gebhart/patrepeval huggingface dataset:
Biosynthesis of asparagine-linked oligosaccharides in <i>Saccharomyces cerevisiae</i>: the <i>alg2</i> mutation (1993)

In the yeast Saccharomyces cerevisiae, the alg2 mutation causes temperature-sensitive growth and abnormal accumulation of the lipid-linked oligosaccharide Man2GlcNAc2-PP-Dol (Jackson et al., Arch. Biochem. Biophys., 272, 203-209, 1989; Huffaker and Robbins, Proc. Natl. Acad. Sci. USA, 80, 7466-7470, 1983). A gene having the function and genomic location of ALG2 was cloned from libraries based on the multicopy plasmid YEp24 and on the centromere plasmid YCp50. Alg2 mutants transformed with plasmids containing ALG2 regained the capacity to grow and to synthesize lipid-linked oligosaccharides normally at the previously non-permissive temperature. ALG2 was essential for viability in haploid and diploid yeast. The ALG2 gene was transcribed into a single mRNA of 1.7 kb in size. The stability of ALG2 mRNA, assessed after thermal inactivation of RNA polymerase II in an rpb1-1 mutant (Herrick et al., Mol. Cell. Biol., 10, 2269-2284, 1990) was very low, with a t1/2 of < 5 min. The ALG2 transcript accumulation was growth dependent, and it was at least an order of magnitude lower in stationary phase cells compared to exponentially growing cells. The putative translation product of ALG2 contained a potential dolichol recognition domain similar to that found in all three glycosyltransferases of the lipid-linked pathway that have been sequenced.(ABSTRACT TRUNCATED AT 250 WORDS)
Protein fractionation using electrostatic interactions in membranel filtration (1995)

One of the critical factors limiting the development of membrane systems for protein fractionation has been the poor selectivity that has generally been obtained with these membrane devices. We have demonstrated that it is possible to dramatically improve the selectivity of available membrane systems by exploiting the different electrostatic interactions between the two proteins and the membrane. The separation factor for the albumin-hemoglobin system could be increased to more than 70 simply by reducing the salt concentration and adjusting the pH to around 7 (near the isoelectric point of hemoglobin). This very high selectivity was a direct result of the strong electrostatic exclusion of the charged albumin from the membrane pores under these conditions. This high selectivity makes it possible to very effectively separate these albumin-hemoglobin mixtures using membrane filtration, and this was demonstrated experimentally using both a simple batch filtration process and a continuous diafiltration system. The hemoglobin recovery in the diafiltration experiment was greater than 70% after a 3-diavolume filtration, with the Hb purification factor being around 100 under these conditions. These results clearly demonstrate the potential of membrane systems for the fractionation of proteins even with very similar molecular weights.
Near-minimum-time maneuvers of flexible vehicles - A Liapunov control law design method (1990)

Introduction C recent research has been directed toward the problem of maneuvering a flexible spacecraft. In Ref. 1 we present a fairly comprehensive treatment of this family of problems up through 1985. Other analytical and experimental investigations have been carried out to evaluate 1) feedback control laws based on minimizing quadratic indices; 2) near-minimum-time and switching-type controllers; and 3) implementation issues. The main configuration of interest in the present discussion is similar to the structure of the Vander Velde and He study; however, we address the use of variable torque actuation via a reaction wheel instead of on/off thrusters, utilize Liapunov control design approaches, and establish stable tracking-type control laws for distributed-parameter systems. We present a method for generating globally stable feedback control laws for maneuvers of distributed-parameter structural systems. The method can accommodate nonlinearity, and our proof of stability does not rely on spatially discretizing distributed-parameter systems. The most fundamental developments are related to similar ideas presented in Refs. 3 and 6 and lead to controls that drive the system to a target fixed point in the state space. However, we extend these ideas to achieve near-minimum-time control. We present novel tracking-type control laws to null the departure motion of the system state from an arbitrary smooth target trajectory and develop the global conditions for stability of the closed-loop system. The
Computational Biology using R (2018)

This is an introductory level course on computational biology.
Mutual Authentication Protocol for Low-cost RFID (2005)

