gebhart/patrepeval huggingface dataset:
Platelet Shape Change Evoked by Selective Activation of P2X1 Purinoceptors with α,β-Methylene ATP (2001)

Simultaneous measurements of [Ca2+]i and light transmission were used to examine the relationship between P2X1 receptor activation and functional platelet responses. The P2X1 agonist alpha,beta-MeATP evoked a transient [Ca2+]i increase and a reversible decrease in light transmission; both responses required external Ca2+ and the nucleotidase apyrase. The transmission response was due to shape change only, verified by scanning electron microscopy and insensitivity to Reopro, a GPIIbIIIa antagonist. Alpha,beta-MeATP stimulated smaller shape changes than ADP, however P2X1 responses had a lifespan of <2 h following resuspension in saline and may be considerably larger in vivo. A peak [Ca2+]i increase of >50 nM was required for detectable shape change. Overlap of concentration-response relationships for alpha,beta-MeATP-evoked [Ca2+]i and shape change suggests that other second messengers are not involved. Therefore, the physiological P2X1 agonist ATP can contribute to platelet activation, in contrast to its previously described inhibitory action at metabotropic platelet purinoceptors.
Probing Brain Reward System Function in Major Depressive Disorder (2002)

The results suggest the presence of a hypersensitive response is present in the brain reward system of depressed patients, which may reflect a hypofunctional state and may provide a novel pathophysiologic and therapeutic target for future studies.
Immunotherapy for neuroblastoma using syngeneic fibroblasts transfected with IL-2 and IL-12 (2007)

Cytokine-modified tumour cells have been used in clinical trials for immunotherapy of neuroblastoma, but primary tumour cells from surgical biopsies are difficult to culture. Autologous fibroblasts, however, are straightforward to manipulate in culture and easy to transfect using nonviral or viral vectors. Here we have compared the antitumour effect of fibroblasts and tumour cells transfected ex vivo to coexpress interleukin-2 (IL-2) and IL-12 in a syngeneic mouse model of neuroblastoma. Coinjection of cytokine-modified fibroblasts with Neuro-2A tumour cells abolished their in vivo tumorigenicity. Treatment of established tumours with three intratumoral doses of transfected fibroblasts showed a significant therapeutic effect with reduced growth or complete eradication of tumours in 90% of mice, associated with extensive leukocyte infiltration. Splenocytes recovered from vaccinated mice showed enhanced IL-2 production following Neuro-2A coculture, and increased cytotoxicity against Neuro-2A targets compared with controls. Furthermore, 100% of the tumour-free mice exhibited immune memory against tumour cells when rechallenged three months later. The potency of transfected fibroblasts was equivalent to that of tumour cells in all experiments. We conclude that syngeneic fibroblasts cotransfected with IL-2 and IL-12 mediate therapeutic effects against established disease, and are capable of generating immunological memory. Furthermore, as they are easier to recover and manipulate than autologous tumour cells, fibroblasts provide an attractive alternative immunotherapeutic strategy for the treatment of neuroblastoma.
SecureML: A System for Scalable Privacy-Preserving Machine Learning (2017)

Machine learning is widely used in practice to produce predictive models for applications such as image processing, speech and text recognition. These models are more accurate when trained on large amount of data collected from different sources. However, the massive data collection raises privacy concerns. In this paper, we present new and efficient protocols for privacy preserving machine learning for linear regression, logistic regression and neural network training using the stochastic gradient descent method. Our protocols fall in the two-server model where data owners distribute their private data among two non-colluding servers who train various models on the joint data using secure two-party computation (2PC). We develop new techniques to support secure arithmetic operations on shared decimal numbers, and propose MPC-friendly alternatives to non-linear functions such as sigmoid and softmax that are superior to prior work. We implement our system in C++. Our experiments validate that our protocols are several orders of magnitude faster than the state of the art implementations for privacy preserving linear and logistic regressions, and scale to millions of data samples with thousands of features. We also implement the first privacy preserving system for training neural networks.
The Use of Oncolytic Vaccinia Viruses in the Treatment of Cancer: A New Role for an Old Ally? (2005)

