gebhart/patrepeval huggingface dataset:
Bringing Functional Context to Emerging Proximity-Mapping Proteomics Tools (2022)

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current state-of-the-art and discusses key limitations underlying these emerging approaches, in particular, the limited functional knowledge they provide in understanding local proteomes / interactomes. This limitation is directly linked to the use of non-biologically- or non-pharmaceutically-relevant reactive intermediates in the course of covalently labeling the local proteomes. As such, these methods cannot report on specific functions of localized protein players, nor can they scrutinize whether the specific functions of such proteins/interactomes can be directly manipulated by pharmacologically-relevant small-molecule ligands. The latest data hint that precision localized electrophile delivery concept ushers a means to address this limitation with high spatiotemporal resolution, and ultimately, in relevant live animals.
ChemInform Abstract: Diastereoselective Carbocyclization of 1,6‐Heptadienes Triggered by Rhodium‐Catalyzed Activation of an Olefinic C—H Bond. (2014)

Abstract The first example of a metal‐catalyzed functionalization of an olefinic C—H bond, i.
Serum amyloid alpha 1-2 are not required for systemic inflammation in the 4T1 murine breast cancer model (2022)

Abstract Cancers induce the production of acute phase proteins such as serum amyloid alpha (SAA) in the liver and cause systemic inflammation. Despite the well-known coincidence of acute phase response and systemic inflammation, the direct roles of SAA proteins in systemic inflammation in the cancer context remains incompletely characterized, particularly in vivo. Here, we investigate the in vivo significance of SAA proteins in systemic inflammation in the 4T1 murine breast cancer model. 4T1 cancers elevate the expression of SAA1 and SAA2, the two major murine acute phase proteins in the liver. The elevation of Saa1-2 correlates with the up-regulation of immune cell-related genes including neutrophil markers. To examine this correlation in detail, we generate mice that lack Saa1-2 and investigate immune-cell phenotypes. RNA-seq experiments reveal that deletion of Saa1-2 does not strongly affect 4T1-induced activation of immune cell-related genes in the liver and bone marrow. Flow cytometry experiments demonstrate the dispensable roles of SAA1-2 in cancer-dependent neutrophil infiltration to the liver. This study clarifies the negligible contribution of SAA1-2 proteins in systemic inflammation in the 4T1 breast cancer model.
Miniaturized tunable terahertz antenna based on graphene (2014)

A tunable terahertz nanoantenna based on graphene is presented. The proposed antenna has a characteristic of dynamic frequency reconfiguration, high miniaturization, easy integration, low reflection coefficient, and good omnidirectional radiation pattern. The attractive properties of the graphene antenna has the potential to be used in nanoscale wireless communications and sensing systems. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:1792–1794, 2014
Execution Risk and Arbitrage Opportunities in the Foreign Exchange Markets (2020)

With the high-frequency data of firm quotes in the transaction platform of foreign exchanges, arbitrage profit opportunities-in the forms of a negative bid-ask spread of a currency pair and triangular transactions involving three currency pairs-can be detected to emerge and disappear in the matter of seconds. The frequency and duration of such arbitrage opportunities have declined over time, most likely due to the emergence of algorithmic trading. When a human trader detects such an arbitrage opportunity and places orders for multiple transactions-two in negative spreads and three in triangular arbitrage-there is no guarantee all of those orders are fulfilled in a fraction of one second. Thus, the arbitrageur has to consider execution risk, when he/ she/it detects the emergence of such an opportunity. The novelty of this paper is to show that those arbitrage opportunities were exploitable and executable, before the mid-2000s, even considering the transactions costs and execution risk. After many algorithmic computers were allowed to be connected directly to the EBS transaction platform in the mid-2000s, the frequency of free lunch cases has declined and probabilities of successful executions of all legs for arbitrage declined. We calculate the change in the expected profit of an attempt to execute necessary transactions to reap benefits from arbitrage opportunity.
Pharmacokinetics of Recombinant Murine Interferon-γ and Human Interferon-αA/D(Bgl) Administered in Concert and Their Influence on Natural Killer Cell Function in Mice (1988)

The pharmacokinetics of recombinant murine interferon-gamma (rMuIFN-gamma) administered alone and in combination with recombinant hybrid human interferon-alpha (rHuIFN-alpha A/D-[Bgl]) were studied following intravenous (i.v.) and intramuscular (i.m.) injections into mice. The concomitant influence of these IFNs on splenic natural killer (NK) cell function was also examined. The coinjection of both IFNs did not affect the pharmacokinetics of either after i.v. administration. However, simultaneous injection of both IFNs i.m. does result in statistically significant changes in the serum concentrations of rHuIFN-alpha A/D(Bgl). The clinical benefits of the increased bioavailability of rHuIFN-alpha A/D(Bgl) are not apparent since NK cell enhancement after both IFNs were injected together was the same as that obtained after injection of rHuIFN-alpha A/D(Bgl) alone. NK cell enhancement after both IFNs were injected together was the same as that obtained after injection of rHuIFN-alpha A/D(Bgl) alone. Correspondingly, the coinjection of both IFNs did not affect the pharmacokinetics of either.
Chemical and enzymatic synthesis of glycopeptides (1995)

