuristic that rejects links if nodes share a certain number of common neighbors produces far shorter paths across the network.
Continuous Left Ventricular Ejection Fraction Monitoring by Central Aortic Pressure Waveform Analysis (2006)

Left ventricular ejection fraction (EF) is perhaps the most clinically significant index of global ventricular function. EF is measured in clinical practice via imaging methods such as echocardiography. However, these methods generally require a well-trained operator and expensive capital equipment. Thus, EF measurements are only obtained in the clinical setting and are usually made few and far between. To expand the measurement of this critical hemodynamic variable, our overarching hypothesis is that EF may be continuously (i.e., automatically) monitored by mathematical analysis of routinely measured blood pressure waveforms. Here, we introduce a novel technique for estimating the absolute EF by model-based analysis of only a central aortic pressure (CAP) waveform. We then demonstrate the validity of the technique with respect to five conscious dogs in which reference EF was independently measured before and after chronic pacing induced heart failure. With further successful testing, the technique may potentially be utilized for continuous EF monitoring in research and clinical settings in which an aortic catheter is employed as well as for ambulatory EF monitoring in conjunction with recently developed implantable devices for measuring CAP.
Innovation technologique – Liliane Bettencourt (2012)

Les grandes tendances de l’innovation biomédicale au xxie siècle Les cours de l’année 2011 du Pr Elias Zerhouni sont la résultante d’une expérience professionnelle qui a été développée dans la leçon inaugurale du 20 janvier 2011. Cette leçon est éditée en ligne (http://lecons-cdf.revues.org/403) et sous forme imprimée (Editions Fayard). Elle est aussi disponible sous forme audiovisuelle sur le site Internet du Collège de France (http://www.college-de-france.fr). L’enseignement a porté sur la ...
Music and computer composition (1972)

The problem discussed is that of simulating human composition of Western popular music by computer and some relevant theories of music and harmony are given. Problems with this kind of program and several schemes that are known not to work are discussed. Several previous computer compositions are discussed, including the ILLIAC Suite. A program to generate short melody fragments was written to simulate some of the aspects of human composition. Five samples of its output are presented and discussed. It was discovered that although the fragments show many of the characteristics of popular melodies, they have a strangely alien sound. It is theorized that this is because the relevant probabilities which would discriminate against unfamiliar sequences were not used.
Nonintrusive performance measurement of a gas turbine engine in real time (2023)

Performance of a gas turbine engine is monitored by computing a mass flow rate through the engine. Acoustic time-of-flight measurements are taken between acoustic transmitters and receivers in the flow path of the engine. The measurements are processed to determine average speeds of sound and gas flow velocities along those lines-of-sound. A volumetric flow rate in the flow path is computed using the gas flow velocities together with a representation of the flow path geometry. A gas density in the flow path is computed using the speeds of sound and a measured static pressure. The mass flow rate is calculated from the gas density and the volumetric flow rate.
Crystal Structure of γ‐Oxapentamidine Complexed with d(CGCGAATTCGCG)2 (1994)

The crystal structure of the complex of gamma-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.
Mechanistic and Preparative Studies of Radical Chain Homolytic Substitution Reactions of N-Heterocyclic Carbene Boranes and Disulfides (2013)

Reactions of 1,3-dimethylimidazol-2-ylidene-borane (diMe-Imd-BH3) and related NHC-boranes with diaryl and diheteroaryl disulfides provide diverse NHC-boryl monosulfides (diMe-Imd-BH2SAr) and NHC-boryl disulfides (diMe-Imd-BH(SAr)2). Heating in the dark with 1 equiv of disulfide favors monosulfide formation, while irradiation with 2 equiv disulfide favors disulfide formation. With heteroaryl disulfides, the NHC-borane in the primary NHC-boryl sulfide product migrates from sulfur to nitrogen to give new products with a thioamide substructure. Most substitution reactions are thought to proceed through radical chains in which homolytic substitution of a disulfide by an NHC-boryl radical is a key step. However, with electrophilic disulfides under dark conditions, a competing ionic path may also be possible.
MagneLayer: Force Field Fabrication by Layered Magnetic Sheets (2020)

Magnets are very useful for the rapid prototyping of haptic interactions. However, it is difficult to arrange fine and complex magnetic fields rapidly. Therefore, we invented a method for fabricating complex geometric magnetic patterns by overlaying multiple magnetic rubber sheets. This method resolves the tradeoff between magnetized pattern complexity and the time required for magnetization. By layering multiple magnetic sheets that have simple magnetic patterns, various types of geometric magnetic patterns, such as checkered and diamond ones, can be generated on the top surface. By applying superposed magnetic fields, various types of tactile stimuli and haptic interaction can be created rapidly. Furthermore, the superposed magnetic fields can be changed dynamically by rotating the layered magnetic sheets. In this paper, we clarify the material requirements and describe the design method for creating these geometric magnetic patterns. We also demonstrate several of their applications.
ChemInform Abstract: Anthranicine, an Unusual Cyclic Hexapeptide from Acremonium sp. A29‐2004. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
<title>Infinitely selective repair buffer for EUVL reticles</title> (2001)

