gebhart/patrepeval huggingface dataset:
N-Glycosylation of Recombinant Pharmaceutical Glycoproteins Produced in Transgenic Plants Towards an Humanisation of Plant N-Glycans (2000)

The number of therapeutic proteins successfully produced in plants is steadily increasing and is expected to grow even more rapidly in the future. Most therapeutic proteins are glycoproteins and N-glycosylation is often essential for their stability, folding and biological activity. Recombinant glycoproteins of mammalian origin expressed in transgenic plants largely retain their biological activity. However, plants are not ideal for production of pharmaceutical proteins because they produce molecules with glycans that are not compatible with therapeutic applications in humans. As a consequence, strategies to humanise plant N-glycans are now developed. Some of these strategies involve the retention of the recombinant glycoprotein in the endoplasmic reticulum while others are related to the inhibition of endogenous Golgi glycosyltransferases or addition of "new" glycosyltransferases. Data on both the N-glycosylation of therapeutic glycoproteins produced in transgenic plants and current strategies to humanise their N-glycosylation will be discussed in this review.
Compact optical pulse train generator (1992)

A device that is capable of creating a series of equally spaced,i denticalp ulses from a inglep ulse is presented. It is useful for studying the time development of transient phenomena.
Homologous recombination repair pathway alterations and their relationship to homologous recombination deficiency in advanced pancreatic cancer patients. (2022)

609 Background: Homologous recombination repair (HRR) is critical for limiting DNA damage arising from double strand breaks. Disrupting HRR has emerged as a therapeutic strategy in pancreatic cancer given the development of PARP inhibitors that can specifically target tumors with homologous recombination deficiency (HRD). While HRD is strongly associated with loss-of-function mutations in BRCA1/2, a broad range of pathogenic alterations have been identified in other HRR genes. Identification of pathogenic alterations that predict response to PARP inhibition remains a critical knowledge gap in the field. Methods: We retrospectively analyzed de-identified records from 895 patients with advanced pancreatic cancer that underwent next generation sequencing (NGS) with the Tempus|xT assay (DNA-seq of 648 genes at 500x coverage, matched normal, full transcriptome RNA-seq). HRD-positivity and genome-wide loss of heterozygosity (LOH) were compared across groups, which were defined based on alterations to BRCA1/2 or other HRR pathway genes. Results: We identified 293/895 (33%) pancreatic cancer patients to be HRD-positive. Among HRD positive patients, 23/895 (2.6%) tumors harbored two alterations in BRCA1/2 (BRCA++), 179/895 (20%) harbored a single alteration in BRCA1/2 (BRCA+), 25/895 (2.8%) harbored two alterations in at least one other non-BRCA HRR gene (other HRR++), 367/895 (41%) harbored a single alteration in one other HRR gene (other HRR+), and 143/895 (16%) had pathogenic alterations in neither BRCA1/2 nor other HRR genes. In terms of HRD status, 23/23 (100%) of BRCA++ cases, 179/337 (53%) of BRCA+ cases, 4/25 (16%) of other HRR++ cases, and 87/367 (24%) of other HRR+ cases were HRD-positive. We observed no cases that were HRD-positive without an alteration in either BRCA1/2 or other HRR gene. Within the other HRR+ group, we found that single alterations in CHEK1/2, FANCA/L, MRE11, PALB2, and RAD51B were all significantly associated with HRD-positivity whereas CDK12, for instance, was not (Table). Conclusions: Comprehensive genomic profiling demonstrates that approximately 1 in 4 patients without BRCA alterations may potentially benefit from PARP inhibition due to alterations in other HRR genes. Future studies may examine the role of PARP inhibition in this population of HRR+ pancreatic cancer patients.[Table: see text]
Performance comparison between six-port and five-port reflectometer (2003)

This paper presents a feasibility study for replacing six-port reflectometers by five-port reflectometers for vector measurements in microwave frequency bands. A new calibration technique is proposed for calibrating the five-port reflectometer. This procedure requires only a short circuit as a standard. The comparison of the practical results obtained by the five-port system with those measured by six-port reflectometers proves its efficiency.
Bioavailability of Nickel in Single‐Wall Carbon Nanotubes (2007)

The biomolecular mechanism of nickel carcinogenicity is driven by intracellular Ni cation. The role of nickel catalyst in single-wall carbon nanotube toxicity will therefore depend on its bioavailability, which is highly uncertain due to encapsulation by carbon shells. This article measures the material-specific Ni release into extra- and intracellular physiological fluid phases and suggests practical techniques for managing the metals contribution to SWNT toxicity. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c2696_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Evaluating Wagner Oxidation Criteria for Protective Al2O3 Scale Formation in Ni-Based Superalloys (2023)