Progress recently made in the synthesis of biologically relevant N- and O-glycopeptides is illustrated by examples. In this context, developments in the preparation of complex saccharide side chains and in the subsequent coupling to peptide portions is described. Special emphasis is given to the synthesis of Lewis antigen-type structures. Furthermore, modern methods in solid phase peptide syntheses utilizing glycosylated building blocks are presented. Recent advances in glycopeptide syntheses employing enzymatic methods in deprotection steps as well as in peptide/saccharide chain elongation are reported.
Effect of noradrenaline and dopamine on progesterone and estradiol secretion of human granulosa cells (1993)

The aim of this study was to explore the direct action of noradrenaline and dopamine on progesterone and estradiol secretion of human granulosa cells cultured in serum-free medium. Progesterone and estradiol production was measured in the presence and absence of noradrenaline, dopamine or propranolol using radioimmunoassays; statistical analysis was performed by analysis of variance and Newman-Keul's multiple range test. Twenty-six women aged 31 +/- 3 years undergoing in vitro fertilization and embryo transfer for infertility treatment at University Women's Hospital, University of Tübingen, Germany, took part in this study. Noradrenaline significantly inhibited progesterone production by human granulosa cells in a dose-related manner at a concentration of 10(-4)-10(-6) mol/l. Dopamine significantly stimulated estradiol secretion by granulosa cells in an inverse dose-related manner. Both effects were blocked by propranolol. The results suggest that catecholaminergic actions switch over the steroid production of human granulosa cells cultured in serum-free medium from progesterone to estradiol.
Non-equilibrium memories with levitated nanoparticles: experimental verification of the generalised Landauer’s principle (2020)

Optical levitation of nanoscale particles promises a completely new experiment in force sensing and the foundations of quantum physics and thermodynamics. However, most of these experiments have hardly made use of the extraordinary versatility of optical micromanipulation technology. We present a novel optical holographic trapping platform that levitates a nanosphere in vacuum in a fully controllable double-well potential. We show the power and versatility of our platform by demonstrating a generalised version of Landauer’s principle, where a memory is first encoded in an out-of-equilibrium classically-squeezed state. We infer produced work and heat over a large number of repetitions of the protocols, and we observe that the energy cost to erase a memory is greatly reduced and can in principle be made negative. Our results pave the way to fully customizable vacuum optical trapping in arbitrary potentials, and opens up to the study of non-linearities in ground-state cooled particles.
Enhancement of delayed-type hypersensitivity by bestatin, an inhibitor of aminopeptidase B and leucine aminopeptidase. (1976)

We found that aminopeptidase B and leucine aminopeptidase appear on the surface of various mammalian cells and hydrolyse substrates.
Studies on evaluation and utilization of activated carbon. 4. Batch and continuous reactivation of activated carbon with a 100mm.PHI. fluidized bed reactor. (1978)

High temperature reactivation of activated carbons used for treatments of phenolic wastewater efluents was investigated by using a 100mmφ fluidized bed reactor equipped with a screw feeder. Reactivation could be carried out in both batch and continuous systems. Batch reactivation was carried out by using a reactor installed with one perforate plate (that is, one hearth), and continuous reactivation was performed by using a reactor installed with one additional perforate plate (that is, a co-current two-hearth fluidized bed reactor).Specific surface area and methylene blue adsorption capacity of the spent carbon could be regenerated to 90% of the levels of the virgin carbon by simple heat treatment in nitrogen.Improvement of such properties as specific surface area and methylene blue adsorption capacity through reactivation with steam was slightly less in the continuous system than in the batch system due to the apparent decrease in the reactivation yield caused by the burning of the carbon with the coexisting air and the loss of fine particles produced in the screw feeder. However, sufficiently effective regeneration could be achieved in both systems.The decrease in strength of carbon by reactivation and reactivation losses were larger in the presence of air.The carbon obtained with a yield of about 95-96% in either batch system or in continuous system could be used for the treatment of phenolic wastewater effluents.
INTERSTITIAL MICROWAVE THERMAL THERAPY FOR PROSTATE CANCER: METHOD OF TREATMENT AND RESULTS OF A PHASE I/II TRIAL (2001)

