gebhart/patrepeval huggingface dataset:
Role of the Two Catalytic Domains of DSR-E Dextransucrase and Their Involvement in the Formation of Highly α-1,2 Branched Dextran (2004)

The dsrE gene from Leuconostoc mesenteroides NRRL B-1299 was shown to encode a very large protein with two potentially active catalytic domains (CD1 and CD2) separated by a glucan binding domain (GBD). From sequence analysis, DSR-E was classified in glucoside hydrolase family 70, where it is the only enzyme to have two catalytic domains. The recombinant protein DSR-E synthesizes both alpha-1,6 and alpha-1,2 glucosidic linkages in transglucosylation reactions using sucrose as the donor and maltose as the acceptor. To investigate the specific roles of CD1 and CD2 in the catalytic mechanism, truncated forms of dsrE were cloned and expressed in Escherichia coli. Gene products were then small-scale purified to isolate the various corresponding enzymes. Dextran and oligosaccharide syntheses were performed. Structural characterization by (13)C nuclear magnetic resonance and/or high-performance liquid chromatography showed that enzymes devoid of CD2 synthesized products containing only alpha-1,6 linkages. On the other hand, enzymes devoid of CD1 modified alpha-1,6 linear oligosaccharides and dextran acceptors through the formation of alpha-1,2 linkages. Therefore, each domain is highly regiospecific, CD1 being specific for the synthesis of alpha-1,6 glucosidic bonds and CD2 only catalyzing the formation of alpha-1,2 linkages. This finding permitted us to elucidate the mechanism of alpha-1,2 branching formation and to engineer a novel transglucosidase specific for the formation of alpha-1,2 linkages. This enzyme will be very useful to control the rate of alpha-1,2 linkage synthesis in dextran or oligosaccharide production.
DAG 4m telescope: assembly, integration and testing (2018)

AMOS with EIE as a main subcontractor, was awarded a contract in November 2014 for the design, manufacturing and installation of a 4m-class telescope for the Turkish Eastern Anatolia Observatory (DAG) situated at 3170 m above the sea level in Palandöken mountains. The telescope is based on a Ritchey-Chretien configuration with two folded Nasmyth focal planes and a focal length of 56m. Diffraction-limited performances will be reached thanks to the combination of the active optics system and the adaptive optics system that will be implemented on one of the Nasmyth ports. The active optics system aims at controlling the shape of the primary mirror by means of 66 axial force actuators and positioning actively the secondary and tertiary mirrors by means of hexapods. More than 30 years of experience in testing instruments and telescopes, including optical testing, alignment, metrology, mechanical static and dynamic measurements, system identification, etc. allow to implement an adequate verification strategy combining component level verifications with factory and site test in the most efficient and reliable manner. As a main contractor, AMOS is in charge of the overall project management, the system engineering, the optical design and the active optics development. As a main sub-contractor and partner of AMOS, EIE is in charge of the development of the mount. The factory test therefore takes place in EIE premises. In this paper is shortly presented the overall design of the telescope with a review of the specification, the optical design and a description of the major sub-systems, including the optics. The assembly, integration et test plan is outlined. The assembly sequence and the tests of the active optics and the mount are discussed. Finally, the site integration and tests are explained. The process to assess the image quality of the telescope and the verification instrument developed for this purpose by AMOS are presented.
Tumorspheres but Not Adherent Cells Derived from Retinoblastoma Tumors Are of Malignant Origin (2013)

