gebhart/patrepeval huggingface dataset:
Estimation of the covariance structure from SNP allele frequencies (2022)

Abstract We propose two new statistics, <m:math xmlns:m="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <m:mrow> <m:mover accent="true"> <m:mrow> <m:mi>V</m:mi> </m:mrow> <m:mo stretchy="false">̂</m:mo> </m:mover> </m:mrow> </m:math> $\hat{V}$ and <m:math xmlns:m="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <m:mrow> <m:mover accent="true"> <m:mrow> <m:mi>S</m:mi> </m:mrow> <m:mo stretchy="false">̂</m:mo> </m:mover> </m:mrow> </m:math> $\hat{S}$ , to disentangle the population history of related populations from SNP frequency data. If the populations are related by a tree, we show by theoretical means as well as by simulation that the new statistics are able to identify the root of a tree correctly, in contrast to standard statistics, such as the observed matrix of F 2 -statistics (distances between pairs of populations). The statistic <m:math xmlns:m="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <m:mrow> <m:mover accent="true"> <m:mrow> <m:mi>V</m:mi> </m:mrow> <m:mo stretchy="false">̂</m:mo> </m:mover> </m:mrow> </m:math> $\hat{V}$ is obtained by averaging over all SNPs (similar to standard statistics). Its expectation is the true covariance matrix of the observed population SNP frequencies, offset by a matrix with identical entries. In contrast, the statistic <m:math xmlns:m="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <m:mrow> <m:mover accent="true"> <m:mrow> <m:mi>S</m:mi> </m:mrow> <m:mo stretchy="false">̂</m:mo> </m:mover> </m:mrow> </m:math> $\hat{S}$ is put in a Bayesian context and is obtained by averaging over pairs of SNPs, such that each SNP is only used once. It thus makes use of the joint distribution of pairs of SNPs. In addition, we provide a number of novel mathematical results about old and new statistics, and their mutual relationship.
A Comparison of Four Methods of Weighting Double Difference Pseudorange Measurements (1995)

Abstract Differential GPS pseudorange measurements can be used to achieve metre level positions suitable for a wide variety of applications. The most significant detrimental factor affecting position estimates determined using pseudorange measurements is signal multipath. Multipath errors are typically a maximum at low satellite elevations, where most physical obstructions are located. Pseudorange measurements can be weighted appropriately in an attempt to minimise the effects of multipath on computed positions. The satellite elevation and signal strength (as defined by the signal to noise ratio) are two factors which can be used either separately or in combination. This paper presents an analysis of four weighting schemes, one based solely on satellite elevation, another solely on signal to noise ratio, a third on a combination of the first two schemes and finally a scheme which applies equal weight to all measurements. The results of a test conducted over a twenty-four hour period indicate that inferior horizontal and three-dimensional position estimates are generated when the fixed variance (equal) weighting scheme is used as opposed to the other three schemes, which all yield comparable results.
The light rail revolution - a safety risk perspective (2016)

Modern light rail (LR) transit networks offer an efficient and reliable mode of public transport, particularly in congested urban conditions where there are frequent interactions between various road users. But how do we ensure the safety of passengers, public and other road users? The safety risks associated with light rail are somewhat less explored and understood, in comparison to the more established transport modes of buses and heavy rail. Quantitative Risk Assessment (QRA) is a common method for evaluating the risk profiles of complex systems, such as public transportation networks. QRA is often applied as a basis for driving business decisions and as part of a risk management framework to satisfy legislative duties in relation to safety issues. This technical paper will gauge public perceptions of risks associated with light rail operations and outline the legal requirements (or guidelines) with regards to undertaking QRA on public transport projects. The common QRA techniques will be explored, with the benefits and corresponding challenges noted, with respect to light rail applications. We will also present case studies on QRA, as applied to light rail projects, to better understand the current risk management practices in the light rail industry.
Development of a Low-Reynolds Number, Nonlinear kappa-epsilon Model for the Reduced Navier-Stokes Equations (1997)

Previous work at NASA LeRC has shown that flow distortions in aircraft engine inlet ducts can be significantly reduced by mounting vortex generators, or small wing sections, on the inside surface of the engine inlet. The placement of the vortex generators is an important factor in obtaining the optimal effect over a wide operating envelope. In this regard, the only alternative to a long and expensive test program which would search out this optimal configuration is a good prediction procedure which could narrow the field of search. Such a procedure has been developed in collaboration with NASA LeRC, and results obtained by NASA personnel indicate that it shows considerable promise for predicting the viscous turbulent flow in engine inlet ducts in the presence of vortex generators. The prediction tool is a computer code which numerically solves the reduced Navier-Stokes equations and so is commonly referred to as RNS3D. Obvious deficiencies in RNS3D have been addressed in previous work. Primarily, it is known that the predictions of the mean velocity field of a turbulent boundary layer flow approaching separation are not in good agreement with data. It was suggested that the use of an algebraic mixing-length turbulence model in RNS3D is at least partly to blame for this. Additionally, the current turbulence model includes an assumption of isotropy which will ultimately fail to capture turbulence-driven secondary flow known to exist in noncircular ducts.
Elite control of HIV infection: implications for vaccines (2006)