The online version contains supplementary material available at 10.1007/s11085-023-10163-5.
On the Mechanism of Thiamine Action. IV.1 Evidence from Studies on Model Systems (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn the Mechanism of Thiamine Action. IV.1 Evidence from Studies on Model SystemsRonald BreslowCite this: J. Am. Chem. Soc. 1958, 80, 14, 3719–3726Publication Date (Print):July 1, 1958Publication History Published online1 May 2002Published inissue 1 July 1958https://pubs.acs.org/doi/10.1021/ja01547a064https://doi.org/10.1021/ja01547a064research-articleACS PublicationsRequest reuse permissionsArticle Views10010Altmetric-Citations1488LEARN 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
[Significance of simultaneous fusion and surgical decompression in lumbar spinal stenosis]. (1993)

In a prospective study 45 patients with clinically relevant spinal stenosis of the lumbar spine were randomized in three groups. Group 1 underwent isolated decompression without fusion, group 2 had decompression and selected fusion, and group 3 underwent fusion of all decompressed segments. Patients with previous surgery of the lumbar spine or obvious instability, such as spondylolisthesis, were excluded from the study. The results were dominated by the relevant clinical improvement in the symptoms of spinal stenosis in all three groups. There were no statistical significant differences in the clinical results between the patients with and without fusion. We conclude that in the absence of obvious segmental instability, no fusion is required for decompressive surgery in degenerative lumbar spinal stenosis.
Role of photoproducts in the cytotoxic action of selenomerocyanine-mediated photodynamic therapy (2005)

Many Type II photosensitizers are substrates of the singlet oxygen they generate. They are, therefore, converted to photoproducts when exposed to light in the presence of oxygen. While most photoproducts appear to be biologically inert, one of the photoproducts generated by selenomerocyanine photosensitizers is a form of elemental selenium that is surprisingly toxic to tumor cells if allowed to form conjugates with serum albumin or lipoproteins. Albumin and lipoproteins act as delivery vehicles for the cytotoxic entity, exploiting the fact that many tumor cells have an increased capacity to bind and internalize albumin and/or lipoproteins. The cytotoxic mechanism of Se(0)-protein conjugates is not yet fully understood but is obviously quite different from the singlet oxygen-mediated mechanism of merocyanine-mediated photodynamic therapy (PDT). Whereas merocyanine-PDT is directed against the plasma membrane, is more effective at 4 °C than at room temperature, and is inhibited by excess albumin and lipoproteins, selenomerocyanine-derived cytotoxic photoproducts act on intracellular targets, are ineffective at low temperatures, and require albumin or lipoproteins as carrier molecules. The discovery of cytotoxic Se(0)-protein conjugates provides a rare example of photoproducts contributing substantially to the cytotoxic effect of PDT and challenges the widely held notion that elemental selenium is biologically inert.
Symptoms, Signs, and Functional Disability in Adult Spondylolisthesis (2000)

Study Design. A cross-sectional clinical study. Objectives. To determine whether there are specific symptoms, signs, and functional disability associated with adult spondylolisthesis. Summary of Background Data. In spite of the common occurrence of adult spondylolisthesis, the symptoms, signs, and disability associated with it have not been analyzed in a large, well-defined group of patients. Methods. The symptoms, signs, and disability of 111 consecutive patients with adult spondylolisthesis, before randomized treatment with fusion or physiotherapy, were compared with those of 39 patients with nonspecific low back pain before lumbar fusion. The patients completed a questionnaire covering clinical history and symptoms and submitted a pain drawing. The signs were documented. Functional disability and pain were quantified by 12-function and 2-pain visual analog scales, respectively. Results. Sixty-two percent of the patients reported low back pain as well as sciatica, 7% sciatica only, and 31% low back pain only. Specific signs were infrequent. A positive straight leg raising test result in 12% and an L5 sensory disturbance in 13% were the most common. The symptoms were similar in patients with spondylolisthesis and chronic low back pain, but the chronic low back pain group reported more functional disability. Patients with a nonorganic pain drawing (widespread, nonspecific pain) were more often blue collar workers; were more often and longer on sick leave; and reported reduced mental condition, sexual function, functional ability, and more pain than patients with an organic pain drawing (localized, specific pain). Conclusions. The clinical pattern and functional disability in adult spondylolisthesis and in low back pain of nonspecific origin are similar. Sciatica in adult spondylolisthesis is typically not associated with a positive straight leg raising test result.
Dornase alfa in early cystic fibrosis lung disease (2002)