Interstitial microwave thermal therapy for prostate cancer was developed to heat the prostate safely to a cytotoxic temperature. Experience with 25 patients in whom external beam radiation therapy for prostate cancer had failed indicates that the treatment is safe. Although our series indicates that this therapy may be effective, further studies and longer followup are required in larger patient groups to confirm the potential role of this therapy as an option for recurrent and primary prostate cancer.
Detection and Prevention of Insider Threats in Database Driven Web Services (2009)

In this paper, we take the first step to address the gap between the security needs in outsourced hosting services and the protection provided in the current practice. We consider both insider and outsider attacks in the third-party web hosting scenarios. We present SafeWS, a modular solution that is inserted between server side scripts and databases in order to prevent and detect website hijacking and unauthorized access to stored data. To achieve the required security, SafeWS utilizes a combination of lightweight cryptographic integrity and encryption tools, software engineering techniques, and security data management principles. We also describe our implementation of SafeWS and its evaluation. The performance analysis of our prototype shows the overhead introduced by security verification is small. SafeWS will allow business owners to significantly reduce the security risks and vulnerabilities of outsourcing their sensitive customer data to third-party providers.
Gallager Bounds for Noncoherent Decoders in Fading Channels (2007)

Recently, Gallager's bounding techniques have been used to derive tight performance bounds for coded systems in fading channels. Most works in this field have thus far dealt with coherent decoding. This paper develops Gallager bounds for noncoherent systems in fading channels. Unlike coherent decoding, the exact error probability of a noncoherent decoder/detector conditioned on the fading coefficients does not admit a closed-form expression. This difficulty is overcome in this paper by employing the Chernoff technique. Although it weakens the bounds to some extent, the Chernoff technique enables the derivations of the limit-before-average (LBA) bound and Gallager bounds in closed form for noncoherent fading channels. Numerical examples show that the proposed bounds are convergent and are tighter than the conventional union bound.
A Short and Versatile Approach for the Synthesis of Pyrrolizidinones (2021)

Abstract Herein we describe a novel 3‐step synthesis of pyrrolizidinone derivatives with good overall yield. This sequence relies on first a [2+2] cycloaddition between a keteniminium salt intermediate, bearing an alkyl chloride side chain, and an alkene partner furnishing the corresponding cyclobutanone after hydrolysis of the resulting cyclobutaniminium. Then ring expansion towards the γ‐lactam using a Beckmann ‐type rearrangement followed by intramolecular S N 2 reaction in the presence of a base triggers the second ring formation of the process. This approach, which is particularly straightforward, allows a broad diversification of pyrrolizidinones by changing the nature of the substituents on the starting alkene and on the keteniminium precursor. Additionally, a computational study was conducted to assess the activation barrier of the S N 2 step on different intermediates as well as the nitrogen pyramidalization of the resulting pyrrolizidinones adducts.
Organocobalt cluster complexes. XI. Carbonium ion derivatives (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganocobalt cluster complexes. XI. Carbonium ion derivativesDietmar. Seyferth, Gary H. Williams, and John E. HallgrenCite this: J. Am. Chem. Soc. 1973, 95, 1, 266–267Publication Date (Print):January 1, 1973Publication History Published online1 May 2002Published inissue 1 January 1973https://pubs.acs.org/doi/10.1021/ja00782a060https://doi.org/10.1021/ja00782a060research-articleACS PublicationsRequest reuse permissionsArticle Views48Altmetric-Citations31LEARN 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
Molecular Screening and Association Analyses of the Interleukin 6 Receptor Gene Variants with Type 2 Diabetes, Diabetic Nephropathy, and Insulin Sensitivity (2005)

IL-6 levels and polymorphisms have been implicated in type 2 diabetes mellitus (T2DM) and insulin resistance. The IL-6 receptor (IL-6R) comprises two subunits, IL-6R and gp130, of which IL-6R confers specificity to IL-6 action and is located in a region of replicated linkage to T2DM on chromosome 1q21. We screened this gene for variation in Northern European Caucasian and African-American ethnic groups. We identified 11 variants with a minor allele frequency over 5%, including two amino acid changes (D358A and V385I) and four variants in the 3' untranslated region. No variant was associated with obesity or measures of insulin sensitivity, but two single nucleotide polymorphisms in the 3' untranslated region showed a trend to an association with T2DM in all Caucasians, and three single nucleotide polymorphisms, including D358A, showed a trend (P < 0.06) to an association with T2DM among the subset of Northern European Caucasians. Variant V385I was unique to African-Americans and was significantly associated with diabetes and diabetic nephropathy (P < 0.05). Among individuals heterozygous for the four variants in the transcribed sequence, one allele was significantly overrepresented, thus suggesting the existence of a regulatory variant controlling mRNA stability or expression. IL-6R is not likely to explain the linkage to diabetes in this region, but our work supports a minor role of variants in T2DM risk and suggests that sequence variants may alter IL-6R mRNA levels and possibly levels of soluble IL-6R.
Detection of K-ras Oncogene Mutations in Bronchoalveolar Lavage Fluid for Lung Cancer Diagnosis (1995)

