gebhart/patrepeval huggingface dataset:
A Micromachined Chip-Based Electrospray Source for Mass Spectrometry (1999)

A micromachining process is described for fabricating a mass spectrometry electrospray source on a silicon chip. The process utilizes polymer (parylene) layers to form a system of chambers, filters, channels, and hollow needle structures (electrospray emitters) that extend more than a millimeter beyond the edge of the silicon substrate. The use of photoresist as the sacrificial layer facilitates the creation of long channels. Access to the channel structures on the chip is through a port etched through the silicon substrate that also serves as a sample reservoir. A reusable chip holder consisting of two plastic plates and an elastomer gasket provides the means to mount the chip in front of the mass spectrometer inlet and make electrical and gas connections. The electrospray emitters have tapered tips with 5 microns x 10 microns rectangular openings. The shape of the tip can be varied depending on the shape of the mask used to protect the parylene structures during the final plasma etch. The parylene emitters are physically robust and require only a high electric field to achieve stable electrospray operation over a period of a few hours. Direct comparisons with conventional glass or fused silica emitters indicated very similar performance with respect to signal strength and stability, spectral quality, and endurance. The automated MS/MS analysis of a mixture of tryptic peptides was no more difficult and yielded nearly identical results as the analysis of the same sample using a conventional nanospray device. This work demonstrates that an efficient electrospray interface to mass spectrometry can be integrated with other on-chip structures and mass-produced using a batch process.
Phase-conjugate interferometric analysis of thin films (1991)

We used phase-conjugate interferometry to determine the optical parameters of absorbing thin films: the refractive index, the extinction coefficient, and the thickness. The use of self-pumped phase-conjugate reflectors in place of mirrors causes optical distortions in the substrate to cancel and makes the interferometer self-aligning. The results of measurement of single-layer absorbing thin films are presented.
Wastewater treatment and algal production in high rate algal ponds with carbon dioxide addition (2010)

High rate algal ponds (HRAPs) provide improved wastewater treatment over conventional wastewater stabilisation ponds; however, algal production and recovery of wastewater nutrients as algal biomass is limited by the low carbon:nitrogen ratio of wastewater. This paper investigates the influence of CO(2) addition (to augment daytime carbon availability) on wastewater treatment performance and algal production of two pilot-scale HRAPs operated with different hydraulic retention times (4 and 8 days) over a New Zealand Summer (November-March, 07/08). Weekly measurements were made of influent and effluent flow rate and water qualities, algal and bacterial biomass production, and the percentage of algae biomass harvested in gravity settling units. This research shows that the wastewater treatment HRAPs with CO(2) addition achieved a mean algal productivity of 16.7 g/m(2)/d for the HRAP(4d) (4 d HRT, maximum algae productivity of 24.7 g/m(2)/d measured in January 08) and 9.0 g/m(2)/d for the HRAP(8d) (8 d HRT)). Algae biomass produced in the HRAPs was efficiently harvested by simple gravity settling units (mean harvested algal productivity: 11.5 g/m(2)/d for the HRAP(4d) and 7.5 g/m(2)/d for the HRAP(8d) respectively). Higher bacterial composition and the larger size of algal/bacterial flocs of the HRAP(8d) biomass increased harvestability (83%) compared to that of HRAP(4d) biomass (69%).
Identification of healed terminal DNA fragments in linear minichromosomes of Schizosaccharomyces pombe. (1987)