I am grateful to Prof. Adi Shamir of the Weizmann
Institute in Israel for his precious comments and kind
advice on our protocol during his visit to ICU during
Asiacryt2004.
Integrating Torrefaction in the Wood Pellet Industry: A Critical Review (2016)

As an established bioenergy industry, the global wood pellet sector is ideally positioned to adopt biomass torrefaction technologies. In this review, potential benefits and challenges of integrating torrefaction within the pellet industry are reviewed and the required technological interventions to enable this integration are analyzed. It is apparent that integration would accelerate the commercialization of biomass torrefaction and benefit the wood pellet industry, torrefaction developers, as well as coal-based utilities. Torrefied pellets are expected to have distinct applications in power generation and help coal-based utilities to reduce their emission levels and comply with increasingly stringent regulations. Co-firing coal with black pellets requires little-to-no retrofit of the existing power plant and, therefore, can offer a low-cost solution. Two potential pathways, in either an upstream or downstream configuration, for retrofitting torrefaction within a white pellet facility are assessed. A successful upstream integration can potentially produce highly dense and durable torrefied pellets. However, the current limitations with this approach are (a) greater reactor volume required for torrefying wood chips and consequently high capital expenses (CAPEX); (b) difficulty in densification; (c) frequent maintenance requirements due to the abrasive nature of torrefied biomass; and (d) safety concerns from fine generation. Torrefaction as a downstream operation, wherein white pellets are subsequently torrefied to produce black pellets, has the benefit of being a simple bolt-on integration. Downstream integration eliminates the need for additional grinding and pelletizing capacity, while minimizing plant-wide contamination due to dust generated from the processing of torrefied biomass. Furthermore, CAPEX can be reduced, as a typical torrefier has significantly higher throughput when processing pellets compared to wood chips. The limitation of downstream integration includes the potential compromise in pellet quality, especially a loss in strength and density. While the benefits of integrating torrefaction are numerous, the techno-economics for each pathway should be further examined.
<i>In vitro</i> growth of murine T cells. V. The isolation and growth of lymphoid cells infiltrating syngeneic solid tumors. (1980)

A method has been developed for isolating and growing lymphoid cells infiltrating murine solid tumors. When tumor cell suspensions are placed in T cell growth factor (TCGF) lymphoid cells and not tumor cells proliferate. By 7 to 9 days lymphoid cells free of tumor can be harvested and grown continuously in TCGF. The growth of these cells is dependent on the presence of TCGF but not on the presence of concanavalin-A. Tumor cell suspensions that have been freed of T lymphoid cells by treatment with anti-Thy-1.2 serum and complement or by fractionation on Ficoll gradients exhibit no cell out-growth in TCGF. The lymphoid cells growing in TCGF exhibit significant cytotoxicity for syngeneic tumor cells and normal fibroblasts grown in culture but do no lyse normal lymphoid cells.
Multi-view multi-label active learning for image classification (2009)

Image classification is an important topic in multimedia analysis, among which multi-label image classification is a very challenging task with respect to the large demand for human annotation of multi-label samples. In this paper, we propose a multi-view multi-label active learning strategy, which integrates the mechanism of active learning and multi-view learning. On one hand we explore the sample and label uncertainties within each view; on the other hand we capture the uncertainty over different views based on multi-view fusion. Then the overall uncertainty along the sample, label and view dimensions are obtained to detect the most informative sample-label pairs. Experimental results demonstrate the effectiveness of the proposed scheme.
Technetium-99m-iminodiacetic acid organic anions: Review of biokinetics and clinical application in hepatology (1989)

Technetium-99m-labeled iminodiacetic acid analogs are a new class of organic anions, taken up and secreted by hepatocyte into hepatic bile by a carrier-mediated organic anion pathway. They provide a new dimension in the assessment of pathophysiology and morphology of the hepatobiliary system. The amount of uptake and the rapidity of its elimination from the liver is dependent upon the structural configuration of the agent as well as the functional integrity of the hepatocyte and the patency of the biliary system. The clinical areas for application are wide and include most of the hepatobiliary diseases. Technetium-99m-iminodiacetic acid, an agent well suited for both planar and single photon tomographic scintigraphy, is ideal for early diagnosis prior to anatomical changes in the hepatobiliary system. The data collection directly from the liver provides quantitation of both regional and global liver diseases. The count-based method for measuring gallbladder emptying overcomes the theoretical disadvantages of geometric tests. Biokinetics and current clinical application of six of the 99mTc-iminodiacetic acid agents are reviewed, and the potential future clinical and research areas of application are indicated.
Stage‐specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis (2006)