Verification that cell lines used for cancer research are derived from malignant cells in primary tumors is imperative to avoid invalidation of study results. Retinoblastoma is a childhood ocular tumor that develops from loss of functional retinoblastoma protein (pRb) as a result of genetic or epigenetic changes that affect both alleles of the RB1 gene. These patients contain unique identifiable genetic signatures specifically present in malignant cells. Primary cultures derived from retinoblastoma tumors can be established as non-adherent tumorspheres when grown in defined media or as attached monolayers when grown in serum-containing media. While the RB1 genotypes of tumorspheres match those of the primary tumor, adherent cultures have the germline RB1 genotype. Tumorspheres derived from pRb-negative tumors do not express pRb and express the neuroendocrine tumor markers synaptophysin and microtubule-associated protein 2 (MAP2). Adherent cells are synaptophysin-negative and express pRb, the epithelial cell marker cytokeratin that is expressed in the retinal pigmented epithelium and the vascular endothelial cell marker CD34. While tumorspheres are of malignant origin, our results cast doubt on the assumption that adherent tumor-derived cultures are always valid in vitro models of malignant cells and emphasize the need for validation of primary tumor cultures.
Privacy-Preserving Anomaly Detection in Cloud Manufacturing Via Federated Transformer (2022)

With the rapid development of cloud manufacturing, industrial production with edge computing as the core architecture has been greatly developed. However, edge devices often suffer from abnormalities and failures in industrial production. Therefore, detecting these abnormal situations timely and accurately is crucial for cloud manufacturing. As such, a straightforward solution is that the edge device uploads the data to the cloud for anomaly detection. However, Industry 4.0 puts forward higher requirements for data privacy and security so that it is unrealistic to upload data from edge devices directly to the cloud. Considering the abovementioned severe challenges, this article customizes a weakly supervised edge computing anomaly detection framework, i.e., federated learning-based transformer framework ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FedAnomaly</i> ), to deal with the anomaly detection problem in cloud manufacturing. Specifically, we introduce federated learning (FL) framework that allows edge devices to train an anomaly detection model in collaboration with the cloud without compromising privacy. To boost the privacy performance of the framework, we add differential privacy noise to the uploaded features. To further improve the ability of edge devices to extract abnormal features, we use the transformer to extract the feature representation of abnormal data. In this context, we design a novel collaborative learning protocol to promote efficient collaboration between FL and transformer. Furthermore, extensive case studies on four benchmark datasets verify the effectiveness of the proposed framework. To the best of our knowledge, this is the first time integrating FL and transformer to deal with anomaly detection problems in cloud manufacturing.
The biology and biochemistry of cereal seed prolamins (1978)

Biochemical characteristics of prolamines, and studies on the location of structural genes specifying different prolamine components, are reviewed. Genetic studies apparently show that the structural genes are located in closely linked groups
Transgene‐mediated GDNF expression enhances synaptic connectivity and GABA transmission to improve functional outcome after spinal cord contusion (2010)

Glial cell line-derived trophic factor (GDNF) is a peptide with pleiotropic survival and growth-promoting effects on neurons. We found that intraspinal injection of a non-replicating herpes simplex virus-based vector coding for GDNF 2 h after blunt trauma to the thoraco-lumbar spinal cord produced sustained improvement in motor behavioral outcomes up to 5 weeks following injury. The improvement in behavior correlated with an increase in synaptophysin and glutamic acid decarboxylase (GAD) in the spinal cord at the level of injury. Addition of recombinant GDNF protein to primary spinal cord neurons in-vitro resulted in enhanced neurite growth and a marked increase in protein levels of GAD65 and GAD67, synapsin I and synaptophysin. GDNF-mediated increases in GAD and the synaptic markers were blocked by the MEK inhibitor UO126, but not by the phosphoinositide 3-kinase inhibitor LY294002. These results suggest that GDNF, acting through the MEK-ERK pathway enhances axonal sprouting, synaptic connectivity, and GABAergic neurotransmission in the spinal cord, that result in improved behavioral outcomes after spinal cord contusion injury.
Improving operating system availability with dynamic update (2004)