The minichromosome Ch16 of the fission yeast Schizosaccharomyces pombe is derived from the centromeric region of chromosome III. We show that Ch16 and a shorter derivative, Ch12, made by gamma-ray cleavage, are linear molecules of 530 and 280 kilobases, respectively. Each minichromosome has two novel telomeres, as shown by genomic Southern hybridization with an S. pombe telomere probe. Comparison by hybridization of the minichromosomes and their chromosomal counterparts showed no signs of gross rearrangement. Cosmid clones covering the ends of the long arms of Ch16 and Ch12 were isolated, and subcloned fragments that contained the breakage sites were identified. They are apparently unique in the genome. By hybridization and Bal 31 digestion, the ends appear to consist of the broken-end sequences directly associated with short stretches (about 300 base pairs) of new DNA that hybridizes to a cloned S. pombe telomere. They do not contain the telomere-adjacent repeated sequences that are present in the normal chromosomes. The sizes of the short telomeric stretches are roughly the same as those of the normal chromosomes. Our results show that broken chromosomal ends in S. pombe can be healed by the de novo addition of the short telomeric repeats. The formation of Ch16 must have required two breakage-healing events, whereas a single cleavage-healing event in the long arm of Ch16 yielded Ch12.
Targeted mutations that ablate either the adenylate cyclase or hemolysin function of the bifunctional cyaA toxin of Bordetella pertussis abolish virulence. (1992)

Bordetella pertussis, the causative agent of whooping cough, secretes several toxins implicated in this disease. One of these putative virulence factors is the adenylate cyclase (AC) toxin that elevates intracellular cAMP in eukaryotic cells to cytotoxic levels. This toxin is a bifunctional protein comprising both AC and hemolysin (HLY) enzymatic domains. The gene encoding the AC toxin (cyaA) is expressed as part of an operon that includes genes required for secretion or activation of the toxin. Because of this genetic organization, it is difficult to create B. pertussis mutants of cyaA that are ablations of a single enzyme function by conventional means, such as transposon mutagenesis. Therefore, to clarify the role of individual toxin functions in the virulence of B. pertussis, we have used site-directed or deletion mutagenesis and genetic recombination to specifically target the cyaA gene of B. pertussis to produce mutants that lack only the AC or HLY activity of this toxin. A point mutant of B. pertussis with abolished AC catalytic activity was greater than 1000 times less pathogenic to newborn mice than wild-type bacteria, directly demonstrating the importance of the AC toxin in pertussis virulence. Similarly, an in-frame deletion mutant of B. pertussis that lacks HLY is equally avirulent, supporting observations that the HLY domain plays a critical role in AC toxin entry into cells. Furthermore, the genetically inactivated AC toxin produced by the point mutant is antigenically similar to the native toxin, suggesting that this strain may be useful in the development of pertussis component vaccines.
<title>Determination and correction of the wobble of a C-arm gantry</title> (2000)

Digital subtraction angiographic image sequences of a calibration phantom are acquired at 30 frames per second from a C-arm gantry covering an angular arc of more than 180 degrees rotating at 40 degrees/s. For each frame, after XRII distortion correction, the relation between the source and its image plane orientation in 3D space is estimated from fiducial markers in the calibration phantom. This gives a mapping between the three-dimensional calibration object and its two- dimensional projection at each gantry angle. We derive eleven mapping coefficients as a function of gantry angle. We use the coefficients to backproject the contribution to any physical voxel. Thus the wobble correction is incorporated directly into cone-beam backprojection. In the absence of gantry wobble, this method is equivalent to the short-scan Feldkamp algorithm, any deviation of the coefficients from those perfect values can be taken as a measure of the gantry wobble. The mapping method requires no special knowledge of the system geometry and any wobble, twisting of the C-arm or XRII during rotation is automatically included. A phantom with tungsten- carbide beads is reconstructed. Accuracy is obtained by comparing reprojections of the center of the tungsten beads with their known values.
An Optically Assisted Program Method for Capacitorless 1T-DRAM (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> This work is aimed at a novel program method that is assisted by light for capacitorless 1T-DRAM based on parasitic bipolar junction transistor operation. Experimental results clearly show that a flash of light triggers a distinctive binary memory state in the capacitorless 1T-DRAM. During the operation of the 1T-DRAM, the gate voltage is sustained at a negative, constant value. The sensing margin is 54 <formula formulatype="inline"><tex Notation="TeX">$\mu \hbox{A}$</tex></formula> and the hold state corresponding to the data retention time is retained over a few seconds. The proposed program method can therefore be considered as a promising candidate for future DRAM applications based on an optical interconnection system. </para>
Sequences in the Coding Region of Clotting Factor VIII Act as Dominant Inhibitors of RNA Accumulation and Protein Production (1993)

