gebhart/patrepeval huggingface dataset:
Efficient Delaunay triangulation using rational arithmetic (1991)

Many fundamental tests performed by geometric algorithms can be formulated in terms of finding the sign of a determinant. When these tests are implemented using fixed precision arithmetic such as floating point, they can produce incorrect answers; when they are implemented using arbitrary-precision arithmetic, they are expensive to compute. We present adaptive-precision algorithms for finding the signs of determinants of matrices with integer and rational elements. These algorithms were developed and tested by integrating them into the Guibas-Stolfi Delaunay triangulation algorithm. Through a combination of algorithm design and careful engineering of the implementation, the resulting program can triangulate a set of random rational points in the unit circle only four to five times slower than can a floating-point implementation of the algorithm. The algorithms, engineering process, and software tools developed are described.
From Single Atoms to Nanoparticles: Autocatalysis and Metal Aggregation in Atomic Layer Deposition of Pt on TiO<sub>2</sub> Nanopowder (2018)

A fundamental understanding of the interplay between ligand-removal kinetics and metal aggregation during the formation of platinum nanoparticles (NPs) in atomic layer deposition of Pt on TiO<sub>2</sub> nanopowder using trimethyl(methylcyclo-pentadienyl)platinum(IV) as the precursor and O<sub>2</sub> as the coreactant is presented. The growth follows a pathway from single atoms to NPs as a function of the oxygen exposure (P<sub>O2</sub> × time). The growth kinetics is modeled by accounting for the autocatalytic combustion of the precursor ligands via a variant of the Finke-Watzky two-step model. Even at relatively high oxygen exposures (<120 mbar s) little to no Pt is deposited after the first cycle and most of the Pt is atomically dispersed. Increasing the oxygen exposure above 120 mbar s results in a rapid increase in the Pt loading, which saturates at exposures >> 120 mbar s. The deposition of more Pt leads to the formation of NPs that can be as large as 6 nm. Crucially, high P<sub>O2</sub> (≥5 mbar) hinders metal aggregation, thus leading to narrow particle size distributions. The results show that ALD of Pt NPs is reproducible across small and large surface areas if the precursor ligands are removed at high P<sub>O2</sub> .
A power based memory BIST grouping methodology (2015)

For System-on-Chips (SoCs) one of the most critical design constraints is power consumption. This paper presents memory built-in self-test (BIST) grouping methodology which takes into account the given peak power, power domains based on Unified Power Format (UPF) and optimal test time. The mentioned grouping criteria enable to perform power-aware memory BIST design at early stages of SoC design. To apply this methodology, there is a need for a method to estimate the power consumption from a design description of the circuit at high level of abstraction. We propose a fast power estimation methodology for register-transfer level (RTL) compilers which is based on linear and polynomial approximation. The obtained approximate functions are embedded in a script developed for automated estimation of power consumption. Memory BIST grouping methodology is based on and uses the data of power consumption estimation script as input information.
Efficient transmission of compressed data for remote volume visualization (2006)

One of the goals of telemedicine is to enable remote visualization and browsing of medical volumes. There is a need to employ scalable compression schemes and efficient client-server models to obtain interactivity and an enhanced viewing experience. First, we present a scheme that uses JPEG2000 and JPIP (JPEG2000 Interactive Protocol) to transmit data in a multi-resolution and progressive fashion. The server exploits the spatial locality offered by the wavelet transform and packet indexing information to transmit, in so far as possible, compressed volume data relevant to the clients query. Once the client identifies its volume of interest (VOI), the volume is refined progressively within the VOI from an initial lossy to a final lossless representation. Contextual background information can also be made available having quality fading away from the VOI. Second, we present a prioritization that enables the client to progressively visualize scene content from a compressed file. In our specific example, the client is able to make requests to progressively receive data corresponding to any tissue type. The server is now capable of reordering the same compressed data file on the fly to serve data packets prioritized as per the client's request. Lastly, we describe the effect of compression parameters on compression ratio, decoding times and interactivity. We also present suggestions for optimizing JPEG2000 for remote volume visualization and volume browsing applications. The resulting system is ideally suited for client-server applications with the server maintaining the compressed volume data, to be browsed by a client with a low bandwidth constraint.
The BRCA1-RAP80 Complex Regulates DNA Repair Mechanism Utilization by Restricting End Resection (2011)