Dynamic update is a mechanism that allows software updates and patches to be applied without loss of service or down-time. Dynamic update of an operating system enables administrators to defer rebooting or restarting services and the resultant disruption, without trading off the ability to apply important security fixes or improve functionality and performance through software updates. We have considered the problem of building a dynamically updatable operating system, and have designed and implemented a prototype update mechanism for the K42 research operating system. Although the prototype utilises the hot-swapping features of K42, many aspects of the design would be relevant for other operating systems. In this paper we categorise and discuss these issues, and where possible propose solutions. We also describe our current prototype. 1
Analysis of cyt0kine gene expression in stimulated T cells of small children by semi‐quantitative PCR (1995)

Only limited amounts of peripheral blood samples can be obtained from small children. Therefore, a polymerase chain reaction (PCR) aided analysis of cytokine gene expression by PBMC or T cells is a valuable tool. We present a combination of procedures to obtain an accurate estimation of the expression of the cytokines IL-4 and IFN-gamma. This can be performed on T cells purified from blood samples of up to 5 ml in volume from children aged 0-4 years with allergic asthma and atopic dermatitis. This procedure includes multiple sampling of PCR products to determine the linear phase of the PCR; inter-experiment correction using a helper T-cell clone, expressing both IL-4 and IFN-gamma; interpatient correction by comparing the expression of a housekeeping gene (HPRT); and finally the development of specific software to analyse densitometric data obtained by scanning photographs of agarose gels, separating PCR products. In this way it is possible to study cytokine gene expression from a very small amount of material.
Bubble Contact Angle Method for Evaluating Substratum Interfacial Characteristics and Its Relevance to Bacterial Attachment (1982)

A bubble contact angle method was used to determine interfacial free-energy characteristics of polystyrene substrata in the presence and absence of potential surface-conditioning proteins (bovine glycoprotein, bovine serum albumin, fatty acid-free bovine serum albumin), a bacterial culture supernatant, and a bacterial exopolymer. Clean petri dish substrata gave a contact angle of 90 degrees , but tissue culture dish substrata were more hydrophilic, giving an angle of 29 degrees or less. Bubble contact angles at the surfaces exposed to the macromolecular solutions varied with the composition and concentration of the solution. Modification by pronase enzymes of the conditioning effect of proteins depended on the nature of both the substratum and the protein, as well as the time of addition of the enzyme relative to the conditioning of the substratum. The effects of dissolved and substratum-adsorbed proteins on the attachment of Pseudomonas sp. strain NCMB 2021 to petri dishes and tissue culture dishes were consistent with changes in bubble contact angles (except when proteins were adsorbed to tissue culture dishes before attachment) as were alterations in protein-induced inhibition of bacterial attachment to petri dishes by treatment with pronase. Differences between the attachment of pseudomonads to petri dishes and tissue culture dishes suggested that different mechanisms of adhesion are involved at the surfaces of these two substrata.
Which Graphical Approaches should be Used to Represent Medical Knowledge? (2005)

Medical knowledge is growing both in quantity and complexity. Although sources of medical knowledge have been digitalized, the way the knowledge they contain is presented to users has not changed and is still highly text-based. However, it has been shown that this information could be presented more efficiently using graphical approaches, such as graphical languages and information visualization. We present here a survey of existing methods and applications, and discuss the potential value of these methods for medical practice. These graphical approaches have great potential for improving medical knowledge consultation, provided they are well-designed, well-evaluated and standardized for re-use.
A Microprocessor Tester for the Treat Upgrade Reactor Trip System (1985)

The upgrading of the Transient Reactor Test (TREAT) Facility at ANL-Idaho has been designed to provide additional experimental capabilities for the study of core disruptive accident (CDA) phenomena. In addition, a programmable Automated Reactor Control System (ARCS) will permit high-power transients up to 11,000 MW having a controlled reactor period of from 15 to 0.1 sec. These modifications to the core neutronics will improve simulation of LMFBR accident conditions. Finally, a sophisticated, multiply-redundant safety system, the Reactor Trip System (RTS), will provide safe operation for both steady state and transient production operating modes. To insure that this complex safety system is functioning properly, a Dedicated Microprocessor Tester (DMT) has been implemented to perform a thorough checkout of the RTS prior to all TREAT operations.
Fabrication of a multi‐applicable removable intraoral denture system for rodent research (2011)

