gebhart/patrepeval huggingface dataset:
Complete NMR Assignment of Succinimide and Its Detection and Quantification in Peptides and Intact Proteins (2017)

Detecting and quantifying post-translational modifications (PTMs) in full-length proteins is a challenge, especially in the case of spontaneously occurring, nonenzymatic PTMs. Such a PTM is the formation of succinimide (Snn) in a protein that occurs spontaneously in prone primary sequences and leads typically to an equilibrium between Snn and its hydrolysis products isoaspartate (isoAsp) and aspartate. In order to detect these modifications in proteins by NMR spectroscopy, chemical shift assignments of reference compounds are required. We used peptide synthesis and 2D NMR spectroscopy to assign all <sup>1</sup>H and <sup>13</sup>C chemical shifts of Snn and isoAsp and found characteristic chemical shift correlations. To provide chemical shift reference data suitable for comparison with data of denatured proteins, we repeated the assignment in 7 M urea (pH 2.3) and in DMSO. Most characteristic of Snn are the two downfield shifted carbonyl chemical shifts, the chemical shift correlations of Cβ-Hβ of Snn and Cα-Hα of the succeeding residue which are clearly distinct from random coil chemical shift correlations. The characteristic 2D NMR fingerprints of Snn were used to detect and quantify this PTM in the model protein lysozyme, the biotherapeutic filgrastim, and the Fc part of immunoglobulin G1. Mass spectrometry (MS) was applied as an additional independent method. The orthogonality of the NMR and MS techniques allows cross-validation, which is especially important to search for subtle PTMs in proteins. Studying PTMs by NMR spectroscopy is a promising method to analyze proteins and peptides from natural sources, recombinant expression, or chemical synthesis.
Exact BER Analysis of NOMA with Arbitrary Number of Users and Modulation Orders (2021)

&lt;div&gt;&lt;div&gt;Non-orthogonal multiple access (NOMA) is a promising candidate for future mobile networks as it enables improved spectral-efficiency, massive connectivity and low latency. This paper derives exact and asymptotic bit error rate (BER) expressions under Rayleigh fading channels for NOMA systems with arbitrary number of users and arbitrary number of receiving antennas and modulation orders, including binary phase-shift keying and rectangular/square quadrature amplitude modulation. Furthermore, the power coefficients' bounds, which ensure users' fairness, and solve the constellation ambiguity problem, are derived for N=2 and 3 users cases with any modulation orders. In addition, this paper determines the optimal power assignment that minimizes the system's average BER. These results provide valuable insight into the system's BER performance and power assignment granularity. For instance, it is shown that the feasible power coefficients range becomes significantly small as the modulation order, or N, increases, where the BER performance degrades due to the increased inter-user interference. Hence, the derived expressions can be crucial for the system scheduler in allowing it to make accurate decisions of selecting appropriate N, modulation orders, and power coefficients to satisfy the users' requirements. The presented expressions are corroborated via Monte Carlo simulations.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;
2-Substituted 1,2-dihydro-3H-dibenz[de,h]isoquinoline-1,3-diones. A new class of antitumor agent (1993)

A new class of antitumor agents, having structural analogy to amonafide, but differing by the addition of a fourth ring in the nucleus, was synthesized conveniently from anthracene. Compounds with a variety of substituents, containing a basic nitrogen atom and located on the imide nitrogen, were prepared. Thirteen of 19 new compounds had greater growth inhibitory potency than amonafide in a panel of cultured murine and human tumor cells using the sulforhodamine B and MTT dye assays. The most active agents were similarly more toxic than amonafide to normal neonatal rat myocytes in vitro, but they had better chemotherapeutic indexes. From these compounds, the one with a 2-(dimethylamino)ethyl side chain (named azonafide) was chosen for further study. It showed high potency against a panel of cultured human colon cancer cells and it was active against ip P388 leukemia and subcutaneous B16 melanoma in mice. Preliminary structure-activity correlations suggest that the basicity of the side-chain nitrogen and the length of side chain are important determinants of antitumor potency in vitro. Steric hindrance and rigidity of the side chains might be other determinants.
Airspace Sectorization Method for Flexible Airspace Management (2018)