Although development of an effective AIDS vaccine to provide sterilizing immunity remains an elusive goal, vaccine protection from disease progression has been achieved in animal models, supporting this approach as a realistic goal for first generation vaccines for humans. The global epidemic would be expected to contract as long as viral load could be durably sustained at levels below 2000 RNA copies/ml, a level at which the probability of transmission and of disease progression are markedly reduced. Such control occurs in a subset of infected persons, but the immune responses in these persons have not been systematically defined. Here we examine HIV-specific cellular and humoral immune function in persons who have achieved such viral control without the need for medications, including those who maintain plasma virus below the level of detection (< 50–75 copies/ml, aviremic controllers, n = 64), persons with persistent low level viremia (75–2000 copies, viremic controllers, n = 60) and persons with chronic uncontrolled infection (n = 30). Results to be presented indicate substantial individual heterogeneity in adaptive immune responses among HIV controllers, and none of the parameters tested predicts the ability to contain virus. These results have important implications for current HIV vaccine development strategies aimed at durable maintenance of low level viremia.
Integration of holographic optical elements with polymer gelatin waveguides on GaAs, LiNbO_3, glass, and aluminum (1989)

We have observed waveguiding in thin films of polymer gelatin on GaAs, LiNbO(3), glass, and aluminum substrates. A graded-index profile can be induced in the gelatin layer and tuned by wet processing. This makes it possible to form waveguides on any smooth surface. Locally sensitizing the gelatin waveguide with ammonium dichromate allows us to integrate single and multiplexed gratings on the same substrate to perform various functions for optical interconnects and signal processing. A waveguide grating coupler that converts free-space TEM(00) laser light to a two-dimensional spherical guided wave with 50 degrees angle of divergence has also been demonstrated. An optical clock distribution network on wafer-scale integrated circuits is feasible with this new technology.
Model for the mechanism of action of coenzyme B12 dependent enzymes. Evidence for .sigma..dbr..pi. rearrangements in cobaloximes (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModel for the mechanism of action of coenzyme B12 dependent enzymes. Evidence for .sigma..dbr..pi. rearrangements in cobaloximesRichard B. Silverman, D. Dolphin, and Bernard M. BabiorCite this: J. Am. Chem. Soc. 1972, 94, 11, 4028–4030Publication Date (Print):May 1, 1972Publication History Published online1 May 2002Published inissue 1 May 1972https://pubs.acs.org/doi/10.1021/ja00766a072https://doi.org/10.1021/ja00766a072research-articleACS PublicationsRequest reuse permissionsArticle Views74Altmetric-Citations33LEARN 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
Does FLT3 mutation impact survival after hematopoietic stem cell transplantation for acute myeloid leukemia? A Center for International Blood and Marrow Transplant Research (CIBMTR) analysis: Impact of FLT3 on OS Post-HCT for AML (2020)

BACKGROUND: Patients with FMS like tyrosine kinase 3 (FLT3)-mutated acute myeloid leukemia (AML) have a poor prognosis and are referred for early allogeneic hematopoietic stem cell transplantation (HCT). METHODS: Data from the Center for International Blood and Marrow Transplant Research (CIBMTR) were used to evaluate 511 adult patients with de novo AML who underwent HCT during 2008 through 2011 to determine whether FLT3 mutations had an impact on HCT outcomes. RESULTS: In total, 158 patients (31%) had FLT3 mutations. Univariate and multivariate analyses revealed an increased risk of relapse at 3 years in the FLT3 mutated group compared with the wild-type (WT) group (38% [95% confidence interval (CI), 30%-45%] vs 28% [95% CI, 24%-33%]; P = .04; relative risk, 1.60 [95% CI, 1.15-2.22]; P = .0048). However, FLT3 mutation status was not significantly associated with nonrelapse mortality, leukemia-free survival, or overall survival. Although more patients in the FLT3 mutated group died from relapsed primary disease compared with those in the WT group (60% vs 46%), the 3-year overall survival rate was comparable for the 2 groups (mutated group: 49%; 95% CI, 40%-57%; WT group: 55%, 95% CI, 50%-60%; P = .20). CONCLUSIONS: The current data indicate that FLT3 mutation status did not adversely impact overall survival after HCT, and about 50% of patients with this mutation who underwent HCT were long-term survivors. Cancer 2016;122:3005-3014. © 2016 American Cancer Society.
ChemInform Abstract: Inhibitors of Human Leukocyte Elastase. Part 3. Inhibition by Tetrahydrobenzisothiazolinylmethyl Aryl Carboxylates. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
A Fully Integrated SAR ADC Using Digital Correction Technique for Triple-Mode Mobile Transceiver (2014)