Detection of these mutations could lead to earlier cancer diagnosis and less need for invasive diagnostic procedures.
Detection and Occurrence of N-Nitrosamines in Archived Biosolids from the Targeted National Sewage Sludge Survey of the U.S. Environmental Protection Agency (2014)

The occurrence of eight carcinogenic N-nitrosamines in biosolids from 74 wastewater treatment plants (WWTPs) in the contiguous United States was investigated. Using liquid chromatography-tandem mass spectrometry, seven nitrosamines [(N-nitrosodimethylamine (NDMA), N-nitrosomethylethylamine, N-nitrosodi-n-propylamine (NDPA), N-nitrosodibutylamine, N-nitrosopyrrolidine, N-nitrosopiperidine (NPIP), and N-nitrosodiphenylamine (NDPhA)] were detected with varying detection frequency (DF) in 88% of the biosolids samples (n = 80), with five of the seven being reported here for the first time in biosolids. While rarely detected (DF 3%), NDMA was the most abundant compound at an average concentration of 504 ± 417 ng/g dry weight of biosolids. The most frequently detected nitrosamine was NDPhA (0.7-147 ng/g) with a DF of 79%, followed by NDPA (7-505 ng/g) and NPIP (51-1185 ng/g) at 21% and 11%, respectively. The DF of nitrosamines in biosolids was positively correlated with their respective n-octanol-water partition coefficients (R(2) = 0.65). The DF and sum of mean concentrations of nitrosamines in biosolids increased with the treatment capacity of WWTPs. Given their frequent occurrence in nationally representative samples and the amount of U.S. biosolids being applied on land as soil amendment, this study warrants more research into the occurrence and fate of nitrosamines in biosolids-amended soils in the context of crop and drinking water safety.
COMPUTER SIMULATIONS WITH EXPLICIT SOLVENT: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects (1998)

This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.
Discovering active motifs in sets of related protein sequences and using them for classification (1994)

We describe a method for discovering active motifs in a set of related protein sequences. The method is an automatic two step process: (1) find candidate motifs in a small sample of the sequences; (2) test whether these motifs are approximately present in all the sequences. To reduce the running time, we develop two optimization heuristics based on statistical estimation and pattern matching techniques. Experimental results obtained by running these algorithms on generated data and functionally related proteins demonstrate the good performance of the presented method compared with visual method of O'Farrell and Leopold. By combining the discovered motifs with an existing fingerprint technique, we develop a protein classifier. When we apply the classifier to the 698 groups of related proteins in the PROSITE catalog, it gives information that is complementary to the BLOCKS protein classifier of Henikoff and Henikoff. Thus, using our classifier in conjunction with theirs, one can obtain high confidence classifications (if BLOCKS and our classifier agree) or suggest a new hypothesis (if the two disagree).
High-Throughput Sequencing of BACHD Mice Reveals Upregulation of Neuroprotective miRNAs at the Pre-Symptomatic Stage of Huntington’s Disease (2021)

Huntington's disease (HD) is a genetic disorder marked by transcriptional alterations that result in neuronal impairment and death. MicroRNAs (miRNAs) are non-coding RNAs involved in post-transcriptional regulation and fine-tuning of gene expression. Several studies identified altered miRNA expression in HD and other neurodegenerative diseases, however their roles in early stages of HD remain elusive. Here, we deep-sequenced miRNAs from the striatum of the HD mouse model, BACHD, at the age of 2 and 8 months, representing the pre-symptomatic and symptomatic stages of the disease. Our results show that 44 and 26 miRNAs were differentially expressed in 2- and 8-month-old BACHD mice, respectively, as compared to wild-type controls. Over-representation analysis suggested that miRNAs up-regulated in 2-month-old mice control the expression of genes crucial for PI3K-Akt and mTOR cell signaling pathways. Conversely, miRNAs regulating genes involved in neuronal disorders were down-regulated in 2-month-old BACHD mice. Interestingly, primary striatal neurons treated with anti-miRs targeting two up-regulated miRNAs, miR-449c-5p and miR-146b-5p, showed higher levels of cell death. Therefore, our results suggest that the miRNAs altered in 2-month-old BACHD mice regulate genes involved in the promotion of cell survival. Notably, over-representation suggested that targets of differentially expressed miRNAs at the age of 8 months were not significantly enriched for the same pathways. Together, our data shed light on the role of miRNAs in the initial stages of HD, suggesting a neuroprotective role as an attempt to maintain or reestablish cellular homeostasis.