The use of genetically engineered, tumor-targeting viruses as oncolytic agents has recently emerged as a promising new area for the development of novel cancer therapies. The first viruses to enter the clinic, such as ONYX-015 (an oncolytic adenovirus), provided evidence both for the safety and for the anti-tumor potential of this approach. The results of these early trials have also allowed investigators to examine the limitations of these viruses and to develop potentially far more effective approaches. In this review the development of such next generation viruses, in particular the potential use of strains of vaccinia virus, will be discussed. Vaccinia has an enormous history of use in humans and possesses many of the features felt to be beneficial for the creation of a successful virotherapy agent. It causes no known disease in humans, yet is capable of infecting almost all cell types with a subsequent rapid and lytic infection, which subsequently induces a vigorous local CTL immune response at the site of infection. Vaccinia also displays natural tumor tropism, and several approaches have been used to further limit viral replication to tumor cells and to optimize the immune response induced at the site of the tumor. Finally, the large cloning capacity of vaccinia allows for the addition of multiple foreign genes into the viral genome. This has been exploited to increase the bystander effect of the virus by immune modulation or by expression of pro-drug converting enzymes as well as to incorporate safety controls and reporters for in vivo molecular imaging. Initial clinical trials with these viruses further highlights their potential as the next generation of oncolytic agents and as highly effective future cancer therapies.
Polymorphic CAG repeats in the androgen receptor gene, prostate-specific antigen polymorphism and prostate cancer risk (2002)

As the development of prostate cancer is androgen-dependent, it has been hypothesized that variation in transcriptional activity by the androgen receptor (AR) related to polymorphic CAG repeats in exon 1, influences prostate cancer risk. The AR regulates gene transcription by binding to androgen-response elements (AREs) in target genes, such as the prostate-specific antigen (PSA). In the ARE-I sequence of the PSA gene an adenine to guanine polymorphism is described. It has been hypothesized that the AR binds the two PSA alleles (A and G) with differing affinities and may, thereby, differentially influence prostate cancer risk. To examine the role of the polymorphisms in the AR and PSA genes in prostate cancer susceptibility, we conducted a case-control study of Austrian Caucasians with 190 newly diagnosed prostate cancer patients and 190 age-matched control men with benign prostatic hyperplasia (BPH). The polymorphisms were determined by polymerase chain reaction (PCR)-based methods using DNA from peripheral white blood cells. Logistic regressions were performed to calculate odds ratios (OR) and confidence limits (CL) and to control for possible confounders. Our data provide no evidence for an association between prostate cancer and CAG repeat length. However, we found a significant influence of the ARE-I PSA polymorphism on prostate cancer risk, when calculating the combination of the A/G and G/G genotypes relative to subjects with the A/A genotype (OR = 0.63; 95% CL 0.39-0.99; P = 0.048), suggesting that the G allele has a protective effect. In a case analysis according to Gleason score, the PSA G/G genotype was significantly more frequent in patients with Gleason score >7 (35.1%) than in patients with Gleason score <7 (21.5%), providing evidence that the PSA G/G genotype is associated with more advanced disease at time of diagnosis. However, the ambivalent role of the PSA during prostate carcinogenesis needs further investigation.
[Infection syndrome in acute radiation sickness patients subjected to Chernobyl accident]. (2005)

In spite of intensive antimicrobial prophylaxis and therapy, most patients with acute radiation sickness I-IV severity grade (dose of 0.1-13.7 Gy) developed infections caused by bacteria, fungi and viruses. Frequency and intensity of those infections were proportional to the radiation dose and severity grade of radiation sickness.
Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history (2003)

Duplicated genes are important in the evolution and ecology of plant-defences because herbivore and pathogen attack can be countered via functional diversification at two levels: among duplicated loci and within loci. We explore molecular sequence variation for two members of a defence-related gene family, Arabidopsis thaliana trypsin inhibitors (ATTI), in A. thaliana and a closely related species, A. lyrata subspp. petraea. A worldwide sample of the inbreeding annual A. thaliana had less genetic variation at two ATTI loci (piTOTAL <or= 0.0006) than observed previously at other functional loci. A significant excess of high frequency derived alleles in the signal sequence and 5' UTR of ATTI2 was consistent with a model of positive selection. However, demographic processes such as population subdivision and expansion, both likely to have occurred in A. thaliana during the last 10 000 years, can also give rise to similar deviations from neutrality. A single population of A. lyrata subspp. petraea in Germany had up to an order of magnitude more standing genetic variation at ATTI loci than the species-wide sample of A. thaliana. Although the level of variability for ATTI1 and ATTI2 within this single population was similar to, or even greater than, observed species-wide diversity for other loci in A. lyrata, there was little evidence to reject an equilibrium neutral model. A spatially explicit sample of 87 A. lyrata subspp. petraea individuals detected outbreeding (FIS = -0.16; FIT = -0.15) but little population subdivision (FST = 0.006) in this self-incompatible perennial herb. Genetic differences between Arabidopsis species were consistent with, but not fully explained by, divergence in ecology and life history. Diversification appears to have occurred in different functional domains for the tandemly duplicated ATTI1 and ATTI2 genes; the majority of fixed replacements in ATTI1 surround the enzyme binding site of the mature protein, whereas in ATTI2 most functional evolutionary change is located in the signal peptide. This pattern is consistent with a hypothesis of subfunctionalization in trypsin inhibitory function.
Alpha Fetoprotein is More than a Hepatocellular Cancer Biomarker: From Spontaneous Immune Response in Cancer Patients to the Development of an AFP-Based Cancer Vaccine (2011)

