gebhart/patrepeval huggingface dataset:
1‐<i>N</i><sup>6</sup>‐Etheno‐ADP‐ribosylation of elongation factor‐2 by diphtheria toxin (1985)

Diphtheria toxin fragment A is able to inhibit protein synthesis in the eukaryotic cell by ADP-ribosylating the diphthamide residue of elongation factor-2 (EF-2) [(1980) J. Biol. Chem. 255, 10710-10720]. The reaction requires NAD as ADP-ribose donor. This work reports on the capacity of an NAD analog, the nicotinamide 1-N6-ethenoadenine dinucleotide (epsilon NAD), to be a substrate of diphtheria toxin fragment A in the transferring reaction of the fluorescent moiety, the epsilon ADP-ribose, to the EF-2. As a consequence of the transfer of the epsilon ADP-ribosyl moiety to the EF-2, there is an increase in the emission intensity of the fluorophore and a blue shift in its emission maximum. The epsilon ADP-ribosylated EF-2, like ADP-ribosylated EF-2, retains the capacity to bind GTP and ribosome. The utility of introducing a fluorescent probe in a well defined point of the EF-2 molecule for conformational or binding studies is discussed.
A Novel Approach Based on Bipartite Network Recommendation and KATZ Model to Predict Potential Micro-Disease Associations (2019)

Accumulating evidence indicates that the microbes colonizing human bodies have crucial effects on human health and the discovery of disease-related microbes will promote the discovery of biomarkers and drugs for the prevention, diagnosis, treatment, and prognosis of diseases. However clinical experiments of disease-microbe associations are time-consuming, laborious and expensive, and there are few methods for predicting potential microbe-disease association. Therefore, developing effective computational models utilizing the accumulated public data of clinically validated microbe-disease associations to identify novel disease-microbe associations is of practical importance. We propose a novel method based on the KATZ model and Bipartite Network Recommendation Algorithm (KATZBNRA) to discover potential associations between microbes and diseases. We calculate the Gaussian interaction profile kernel similarity of diseases and microbes based on validated disease-microbe associations. Then, we construct a bipartite graph and execute a bipartite network recommendation algorithm. Finally, we integrate the disease similarity, microbe similarity and bipartite network recommendation score to obtain the final score, which is used to infer whether there are some novel disease-microbe interactions. To evaluate the predictive power of KATZBNRA, we tested it with the walk length 2 using global leave-one-out cross validation (LOOV), two-fold and five-fold cross validations, with AUCs of 0.9098, 0.8463 and 0.8969, respectively. The test results also show that KATZBNRA is more accurate than two recent similar methods KATZHMDA and BNPMDA.
Inhibition of Plasmodium yoelii blood-stage malaria by interferon α through the inhibition of the production of its target cell, the reticulocyte (2001)

The effect of a recombinant hybrid human interferon alpha (IFN-alpha) (which cross-reacts with murine cells) on C57BL/6 mice infected with Plasmodium yoelii sporozoites or parasitized erythrocytes was determined. IFN-alpha did not inhibit the development of the parasite in the liver, but it did reduce the blood parasite load and the hepatosplenomegaly induced by the infection in mice injected with blood-stage parasites. The extent of anemia in IFN-alpha-treated and control mice was similar, despite the lower parasite load in the IFN-alpha-treated mice. The reduced blood parasite load in IFN-alpha-treated mice was associated with reduced erythropoiesis and reticulocytosis. As reticulocytes are the preferred target cells for the strain of P yoelii used (P yoelii yoelii 265 BY), it was postulated that the inhibition of reticulocytosis in IFN-alpha-treated mice was causally related to the observed decreased blood parasite load. This was supported by the finding that IFN-alpha inhibited a different strain of P yoelii (17X clone A), which also displays a tropism for reticulocytes, but not a line of Plasmodium vinckei petteri, which infects only mature red blood cells. As human malaria species also display different tropism for reticulocytes, these findings could be relevant for people coinfected with multiple Plasmodium species or strains or coinfected with Plasmodium and virus. (Blood. 2001;97:3966-3971)
Forked and integrated variants in an open-source firmware project (2015)