A method for airspace sectorization is developed based on initial airspace configuration. The method begins with identifying Traffic Mass (TM) situations in all sectors ahead of time, especially for the sectors that exceeds the defined controller capability to manage (called overloaded sectors) as well as for those that are under-utilized (called under-utilized sectors). Then, for the overloaded sectors, the method implements the removal of excessive Traffic Mass by moving sector boundaries from the sector with low TM to the overloaded sector in conjunction with a diffusion algorithm. Alternatively, for the under-utilized sectors, they can be combined with their neighbors using General-Clustering-Algorithm. The simulation demonstrates that the method not only removes excessive TM but also improves efficiency. More importantly, the designed sectors which follow the candidate boundary strategy reduce controller's cognitive difficulty, this helps to keep controllers in as much clear-headed situation as possible to ensure flight safety.
Impact of Modifiable Risk Factors on Long-Term Outcomes after Coronary Artery Bypass Surgery (2020)

In patients undergoing CABG, diabetes, hyperlipidemia, and smoking, as documented preoperatively, were potentially modifiable risk factors that were independently and cumulatively associated with long-term risk of ACS or coronary revascularization, highlighting the importance of early identification and risk factors control for improving cardiovascular health after CABG.
Protein arginine methyltransferase 7 promotes breast cancer cell invasion through the induction of MMP9 expression (2014)

Recent evidence points to the protein arginine methyltransferase (PRMT) family of enzymes playing critical roles in cancer. PRMT7 has been identified in several gene expression studies to be associated with increased metastasis and decreased survival in breast cancer patients. However, this has not been extensively studied. Here we report that PRMT7 expression is significantly upregulated in both primary breast tumour tissues and in breast cancer lymph node metastases. We have demonstrated that reducing PRMT7 levels in invasive breast cancer cells using RNA interference significantly decreased cell invasion in vitro and metastasis in vivo. Conversely, overexpression of PRMT7 in non-aggressive MCF7 cells enhanced their invasiveness. Furthermore, we show that PRMT7 induces the expression of matrix metalloproteinase 9 (MMP9), a well-known mediator of breast cancer metastasis. Importantly, we significantly rescued invasion of aggressive breast cancer cells depleted of PRMT7 by the exogenous expression of MMP9. Our results demonstrate that upregulation of PRMT7 in breast cancer may have a significant role in promoting cell invasion through the regulation of MMP9. This identifies PRMT7 as a novel and potentially significant biomarker and therapeutic target for breast cancer.
Anatomic Proximity of the Esophagus to the Coronary Sinus: Implication for Catheter Ablation Within the Coronary Sinus (2006)

In 57% of our patients, the esophagus was in direct contact with the CS, and a significantly shorter distance between the esophagus and the CS ostium was noted in these patients. It is important to prevent esophageal damage when applying energy within the CS.
Antitumour activity mediated by CD4+ cytotoxic T lymphocytes against MHC class II‐negative mouse hepatocellular carcinoma induced by dendritic cell vaccine and interleukin‐12 (2005)

When BALA/c mice with BNL hepatocellular carcinoma (HCC) were treated with dendritic cells fused with BNL cells (DC/BNL) and recombinant murine interleukin (IL)-12, tumour development was significantly suppressed, whereas treatment with either DC/BNL or IL-12 alone did not show a tumour-suppressive effect. Antitumour activity induced by DC/BNL + IL-12 was abrogated by depletion of CD4+ T cells, but not by depletion of CD8+ T cells or natural killer cells. Splenic CD4+ T cells and CD8+ T cells from DC/BNL-treated mice showed cytotoxic activity against BNL cells after 3 days of incubation with DC/BNL, although BNL cells do not express major histocompatibility complex (MHC) class II molecules even after treatment with interferon (INF)-gamma. Furthermore, CD4+ T cells killed syngeneic-irrelevant CT26 cells and even allogeneic Hepa1-6 cells. This cytotoxicity was blocked by concanamycin A, but not by an anti-Fas ligand (FasL) monoclonal antibody, indicating that cytotoxic activity was mediated by perforin. Immunofluorescence microscopy demonstrated that abundant CD4+ T cells and MHC class II-positive macrophages, but not CD8(+) T cells, had infiltrated tumour tissue in mice treated with DC/BNL + IL-12. Flow cytometric analysis of tumour-infiltrating cells in mice treated with DC/BNL + IL-12 showed increases in CD4+ T cells and MHC class II+ CD11b+ cells but not in CD8+ T cells or MHC class I+ CD11b+ cells. Our results suggest that, in BNL-bearing mice treated with DC/BNL + IL-12, tumour macrophages activated by INF-gamma produced by IL-12-stimulated T cells might present BNL tumour antigens and activate DC/BNL-primed CD4+ cytotoxic T lymphocytes (CTLs) in a MHC class II-dependent manner, leading to perforin-mediated bystander killing of neighbouring MHC class II-negative tumour cells.
Effects of Targeting Higher vs Lower Arterial Oxygen Saturations on Death or Disability in Extremely Preterm Infants (2013)