The tumor suppressor protein BRCA1 is a constituent of several different protein complexes and is required for homology-directed repair (HDR) of DNA double strand breaks (DSBs). The most recently discovered BRCA1-RAP80 complex is recruited to ubiquitin structures on chromatin surrounding the break. Deficiency of any member of this complex confers hypersensitivity to DNA-damaging agents by undefined mechanisms. In striking contrast to other BRCA1-containing complexes that are known to promote HDR, we demonstrate that the BRCA1-RAP80 complex restricts end resection in S/G(2) phase of the cell cycle, thereby limiting HDR. RAP80 or BRCC36 deficiency resulted in elevated Mre11-CtIP-dependent 5' end resection with a concomitant increase in HDR mechanisms that rely on 3' single-stranded overhangs. We propose a model in which the BRCA1-RAP80 complex limits nuclease accessibility to DSBs, thus preventing excessive end resection and potentially deleterious homology-directed DSB repair mechanisms that can impair genome integrity.
Rat cytochrome P450C24 (CYP24) does not metabolize 1,25‐dihydroxyvitamin D<sub>2</sub> to calcitroic acid (2003)

1alpha-Hydroxy-23 carboxy-24,25,26,27-tetranorvitamin D(3) (calcitroic acid) is known to be the major water-soluble metabolite produced during the deactivation of 1,25-(OH)(2)D(3). This deactivation process is carried out exclusively by the multicatalytic enzyme CYP24 and involves a series of oxidation reactions at C(24) and C(23) leading to side-chain cleavage and, ultimately, formation of the calcitroic acid. Like 1,25-(OH)(2)D(3), 1alpha,25-1,25-(OH)(2)D(2) is also known to undergo side-chain oxidation and side-chain cleavage to form calcitroic acid (Zimmerman et al. [2001]. 1,25-(OH)(2)D(2) differs from 1,25-(OH)(2)D(3) by the presence of a double bond at C(22) and a methyl group at C(24). To date, there have been no studies detailing the participation of CYP24 in the production of calcitroic acid from 1,25-(OH)(2)D(2). We, therefore, studied the metabolism of 1,25-(OH)(2)D(3) and 1,25-(OH)(2)D(2) using a purified rat CYP24 system. Lipid and aqueous-soluble metabolites were prepared for characterization. Aqueous-soluble metabolites were subjected to reverse-phase high-pressure liquid chromatography (HPLC) analysis. As expected, 1,23(OH)(2)-24,25,26,27-tetranor D and calcitroic acid were the major lipid and aqueous-soluble metabolites, respectively, when 1,25-(OH)(2)D(3) was used as substrate. However, when 1,25-(OH)(2)D(2) was used as substrate, 1,24(R),25-(OH)(3)D(2) was the major lipid-soluble metabolite with no evidence for the production of either 1,23(OH)(2)-24,25,26,27-tetranor D or calcitroic acid. Apparently, the CYP24 was able to 24-hydroxylate 1,25-(OH)(2)D(2), but was unable to effect further changes, which would result in side-chain cleavage. These data suggest that the presence of either the double bond at C(22) or the C(24) methyl group impedes the metabolism of 1,25-(OH)(2)D(2) to calcitroic acid by CYP24 and that enzymes other than CYP24 are required to effect this process.
Piezoceramic induced strain actuation of one- and two-dimensional structures (1989)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 1989.
A Simple Access to Biologically Important<i>trans</i>-Stilbenes via Ru-Catalyzed Cross Metathesis (2006)

The cross metathesis of methoxy- or acetoxy-substituted styrenes using the Grubbs II catalyst affords unsymmetrical (mixed) E-stilbenes with astonishingly high selectivity (up to 79% yield). This approach offers a short and flexible synthesis of variously substituted stilbenes, which are derivatives or precursors of biologically important compounds such as resveratrol, piceatannol, and pinostilbene.
Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform (2020)