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide, with a poor prognosis and limited therapeutic options. Due to its overexpression in the majority of HCCs, alpha-fetoprotein (AFP) represents one of the most useful markers for hepatocarcinomas and for monitoring patients' response to therapy. Although it was earlier reported that AFP has immunosuppressive properties, it has been recently demonstrated that AFP induces spontaneous T and B cells responses in HCC patients. The characterization of AFP-immunogenic epitopes gives the opportunity to design AFP-based cancer vaccines for human HCC. The activity of AFP-based vaccines has been investigated in HCC mouse models in order to develop novel strategies to treat patients with HCC. This review will discuss the rationale for using the AFP-based vaccination strategy and recent results corroborating the usefulness of AFP vaccines as a potential tool for cancer therapy.
The dielectric properties of biological tissues: III. Parametric models for the dielectric spectrum of tissues (1996)

A parametric model was developed to describe the variation of dielectric properties of tissues as a function of frequency. The experimental spectrum from 10 Hz to 100 GHz was modelled with four dispersion regions. The development of the model was based on recently acquired data, complemented by data surveyed from the literature. The purpose is to enable the prediction of dielectric data that are in line with those contained in the vast body of literature on the subject. The analysis was carried out on a Microsoft Excel spreadsheet. Parameters are given for 17 tissue types.
Enantioselective ring cleavage of meso-epoxides with B-halodiisopinocampheylboranes (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective ring cleavage of meso-epoxides with B-halodiisopinocampheylboranesN. N. Joshi, M. Srebnik, and Herbert C. BrownCite this: J. Am. Chem. Soc. 1988, 110, 18, 6246–6248Publication Date (Print):August 1, 1988Publication History Published online1 May 2002Published inissue 1 August 1988https://pubs.acs.org/doi/10.1021/ja00226a050https://doi.org/10.1021/ja00226a050research-articleACS PublicationsRequest reuse permissionsArticle Views730Altmetric-Citations82LEARN 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
souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes (2019)

Methods to deconvolve single-cell RNA sequencing (scRNAseq) data are necessary for samples containing a natural mixture of genotypes and for scRNAseq experiments that multiplex cells from different donors 1 . Multiplexing across donors is a popular experimental design with many benefits including avoiding batch effects 2 , reducing costs, and improving doublet detection. Using variants detected in the RNAseq reads, it is possible to assign cells to the individuals from which they arose. These variants can also be used to identify and remove cross-genotype doublet cells that may have highly similar transcriptional profiles precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA in the system. Ambient RNA is caused by cell lysis prior to droplet partitioning and is an important confounder of scRNAseq analysis 3 . Souporcell is a novel method to cluster cells using only the genetic variants detected within the scRNAseq reads. We show that it achieves high accuracy on genotype clustering, doublet detection, and ambient RNA estimation as demonstrated across a wide range of challenging scenarios.
Landmark methods for forms without landmarks: localizing group differences in outline shape (1996)

Procrustes superposition and the thin-plate spline each principally developed within the context of discrete landmark data, can be combined in a novel adaptive filter for detecting localized group differences of outline shape.
ChemInform Abstract: Hydrogen Storage in Single‐Walled Carbon Nanotubes at Room Temperature. (2000)

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.
MR thermometry (2008)

Minimally invasive thermal therapy as local treatment of benign and malignant diseases has received increasing interest in recent years. Safety and efficacy of the treatment require accurate temperature measurement throughout the thermal procedure. Noninvasive temperature monitoring is feasible with magnetic resonance (MR) imaging based on temperature-sensitive MR parameters such as the proton resonance frequency (PRF), the diffusion coefficient (D), T1 and T2 relaxation times, magnetization transfer, the proton density, as well as temperature-sensitive contrast agents. In this article the principles of temperature measurements with these methods are reviewed and their usefulness for monitoring in vivo procedures is discussed. Whereas most measurements give a temperature change relative to a baseline condition, temperature-sensitive contrast agents and spectroscopic imaging can provide absolute temperature measurements. The excellent linearity and temperature dependence of the PRF and its near independence of tissue type have made PRF-based phase mapping methods the preferred choice for many in vivo applications. Accelerated MRI imaging techniques for real-time monitoring with the PRF method are discussed. Special attention is paid to acquisition and reconstruction methods for reducing temperature measurement artifacts introduced by tissue motion, which is often unavoidable during in vivo applications.
A Longitudinal Biomarker for the Extent of Skin Disease in Patients With Diffuse Cutaneous Systemic Sclerosis (2015)