A variety of retroviral vectors for transduction and expression of clotting factor VIII (FVIII) were constructed by using truncated forms of a FVIII cDNA lacking part or all of the nonessential B-domain sequences. Both the titer of virus and FVIII protein production from the vectors was about 2 orders of magnitude lower than the virus titer and protein production from identical retroviral vectors containing other cDNAs, including clotting factor IX. These decreases could be entirely explained by an observed 100-fold lower accumulation of vector RNAs containing the FVIII sequences in comparison to vectors containing other cDNA sequences. Deletion analysis of one of the FVIII vectors demonstrated that diffuse sequences within the FVIII coding region had a deleterious effect upon vector titer and RNA accumulation. One inhibitory signal could be localized to a 1.2-kb stretch of DNA, but further localization was not possible as additional size reduction abolished the activity. These results indicate that expression of FVIII is regulated by signals within FVIII coding sequence that result in decreased RNA accumulation and FVIII protein production. Alteration of these inhibitory signals to permit high-level FVIII production may be difficult due to the wide distribution of these signals within the coding region of the protein.
Neurotrophic and Neurotoxic Effects of Amyloid β Protein: Reversal by Tachykinin Neuropeptides (1990)

The amyloid beta protein is deposited in the brains of patients with Alzheimer's disease but its pathogenic role is unknown. In culture, the amyloid beta protein was neurotrophic to undifferentiated hippocampal neurons at low concentrations and neurotoxic to mature neurons at higher concentrations. In differentiated neurons, amyloid beta protein caused dendritic and axonal retraction followed by neuronal death. A portion of the amyloid beta protein (amino acids 25 to 35) mediated both the trophic and toxic effects and was homologous to the tachykinin neuropeptide family. The effects of the amyloid beta protein were mimicked by tachykinin antagonists and completely reversed by specific tachykinin agonists. Thus, the amyloid beta protein could function as a neurotrophic factor for differentiating neurons, but at high concentrations in mature neurons, as in Alzheimer's disease, could cause neuronal degeneration.
Three-terminal adaptive nematic liquid-crystal lens device (1994)

A 1 mm x 1 mm nematic liquid-crystal three-terminal device for optical beam forming (focusing/spoiling) is fabricated. A thin-film-resistor network on the device substrate layer is used to control the voltages on the 98 internal lens electrodes by use of only one variable external driver. By using a high-resistance thin-film layer of amorphous silicon under the 98-element parallel electrode structure layer, we generate a near-continuous index perturbation to form a cylindrical lens. The focal length of this lens is continuously variable from inifinity to 12 cm by use of a variable 1-4-V-peak 1-kHz square-wave external terminal control signal.
New approaches in metastatic melanoma: biological and molecular targeted therapies (2007)

Classical metastatic melanoma therapy is disappointing but important progress has been made in the understanding of melanoma biology. Genetic lesions and several intracellular signaling pathways that could serve as targets for novel therapy have been identified and a number of new agents are under evaluation. Promising tumor cell targets were identified in the cell membrane, cytoplasm and nucleus. New therapeutic approaches, besides monoclonal antibodies and vaccination, include an increasing number of small molecules that have been shown to interfere restrictively with intracellular signaling pathways in melanoma and decrease proliferation, survival, migration or invasion. Other agents can interfere with stromal components of melanoma, such as angiogenesis and components of the immune system.
Parallel Computer Architecture: A Hardware/Software Approach (1998)

The most exciting development in parallel computer architecture is the convergence of traditionally disparate approaches on a common machine structure. This book explains the forces behind this convergence of shared-memory, message-passing, data parallel, and data-driven computing architectures. It then examines the design issues that are critical to all parallel architecture across the full range of modern design, covering data access, communication performance, coordination of cooperative work, and correct implementation of useful semantics. It not only describes the hardware and software techniques for addressing each of these issues but also explores how these techniques interact in the same system. Examining architecture from an application-driven perspective, it provides comprehensive discussions of parallel programming for high performance and of workload-driven evaluation, based on understanding hardware-software interactions.


