gebhart/patrepeval huggingface dataset:
Estimating Common Parameters of Lognormally Distributed Environmental and Biomonitoring Data: Harmonizing Disparate Statistics from Publications (2014)

The progression of science is driven by the accumulation of knowledge and builds upon published work of others. Another important feature is to place current results into the context of previous observations. The published literature, however, often does not provide sufficient direct information for the reader to interpret the results beyond the scope of that particular article. Authors tend to provide only summary statistics in various forms, such as means and standard deviations, median and range, quartiles, 95% confidence intervals, and so on, rather than providing measurement data. Second, essentially all environmental and biomonitoring measurements have an underlying lognormal distribution, so certain published statistical characterizations may be inappropriate for comparisons. The aim of this study was to review and develop direct conversions of different descriptions of data into a standard format comprised of the geometric mean (GM) and the geometric standard deviation (GSD) and then demonstrate how, under the assumption of lognormal distribution, these parameters are used to answer questions of confidence intervals, exceedance levels, and statistical differences among distributions. A wide variety of real-world measurement data sets was reviewed, and it was demonstrated that these data sets are indeed of lognormal character, thus making them amenable to these methods. Potential errors incurred from making retrospective estimates from disparate summary statistics are described. In addition to providing tools to interpret "other people's data," this review should also be seen as a cautionary tale for publishing one's own data to make it as useful as possible for other researchers.
Localized Rac Activation Dynamics Visualized in Living Cells (2000)

Signaling proteins are thought to be tightly regulated spatially and temporally in order to generate specific and localized effects. For Rac and other small guanosine triphosphatases, binding to guanosine triphosphate leads to interaction with downstream targets and regulates subcellular localization. A method called FLAIR (fluorescence activation indicator for Rho proteins) was developed to quantify the spatio-temporal dynamics of the Rac1 nucleotide state in living cells. FLAIR revealed precise spatial control of growth factor-induced Rac activation, in membrane ruffles and in a gradient of activation at the leading edge of motile cells. FLAIR exemplifies a generally applicable approach for examining spatio-temporal control of protein activity.
TeSR: A robust Temporal Self-Referencing approach for Hardware Trojan detection (2011)

Malicious modification of integrated circuits, referred to as Hardware Trojans, in untrusted fabrication facility has emerged as a major security threat. Logic testing approaches are not very effective for detecting large sequential Trojans which require multiple state transitions often triggered by rare circuit events in order to activate and cause malfunction. On the other hand, side-channel analysis has emerged as an effective approach for detection of such large sequential Trojans. However, existing side-channel approaches suffer from large reduction in detection sensitivity with increasing process variations or decreasing Trojan size. In this paper, we propose TeSR, a Temporal Self-Referencing approach that compares the current signature of a chip at two different time windows to completely eliminate the effect of process noise, thus providing high detection sensitivity for Trojans of varying size. Furthermore, unlike existing approaches, it does not require golden chip instances as a reference. Simulation results for three complex designs and three representative sequential Trojan circuits demonstrate the effectiveness of the approach under large inter- and intra-die process variations.
Exons 45–55 Skipping Using Mutation-Tailored Cocktails of Antisense Morpholinos in the DMD Gene (2019)

Mutations in the dystrophin (DMD) gene and consequent loss of dystrophin cause Duchenne muscular dystrophy (DMD). A promising therapy for DMD, single-exon skipping using antisense phosphorodiamidate morpholino oligomers (PMOs), currently confronts major issues in that an antisense drug induces the production of functionally undefined dystrophin and may not be similarly efficacious among patients with different mutations. Accordingly, the applicability of this approach is limited to out-of-frame mutations. Here, using an exon-skipping efficiency predictive tool, we designed three different PMO cocktail sets for exons 45-55 skipping aiming to produce a dystrophin variant with preserved functionality as seen in milder or asymptomatic individuals with an in-frame exons 45-55 deletion. Of them, the most effective set was composed of select PMOs that each efficiently skips an assigned exon in cell-based screening. These combinational PMOs fitted to different deletions of immortalized DMD patient muscle cells significantly induced exons 45-55 skipping with removing 3, 8, or 10 exons and dystrophin restoration as represented by western blotting. In vivo skipping of the maximum 11 human DMD exons was confirmed in humanized mice. The finding indicates that our PMO set can be used to create mutation-tailored cocktails for exons 45-55 skipping and treat over 65% of DMD patients carrying out-of-frame or in-frame deletions.
A 1.8-GHz low-phase-noise spiral-LC CMOS VCO (2002)