Abstract Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast IBD estimates robust to genotype and phasing errors. Using haplotype data simulated over pedigrees with realistic genotyping and phasing errors we show that the TPBWT outperforms other state-of-the-art IBD inference algorithms in terms of speed and accuracy. For each phase-aware method, we explore the false positive and false negative rates of inferring IBD by segment length and characterize the types of error commonly found. Our results highlight the fragility of most phased IBD inference methods; the accuracy of IBD estimates can be highly sensitive to the quality of haplotype phasing. Additionally we compare the performance of the TPBWT against a widely used phase-free IBD inference approach that is robust to phasing errors. We introduce both in-sample and out-of-sample TPBWT-based IBD inference algorithms and demonstrate their computational efficiency on massive-scale datasets with millions of samples. Furthermore we describe the binary file format for TPBWT-compressed haplotypes that results in fast and efficient out-of-sample IBD computes against very large cohort panels. Finally, we demonstrate the utility of the TPBWT in a brief empirical analysis exploring geographic patterns of haplotype sharing within Mexico. Hierarchical clustering of IBD shared across regions within Mexico reveals geographically structured haplotype sharing and a strong signal of isolation by distance. Our software implementation of the TPBWT is freely available for non-commercial use in the code repository https://github.com/23andMe/phasedibd .
Electric Grid Integration Costs for Plug-In Electric Vehicles (2014)

<div class="section abstract"><div class="htmlview paragraph">This paper evaluates the hidden costs of Plug-In Electric Vehicle (PEV) integration into the electric grid. The topic of PEV infrastructure is traditionally associated with the direct costs of installing chargers. However, there is also the indirect cost of infrastructure upgrades required upstream of the customer service point (meter). This is a case study of indirect infrastructure costs for PEV integration along with ways to mitigate and manage this cost transferred to customers for the Sacramento Municipal Utility District (SMUD). The costs are estimated using Monte Carlo methods applied to the geospatial and temporal diversity of SMUD's distribution network. An estimate of economic value added by Time of Use (TOU) incentives and Smart Charging for SMUD's service region is also provided.</div></div>
Mutational analysis and properties of the <i>msbA</i> gene of <i>Escherichia coli</i>, coding for an essential ABC family transporter (1996)

The htrB gene was discovered because its insertional inactivation interfered with Escherichia coli growth and viability at temperatures above 32.5 degrees C, as a result of accumulation of phospholipids. The msbA gene was originally discovered because when cloned on a low-copy-number plasmid vector it was able to suppress the temperature-sensitive growth phenotype of an htrB null mutant as well as the accumulation of phospholipids. The msbA gene product belongs to the superfamily of ABC transporters, a universally conserved family of proteins characterized by a highly conserved ATP-binding domain. The msbA gene is essential for bacterial viability at all temperatures. In order to understand the physiological role of the MsbA protein, we mutated the ATP-binding domain using random PCR mutagenesis. Six independent mutants were isolated and characterized. Four of these mutations resulted in single-amino-acid substitutions in non-conserved residues and were able to support cell growth at 30 degrees C but not at 43 degrees C. The remaining two mutations behaved as recessive lethals, and resulted in single-amino-acid substitutions in Walker motif B, one of the two highly conserved regions of the ATP-binding domain. Despite the fact that neither of these two mutant proteins can support E. coli growth, they both retained the ability to bind ATP in vitro. In addition, we present evidence to show that N-acetyl [3H]-glucosamine, a precursor of lipopolysaccharides, accumulates at the non-permissive temperature in the inner membrane of either htrB null or msbA conditional lethal strains. Translocation of the precursor to the outer membrane is restored by transformation with a plasmid containing the wild-type msbA gene. A possible role for MsbA as a translocator of lipopolysaccharides or its precursors is discussed.
The borohydride-catalyzed reaction of diborane with epoxides. The anti-Markovnikov opening of trisubstituted epoxides (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe borohydride-catalyzed reaction of diborane with epoxides. The anti-Markovnikov opening of trisubstituted epoxidesHerbert C. Brown and Nung Min YoonCite this: J. Am. Chem. Soc. 1968, 90, 10, 2686–2688Publication Date (Print):May 1, 1968Publication History Published online1 May 2002Published inissue 1 May 1968https://pubs.acs.org/doi/10.1021/ja01012a039https://doi.org/10.1021/ja01012a039research-articleACS PublicationsRequest reuse permissionsArticle Views868Altmetric-Citations60LEARN 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 Get e-Alerts
G Protein-Coupled Receptors Disrupted in Human Genetic Disease (2008)