To identify sequential alterations of the genome, transcriptome, and proteome during colorectal cancer progression, we have analyzed tissue samples from 36 patients, including the complete mucosa-adenoma-carcinoma sequence from 8 patients. Comparative genomic hybridization (CGH) revealed patterns of stage specific, recurrent genomic imbalances. Gene expression analysis on 9K cDNA arrays identified 58 genes differentially expressed between normal mucosa and adenoma, 116 genes between adenoma and carcinoma, and 158 genes between primary carcinoma and liver metastasis (P < 0.001). Parallel analysis of our samples by CGH and expression profiling revealed a direct correlation of chromosomal copy number changes with chromosome-specific average gene expression levels. Protein expression was analyzed by two-dimensional gel electrophoresis and subsequent mass spectrometry. Although there was no direct match of differentially expressed proteins and genes, the majority of them belonged to identical pathways or networks. In conclusion, increasing genomic instability and a recurrent pattern of chromosomal imbalances as well as specific gene and protein expression changes correlate with distinct stages of colorectal cancer progression. Chromosomal aneuploidies directly affect average resident gene expression levels, thereby contributing to a massive deregulation of the cellular transcriptome. The identification of novel genes and proteins might deliver molecular targets for diagnostic and therapeutic interventions.
Control of Plant Virus Diseases by Pathogen-Derived Resistance in Transgenic Plants (1993)

Plant viruses have an enormous negative impact on agricultural crop production throughout the world, and, consequently, agronomists and plant pathologists have devoted considerable effort toward controlling virus diseases during this century. Prior to the advent of genetic engineering, traditional plant breeding methodology was sometimes successfully applied to develop resistance to viruses of agronomically important crops. In addition, standard techniques of plant pathology, including quarantine, eradication, crop rotation, and certified virus-free stock, have been important tools to control virus diseases, although each has disadvantages, such as expense, questionable effectiveness, and lack of reliability on a yearly basis. The prospects for pathogen-mediated intervention in virus disease development were first realized in 1929 when H.H. McKinney demonstrated that tobacco could be protected from infection by a severe strain of TMV by prior inoculation with
Isonitrile, I. Darstellung von Isonitrilen aus monosubstituierten Formamiden durch Wasserabspaltung (1960)

Abstract Es wird über die Darstellung von Isonitrilen aus monosubstituierten Formamiden durch Wasserabspaltung mittels Phosphoroxychlorids in Gegenwart von Pyridin oder Kalium‐tert.‐butylat berichtet. An 18 Beispielen wird gezeigt, daß die Methode allgemein anwendbar ist und auch die Darstellung von Isonitrilen erlaubt, die bisher nicht zugänglich waren. Die Konstitutionsabhängigkeit der UV‐Absorption sowie der IR‐Absorptions‐Frequenzen und Intensitäten von Isonitrilen werden diskutiert.
Novel members of the mitogen-activated protein kinase activator family in Xenopus laevis. (1993)

Mitogen-activated protein (MAP) kinases comprise an evolutionarily conserved family of proteins that includes at least three vertebrate protein kinases (p42, p44, and p55 MAPK) and five yeast protein kinases (SPK1, MPK1, HOG1, FUS3, and KSS1). Members of this family are activated by a variety of extracellular agents that influence cellular proliferation and differentiation. In Saccharomyces cerevisiae, there are multiple physiologically distinct MAP kinase activation pathways composed of structurally related kinases. The recently cloned vertebrate MAP kinase activators are structurally related to MAP kinase activators in these yeast pathways. These similarities suggest that homologous kinase cascades are utilized for signal transduction in many, if not all, eukaryotes. We have identified additional members of the MAP kinase activator family in Xenopus laevis by a polymerase chain reaction-based analysis of embryonic cDNAs. One of the clones identified (XMEK2) encodes a unique predicted protein kinase that is similar to the previously reported activator (MAPKK) in X. laevis. XMEK2, a highly expressed maternal mRNA, is developmentally regulated during embryogenesis and expressed in brain and muscle. Expression of XMEK2 in yeast cells suppressed the growth defect associated with loss of the yeast MAP kinase activator homologs, MKK1 and MKK2. Partial sequence of a second cDNA clone (XMEK3) identified yet another potential MAP kinase activator. The pattern of expression of XMEK3 is distinct from that of p42 MAPK and XMEK2. The high degree of amino acid sequence similarity of XMEK2, XMEK3, and MAPKK suggests that these three are related members of an amphibian family of protein kinases involved in the activation of MAP kinase. Discovery of this family suggests that multiple MAP kinase activation pathways similar to those in yeast cells exist in vertebrates.
Stable and unstable phases of a diblock copolymer melt (1994)