* synthesizes a decade of research and development for practicing engineers, graduate students, and researchers in parallel computer architecture, system software, and applications development

* presents in-depth application case studies from computer graphics, computational science and engineering, and data mining to demonstrate sound quantitative evaluation of design trade-offs 

* describes the process of programming for performance, including both the architecture-independent and architecture-dependent aspects, with examples and case-studies

* illustrates bus-based and network-based parallel systems with case studies of more than a dozen important commercial designs

Table of Contents

1 Introduction 
2 Parallel Programs 
3 Programming for Performance 
4 Workload-Driven Evaluation 
5 Shared Memory Multiprocessors 
6 Snoop-based Multiprocessor Design 
7 Scalable Multiprocessors
8 Directory-based Cache Coherence
9 Hardware-Software Tradeoffs 
10 Interconnection Network Design 
11 Latency Tolerance 
12 Future Directions 
APPENDIX A Parallel Benchmark Suites
A relational model of data for large shared data banks (1983)

Future users of large data banks must be protected from having to know how the data is organized in the machine (the internal representation). A prompting service which supplies such information is not a satisfactory solution. Activities of users at terminals and most application programs should remain unaffected when the internal representation of data is changed and even when some aspects of the external representation are changed. Changes in data representation will often be needed as a result of changes in query, update, and report traffic and natural growth in the types of stored information. Existing noninferential, formatted data systems provide users with tree-structured files or slightly more general network models of the data. In Section 1, inadequacies of these models are discussed. A model based on n -ary relations, a normal form for data base relations, and the concept of a universal data sublanguage are introduced. In Section 2, certain operations on relations (other than logical inference) are discussed and applied to the problems of redundancy and consistency in the user's model.
Identification of a Human Cyclin D1-Derived Peptide that Induces Human Cytotoxic CD4 T Cells (2009)

Cyclin D1 is over-expressed in various human tumors and therefore can be a potential oncogenic target antigen. However, only a limited number of T cell epitopes has been characterized. We aimed at identifying human cyclin D1-derived peptides that include both CD4 and CD8 T cell epitopes and to test if such multi-epitope peptides could yield improved cytotoxic CD8 T cell responses as well as cytotoxic CD4 T cells. Five HLA-DR.B1-binding peptides containing multiple overlapping CD4 epitopes and HLA-A0201-restricted CD8 T cell epitopes were predicted by computer algorithms. Immunogenicity of the synthetic peptides was assessed by stimulating T cells from healthy donors in vitro and the epitope recognition was measured by IFN-gamma ELISPOT and (51)Chromium release assays. A HLA-DR.B1 peptide, designed "DR-1", in which a HLA-A0201-binding epitopes (D1-1) was imbedded, induced CD3 T cell responses against both DR-1 and D1-1 peptides in IFN-gamma ELISPOT assay. This suggested processing of the shorter D1-1 epitope from the DR-1 sequence. However, only DR-1-stimulated CD4 or CD3 T cells possessed cytotoxicity against peptide-pulsed autologous DCs and a cancer cell line, that expresses a high level of cyclin D1. Monoclonal antibody to HLA-DR abrogated the epitope-specific responses of both CD3 and CD4 T cells, demonstrating class II-mediated killing. Our studies suggest a possible role of CD4 T cells in anti-tumor immunity as cytotoxic effectors against HLA-DR expressing cancers and provide a rationale for designing peptide vaccines that include CD4 epitopes.
A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site. (1982)