Genetic variation in G protein-coupled receptors (GPCRs) results in the disruption of GPCR function in a wide variety of human genetic diseases. In vitro strategies have been used to elucidate the molecular pathologies that underlie naturally occurring GPCR mutations. Various degrees of inactive, overactive, or constitutively active receptors have been identified. These mutations often alter ligand binding, G protein coupling, receptor desensitization, and receptor recycling. The role of inactivating and activating calcium-sensing receptor (CASR) mutations is discussed with respect to familial hypocalciuric hypercalemia (FHH) and autosomal dominant hypocalemia (ADH). Among ADH mutations, those associated with tonic-clonic seizures are discussed. Other receptors discussed include rhodopsin, thyrotropin, parathyroid hormone, melanocortin, follicle-stimulating hormone, luteinizing hormone, gonadotropin-releasing hormone (GnRHR), adrenocorticotropic hormone, vasopressin, endothelin-beta, purinergic, and the G protein associated with asthma (GPRA). Diseases caused by mutations that disrupt GPCR function are significant because they might be selectively targeted by drugs that rescue altered receptors. Examples of drug development based on targeting GPCRs mutated in disease include the calcimimetics used to compensate for some CASR mutations, obesity therapeutics targeting melanocortin receptors, interventions that alter GnRHR loss from the cell surface in idiopathic hypogonadotropic hypogonadism and novel drugs that might rescue the P2RY12 receptor in a rare bleeding disorder. The discovery of GPRA suggests that drug screens against variant GPCRs may identify novel drugs. This review of the variety of GPCRs that are disrupted in monogenic disease provides the basis for examining the significance of common pharmacogenetic variants.
Tunable infrared detector with integrated micromachined Fabry-Perot filter (2008)

We report the design, fabrication, and test results of a tunable pyroelectric detector with an integrated micromachined Fabry-Perot FP filter for gas analysis in the mid-wave infrared MWIR. The new approach is based on a bulk micromachined Fabry-Perot interferometer with an air cavity, which is electrostatically tuned. Various types of movable reflectors and spring configurations are fabricated to determine the optimum solution with respect to maximum tuning range, low gravity influence on center wavelength, and suitable filter bandwidth. Short and long cavity filters are designed for the spectral ranges of 3 to 4.3 m and 3.7 to 5.0 m, respectively. The tunable filter is arranged on top of a current mode pyroelectric detector with a flat spectral response. It is shown that the main challenge is to achieve a high finesse in spite of nonperfect parallelism, mirror curvature, and the additional phase shift caused by the Bragg reflectors.
<i>Staphylococcus aureus</i> HrtA Is an ATPase Required for Protection against Heme Toxicity and Prevention of a Transcriptional Heme Stress Response (2008)

During systemic infection, Staphylococcus aureus acquires nutrient iron from heme, the cofactor of vertebrate myoglobin and hemoglobin. Upon exposure to heme, S. aureus up-regulates the expression of the heme-regulated transporter, HrtAB. Strains lacking hrtAB exhibit increased sensitivity to heme toxicity, and upon heme exposure they elaborate a secreted protein response that interferes with the recruitment of neutrophils to the site of infection. Taken together, these results have led to the suggestion that hrtAB encodes an efflux system responsible for relieving the toxic effects of accumulated heme. Here we extend these observations by demonstrating that HrtA is the ATPase component of the HrtAB transport system. We show that HrtA is an Mn(2+)/Mg(2+)-dependent ATPase that functions at an optimal pH of 7.5 and exhibits in vitro temperature dependence uncommon to ABC transporter ATPases. Furthermore, we identify conserved residues within HrtA that are required for in vitro ATPase activity and are essential for the functionality of HrtA in vivo. Finally, we show that heme induces an alteration in the gene expression pattern of S. aureus Delta hrtA, implying the presence of a novel transcriptional regulatory mechanism responsible for the previously described immunomodulatory characteristics of hrtA mutants exposed to heme.
원보 : 머위 분획물의 In Vitro 라디칼 소거능 및 신경세포의 산화적 스트레스 보호 효과 (2014)