Leukocytes that infiltrate cystic fibrosis (CF) sputum as a result of infection have long been known to liberate large amounts of DNA, which increases sputum viscosity and promotes the cycle of chronic lung infection and inflammation that ultimately leads to respiratory failure and death. It was only recently recognized that this vicious cycle begins in infancy, and that architectural damage to CF lungs is detectable even in children with normal pulmonary function tests. Dornase alfa cleaves DNA and improves sputum viscosity in CF. Although its efficacy in reducing the risk of acute infectious exacerbations and improving pulmonary function has been recognized for a decade, there is growing interest in its potential for long-term benefit in young patients with mild lung function abnormalities. The Pulmozyme Early Intervention Trial (PEIT) study demonstrated that dornase alfa reduces the risk of pulmonary exacerbations requiring i.v. antibiotic treatment by 34% and improves forced expiratory flow at 25-75% of forced vital capacity (FEF(25-75)), mid-expiratory flow at 50% of forced vital capacity (MEF), and forced expired volume in 1 sec (FEV(1)) over a 2-year period in CF patients with almost normal lung function. A post hoc subgroup analysis suggests that the magnitude of pulmonary function test (PFT) changes may vary, depending on the initial degree of lung function impairment, but that the reduction in exacerbations appears to be a consistent benefit. These results support the current view that CF patients benefit from intervention early in the course of their lung disease.
A Model for Programming Data-Intensive Applications on FPGAs: A Genomics Case Study (2012)

Genomics computing is indispensable in basic medical research as well as in practical applications such as disease prevention, pharmaceutical development, and criminal forensics. DNA sequencing, assembly and analysis are key components of genomics computing. Coupled with the increased use of computation for both synthesis and analysis of data in genomics is the astounding increase in the rate at which next-generation sequencing platforms are producing genomic data. Keeping up with the combination of increasing levels of algorithmic demands and an exponential increase in data represents a huge computational challenge that requires a corresponding revolution in how we process the data. Field Programmable Gate Arrays (FPGAs) are particularly well suited to the type of highly parallel, bit-level computations found in genomics algorithms. Unfortunately, the use of FPGA platforms among genomics researchers has been limited by the specialized hardware design expertise currently required to use these platforms. Another limiting factor has been a proliferation of FPGA platform architectures, each generally requiring a re-implementation of the algorithm. This paper describes a new programming model called Elan and an associated compiler that we are developing for FPGA-based genomic applications. The Elan model and compiler allow a programmer to use familiar concepts from parallel and distributed computing to develop an application at a relatively high level of abstraction, which can then be compiled automatically to large-scale FPGA platforms. One of the goals of Elan is to allow an application to be run seamlessly across both the CPU and FPGA portions of a platform, and to be parallelized easily across a system comprising many FPGAs and CPUs. We use the short read alignment application as the motivating example.
Heat Shield for Extreme Entry Environment Technology (HEEET) (2017)

Heat-shield for Extreme Entry Technology (HEEET) project is based on the 3-D Woven TPS, an emerging innovative and game changing technology funded by SMD and STMD to fill the ablative TPS gap that exists currently for reaching the depths of Saturn and Venus. Woven TPS technology will address the challenges currently faced by the Venus, Saturn, and higher speed sample return mission Science community due to lack of availability of the only TPS, namely Carbon Phenolic and enable the Science community to move forward with proposals in this decade with Woven TPS. This presentation describes the approach in maturing the technology in the next three years enabling NF-4 mission proposers to address the challenges of Venus, Saturn or higher speed sample return missions.
Continuous Quantum Nondemolition Measurement of the Transverse Component of a Qubit (2016)

Quantum jumps of a qubit are usually observed between its energy eigenstates, also known as its longitudinal pseudospin component. Is it possible, instead, to observe quantum jumps between the transverse superpositions of these eigenstates? We answer positively by presenting the first continuous quantum nondemolition measurement of the transverse component of an individual qubit. In a circuit QED system irradiated by two pump tones, we engineer an effective Hamiltonian whose eigenstates are the transverse qubit states, and a dispersive measurement of the corresponding operator. Such transverse component measurements are a useful tool in the driven-dissipative operation engineering toolbox, which is central to quantum simulation and quantum error correction.
Application of sol–gel based molecularly imprinted xerogel for on-line capillary microextraction of fentanyl from urine and plasma samples (2013)