We have identified the promoter region of the GAL10 gene (whose product is UDP-galactose epimerase) of Saccharomyces cerevisiae; this promoter mediates galactose induction of transcription in conjunction with the product of the GAL4 regulatory gene. This identification was achieved by excising a 365-base-pair fragment of GAL10 leader DNA with a GAL10 proximal endpoint greater than 100 base pairs upstream of the transcriptional start site and substituting it in place of the upstream activation site of the CYC1 (iso-1-cytochrome c) promoter [Guarente, L. & Ptashne, M. (1981) Proc. Natl. Acad. Sci. USA 78, 2199-2203]. The hybrid promoter is composed of DNA encoding CYC1 mRNA start sites and the GAL segment upstream of these sites. This promoter is regulated in a manner analogous to GAL10; i.e., it is induced by galactose and responds to mutations in the GAL4 and GAL80 regulatory loci. The activity of the hybrid promoter requires sequences in the region of the CYC1 mRNA start sites but does not require a precise spacing between these sequences and the GAL segment. The transposed GAL segment appears not to contain sequences that mediate glucose repression. Thus, the picture of the GAL10 promoter that emerges is one of an upstream activation site that responds to the GAL4 product plus galactose, and a region of transcription initiation that may contain sequences that mediate glucose repression. Experiments employing strains inducible (GAL80) or constitutive (gal80) for GAL10 expression indicate that an additional component of glucose repression is inducer exclusion.
Cyclodextrin-Containing Polymers. 1. Preparation of Polymers (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclodextrin-Containing Polymers. 1. Preparation of PolymersAkira Harada, Masaoki Furue, and Shun-ichi NozakuraCite this: Macromolecules 1976, 9, 5, 701–704Publication Date (Print):September 1, 1976Publication History Published online1 May 2002Published inissue 1 September 1976https://pubs.acs.org/doi/10.1021/ma60053a003https://doi.org/10.1021/ma60053a003research-articleACS PublicationsRequest reuse permissionsArticle Views1543Altmetric-Citations115LEARN 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
Molecular Cloning and Characterization of a Human Mitochondrial Ceramidase (2000)

We have recently purified a rat brain membrane-bound nonlysosomal ceramidase (El Bawab, S., Bielawska, A., and Y. A. Hannun (1999) J. Biol. Chem. 274, 27948-27955). Using peptide sequences obtained from the purified rat brain enzyme, we report here the cloning of the human isoform. The deduced amino acid sequence of the protein did not show any similarity with proteins of known function but was homologous to three putative proteins from Arabidospis thaliana, Mycobacterium tuberculosis, and Dictyostelium discoideum. Several blocks of amino acids were highly conserved in all of these proteins. Analysis of the protein sequence revealed the presence at the N terminus of a signal peptide followed by a putative myristoylation site and a putative mitochondrial targeting sequence. The predicted molecular mass was 84 kDa, and the isoelectric point was 6.69, in agreement with rat brain purified enzyme. Northern blot analysis of multiple human tissues showed the presence of a major band corresponding to a size of 3.5 kilobase. Analysis of this major band on the blot indicated that the enzyme is ubiquitously expressed with higher levels in kidney, skeletal muscle, and heart. The enzyme was then overexpressed in HEK 293 and MCF7 cells using the pcDNA3. 1/His-ceramidase construct, and ceramidase activity (at pH 9.5) increased by 50- and 12-fold, respectively. Next, the enzyme was characterized using lysate of overexpressing cells. The results confirmed that the enzyme catalyzes the hydrolysis of ceramide in the neutral alkaline range and is independent of cations. Finally, a green fluorescent protein-ceramidase fusion protein was constructed to investigate the localization of this enzyme. The results showed that the green fluorescent protein-ceramidase fusion protein presented a mitochondrial localization pattern and colocalized with mitochondrial specific probes. These results demonstrate that this novel ceramidase is a mitochondrial enzyme, and they suggest the existence of a topologically restricted pathways of sphingolipid metabolism.