ISRCTN Identifier: 62491227; ClinicalTrials.gov Identifier: NCT00637169.
Band-gap measurements of bulk and nanoscale hematite by soft x-ray spectroscopy (2009)

Chemical and photochemical processes at semiconductor surfaces are highly influenced by the size of the band gap, and ability to control the band gap by particle size in nanomaterials is part of their promise. The combination of soft x-ray absorption and emission spectroscopies provides band-gap determination in bulk and nanoscale itinerant electron semiconductors such as CdS and ZnO, but this approach has not been established for materials such as iron oxides that possess band-edge electronic structure dominated by electron correlations. We performed soft x-ray spectroscopy at the oxygen $K$-edge to reveal band-edge electronic structure of bulk and nanoscale hematite. Good agreement is found between the hematite band gap derived from optical spectroscopy and the energy separation of the first inflection points in the x-ray absorption and emission onset regions. By applying this method to two sizes of phase-pure hematite nanoparticles, we find that there is no evidence for size-driven change in the band gap of hematite nanoparticles down to around 8 nm.
Duplication and Divergence of 2 Distinct Pancreatic Ribonuclease Genes in Leaf-Eating African and Asian Colobine Monkeys (2006)

Unique among primates, the colobine monkeys have adapted to a predominantly leaf-eating diet by evolving a foregut that utilizes bacterial fermentation to breakdown and absorb nutrients from such a food source. It has been hypothesized that pancreatic ribonuclease (pRNase) has been recruited to perform a role as a digestive enzyme in foregut fermenters, such as artiodactyl ruminants and the colobines. We present molecular analyses of 23 pRNase gene sequences generated from 8 primate taxa, including 2 African and 2 Asian colobine species. The pRNase gene is single copy in all noncolobine primate species assayed but has duplicated more than once in both the African and Asian colobine monkeys. Phylogenetic reconstructions show that the pRNase-coding and noncoding regions are under different evolutionary constraints, with high levels of concerted evolution among gene duplicates occurring predominantly in the noncoding regions. Our data suggest that 2 functionally distinct pRNases have been selected for in the colobine monkeys, with one group adapting to the role of a digestive enzyme by evolving at an increased rate with loss of positive charge, namely arginine residues. Conclusions relating our data to general hypotheses of evolution following gene duplication are discussed.
An access control language for web services (2002)

This paper presents an approach for formally specifying and enforcing security policies on web service implementations. Networked services in general, and web services in particular, require extensive amounts of code to ensure that clients respect site-integrity constraints. We provide a language by which these constraints can be expressed and enforced automatically, portably and efficiently. Security policies in our system are specified in a language based on temporal logic, and are processed by an enforcement engine to yield site and platform-specific access control code. This code is integrated with a web server and platform-specific libraries to enforce the specified policy on a given web service. Our approach decouples the security policy specification from service implementations, provides a mandatory access control model for web services, and achieves good performance. We show that up to 22% of the code in a traditional web service module is dedicated to security checking functionality, including checks for client sequencing and parameter validation. We show that our prototype language implementation, WebGuard, enables web programmers to significantly reduce the amount of security checking code they need to develop manually. The quality of the code generated by WebGuard from formal policy specifications is competitive with the latency of handcrafted code to within a few percent.
Rapid bioparticle concentration and detection by combining a discharge driven vortex with surface enhanced Raman scattering (2007)

