gebhart/patrepeval huggingface dataset:
The Massively Parallel Processor (1985)

From the Publisher:
The development of parallel processing, with the attendant technology of advanced software engineering, VLSI circuits, and artificial intelligence, now allows high-performance computer systems to reach the speeds necessary to meet the challenge of future complex scientific and commercial applications. This collection of articles documents the design of one such computer, a single instruction multiple data stream (SIMD) class supercomputer with 16,834 processing units capable of over 6 billion 8 bit operations per second. It provides a complete description of the Massively Processor (MPP), including discussions of hardware and software with special emphasis on applications, algorithms, and programming. 
This system with its massively parallel hardware and advanced software is on the cutting edge of parallel processing research, making possible AI, database, and image processing applications that were once thought to be inconceivable. massively parallel processor represents the first step toward the large-scale parallelism needed in the computers of tomorrow. Orginally built for a variety of image-processing tasks, it is fully programmable and applicable to any problem with sizeable data demands. 
Contents: History of the MPP, D. Schaefer; Structures for Implementing the Classy Algorithm on the MPP, R. White; Inversion of Positive Definite Matrices on the MPP, R. White; LANDSAT-4 Thematic Mapper Data Processing with the MPP, R. O. Faiss; Fluid Dynamics Modeling, E. J. Gallopoulas; Database Management, E. Davis; List Based Processing on the MPP, J. L. Potter; The Massively Processor System Overvew, K. E. Batcher; Array Unit, K. E.Batcher; Array Control Unit, K. E. Batcher; Staging Memory, K. E. Batcher; PE Design, J. Burkley; Programming the MPP, J. L. Potter; Parallel Pascal and the MPP, A. P Reeves; MPP System Software, K. E. Batcher; MPP Program Development and Simulation, E. J. Gallopoulas. 
J. L. Potter is Associate Professor of Computer Science at Kent State University. Massively Processor is included in the Scientific Computation Series, edited by Dennis Gannon.
High‐level rapid production of full‐size monoclonal antibodies in plants by a single‐vector DNA replicon system (2009)

Plant viral vectors have great potential in rapid production of important pharmaceutical proteins. However, high-yield production of hetero-oligomeric proteins that require the expression and assembly of two or more protein subunits often suffers problems due to the "competing" nature of viral vectors derived from the same virus. Previously we reported that a bean yellow dwarf virus (BeYDV)-derived, three-component DNA replicon system allows rapid production of single recombinant proteins in plants (Huang et al., 2009. Biotechnol Bioeng 103: 706-714). In this article, we report further development of this expression system for its application in high-yield production of oligomeric protein complexes including monoclonal antibodies (mAbs) in plants. We showed that the BeYDV replicon system permits simultaneous efficient replication of two DNA replicons and thus, high-level accumulation of two recombinant proteins in the same plant cell. We also demonstrated that a single vector that contains multiple replicon cassettes was as efficient as the three-component system in driving the expression of two distinct proteins. Using either the non-competing, three-vector system or the multi-replicon single vector, we produced both the heavy and light chain subunits of a protective IgG mAb 6D8 against Ebola virus GP1 (Wilson et al., 2000. Science 287: 1664-1666) at 0.5 mg of mAb per gram leaf fresh weight within 4 days post-infiltration of Nicotiana benthamiana leaves. We further demonstrated that full-size tetrameric IgG complex containing two heavy and two light chains was efficiently assembled and readily purified, and retained its functionality in specific binding to inactivated Ebola virus. Thus, our single-vector replicon system provides high-yield production capacity for hetero-oligomeric proteins, yet eliminates the difficult task of identifying non-competing virus and the need for co-infection of multiple expression modules. The multi-replicon vector represents a significant advance in transient expression technology for antibody production in plants.
Chemoenzymatic Synthesis of Glycosylated Glucagon-like Peptide 1: Effect of Glycosylation on Proteolytic Resistance and in Vivo Blood Glucose-Lowering Activity (2009)