A completely integrated 1.8-GHz low-phase-noise voltage-controlled oscillator is presented. The design relies heavily on the integrated spiral inductors, which are constructed with only two metal layers and without etching. The effects of eddy currents and losses in the heavily doped substrate have been simulated and modeled with finite-element analyses. The achieved phase noise is as low as -116 dBc/Hz at 600 kHz offset, at a power consumption of only 6 mW. The VCO's tuning range is 250 MHz.
EFFECT OF FATTY ACIDS ON THE VENTRICULAR ARRHYTHMIA THRESHOLD IN THE ISOLATED HEART OF THE RABBIT (1981)

1 The ventricular arrhythmia threshold (VAT) was measured in the isolated Ringer-perfused rabbit heart (Langendorff preparation) by applying a single 10 ms square-wave pulse of current to the left ventricle during the vulnerable period of the late systole under normoxic and hypoxic conditions. 2 The sodium salt of the fatty acid was bound to albumen and incorporated in the Krebs-Henseleit solution which was maintained at 37 degrees C and gassed with 95% O2 and 5% CO2 (normoxia) or 5% CO2 in air (hypoxia). 3 Saturated fatty acids failed to alter the VAT under normoxia. 4 Naturally occurring long-chained saturated and mono-unsaturated fatty acids with chain lengths varying from 14 to 20 carbons, but not the 12 carbon lauric acid, potentiated the effect of the hypoxia in lowering the VAT. 5 Short-chained 8 and 10 carbon saturated and long-chained polyunsaturated fatty acids antagonized the effect of hypoxia on the VAT. 6 In addition the polyunsaturated acids antagonized the potentiating effect of the long-chained saturated and mono-unsaturated acids on the hypoxia in lowering the VAT. 7 The fatty acids did not alter the duration or type of the induced arrhythmia.
A multiray model for calculating electron pencil beam distribution (1988)

Based on the Fermi-Eyges theory, a set of recursion relations was derived for calculating electron distributions in the layered geometry. The electron distribution at a specific depth was obtained by convolving the upstream electron distribution with a kernel determined by the scattering parameters of the layer. Modifications were made to overcome some inherent limitations of the Fermi-Eyges theory. For each point in the medium, the most probable, or mean, path traversed by the electrons in reaching the point was derived. The skewness of the mean paths and the related energy degradation were included in a multiray model for pencil beam calculations. The resultant electron planar fluence distributions are no longer Gaussian as predicted by the original theory. The effects of edges or localized inhomogeneities are also included. Comparisons between our calculations and Monte Carlo simulations show good agreement.
Electron Paramagnetic Resonance Studies of the Electronic Structures of Bis(maleonitriledithiolato)copper(II), -nickel(III), -cobalt(II), and -rhodium(II) Complexes (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectron Paramagnetic Resonance Studies of the Electronic Structures of Bis(maleonitriledithiolato)copper(II), -nickel(III), -cobalt(II), and -rhodium(II) ComplexesA. H. Maki, N. Edelstein, A. Davison, and R. H. HolmCite this: J. Am. Chem. Soc. 1964, 86, 21, 4580–4587Publication Date (Print):November 1, 1964Publication History Published online1 May 2002Published inissue 1 November 1964https://pubs.acs.org/doi/10.1021/ja01075a013https://doi.org/10.1021/ja01075a013research-articleACS PublicationsRequest reuse permissionsArticle Views1261Altmetric-Citations272LEARN 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
Physical Unclonable Functions and Applications: A Tutorial (2014)

This paper describes the use of physical unclonable functions (PUFs) in low-cost authentication and key generation applications. First, it motivates the use of PUFs versus conventional secure nonvolatile memories and defines the two primary PUF types: “strong PUFs” and “weak PUFs.” It describes strong PUF implementations and their use for low-cost authentication. After this description, the paper covers both attacks and protocols to address errors. Next, the paper covers weak PUF implementations and their use in key generation applications. It covers error-correction schemes such as pattern matching and index-based coding. Finally, this paper reviews several emerging concepts in PUF technologies such as public model PUFs and new PUF implementation technologies.
Shedding Light on the Use of Heat to Treat HIV Infections (1993)