Code cloning has been reported both on small (code fragments) and large (entire projects) scale. Cloning-in-the-large, or forking, is gaining ground as a reuse mechanism thanks to availability of better tools for maintaining forked project variants, hereunder distributed version control systems and interactive source management platforms such as Github. We study advantages and disadvantages of forking using the case of Marlin, an open source firmware for 3D printers. We find that many problems and advantages of cloning do translate to forking. Interestingly, the Marlin community uses both forking and integrated variability management (conditional compilation) to create variants and features. Thus, studying it increases our understanding of the choice between integrated and clone-based variant management. It also allows us to observe mechanisms governing source code maturation, in particular when, why and how feature implementations are migrated from forks to the main integrated platform. We believe that this understanding will ultimately help development of tools mixing clone-based and integrated variant management, combining the advantages of both.
Lateral Diffusion of Lipids in Silane-, Dextran-, and S-Layer-Supported Mono- and Bilayers (1999)

Supported lipid bilayers on planar silicon substrates have been formed using crystalline bacterial cell surface (S-layer) protein as support onto which DMPC (pure or mixture with 30 mol % cholesterol) or DPPC bilayers were deposited. Lateral diffusion of fluorescence lipid probes in these layers have been investigated with fluorescence recovery after photobleaching technique (FRAP). For comparison, hybrid lipid bilayers (lipid monolayer on alkylsilanes) and lipid bilayers on dextran composed of the same lipids as for S-layer-supported systems were studied. The mobility of lipids was highest in the S-layer-supported bilayers. No significant difference in mobility was observed for supports of the two S-layer proteins from Bacillus coagulans E38-66 or Bacillus sphaericus CCM2177. DMPC/cholesterol-layers revealed mostly a homogeneous structure, whereas in planar DPPC layers defects could be observed. In S-layer-supported DPPC bilayers, clear cracks could be seen below Tm whereas above Tm inhomogeneous round structures were formed. In another set of experiments the supported bilayers have been covered by S-layer proteins using three different techniques for protein recrystallization (trough, vertical, and horizontal). The recrystallization of S-layers was visualized in large scale by electron microscopy (EM) and more specific on the different substrates by atomic force microscopy (AFM). The S-layer cover induced an enhanced mobility of the probe in the lipid layer. Furthermore it was noticed that the S-layer lattice cover could prevent the formation of cracks and other inhomogenities in the bilayers.
The liver and IgA: Immunological, cell biological and clinical implications (1989)

Secretory immunoglobulin A is the characteristic and predominant immunoglobulin of the mucosal immune system; it participates in immunological protection at the level of mucous membrane surfaces. During the past 10 to 15 years, a great deal of experimental and clinical evidence has shown that the liver is very much involved in the sIgA system. In certain animals (rats, mice, rabbits), polymeric forms of IgA are efficiently cleared by the liver and transported into bile by a receptor-mediated vesicular pathway across hepatocytes. Taking advantage of this easily accessible pathway, investigators have defined many of the events in the external secretion of pIgA, including details about the synthesis and secretion of its receptor, secretory component. In the rat hepatocyte, secretory component is synthesized as a transmembrane glycoprotein and is expressed preferentially on the sinusoidal plasma membrane; circulating pIgA that binds to secretory component is internalized into endocytic vesicles and transported across the hepatocyte to the bile canalicular membrane, where the pIgA is released into bile as a soluble complex with a portion of the secretory component, the complex being secretory IgA. In some other animals (dog, guinea pig, sheep) as well as man, biliary epithelial cells, not hepatocytes, express secretory component and perform the transcytosis and secretion of pIgA into bile. In those species, much of the pIgA that reaches bile is synthesized locally in plasma cells that populate the biliary tree; this design is analogous to the release of sIgA into various mucosae in the body. The major biological functions ascribed to the secretion of IgA into bile are enhancement of immunological defense of the biliary and upper intestinal tracts and the clearance of harmful antigens from the circulation as IgA-antigen complexes. However, the importance of biliary IgA antibodies is largely unclarified, and man lacks the capacity for effective clearance of IgA-antigen complexes via the secretory component-mediated transhepatocellular pathway; whether this deficit contributes to the propensity for man to develop IgA immune complex diseases should be clarified. Among liver diseases, alcoholic disease is most closely linked to alterations in IgA metabolism. This association is manifested principally by the deposition of IgA along the sinusoids in the livers of the majority of alcoholics and in the renal mesangium of many. The IgA1 subclass of IgA predominates in the IgA deposits in both tissues; the possibility that this predominance is related to abnormalities in the removal of circulating IgA1 by asialoglycoprotein receptors on hepatocytes is an intriguing consideration. Thus, the liver plays a unique role in mucosal immunity and in the physiology of IgA in normal and disease states. Further study of the associations between the liver and IgA, particularly in man, is clearly needed.
Serum insulin-like growth factor-I in 1030 healthy children, adolescents, and adults: relation to age, sex, stage of puberty, testicular size, and body mass index. (1994)