Glucagon-like peptide 1 (7-36) amide (GLP-1) has been attracting considerable attention as a therapeutic agent for the treatment of type 2 diabetes. In this study, we applied a glycoengineering strategy to GLP-1 to improve its proteolytic stability and in vivo blood glucose-lowering activity. Glycosylated analogues with N-acetylglucosamine (GlcNAc), N-acetyllactosamine (LacNAc), and alpha2,6-sialyl N-acetyllactosamine (sialyl LacNAc) were prepared by chemoenzymatic approaches. We assessed the receptor binding affinity and cAMP production activity in vitro, the proteolytic resistance against dipeptidyl peptidase-IV (DPP-IV) and neutral endopeptidase (NEP) 24.11, and the blood glucose-lowering activity in diabetic db/db mice. Addition of sialyl LacNAc to GLP-1 greatly improved stability against DPP-IV and NEP 24.11 as compared to the native type. Also, the sialyl LacNAc moiety extended the blood glucose-lowering activity in vivo. Kinetic analysis of the degradation reactions suggested that the sialic acid component played an important role in decreasing the affinity of peptide to DPP-IV. In addition, the stability of GLP-1 against both DPP-IV and NEP24.11 incrementally improved with an increase in the content of sialyl LacNAc in the peptide. The di- and triglycosylated analogues with sialyl LacNAc showed greatly prolonged blood glucose-lowering activity of up to 5 h after administration (100 nmol/kg), although native GLP-1 showed only a brief duration. This study is the first attempt to thoroughly examine the effect of glycosylation on proteolytic resistance by using synthetic glycopeptides having homogeneous glycoforms. This information should be useful for the design of glycosylated analogues of other bioactive peptides as desirable pharmaceuticals.
Lactam Formation through Aminolysis of α-Amino-γ-butyrolactone. 2-Amino-4-hydroxybutyramides and 1-Aryl 3-Aminopyrrolidin-2-ones (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLactam Formation through Aminolysis of α-Amino-γ-butyrolactone. 2-Amino-4-hydroxybutyramides and 1-Aryl 3-Aminopyrrolidin-2-onesY. Knobler, E. Bonni, and T. SheradskyCite this: J. Org. Chem. 1964, 29, 5, 1229–1236Publication Date (Print):May 1, 1964Publication History Published online1 May 2002Published inissue 1 May 1964https://pubs.acs.org/doi/10.1021/jo01028a059https://doi.org/10.1021/jo01028a059research-articleACS PublicationsRequest reuse permissionsArticle Views254Altmetric-Citations10LEARN 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
Thrombopoietin is a major limiting factor for selective outgrowth of human umbilical cord blood cells in non‐obese diabetic/severe combined immunodeficient recipient mice (2003)

A single dose (0.3 microg) of recombinant human thrombopoietin (TPO) was injected into sublethal irradiated non-obese diabetic/severe combined immunodeficient (NOD/SCID) mice immediately after transplantation of 1.5 x 10(5) purified CD34+ umbilical cord blood (UCB) cells. Bone marrow (BM) was analysed for human cells by immunophenotyping and colony culture at d 35. TPO treatment produced a two- to sixfold increase in the frequency and number of human CD45+ cells. The lineage distributions among the human cells were similar irrespective of TPO treatment; however, a prominent increase was observed in CD71+GpA- cells, reflecting the proliferative stimulus provided by TPO. The frequency of immature CD34+ cells and human granulocyte-macrophage colony-forming units and erythroid burst-forming units in TPO-treated mice was similar to that of untreated mice, but their absolute numbers had increased proportionally to the increase in human cells. The results demonstrate that human TPO is a major limiting factor for multilineage outgrowth of human UCB cells in NOD/SCID mice and can be conveniently supplemented by single-dose treatment immediately after transplantation. TPO did not affect the survival of mice after transplantation and did not significantly increase the number of immature CD34+CD38- cells; secondary transplantation revealed that TPO administration also had no significant effect on long-term repopulation. The findings demonstrate that human TPO is required for proper outgrowth of human haematopoietic stem cells after transplantation. In addition, a single administration of TPO may improve the efficiency and reproducibility of the NOD/SCID mouse assay for human immature transplantable progenitor cells.
Gene Expression Profiling of Blood for the Prediction of Ischemic Stroke (2010)