Considering the lack of effectiveness of current therapies to treat HIV disease, the authors present observations that provide a strong cogent argument for critically designed and meticulously performed clinical trials employing whole body hyperthermia with or without other therapeutic modalities. Only as a result of such clinical trials will it be possible to fairly evaluate the role of hyperthermia as a potential therapy for treatment of chronic HIV infection.
Hydroboration. XXXVI. Direct route to 9-borabicyclo[3.3.1]nonane via the cyclic hydroboration of 1,5-cyclooctadiene. 9-Borabicyclo[3.3.1]nonane as a uniquely selective reagent for the hydroboration of olefins (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroboration. XXXVI. Direct route to 9-borabicyclo[3.3.1]nonane via the cyclic hydroboration of 1,5-cyclooctadiene. 9-Borabicyclo[3.3.1]nonane as a uniquely selective reagent for the hydroboration of olefinsHerbert C. Brown, Evord F. Knights, and Charles G. ScoutenCite this: J. Am. Chem. Soc. 1974, 96, 25, 7765–7770Publication Date (Print):December 1, 1974Publication History Published online1 May 2002Published inissue 1 December 1974https://pubs.acs.org/doi/10.1021/ja00832a025https://doi.org/10.1021/ja00832a025research-articleACS PublicationsRequest reuse permissionsArticle Views2809Altmetric-Citations173LEARN 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
Epiligrin, a component of epithelial basement membranes, is an adhesive ligand for alpha 3 beta 1 positive T lymphocytes. (1993)

The cutaneous T cell lymphomas (CTCL), typified by mycosis fungoides, and several chronic T cell mediated dermatoses are characterized by the migration of T lymphocytes into the epidermis (epidermotropism). Alternatively, other types of cutaneous inflammation (malignant cutaneous B cell lymphoma, CBCL, or lymphocytoma cutis, non-malignant T or B cell type) do not show evidence of epidermotropism. This suggests that certain T lymphocyte subpopulations are able to interact with and penetrate the epidermal basement membrane. We show here that T lymphocytes derived from patients with CTCL (HUT 78 or HUT 102 cells), adhere to the detergent-insoluble extracellular matrix prepared from cultured basal keratinocytes (HFK ECM). HUT cell adhesion to HFK ECM was inhibitable with monoclonal antibodies (mAbs) directed to the alpha 3 (P1B5) or beta 1 (P4C10) integrin receptors, and could be up-regulated by an activating anti-beta 1 mAb (P4G11). An inhibitory mAb, P3H9-2, raised against keratinocytes identified epiligrin as the ligand for alpha 3 beta 1 positive T cells in HFK ECM. Interestingly, two lymphocyte populations could be clearly distinguished relative to expression of alpha 3 beta 1 by flow cytometry analysis. Lymphokine activated killer cells, alloreactive cytotoxic T cells and T cells derived from patients with CTCL expressed high levels of alpha 3 beta 1 (alpha 3 beta 1high). Non-adherent peripheral blood mononuclear cells, acute T or B lymphocytic leukemias, or non-cutaneous T or B lymphocyte cell lines expressed low levels of alpha 3 beta 1 (alpha 3 beta 1low). Resting PBL or alpha 3 beta 1low T or B cell lines did not adhere to HFK ECM or purified epiligrin. However, adhesion to epiligrin could be up-regulated by mAbs which activate the beta 1 subunit indicating that alpha 3 beta 1 activity is a function of expression and affinity. In skin derived from patients with graft-vs.-host (GVH) disease, experimentally induced delayed hypersensitivity reactions, and CTCL, the infiltrating T cells could be stained with mAbs to alpha 3 or beta 1 and were localized in close proximity to the epiligrin-containing basement membrane. Infiltrating lymphocytes in malignant cutaneous B disease (CBCL) did not express alpha 3 beta 1 by immunohistochemical techniques and did not associate with the epidermal basement membrane. The present findings clearly define a function for alpha 3 beta 1 in T cells and strongly suggest that alpha 3 beta 1 interaction with epiligrin may be involved in the pathogenesis of cutaneous inflammation.
Epidemiology of Major Depressive Disorder (2005)

This large survey suggests a higher prevalence of MDD in the US population than large-sample estimates from the 1980s and 1990s. The shift in highest lifetime risk from young to middle-aged adults is an important transformation in the distribution of MDD in the United States and specificity in risk for an age-period cohort. Associations between MDD and Axis I and II disorders were strong and significant, with variation within broad categories by specific diagnoses signaling the need for attention to the genetic and environmental reasons for such variation, as well as the implications for treatment response.
Nisin, a peptide antibiotic: cloning and sequencing of the nisA gene and posttranslational processing of its peptide product (1989)