The objective was to engineer an inexpensive intraoral removable denture system for rodents that can be utilised in numerous oral health research applications. At the forefront is biofilm research related to Candida-associated denture stomatitis. Previously described intraoral devices are primitive and inadequate. The denture system was engineered consisting of a fixed part that is anchored to the posterior palate by orthodontic wires and acrylic resin and a removable part fitted to the anterior palate that is retained by magnets embedded in the fixed part. Both parts are custom fitted to the rodent palate by impression making and cast fabrication. Rats fitted with the intraoral denture system maintained body weight and normal activity with the device maintaining integrity and durability for upwards of 8 weeks. The denture system was used successfully to establish a working model of denture stomatitis. This newly engineered inexpensive intraoral removable denture system for rodents can be utilised in numerous oral health research applications, including denture-associated infections, biofilms and a variety of biomaterial applications. The removable portion is advantageous for longitudinal analyses and charging/discharging of biomaterials.
MO‐D‐BRB‐03: Using a Database of Patient Geometric and Dosimetric Information for Quantitative IMRT Plan Quality Control (2009)

Purpose: To empower IMRT treatment planners with the ability to judge new plans against the performance of similar past plans. Method and Materials: This is accomplished by searching a database of treated patients using the geometric relationships between targets and organs at risk (OARs). We introduce the concept of a shape relationship descriptor to quantify this intuitively important relationship. The overlap volume histogram (OVH) simplifies the complex 3D relationship between a target and an OAR. The OVH is the normalized 1D histogram of the OAR volume within a distance of the target. The OVH descriptor was used to search a patient database, providing a patient specific set of dose volume histograms (DVHs). These DVHs were then presented to the planner to aid their decisions. Results: The method was applied to both parotids of 32 treated head‐and‐neck patients. The 17 parotids that promised the greatest reduction in D 50 were selected for re‐planning. These 17 parotids came from 13 patients. Our method indicated that the doses of the other nine parotids of the 13 patients could not be reduced, so they were included in the re‐planning process as controls. Re‐planning with an effort to reduce D 50 was conducted on the 26 parotids of these 13 patients. Average reductions of D 50 were 6.6Gy for the 17 improvement candidates and 1.9Gy for the controls. Originally, several parotids violated the RTOG planning goal of V (30Gy)⩽50%. Eleven of these were improvement candidates, and re‐planning reduced this number to three. Re‐planning had no impact on the five control parotids that were violating the RTOG planning goal. According to the physician reviews, re‐planning did not degrade target coverage or OAR sparing. Conclusions: Our method offers a patient specific DVH evaluation for OARs, providing an effective mechanism of quantitative IMRT plan quality control.
Dry reforming of methane in the presence of ruthenium-based catalysts (2009)

The catalytic activities of ruthenium-based catalysts (5 wt% Ru) supported on alumina, ceria and ceria/alumina with different proportions of ceria ( n Ce10Al, n = 1, 3, 5; n = atomic ratio) were studied for the methane reforming reaction with CO 2 (CH 4 /CO 2 = 1) in the temperature range of 400–800 °C. Evaluation of coke deposited after the reaction showed carbon deposition on Ru catalysts supported on CeO 2 , 1Ce10Al and 3Ce10Al, but not on Ru/Al 2 O 3 and Ru/5Ce10Al. Moreover, the sample Ru/5Ce10Al exhibited a higher activity than the other catalysts.
Human Properdin Released By Infiltrating Neutrophils Can Modulate Influenza A Virus Infection (2021)