Serum levels of insulin-like growth factor-I (IGF-I) increase with age and pubertal development. The large variation in circulating IGF-I levels in adolescence makes it difficult to use the IGF-I value of a single child in the assessment of his growth status. In addition, the interference of IGF-binding proteins in many IGF-I assays contributes to this problem. We measured IGF-I in acid-ethanol-extracted serum from 1030 healthy children, adolescents, and adults, employing a RIA that reduces interference of IGF-binding proteins by using monoiodinated Tyr31-[125I]des-(1-3)IGF-I as radioligand. Mean serum IGF-I concentrations increased slowly in prepubertal children from 80-200 micrograms/L with a further steep increase during puberty to approximately 500 micrograms/L. After puberty, a subsequent continuous fall in circulating IGF-I levels was apparent throughout adulthood to a mean of 100 micrograms/L at the age of 80 yr (P < 0.0001). Girls had maximal IGF-I levels at 14.5 yr of age, whereas boys had peak IGF-I levels 1 yr later. This is almost 2 yr later than average peak height velocity. The large variation in serum IGF-I levels during puberty was diminished when data were separated according to sex and Tanner stage of puberty. Interestingly, we found a significant variation with age within the Tanner stages; there was an increase in serum IGF-I concentrations with age in the early pubertal stages and a decrease in the late stages (P < 0.05). Serum IGF-I increased concomitantly with increasing testicular volume. Multiple regression analysis revealed that serum IGF-I levels predicted height velocity in the following year (r = 0.33; P < 0.0001). Body mass index did not correlate significantly with serum IGF-I in prepubertal children in a multiple regression analysis. In conclusion, there was a significant variation in serum IGF-I levels with age within a given Tanner stage of puberty in addition to the well known increase with increasing age or pubertal stage. Accordingly, the effects of sex, age, and puberty on serum IGF-I cannot be separated into simple additive components when studying 1030 children in a cross-sectional design. Thus, the age-, sex-, and puberty-corrected IGF-I values may, in fact, improve the use of serum IGF-I as a diagnostic tool to distinguish between a child with retarded puberty and a GH-deficient individual.
Joint Beamforming and Scheduling for a Multi-Antenna Downlink with Imperfect Transmitter Channel Knowledge (2007)