Rapid concentration and detection of bacteria in integrated chips and microfluidic devices is needed for the advancement of lab-on-a-chip devices because current detection methods require high concentrations of bacteria which render them impractical. We present a new chip-scale rapid bacteria concentration technique combined with surface-enhanced Raman scattering (SERS) to enhance the detection of low bacteria count samples. This concentration technique relies on convection by a long-range converging vortex to concentrate the bacteria into a packed mound of 200 mum in diameter within 15 min. Concentration of bioparticle samples as low as 10(4) colony forming units (CFU)ml are presented using batch volumes as large as 150 mul. Mixtures of silver nanoparticles with Saccharomyces cerevisiae, Escherichia coli F-amp, and Bacillus subtilis produce distinct and noticeably different Raman spectra, illustrating that this technique can be used as a detection and identification tool.
Phosphorus-Based Absolutely Quantified Standard Peptides for Quantitative Proteomics (2009)

An innovative method for the production of absolutely quantified peptide standards is described. These are named phosphorus-based absolutely quantified standard (PASTA) peptides. As the first step, synthetic phosphopeptides are calibrated via a hybrid LC-(ICP+ESI)-MS system. Quantification is achieved by ICP-MS detection of 31P, and identification is performed by ESI-MS. Generation of phosphopeptide standard solutions with this system is demonstrated to provide absolute concentrations with an accuracy better than 10%. The concept was extended to the production of peptide standards by subjecting a PASTA phosphopeptide to gentle and complete dephosphorylation to obtain the cognate PASTA peptide. It is demonstrated that both enzymatic hydrolysis by alkaline or antarctic phosphatase or chemical hydrolysis by hydrofluoric acid can be employed for this purpose. Further, the introduction of one or more stable isotope-labeled amino acids (preferably labeled by 13C, 15N) results in the production of a labeled PASTA peptide, which then can be employed as an internal standard for quantitative analysis by LC-ESI-MS. Using a 1:1 mixture of a stable isotope-labeled PASTA peptide/phosphopeptide pair as dual standard, a quantification between active and inactive recombinant MAP kinase p38alpha was performed by a combination of tryptic digestion and nanoLC-MS.
Eudistomins From the New Zealand Ascidian Ritterella sigillinoides (1989)

In addition to the previously reported antiviral and antitumour compounds eudistomin K (la)and eudistomin K sulfoxide (2a), debromoeudistomin K (3a), eudistomin C (4a), eudistomin O (5a) and ß-carboline (5b) have now also been isolated from the New Zealand ascidian Ritterella sigillinoides . The in vitro biological activities of these compounds are compared.
Three-Dimensional Near-Field Microwave Holography Using Reflected and Transmitted Signals (2011)

A new 3-D holographic microwave imaging technique is proposed to reconstruct targets in the near-field range. It is based on the Fourier analysis of the wideband transmission and reflection signals recorded by two antennas scanning together along two rectangular parallel apertures on both sides of the inspected region. The complex scattering parameters of the two antennas are collected at several frequencies and then processed to obtain a representation of the 3-D target in terms of 2-D slice images at all desired range locations. No assumptions are made about the incident field and Green's function, which are derived either by simulation or by measurement. Furthermore, an approach is proposed to reduce the image artifacts along range. To validate the proposed technique, predetermined simulated targets are reconstructed. The effects of random noise, number of sampling frequencies, and dielectric contrast of the targets are also discussed.
ÉTUDE DE L'AJUSTEMENT DE LA CONSOMMATION SPONTANÉE D'ÉNERGIE EN FONCTION DE L'APPORT AZOTÉ CHEZ LE RAT EN CROISSANCE (1963)

Seine-et-
Glaucoma drops control intraocular pressure and protect optic nerves in a rat model of glaucoma. (1998)

Topical glaucoma therapy in this model can prevent IOP elevation and protect optic nerve fibers.
From computational high-throughput screenings to the lab: taking metal–organic frameworks out of the computer (2022)