Skin gene expression can be used effectively to monitor changes in SSc skin disease over time. We implemented 2 relatively simple models on a NanoString platform permitting highly reproducible assays that can be applied directly to samples from patients or collected as part of clinical trials.
Early Predictors of Postinjury Multiple Organ Failure (1994)

Age greater than 55 years, ISS greater than or equal to 25, and greater than 6 U RBC/12 hours are early independent predictors of MOF. Subgroup analyses indicate that BD and lactate levels may add substantial predictive value. Moreover, these results emphasize the predominant role of the initial insult in the pathogenesis of postinjury MOF.
An All‐Optical, Non‐volatile, Bidirectional, Phase‐Change Meta‐Switch (2013)

Non-volatile, bidirectional, all-optical switching in a phase-change metamaterial delivers high-contrast transmission and reflection modulation at near- to mid-infrared wavelengths in device structures down to ≈1/27 of a wavelength thick.
EDMAS: A locally distributed mail system (1984)

The Eden Project is a five-year effort to design, build and test operating system structures for local area networks. A specific goal is to allow users to obtain the advantages of both physical distribution and logical integration. Since Eden is physically distributed, its users can take advantage of personal workstations. Since Eden is logically integrated, system resources can be named and accessed in a location independent way.Edmas, the Eden mail system, was designed to be an early test of Eden's usefulness. This paper describes the design and implementation of Edmas, and presents several of the lessons we have learned about constructing location independent services and about the design of mail systems.
HLA-B37 and HLA-A2.1 molecules bind largely nonoverlapping sets of peptides. (1990)

T-cell recognition of peptides that are bound and presented by class I major histocompatibility complex molecules is highly specific. At present it is unclear what role class I peptide binding plays relative to T-cell receptor specificity in determination of immune recognition. A previous study from our group demonstrated that the HLA-A2.1 molecule could bind to 25% of the members of a panel of unrelated synthetic peptides as assessed by a functional peptide competition assay. To determine the peptide-binding specificity of another HLA class I molecule, we have examined the capacity of this panel of peptides to compete for the presentation of influenza virus nucleoprotein peptide NP-(335-350) by HLA-B37 to NP-peptide-specific HLA-B37-restricted cytotoxic T-lymphocyte lines. Forty-two percent of peptides tested were capable of inhibiting NP-(335-350) presentation by HLA-B37. Remarkably, none of these HLA-B37-binding peptides belong to the subset that was previously shown to bind to the HLA-A2.1 molecule. Only the NP-(335-350) peptide was capable of binding to both HLA-A2.1 and HLA-B37. These findings demonstrate that the peptide-binding specificities of HLA-B37 and HLA-A2.1 are largely nonoverlapping and suggest that, from the universe of peptides, individual HLA class I molecules can bind to clearly distinct subsets of these peptides.
Metal-Based Turn-On Fluorescent Probes for Sensing Nitric Oxide (2006)

Nitric oxide, a reactive free radical, regulates a variety of biological processes. The absence of tools to detect NO directly, rapidly, specifically, and selectively motivated us to synthesize metal-based fluorescent probes to visualize the presence of NO. We prepared and investigated Co(II), Fe(II), Ru(II), Rh(II), and Cu(II) complexes as turn-on fluorescent NO sensors. Our exploration has provided insight into how the interaction of transition-metal centers with nitric oxide can be utilized for NO sensing.
A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics (2004)

Proteomic analysis of complex protein mixtures using proteolytic digestion and liquid chromatography in combination with tandem mass spectrometry is a standard approach in biological studies. Data-dependent acquisition is used to automatically acquire tandem mass spectra of peptides eluting into the mass spectrometer. In more complicated mixtures, for example, whole cell lysates, data-dependent acquisition incompletely samples among the peptide ions present rather than acquiring tandem mass spectra for all ions available. We analyzed the sampling process and developed a statistical model to accurately predict the level of sampling expected for mixtures of a specific complexity. The model also predicts how many analyses are required for saturated sampling of a complex protein mixture. For a yeast-soluble cell lysate 10 analyses are required to reach a 95% saturation level on protein identifications based on our model. The statistical model also suggests a relationship between the level of sampling observed for a protein and the relative abundance of the protein in the mixture. We demonstrate a linear dynamic range over 2 orders of magnitude by using the number of spectra (spectral sampling) acquired for each protein.