This study replicated our previously reported gene expression profile in a larger cohort and identified additional genes that discriminate ischemic stroke from relevant control groups. This multigene approach shows potential for a point-of-care test in acute ischemic stroke.
Nucleotide sequence of the yeastILV2gene which encodes acetolactate synthase (1985)

We have determined the nucleotide sequence of the yeast ILV2 gene which codes for the amino acid biosynthetic enzyme acetolactate synthase (ALS). ALS has recently been shown to be the target in bacteria, yeast and plants, of the potent new herbicide sulfometuron methyl. The coding sequence for the ILV2 polypeptide contains 2061 base pairs. Comparison of deduced amino acid sequences indicates considerable conservation between the yeast protein and the large subunits of the E. coli ALS II and ALS III isozymes. A major distinction between the three proteins is the presence of an additional 90 amino acids at the amino terminal of the yeast protein. The amino acid sequence in this region shows similarities to yeast mitochondrial transit sequences and may function as such, since yeast ALS is localized in the mitochondria. Consensus sequences for initiation and termination of transcription that are consistent with the ends of the ILV2 mRNA, as well as general amino acid control regulatory sequences have been identified.
Catalyzed Pyrolysis of Grape and Olive Bagasse. Influence of Catalyst Type and Chemical Treatment (1997)

Catalyzed pyrolysis of grape and olive bagasse under different experimental conditions has been studied. Variables investigated were temperature and type and concentration of catalysts. Experiments were carried out in an isothermal manner. Products of pyrolysis are gases (H2, CO, CO2, and CH4), liquids (methanol, acetone, furfurylic alcohol, phenol, furfural, naphthalene, and o-cresol), and solids (chars). Temperature is a significant variable, yielding increases of fixed carbon content, gases, and to a lesser extent, ash percentage. Catalyst presence also yields increases of solid phase content, but the amount of liquid components decrease. Among catalysts applied those of Fe and Zn are the most advisable to obtain gases. Chemical treatment of bagasses with sulfuric or phosphoric acid washing leads to lower char yields, although fixed carbon content is higher and ash presence diminishes with respect to catalyst pyrolysis without chemical pretreatment. A pyrolysis kinetic study based on gas generation from thermal decomposition of residues has been carried out. From the model proposed, rate constants for the formation of each gas, reaction order of the catalyst, and activation energies were determined.
Micro-coaxial lines for active hybrid-monolithic circuits (2009)

This paper discusses fundamental properties of rectangular micro-coaxial lines fabricated in the PolyStratatrade process for broadband applications from 2-20 GHz. The possible impedance ranges for coaxial lines implemented with both five and eleven Cu layers are discussed and compared with measured results for the lowest impedance (8 Omega) line. Power handling and thermal properties of these miniature lines are analyzed and measured. A 50 Omega line with outer conductor cross-section of 600 mum by 400 mum is experimentally shown to handle 53 W at 2:5 GHz with a 10% duty cycle. Integration with active components is investigated and a 1-10 GHz measurement of a GaN 50 Omega MMIC amplifier shows minimal performance degradation relative to on-wafer measurements.
Disruption of pioneer growth cone guidance in vivo by removal of glycosyl phosphatidylinositol-anchored cell surface proteins (1992)