This paper presents a fully integrated SAR ADC for GSM/WCDMA/LTE triple-mode transceiver (RFIC) with non-binary DAC structure and digital correction techniques. All blocks including input buffer, ADC core, bias, references and ADC logics are implemented in a single chip with a small die area of 0.044 mm /0.066 mm for ADC core and ADC logic. The proposed ADC does not require off-chip decoupling capacitor for reference voltage by employing charge-sharing topology. Reconfigurable structure is used for multi-mode operation by adjusting ADC speed and noise, where SNDR of 67.0 dB in GSM and 58.2 dB in WCDMA/LTE are achieved at the sampling frequencies of 52 MS/s and 80 MS/s, respectively.
Plasma P-selectin is an early marker of thromboembolism in COVID-19 (2021)

Coagulopathy and thromboembolism are known complications of SARS-CoV-2 infection. The mechanisms of COVID-19-associated hematologic complications involve endothelial cell and platelet dysfunction and have been intensively studied. We leveraged a prospectively collected acute COVID-19 biorepository to study the association of plasma levels of a comprehensive list of coagulation proteins with the occurrence of venous thromboembolic events (VTE). We included in our analysis 305 subjects with confirmed SARS-CoV-2 infection who presented to an urban Emergency Department with acute respiratory distress during the first COVID-19 surge in 2020; 13 (4.2%) were subsequently diagnosed with venous thromboembolism during hospitalization. Serial samples were obtained and assays were performed on two highly-multiplexed proteomic platforms. Nine coagulation proteins were differentially expressed in patients with thromboembolic events. P-selectin, a cell adhesion molecule on the surface of activated endothelial cells, displayed the strongest association with the diagnosis of VTE, independent of disease severity (p=0.0025). This supports the importance of endothelial activation in the mechanistic pathway of venous thromboembolism in COVID-19. P-selectin together with D-dimer upon hospital presentation provided better discriminative ability for VTE diagnosis than D-dimer alone.
Minimum mean squared error interference suppression for direct-sequence spread-spectrum code-division multiple-access (2003)

Demodulation of a direct-sequence spread-spectrum (DS/SS) code-division multiple-access (CDMA) signal in the presence of multiple-access interference is considered. The channel output is first passed through a filter matched to the chip waveform and then sampled at the chip rate. Because of the complexity and coefficient noise associated with such an adaptive filter when N is large, simpler structures with fewer adaptive components are proposed. In each case the multiple samples per symbol are combined via a trapped delay line, where the taps are selected to minimize the mean square error. It is shown that the complexity of both of these schemes are comparable, but that the first scheme is somewhat more effective in cancelling interference. Numerical results are presented for specific examples illustrating the efficacy of the proposed methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Virus excretion in the cervicovaginal secretions of pregnant and nonpregnant HIV-infected women. (1993)

In order to estimate the prevalence of viral excretion in cervicovaginal secretions, we made a cross-sectional study of 55 HIV-infected women. The patient population was diverse, including pregnant and nonpregnant women in different disease stages from three centers. Virus replication was found in the cell-free supernatant from 12 of 55 cervicovaginal samples (21.8%) by coculture on the CD4-positive cell line CEM-C113. In addition, cell-associated virus was detected in five of a subgroup of 22 samples testing negatively on cell-free supernatant. The prevalence of HIV in the cell-free supernatant was not related to disease stage, zidovudine therapy, transmission group, or history of sexually transmitted diseases. Excretion of HIV was significantly higher in our population of pregnant women (eight of 21, 38%) compared with an unmatched group of nonpregnant women (four of 34, 11.8%; p = 0.04). These results provide evidence of cell-free virus shedding as well as the presence of cell-associated virus in the genital secretions of HIV-infected women.
Supplemental Figure 1 from Short- and Long-Term Effects of CDK4/6 Inhibition on Early-Stage Breast Cancer (2023)

&lt;p&gt;Canonical effects of CDK4/6 inhibition&lt;/p&gt;
Orientations actuelles en matière de transporteurs d’oxygène in vivo les émulsions de fluorocarbures (1987)