The complement system is designed to recognise and eliminate invading pathogens <i>via</i> activation of classical, alternative and lectin pathways. Human properdin stabilises the alternative pathway C3 convertase, resulting in an amplification loop that leads to the formation of C5 convertase, thereby acting as a positive regulator of the alternative pathway. It has been noted that human properdin on its own can operate as a pattern recognition receptor and exert immune functions outside its involvement in complement activation. Properdin can bind directly to microbial targets <i>via</i> DNA, sulfatides and glycosaminoglycans, apoptotic cells, nanoparticles, and well-known viral virulence factors. This study was aimed at investigating the complement-independent role of properdin against Influenza A virus infection. As one of the first immune cells to arrive at the site of IAV infection, we show here that IAV challenged neutrophils released properdin in a time-dependent manner. Properdin was found to directly interact with haemagglutinin, neuraminidase and matrix 1 protein Influenza A virus proteins in ELISA and western blot. Furthermore, modelling studies revealed that properdin could bind HA and NA of the H1N1 subtype with higher affinity compared to that of H3N2 due to the presence of an HA cleavage site in H1N1. In an infection assay using A549 cells, properdin suppressed viral replication in pH1N1 subtype while promoting replication of H3N2 subtype, as revealed by qPCR analysis of M1 transcripts. Properdin treatment triggered an anti-inflammatory response in H1N1-challenged A549 cells and a pro-inflammatory response in H3N2-infected cells, as evident from differential mRNA expression of TNF-α, NF-κB, IFN-α, IFN-β, IL-6, IL-12 and RANTES. Properdin treatment also reduced luciferase reporter activity in MDCK cells transduced with H1N1 pseudotyped lentiviral particles; however, it was increased in the case of pseudotyped H3N2 particles. Collectively, we conclude that infiltrating neutrophils at the site of IAV infection can release properdin, which then acts as an entry inhibitor for pandemic H1N1 subtype while suppressing viral replication and inducing an anti-inflammatory response. H3N2 subtype can escape this immune restriction due to altered haemagglutinin and neuraminindase, leading to enhanced viral entry, replication and pro-inflammatory response. Thus, depending on the subtype, properdin can either limit or aggravate IAV infection in the host.
Capillary circulation in the brain. (1992)

A close relationship exists between the local capillary density in different brain structures and their local blood flow and metabolism. Capillary density appears to have developed depending on local functional demands. Investigation of single capillary perfusion has shown that all capillaries are perfused with plasma in the brain at any time point. Theories of capillary cycling and capillary recruitment have been based on experimental artifacts. Indirect evidence exists for a heterogeneity of perfusion under normal conditions, especially with respect to erythrocyte flow. The capillary diffusion capacity depends on, among other things, the available capillary surface area, which would increase with recruitment of capillaries. In the case of capillary perfusion heterogeneity, the capillary diffusion capacity may also be increased by homogenization of the perfusion rate (slowly perfused capillaries becoming faster perfused). This could give a physiological impression of an "apparent" increase in the capillary surface area. It is recommended that the terms "capillary cycling" and "recruitment" should be used in conjunction with more specific explanations, like "recruitment of erythrocytes" and "recruitment of previously nonperfused capillaries".
Role of the radical pool in combustion (1985)

We present numerical solutions of the detailed chemical kinetics mechanisms for the reactions of hydrogen with fluorine and oxygen on a phase plane where temperature is plotted vs the concentration of one of the radicals, F or H. We observe that for given initial reactant concentrations, all solutions follow a common path, after an initial transient, regardless of initial temperature or initial radical concentration. We then analyze the reaction mechanism and find that the rate equations for radical species rapidly reach a stable steady state that couples all of the radicals into a pool. The pool concentration then grows until onset of a reaction that consumes two radicals, resulting in a steady state of the entire pool. Further growth of the pool is due entirely to the temperature dependence of the steady state, which has the form of an equilibrium constant. We show that the rate of temperature increase is proportional to the radical pool concentration, particularly its steady-state value. 26 refs., 3 figs.