This study was focused on the evaluation of radical scavenging effect and the protective activity against oxidative stress of the extract and fractions from Petasites japonicus. P. japonicus was extracted with methanol and then fractionated into 4 fractions [n-butanol, ethyl acetate (EtOAc), methylene chloride, and n-hexane]. The extract and fractions showed strong 1,1- diphenyl-2-picrylhydrazyl radical scavenging activity. Among all the fractions, particularly, the EtOAc fraction showed the strongest effect with the IC50 value of 0.02 μg/ml. In addition, the fractions also showed strong hydroxyl radical scavenging activity and nitric oxide scavenging activity as well. Furthermore, cell viability generated by the P. japonicus extract and 4 fractions were examined under C6 glial cellular model. The C6 glial cells showed high generation of reactive oxygen species (ROS) and decrease in cell viability by the treatment generator of hydrogen peroxide. However, the production of ROS formation was decreased by the treatment of the fractions of P. japonicus and also founded that the EtOAc fraction led to significant increase in the cell viability at concentration 100 μg/ml. Results from this work indicated that P. japonicus showed protective effects against oxidative stress and its EtOAc fraction may be served as a useful natural antioxidant.
Halo size under distance and near conditions in refractive multifocal intraocular lenses (2001)

Under high contrast conditions halos can be stimulated in all patients with multifocal intraocular lenses. The halo size using the distance or the near focus is identical.
Remote sensing of propane and methane by means of a differential absorption lidar by topographic reflection (1996)

The development of a differential absorption lidar (DIAL) system in the mid-IR region for the detection and monitoring of light hydrocarbons is presented. Two lithium niobate optical parametric oscillators provided the signal and reference wavelengths. With the aid of a retroreflector, the system detected 0.63 ppm of propane and 0.05 ppm of methane in the atmosphere at a greater than 1 mile range in the controlled release tests. Subsequently, the system mapped a petroleum deposit in eastern New Mexico.
Serum Fatty Acid‐Binding Protein 4 is Increased in Patients with Psoriasis (2016)

Psoriasis is associated with metabolic syndrome and cardiovascular disease. Fatty acid-binding proteins (FABP) have been recognized as predictors of these systemic disorders. The aim of this study was to assess correlations between levels of serum heart and adipocyte fatty acid-binding proteins (FABP3, FABP4) and disease severity, indicators of inflammation or metabolic disturbances, and topical treatment in psoriatic patients. Thirty-seven patients with relapse of plaque-type psoriasis and 16 healthy volunteers were recruited. Blood samples were collected before and after 14 days of therapy. Serum FABP concentrations were examined by enzyme-linked immunosorbent assay for correlation with Psoriasis Area and Severity Index (PASI), body mass index (BMI), inflammatory or metabolic parameters, and treatment used. The median FABP4 serum levels were significantly increased (p = 0.038) in psoriatic patients, while FABP3 levels did not differ (p = 0.47) compared to the controls. No significant correlations were noted between the proteins and PASI, C-reactive protein (CRP), BMI, or levels of glucose or lipids. FABP3 significantly correlated with white blood count (p = 0.03) and aspartate aminotransferase (p = 0.04). After topical treatment, there was no significant change in serum FABP3 [11.5 (4.9-30.3) vs. 12.9 (3.5-30.3) ng/ml] (p = 0.96), whereas FABP4 was decreased [27,286 (20,344-32,257) vs. 23,034 (18,320-29,874) pg/ml] (p = 0.12), losing its basal significance. FABP4 may be a marker of psoriasis, and FABP3 may be associated with inflammation or liver disorders in psoriatic patients. FABP do not appear to be useful for determining disease severity or the effectiveness of antipsoriatic treatment.