The three-layer absorber stack for EUVL reticles currently consists of an absorber, repair buffer and etch stop layers. The repair buffer should exhibit high etch selectivity during the absorber etch processes (i.e. pattern transfer and focused ion beam (FIB) repair), be thermally and electrically conductive, optimally thin and have high etch selectivity to the silicon-capping layer over the Mo/Si multi-layer mirror. The absorber materials that have been studied in the past are TaSiN and Cr with SiON as the repair buffer on top of a Cr etch stop layer. The SiON repair buffer is insulating, exhibiting low thermal and electrical conductivity. Also, the required thickness for FIB repair is greater than 750 Angstroms using a standard 30-keV Ga<SUP>+</SUP> FIB tool, while the etch selectivity to the silicon capping layer during pattern transfer is less than five to one necessitating a Cr etch stop. A sputtered carbon repair buffer exhibiting the required qualities has been studied. The carbon film is thermally and electrically conductive and exhibits extremely high reactive ion etch selectivity to the silicon-capping layer. Carbon also has the lowest sputter yield out of all the elements opening a larger FIB repair process window without using gas-assisted etching. A conductive repair buffer also prevents the possibility of static charge buildup on the mask that could damage patterns during an electrostatic discharge.
Comparison of Comet Enflow and VA One Acoustic-to-Structure Power Flow Predictions (2010)

Comet Enflow is a commercially available, high frequency vibroacoustic analysis software based on the Energy Finite Element Analysis (EFEA). In this method the same finite element mesh used for structural and acoustic analysis can be employed for the high frequency solutions. Comet Enflow is being validated for a floor-equipped composite cylinder by comparing the EFEA vibroacoustic response predictions with Statistical Energy Analysis (SEA) results from the commercial software program VA One from ESI Group. Early in this program a number of discrepancies became apparent in the Enflow predicted response for the power flow from an acoustic space to a structural subsystem. The power flow anomalies were studied for a simple cubic, a rectangular and a cylindrical structural model connected to an acoustic cavity. The current investigation focuses on three specific discrepancies between the Comet Enflow and the VA One predictions: the Enflow power transmission coefficient relative to the VA One coupling loss factor; the importance of the accuracy of the acoustic modal density formulation used within Enflow; and the recommended use of fast solvers in Comet Enflow. The frequency region of interest for this study covers the one-third octave bands with center frequencies from 16 Hz to 4000 Hz.
Remodeling of the malaria parasite and host human red cell by vesicle amplification that induces artemisinin resistance (2018)

Artemisinin resistance threatens worldwide malaria control and elimination. Elevation of phosphatidylinositol-3-phosphate (PI3P) can induce resistance in blood stages of Plasmodium falciparum The parasite unfolded protein response (UPR) has also been implicated as a proteostatic mechanism that may diminish artemisinin-induced toxic proteopathy. How PI3P acts and its connection to the UPR remain unknown, although both are conferred by mutation in P falciparum Kelch13 (K13), the marker of artemisinin resistance. Here we used cryoimmunoelectron microscopy to show that K13 concentrates at PI3P tubules/vesicles of the parasite's endoplasmic reticulum (ER) in infected red cells. K13 colocalizes and copurifies with the major virulence adhesin PfEMP1. The PfEMP1-K13 proteome is comprehensively enriched in multiple proteostasis systems of protein export, quality control, and folding in the ER and cytoplasm and UPR. Synthetic elevation of PI3P that induces resistance in absence of K13 mutation also yields signatures of proteostasis and clinical resistance. These findings imply a key role for PI3P-vesicle amplification as a mechanism of resistance of infected red cells. As validation, the major resistance mutation K13C580Y quantitatively increased PI3P tubules/vesicles, exporting them throughout the parasite and the red cell. Chemical inhibitors and fluorescence microscopy showed that alterations in PfEMP1 export to the red cell and cytoadherence of infected cells to a host endothelial receptor are features of multiple K13 mutants. Together these data suggest that amplified PI3P vesicles disseminate widespread proteostatic capacity that may neutralize artemisinins toxic proteopathy and implicate a role for the host red cell in artemisinin resistance. The mechanistic insights generated will have an impact on malaria drug development.
Barium Sulfate Scale Removal at Low-Temperature (2021)

Precipitation of the scale in the oil and gas reservoirs, surface and subsurface equipment, and processing and production facilities is a big problem as it affects petroleum production. The scale precipitations decrease the oil and gas production and cause economical loss. Solving this issue requires an engineering investigation to provide a safe, efficient, and economic solution. Consequently, this study proposed a developed dissolver for barium sulfate scales, where two field-scale samples were collected from different locations. The compositional analysis for scale samples showed that sample 1 is 100% barium sulfate where sample 2 has 97.75% barium sulfate and 2.25% of quartz. The composition of the developed dissolver has diethylenetriamine pentaacetic acid (DTPA) as a chelating agent, oxalic acid, and tannic acids as an activator, nonionic surfactant, and water as the base fluid. The new dissolver was investigated with extensive lab tests to determine the dissolution efficiency, precipitation tendency for the dissolved scale solids, corrosion rate, and fluid-rock interaction. The obtained successful results indicated that the developed dissolver had a dissolution efficiency for two real barium scale samples as the results showed 76.9 and 71.2% at 35°C and 91.3 and 78.4% at 90°C for samples 1 and 2, respectively. The new solution has a great performance compared with common scale dissolvers in the oil field as hydrochloric acid, ethylenediaminetetraacetic acid, and diethylenetriamine pentaacetic acid. The developed dissolver showed a very low precipitation tendency for the scale dissolved solids (1.9 and 3.2% for samples 1 and 2, respectively) under 35°C for 24 hours. Without any additives of corrosion inhibitors, the corrosion rate was 0.001835 g/cm2 at 6.9 MPa and 100°C for 6 hours. Injecting the developed dissolver for damaged sandstone core sample with barite mud by flooding test showed a return permeability of 115%.