Using self-consistent field theory, we examine microphases of diblock copolymers and find, in addition to lamellar, hexagonal, and cubic phases, a stable gyroid phase which occurs between the lamellar and hexagonal ones. It terminates at a triple point, with a lamellar to hexagonal transition occurring in the weak-segregation limit. Other phases of experimental interest are studied, and we describe the regions in which they are most nearly stable.
Energy-Efficient Scheduling for Real-Time Systems on Dynamic Voltage Scaling (DVS) Platforms (2007)

Energy-efficient designs have played import roles for hardware and software implementations for a decade. With the advanced technology of VLSI circuit designs, energy-efficiency can be achieved by adopting the dynamic voltage scaling (DVS) technique. In this paper, we survey the studies for energy-efficient scheduling in real-time systems on DVS platforms to cover both theoretical and practical issues.
A quantitative study of differentiated services for the Internet (2000)

The Differentiated Services architecture provides router mechanisms for aggregate traffic, and edge mechanisms for individual flows, that together can be used to build services with varying delay and loss behaviors. In this paper, we compare the loss and delay behaviors that can be provided using the services based on combinations of two router mechanisms, threshold dropping and priority scheduling and two packet marking mechanisms, edge-discarding and edge-marking. In the first part of our work, we compare the delay and loss behaviors of the two router mechanisms coupled with edge-discarding for a wide range of traffic arrivals. We observe that priority scheduling provides lower expected delays to preferred traffic than threshold dropping. In addition, we find that a considerable additional link bandwidth is needed with threshold dropping to provide same delay behavior as priority scheduling. We further observe little difference in the loss incurred by preferred traffic under both router mechanisms, except when sources are extremely bursty, in which case threshold dropping performs better. In the second part of our work, we examine the throughput of a TCP connection that uses a service built upon threshold dropping and edge-marking. Our analysis shows that a significant improvement in throughput can be achieved. However, we find that in order to fully achieve the benefit of such a packet marking, the TCP window must take the edge-marking mechanism into consideration.
Vehicle Powertrain Connected Route Optimization for Conventional, Hybrid and Plug-in Electric Vehicles (2016)

Most navigation systems use data from satellites to provide drivers with the shortest-distance, shortest-time or highway-preferred paths. However, when the routing decisions are made for advanced vehicles, there are other factors affecting cost, such as vehicle powertrain type, battery state of charge (SOC) and the change of component efficiencies under traffic conditions, which are not considered by traditional routing systems. The impact of the trade-off between distance and traffic on the cost of the trip might change with the type of vehicle technology and component dynamics. As a result, the least-cost paths might be different from the shortest-distance or shortest-time paths. In this work, a novel routing strategy has been proposed where the decision-making process benefits from the aforementioned information to result in a least-cost path for drivers. We integrate vehicle powertrain dynamics into route optimization and call this strategy as Vehicle Powertrain Connected Route Optimization (VPCRO). We find that the optimal paths might change significantly for all types of vehicle powertrains when VPCRO is used instead of shortest-distance strategy. About 81% and 58% of trips were replaced by different optimal paths with VPCRO when the vehicle type was Conventional Vehicle (CV) and Electrified Vehicle (EV), respectively. Changed routes had reduced travel costs on an average of 15% up to a maximum of 60% for CVs and on an average of 6% up to a maximum of 30% for EVs. Moreover, it was observed that 3% and 10% of trips had different optimal paths for a plug-in hybrid electric vehicle, when initial battery SOC changed from 90% to 60% and 40%, respectively. Paper shows that using sensory information from vehicle powertrain for route optimization plays an important role to minimize travel costs.
A sulfur isotope study of base metal mineralization in the Willyama Complex, western New South Wales, Australia (1975)