Nisin produced by Streptococcus lactis is used as a food preservative and is the most important member of a group of antibiotics containing lanthionine bridges. To understand the genetic basis of these so-called lantibiotics (Schnell et al., Nature 333:276-278, 1988), we characterized the nisin structural gene, nisA, which is located on a plasmid and codes for a 57-amino-acid prepeptide. The prepeptide is processed posttranslationally to the pentacyclic antibiotic. Although nisin and the recently elucidated lantibiotic epidermin from Staphylococcus epidermidis are produced by different organisms, their gene organization is identical. As with epidermin, the nisin propeptide corresponds to the C-terminus of the prepeptide. The N-terminus of the prepeptide is cleaved at a characteristic splice site (Pro--2 Arg--1 Ile-+1). Remarkably, the N-terminus of prenisin shares 70% similarity with preepidermin, although the propeptide sequences are distinctly different. The structural similarities between these two lantibiotics are consistent with the fact that there is a common mechanism of biosynthesis of these lanthionine-containing antibiotics.
Polyfunctional responses by human T cells result from sequential release of cytokines (2011)

The release of cytokines by T cells defines a significant part of their functional activity in vivo, and their ability to produce multiple cytokines has been associated with beneficial immune responses. To date, time-integrated end-point measurements have obscured whether these polyfunctional states arise from the simultaneous or successive release of cytokines. Here, we used serial, time-dependent, single-cell analysis of primary human T cells to resolve the temporal dynamics of cytokine secretion from individual cells after activation ex vivo. We show that multifunctional, Th1-skewed cytokine responses (IFN-γ, IL-2, TNFα) are initiated asynchronously, but the ensuing dynamic trajectories of these responses evolve programmatically in a sequential manner. That is, cells predominantly release one of these cytokines at a time rather than maintain active secretion of multiple cytokines simultaneously. Furthermore, these dynamic trajectories are strongly associated with the various states of cell differentiation suggesting that transient programmatic activities of many individual T cells contribute to sustained, population-level responses. The trajectories of responses by single cells may also provide unique, time-dependent signatures for immune monitoring that are less compromised by the timing and duration of integrated measures.
Training the elderly on the ability factors of spatial orientation and inductive reasoning. (1986)

We examined the effects of cognitive training with elderly participants from the Seattle Longitudinal Study. Subjects were classified as having remained stable or having declined over the previous 14-year interval on each of two primary abilities, spatial orientation and inductive reasoning. Subjects who had declined on one of these abilities received training on that ability; subjects who had declined on both abilities or who had remained stable on both were randomly assigned to the spatial orientation or inductive reasoning training programs. Training outcomes were examined within an ability-measurement framework with empirically determined factorial structure. Significant training effects, at the level of the latent ability constructs, occurred for both spatial orientation and inductive reasoning. These effects were general, in that no significant interactions with decline status or gender were found. Thus, training interventions were effective both in remediating cognitive decline on the target abilities and in improving the performance of stable subjects.
Oxidative inactivation of plasmin and other serine proteases by copper and ascorbate (1993)

Fibrin thrombi form at sites of injury, where leukocytes release a variety of oxidants. To determine whether oxidants might affect proteins of the fibrinolytic system, we examined the effects of various oxidants on plasmin. Plasmin was not inhibited by micromolar concentrations of hypochlorous acid, chloramine T, or H2O2. Neither Fe nor Cu affected plasmin alone or in the presence of H2O2. However, incubation of plasmin with 5 mumol/L Cu(I or II) in the presence of the reducing agent ascorbic acid resulted in a loss of its hydrolytic activity towards proteins as well as towards small synthetic substrates. The addition of EDTA, but not mannitol, prevented its inactivation. Inactivation was prevented by the addition of catalase and accelerated by hydrogen peroxide. Preincubation of plasmin with the competitive inhibitor alpha-N-acetyl-L-lysine methyl ester prevented inactivation by Cu(II) and ascorbate. These results together suggest site-specific oxidation of plasmin's active site. Treatment of the plasminogen activators tissue plasminogen activator and two-chain urokinase-type plasminogen activator, as well as trypsin, neutrophil elastase, and thrombin with Cu(II) and ascorbate resulted in a loss of their amidolytic and proteolytic activity, indicating the general susceptibility of serine proteases to this type of oxidation. Oxidation of the zymogens Glu-plasminogen and single-chain urokinase-type plasminogen activator by Cu(II) and ascorbate resulted in the failure of these molecules to generate active enzymes when treated with plasminogen activators or plasmin, respectively. The active site His residue may be the target of oxidative inactivation, as evidenced by the partial protection afforded plasmin by the addition of Zn(II), histidine, or the platinum derivative, platinum(II) (2,2′:6′,2″- terpyridine) chloride. Because platelets contain micromolar concentrations of Cu and leukocytes are rich in ascorbate, Cu-dependent site-specific oxidation might play a role in modulating proteolytic events and the life span of thrombi formed at sites of tissue injury.