Metal-organic frameworks (MOFs) are one of the most researched designer materials today, as their high tunability offers scientists a wide space to imagine all kinds of possible structures. Their uniquely flexible customisability spurred the creation of hypothetical datasets and the syntheses of more than 100 000 MOFs officially reported in the Cambridge Structural Database. To scan such large numbers of MOFs, computational high-throughput screenings (HTS) have become the customary method to identify the most promising structure for a given application, and/or to spot useful structure-property relationships. However, despite all these data-mining efforts, only a fraction of HTS studies have identified synthesisable top-performing MOFs that were then further investigated in the lab. In this perspective, we review these specific cases and suggest possible steps to push future HTS more systematically towards synthesisable structures.
Cd1-xZnxS/ZnS core/shell quantum dot ferroelectric liquid crystal composite system: analysis of faster optical response and lower operating voltage (2014)

AbstractCd1−xZnxS/ZnS core/shell-structured quantum dot (QD)-doped ferroelectric liquid crystal (FLC) Felix 17/000 has been investigated in the present study. In the SmC* phase, the effect of QD on the dielectric and electro-optical properties of FLC has been studied as a function of dopant concentration. A substantial change in the different parameters like tilt angle, spontaneous polarisation, response time and relative permittivity has been observed for the composite system. Nearly two times faster response of the composite system with lower operating voltage is one of the promising results of the present study. The faster optical response along with the decreased value of spontaneous polarisation can be utilised in low power consumption liquid crystal displays.Keywords: ferroelectric liquid crystalquantum dotsoptical responseoperating voltage
High-repetition-rate closed-cycle rare gas electrical discharge laser (1976)

The recently developed technology of high-pressure molecular lasers has been combined with ultrahigh-vacuum technology to develop a fast-flow high-pressure laser system capable of long-duration closed-cycle operation with rare gases. The system’s economy, reliability, and capability for long-time operation at a high repetition rate make it suitable for avionics, space, and isotope separation applications. High-repetition-rate laser performance has been demonstrated in He–Xe, Ne–Xe, Ar–Xe, and Kr–Xe. Experimental results for high-pressure He–Xe mixtures are given.
A novel approach to mask defect inspection (2008)

Memory chips, now constituting a major part of semiconductor market, posit a special challenge for inspection, as they are generally produced with the smallest half-pitch available with today's technology. This is true, in particular, to photomasks of advanced memory devices, which are at the forefront of the "low-k<sub>1</sub>" regime. In this paper we present a novel photomask inspection approach, that is particularly suitable for low-k<sub>1</sub> layers of advanced memory chips, owing to their typical dense and periodic structure. The method we present can produce a very strong signal for small mask defects, by suppression of the modulation of the pattern's image. Unlike dark-field detection, however, here a single diffraction order associated with the pattern generates a constant "gray" background image, that is used for signal enhancement. We define the theoretical basis for the new detection technique, and show, both analytically and numerically, that it can easily achieve a detection line past the printability spec, and that in cases it is at least as sensitive as high-resolution based detection. We also demonstrate this claim experimentally on a customer mask, using the platform of Applied Material's newly released Aera2<sup>TM</sup> mask inspection tool. The high sensitivity demonstrates the important and often overlooked concept that resolution is not synonymous with sensitivity. The novel detection method is advantageous in several other aspects, such as the very simple implementation, the high throughput, and the relatively simple pre- and post-processing algorithms required for signal extraction. These features, and in particular the very high sensitivity, make this novel detection method an attractive inspection option for advanced memory devices.
Polymerization of vinyl derivatives of the main group elements (1993)

Abstract A survey of selected novel hybrid organic‐inorganic polymers obtained by polymerization and copolymerzation of main group compounds containing vinyl groups is presented. Examples from groups 13 through 16 are discussed with an emphasis on synthesis and quantitative reactivity studies.
Emergency access to protected health records. (2009)

Digital Rights Management (DRM) schemes are receiving increased attention in the healthcare domain for the protection of sensitive health records as they offer security against insider attacks and advance protection features such as usage control. However, to be accepted by health care providers, a DRM solution has to fulfill specific healthcare requirements including emergency access. In this paper, we propose such DRM solution that can be deployed in highly distributed environments of electronic or personal health record infrastructures.
Characterisation of NAP and CBM, two genes involved in the reproductive development of Arabidopsis thaliana. (2002)

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