We consider the downlink of a wireless system where the base-station has M ges 1 antennas and K user terminals have one antenna each. We study the weighted rate sum maximization in the case of non-perfect Channel State Information at the Transmitter (CSIT). Some relevant downlink optimization problems, such as the stabilization of the transmission queues under random packet arrivals and the proportional fair scheduling for infinite backlogged systems, can be solved as special cases of the proposed problem. We restrict the transmitter strategy to be based on Gaussian coding and beamforming. Even under this simplifying condition, the problem at hand is non-convex and it does not appear to lend itself to a simple algorithmic solution. Therefore, we introduce some approximations that yield a definition of signal-to-interference plus noise ratio (SINR) commonly used in the classical array- processing/beamforming literature. For the simpler (but still non-convex) approximated problem, we propose a powerful heuristic solution based on greedy user selection and a gradient iteration that converges to a local maximum of the objective function. This method yields very competitive results with relatively low computational complexity. Extensive simulations show that, in the case of perfect CSIT, the proposed heuristic scheme performs very closely to the optimal (dirty-paper coding) strategy while, in the case of non-perfect CSIT, it significantly outperforms previously proposed suboptimal approaches, such as random beamforming and approximated zero-forcing with greedy user selection.
Temperature control and in-situ fault detection of wafer warpage (2005)

Wafer warpage is common in microelectronics processing. Warped wafers can affect device performance, reliability and linewidth control in various processing steps. We proposed in this paper an in-situ fault detection technique for wafer warpage in lithography. Early detection will minimize cost and processing time. Based on first principle thermal modeling, we are able to detect warpage fault from available temperature measurements. In this paper, the use of advanced process control resulted in very small temperature disturbance making it suitable for industrial implementation. More importantly, the sensitivity for detecting warpage is not compromised even though the temperature signal is small. Experimental results demonstrate the feasibility of the approach.
Formation of Silver Nanoprisms with Surface Plasmons at Communication Wavelengths (2006)

Abstract Silver nanoprisms with strong absorption in the near‐IR have been synthesized using a modification of the photoinduced method by illuminating preformed silver seeds under different illumination conditions. Low‐intensity light‐emitting diodes and white light combined with different color filters are used as light sources. The lateral dimensions of the nanoprisms are found to be correlated in a quasilinear fashion with the emission wavelength and the position of the main in‐plane dipole plasmon band. The structural characterization of the Ag nanoparticles, carried out using scanning electron microscopy, transmission electron microscopy (TEM), high‐resolution TEM, and electron diffraction, reveal that the particles are flat and have a single‐crystal face‐centered‐cubic structure. Time‐resolved studies suggest that the nanoprisms are formed by steady consumption of the original Ag seeds with little variation of the aspect ratio after a short induction time.
Engineering a cyanobacterium as the catalyst for the photosynthetic conversion of CO2 to 1,2-propanediol (2013)

This work demonstrated that cyanobacteria can be engineered as a catalyst for the photosynthetic conversion of CO2 to 1,2-PDO. This work also characterized two NADPH-dependent sADHs for their catalytic capacity in 1,2-PDO formation, and suggested that they may be useful tools for renewable production of reduced chemicals in photosynthetic organisms.
Rehabilitating the industrial revolution (1992)

Rehabilitating the industrial revolution. Gradualist perspectives now dominate economic and social histories of the industrial revolution. Analyses of economic change which rely on growth accounting and macroeconomic estimates of productivity indicate continuity with the past; social historians have followed in turning aside from the analysis of new class formations. This article challenges these perspectives. Currently accepted economic indicators and recent social history underplay the extent and uniqueness of economic and social transformation. The article emphasizes change in technology, the use of a female and child labour force, regional specialization, demographic behaviour, and political change.
A symmetric diagonal driver transistor SRAM cell with imbalance suppression technology for stable low voltage operation (2002)

A symmetric diagonal driver transistor (SDDT) cell has been developed for low voltage SRAM operation which exhibits high alignment tolerance. This new symmetric cell layout substantially suppresses the imbalance in a pair of cell transistor characteristics and, combined with silicon nitride self-aligned contact (Si/sub 3/N/sub 4/-SAC) and low resistance ground-line structures, results in a minimum operation voltage of 1.9 V, which is 0.3 V lower than that of the conventional split word line cell.
Common Launch Acceptability Region Task Group (2001)