A molecularly imprinted xerogel (MIX) for fentanyl was successfully prepared on the inner surface of a copper tube by sol–gel technology. Primarily, the tube was treated by self-assembly monolayers of 3-(mercaptopropyl) trimethoxysilane and then [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane was employed as a precursor for imprinting the template molecule in acidic conditions. During the sol–gel process influential parameters including volume and concentration of fentanyl were carefully investigated to obtain the most efficient and appropriate xerogel. In parallel, a non-imprinted xerogel (NIX) was synthesized in the absence of fentanyl. The extraction efficiencies achieved from MIX and NIX, showed some degree of selectivity for the MIX coating. Donepezil was used to estimate the selectivity of the imprinted xerogel with respect to the template molecule. The ratio of MIX/NIX, as a criterion of selectivity, was about 2.5 and 1.1 for fentanyl and donepezil, respectively. The linearity of the analyte was in the range of 5–5000 μg L−1. LOD was found to be 3 μg L−1 and the inter- and intra-day RSD% of 5.5 and 6.5 (n = 5) were obtained. The developed method was conveniently applied to plasma and urine samples spiked with the analyte, while the relative recovery percentages for the spiked samples were up to 85%.
Data‐Driven Investigation of Monosilane and Ammonia Co‐Pyrolysis to Silicon‐Nitride‐Based Ceramic Nanomaterials (2020)

With its high strength, high thermal stability, low density, and high electrical resistance, silicon-nitride-based ceramics have been widely used as gate insulating layers, oxidation masks, and passivation layers. Employing SiN nanomaterials in anode applications also improves rate performances and cycling stability of the lithium-ion batteries. However, a fundamental understanding of the SiN synthetic process remains elusive. SiN gas-phase synthesis can be tailored with a comprehensive understanding of the underlying thermodynamics. In comparison to the characterization data available for solid-state SiN materials, high-level theoretical studies on gas-phase materials possessing Si-N bonds and comprehensive investigation of the SiN chemistry, particularly for nanoclusters, are very uncommon. Thus, we performed a theoretical study of Si and SiN alloy acyclic hydrides and polycyclic clusters to predict electronic structures and thermochemistry using quantum chemical calculation and statistical thermodynamics. Electronic properties by way of highest and lowest occupied molecular orbital energy gap and natural bonding orbitals analysis were calculated to explore the influence of elemental composition and geometry on the stability. Our studies provide characteristic data of SiN species for a data-driven approach to map the design space for discovery of novel silicon-nitride-based ceramic materials for advanced electronic and coating applications.
Ultralong photon-echo-based quantum memories using optical locking (2012)

Unlike slow-light-based quantum memories, photon echoes offer the benefit of high speed and wide bandwidth. Over the last decade, the rephasing mechanism of photon echoes has been studied for quantum memories to overcome fundamental limitations in photon echoes, such as population inversion and low retrieval efficiency. Although these limitations have been overcome in modified photon echo schemes, photon storage time is still too short to apply it to long-distance quantum communications. For long-distance quantum communications, ultralong photon storage time of the order of seconds is needed to implement quantum repeaters. In this review article, challenging techniques for ultralong photon storage are presented, where ultralong storage is obtained via a coherence conversion process between optical and spin states by using an optical locking technique. To remove population-inversion-caused quantum noise, a double rephasing scheme is addressed, where rephasing-pulse-caused population inversion hinders photon echoes for quantum memory applications.
Evaluation of Rapid Context Switching on a CSRC Device (2002)

One property that distinguishes reconfigurable computing from rapid prototyping is the ability to configure the computational fabric on-line while an application is running. Conventional reconfigurable computing platforms utilize commodity FPGAs, which typically have relatively long configuration times. Shrinking the configuration time down to the nanosecond region opens possibilities for rapid context switching and virtualizing the computational resources. An experimental context switching FPGA, called the CSRC, has been created by BAE Systems, and gives researchers the opportunity to explore context-switching applications. This paper presents results obtained from constructing both control-driven and data-driven context switching applications on the CSRC device, along with unique properties of the run-time and compile-time environment.
On trust models and trust evaluation metrics for ad hoc networks (2006)

Within the realm of network security, we interpret the concept of trust as a relation among entities that participate in various protocols. Trust relations are based on evidence created by the previous interactions of entities within a protocol. In this work, we are focusing on the evaluation of trust evidence in ad hoc networks. Because of the dynamic nature of ad hoc networks, trust evidence may be uncertain and incomplete. Also, no preestablished infrastructure can be assumed. The evaluation process is modeled as a path problem on a directed graph, where nodes represent entities, and edges represent trust relations. We give intuitive requirements and discuss design issues for any trust evaluation algorithm. Using the theory of semirings, we show how two nodes can establish an indirect trust relation without previous direct interaction. We show that our semiring framework is flexible enough to express other trust models, most notably PGP's Web of Trust. Our scheme is shown to be robust in the presence of attackers.