The Willyama Complex in western New South Wales, Australia, is characterized by the presence of both stratiform and vein-type lead-silver-zinc mineralization; these are known, respectively, as the Broken Hill type (of which the main Broken Hill Lode is the most important example) and the Thackaringa type. Isotopic similarity of the sulfur from the two types of deposits supports the hypothesis that the Thackaringa-type veins were derived from the Broken Hill-type mineralization, possibly during retrograde metamorphism of the Willyama Complex.Variations in sulfur isotope composition among individual Broken Hill-type deposits are consistent with a contribution of sulfur from more than one source, and a multi-basin model is proposed, with the variation being due primarily to differences in the relative proportion of biogenic sulfide contributed in each basin.Although delta 34 S sp-gn measurements show considerable variation, a temperature of metamorphism of the main Broken Hill Lode of the order of 700 degrees C is indicated.
Dehydrooligopeptides. XIV. Syntheses of 2-[(<i>Z</i>)-1-Amino-1-alken-1-yl]oxazole-4-carboxylic Acid and the Main Common Skeleton of Thiostrepton Peptide Antibiotics, A10255G and J (1996)

Abstract The practical synthesis of a unique dehydropentapeptide (2), the common main skeleton of thiostrepton macrocyclic peptide antibiotics, A10255G and J, is described. Peptide 2 is constructed from a novel 2-[(Z)-1-amino-1-propen-1-yl]oxazole-4-carboxylic acid, 2-(1-aminomethyl)- and 2-[(S)-1-aminoethyl]thiazole-4-carboxylic acid residues, besides L-threonine and dehydroalanine residues at the N- and C-termini, respectively. First, the general syntheses of various 2-[(Z)-1-amino-1-alken-1-yl]oxazole-4-carboxylic acid derivatives (11) and preparation of N-terminal dehydrodipeptides (17) containing the acid (11a) were done. Subsequent coupling of 17 with the C-terminal tripeptide comprised of the above two 2-(aminoalkyl)thiazole-4-carboxylic acid moieties (22) and (23) and serine moiety (4), and final β-elimination were tried and gave the desired protected 2 [(P)-2].
Cellular Immune Responses Are Essential for the Development of <i>Helicobacter felis</i> -Associated Gastric Pathology (1999)

The bacteria Helicobacter pylori is a major human pathogen that infects over half of the world's population. Infection initiates a series of changes in the gastric mucosa, beginning with atrophic gastritis and leading in some patients to peptic ulcer disease, mucosa-associated lymphomas, and gastric adenocarcinoma. Although this cascade of events clearly occurs, little is known about the role of the host immune response in disease progression. We have utilized the C57BL/6 Helicobacter felis mouse model to critically analyze the role of the adaptive immune response in the development of Helicobacter-associated gastric pathology. Infection of B and T cell-deficient RAG-1-/- mice or T cell-deficient TCRbetadelta-/- mice with H. felis resulted in high levels of colonization, but no detectable gastric pathology. Conversely, infection of B cell-deficient microMT mice resulted in severe gastric alterations identical with those seen in immunocompetent C57BL/6-infected mice, including gastric mucosal hyperplasia and intestinal metaplasia. These results demonstrate that the host T cell response is a critical mediator of Helicobacter-associated gastric pathology, and that B cells and their secreted Abs are not the effectors of the immune-mediated gastric pathology seen after H. felis infection. These results indicate that in addition to specific Helicobacter virulence factors, the host immune response is an important determinant of Helicobacter-associated disease.
Microwave Photonic Filter (2009)

For microwave photonic filter can process RF signal directly in the optical domain,its response can be easily tuned and its transfer function can reconfigurate fast,microwave photonic filter become an important research content in microwave photonics.In this paper,we have introduced some filter structures with different light sources and structures based on fiber bragg grating,simply analyzed their function characteristics and shortages.