<div class="htmlview paragraph">This paper presents a brief overview of the Common Launch Acceptability Region Approach (CLARA) problem and the history of efforts within the Air Force and SAE to address it. An SAE Task Group has produced top level requirements and a proposed CLAR Methodology consisting of three components (Truth Model, Coefficient Generator and LAR Generator) that provides a solution to the multiple LAR implementation problem. This proposed CLAR methodology fulfills the key requirement of a LAR algorithm that is to be common to all applications and allows updates via tables of coefficients requiring the validation of only those coefficients and not the algorithm. This paper also presents the status of trade studies being conducted by the CLARA TG on mathematical algorithms required to implement the methodology. A key step in these trade studies is development of the appropriate metrics and analysis tools with which to judge alternative algorithms.</div>
Building WDM wide area resilient transport network from 4-node semi-mesh and mesh sub-networks (2002)

This paper deals with optical transport network design using wavelength division multiplexing (WDM) facilities. It proposes a method for building networks from sub-network combinations. Two types of 4-node sub-networks and their properties are presented. For each sub-network, any fiber break can be recovered using re-routing paths. A European network set-up illustrates the method capabilities. The network has 19 nodes connected through 39 links distributed within 9 semi-mesh sub-networks. Comparison is made between local and non-local re-routing and between channel capacities of 2.5 and 10 Gb/s. The use of wavelength converters is also investigated. Advantages and drawbacks of different solutions are given with emphasis on fiber length and optical cross-connect size.
Antibody Glycosylation and Inflammation (2013)

IgG antibodies are the basis of some of the most effective therapeutics developed over the last 20 years. These antibodies are highly specific, have long serum-half lives, and can be produced relatively routinely, making them ideal drugs for immunotherapy. The degree of regulation on IgG antibody effector functions by the composition of the single, N-linked glycan attached to the Fc is increasingly appreciated. IgG antibodies with identical protein sequences can gain a 50-fold potency, in terms of initiating antibody-dependent cellular cytotoxicity (ADCC) by removal of the single fucose residue from the Fc glycan. Conversely, the addition of sialic acid to the terminus of the Fc glycan converts IgG antibodies into anti-inflammatory mediators, capable of suppressing autoantibody driven inflammation. This review will discuss the contribution of the Fc glycan to IgG antibody effector functions, the regulation of the antibody glycosylation in vivo, implications for the rational design of IgG antibody-based therapeutics, and touch upon the contribution of glycosylation to other immunoglobulin isotypes.
Synthesis of some New Disperse Dyes (1996)

Department of Chemistry, D G College, Kanpur-208 001 <em>Manuscript received 17 January 1994, revised 21 October 1994, accepted 2 March 1995</em> Synthesis of some New Disperse Dyes.
Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics (2008)

We describe the practical implementation of a new RP (pH 10 - pH 2) 2D HPLC-ESI/MS scheme for large-scale bottom-up analysis in proteomics. When compared to the common SCX-RP approach, it provides a higher separation efficiency in the first dimension and increases the number of identified peptides/proteins. We also employed the methodology of our sequence-specific retention calculator (SSRCalc) and developed peptide retention prediction algorithms for both LC dimensions. A diverse set of approximately 10,000 tryptic peptides from the soluble protein fraction of whole NK-type cells gave retention time versus hydrophobicity correlations, with R (2) values of 0.95 for pH 10 and 0.945 for pH 2 (formic acid) separation modes. The superior separation efficiency and the ability to use retention prediction to filter out false-positive MS/MS identifications gives promise that this approach will be a method of choice for large-scale proteomics analyses in the future. Finally, the "semi-orthogonal" separation selectivity permits the concatenation of fractions in the first dimension of separation before the final LC-ESI MS step, effectively cutting the analysis time in half, while resulting in a minimal reduction in protein identification.
Autonomic Nervous System Evaluation of Patients With Vasomotor Rhinitis (2000)

Autonomic nervous system dysfunction is significant in patients with vasomotor rhinitis. Possible factors that trigger this dysfunction including nasal trauma and extraesophageal manifestations of gastroesophageal reflux are discussed.