La réalisation d’un transporteur injectable d’oxygène – coordine chimiquement comme avec l’hémoglobine, ou simplement dissous comme dans un fluorocarbure – a pris rang parmi les nouveaux défis de la médecine Les applications potentielles de tels transporteurs concernent en effet de nombreuses situations pathologiques parmi les plus graves et les plus fréquentes, en particulier dans les domaines cardiovasculaire et cérebrovasculaire. Dans le traitement de certains cancers, comme substituts du sang en traumatologie d’urgence, comme agents de contrasto pour le diagnostic, pour la préservation de tissus et transplants, etc Les caractéristiques qui font des fluorocarbures d’excellents vecteurs d’oxygène a usage biomédical sont rappelées Les critères à utiliser pour leur sélection, ainsi que pour celle des autres constituants des émulsions injectables de fluorocarbure, sont définis. Les principales différences qui existent entre ces émulsions et le sang sont détaillées, ainsi que leurs conséquences sur la délivrance de l’oxygène et leurs implications thérapeutiques. Les défauts et insuffisances des premières émulsions utilisées sont analyses, permettant ainsi de désigner les prochains objectifs à atteindre. Les progrès déjà considérables qui ont été réalises par rapport a cette première génération d’émulsions sont passes en revue : fluorocarbures plus purs, plus fiables, meilleure connaissance des relations structures/propriétés en ce qui concerne leur capacité de dissolution d’oxygène et leur vitesse d’excrétion, définition du domaine des masses moléculaires pertinentes, reconnaissance du rôle déterminant des tensioactifs. Développement d’émulsions significativement plus concentrées et plus efficaces, progrès en matière de préparation, caractérisation et évaluation des émulsions. etc. Des progrès restent à faire dans la maîtrise des émulsions. Afin d’augmenter leur stabilité, prolonger leur persistance intravasculaire et permettre une meilleure adaptation de leurs caractéristiques en fonction de l’indication thérapeutique. Ceci dépendra largement de la disponibilité de nouveaux agents tensioactifs et/ou co-tensioactifs plus fluorophiles et plus biocompatibles, dont les caractéristiques souhaitables sont précisées Les principales applications sont revues succinctement.
Purification and characterization of a lectin from the mushroom Hypsizigus marmoreus (2015)

HML (Hypsizigus marmoreus lectin) was isolated from the mushroom Hypsizigus marmoreus using CM cation exchange, bovine submaxillary gland mucin affinity column and TSK-GEL G3000SW gel filtration chromatography. The results of SDS-PAGE, MALDI-TOF MS and gel filtration analysis of HML indicated that the lectin was a dimer with each subunit of 9.5 kDa. The partial amino acid sequences of HML were determined by N-terminal sequencing of peptides obtained by trypsin or Glu-C endopeptidase digest of the lectin. In the hemagglutination inhibition assay, HML did not bind to any mono- or oligo-saccharides tested. Among the glycoproteins examined, asialo-fetuin was the strongest inhibitor.
Boundary-induced trapped state in electro-optic frequency combs (2022)

We show that, when optical energy propagates in the frequency dimension during the generation of electro-optic microcombs, the introduction of a frequency boundary can reflect the energy propagation. Further, we show that two boundaries yield a trapped state in frequency dimension.
Progesterone treatment attenuates brain edema following contusion injury in male and female rats (1992)

To assess the effectiveness of progesterone as a treatment for edema following traumatic brain injury, male and female rats were injected with progesterone or the oil vehicle over a 3-day period following a cortical contusion injury. Oil-treated rats showed significant localized edema as measured by the wet weight/dry weight tissue punch technique. Progesterone-treated rats, both male and female, showed marked attenuation, or in some cases, absence of this post-injury edema. We conclude that progesterone shows promise as a treatment for edema following traumatic brain injury.
Association of blood coagulation factors V and X with phospholipid monolayers (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAssociation of blood coagulation factors V and X with phospholipid monolayersLawrence D. Mayer, Marc Lee Pusey, Mark A. Griep, and Gary L. NelsestuenCite this: Biochemistry 1983, 22, 26, 6226–6232Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/bi00295a029https://doi.org/10.1021/bi00295a029research-articleACS PublicationsRequest reuse permissionsArticle Views29Altmetric-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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Performance tests of a novel electroencephalographic data-acquisition system (2007)

The aim of the this study is to present some performance tests of a novel 256-channel electroencephalographic data-acquisition system. The common mode rejection ratio of the system was measured as 102 dB for signals in the electroencephalography frequency range and 154 dB for de signals. System electrical noise (referred-to-input) is 1.76 mu V (rms) (0.21 mu V/root Hz for 70-Hz bandwidth). The cross-talk rejection was found to be at 58 dB. The dynamic range of the system was found 108 dB. The performance tests and recorded experimental EEG data show that the developed system can be used in conducting source localization experiments.
Spaceborne P-band SAR for BIOMASS mission (2010)

In the frame of the BIOMASS mission promoted by ESA for evaluating and monitoring Earth biomass, the expected performance of a P-band SAR instrument based on very large Direct Radiating Array antenna is addressed, as well as its architecture and the accommodation challenge on a platform.