Cell surface proteins anchored to membranes via covalently attached glycosyl-phosphatidylinositol (GPI) have been implicated in neuronal adhesion, promotion of neurite outgrowth and directed cell migration. Treatment of grasshopper embryos with bacterial phosphatidylinositol-specific phospholipase C (PI-PLC), an enzyme that cleaves the GPI anchor, often induced disruptions in the highly stereotyped migrations of peripheral pioneer growth cones and afferent neuron cell bodies. In distal limb regions of embryos treated with PI-PLC at early stages of pioneer axon outgrowth, growth cones lost their proximal orientation toward the central nervous system (CNS) and turned distally. Pioneer growth cones in treated limbs also failed to make a characteristic ventral turn along the trochanter-coxa (Tr-Cx) segment boundary, and instead continued to grow proximally across the boundary. Treatment at an earlier stage of development caused pre-axonogenesis Cx1 neurons to abandon their normal circumferential migration and reorient toward the CNS. None of these abnormal phenotypes were observed in limbs of untreated embryos or embryos exposed to other phospholipases that do not release GPI-anchored proteins. Incubation of embryos with PI-PLC effectively removed immunoreactivity for fasciclin I, a GPI-anchored protein expressed on a subset of neuronal surfaces. These results suggest that cell surface GPI-anchored proteins are involved in pioneer growth cone guidance and in pre-axonogenesis migration of neurons in the grasshopper limb bud in vivo.
Staphylococcus aureus exopolysaccharide in vivo demonstrated by immunomagnetic separation and electron microscopy (1989)

Staphylococcus aureus strains were separated from mastitis milk samples without cultivation by using monodisperse magnetic polymer particles coated with polyclonal antiserum against an encapsulated S. aureus strain. Exopolysaccharide was verified by transmission electron microscopy and the serum soft-agar culture technique. Capsular polysaccharide was found on virtually all clinical isolates. Surface protein A and S. aureus-specific cell wall components were masked when the strains were cultured on an exopolysaccharide-promoting medium. Masking of surface determinants was dependent on their concentration on the bacterial surface as well as on exopolysaccharide abundance. The polysaccharide layer on in vivo bacteria was reduced markedly after just one transfer from milk to blood agar plates but was reexpressed after culturing was done on a capsule-generating medium.
Dead-in-shell positions of near-term ostrich embryos (2017)

The patterns of embryonic development in ostriches, especially in the last stage of hatching, are still not well understood. This study examined between 3468 and 3484 dead-in-shell (DIS) eggs with chicks that died between day 35 and day 42 of artificial incubation. Most DIS chicks were positioned correctly with their heads towards the air cell (52.6%). DIS chicks that positioned their heads near the equator of the egg amounted to 46.5%, while a small percentage (0.9%) were positioned with their upper body towards the bottom of the egg. More DIS chicks tended to pip internally near the equator of the egg (37.6%) than DIS chicks that pipped internally through the membranes into the air cell (34.4%). Most DIS chicks had their heads turned in the correct position from left to right (54.4%), though their beaks were mostly positioned towards the air cell (52.9%). The highest percentage of DIS chicks had their feet in the upwards position (52.4%), while 46% had their feet across or below the head. The wings of all DIS chicks were positioned next to the body. Results from the study showed that most of the DIS chicks were roughly in the correct position, but were still unable to hatch. This warrants future research to investigate the reasons that prevent correctly positioned chicks from hatching.Keywords: Head position, malposition, pipping position
Bug Auctions: Vulnerability Markets Reconsidered (2004)

Measuring software security is difficult and inexact; as a result, the market for secure software has been compared to a `market of lemons.&amp;apos; Schechter has proposed a vulnerability market in which software producers offer a time-variable reward to free-market testers who identify vulnerabilities. This vulnerability market can be used to improve testing and to create a relative metric of product security. This paper argues that such a market can best be considered as an auction; auction theory is then used to tune the structure of this `bug auction&amp;apos; for efficiency and to better defend against attacks. The incentives for the software producer are also considered, and some fundamental problems with the concept are articulated.
Phase-change random access memory: A scalable technology (2008)

Nonvolatile RAM using resistance contrast in phase-change materials [or phase-change RAM (PCRAM)] is a promising technology for future storage-class memory. However, such a technology can succeed only if it can scale smaller in size, given the increasingly tiny memory cells that are projected for future technology nodes (i.e., generations). We first discuss the critical aspects that may affect the scaling of PCRAM, including materials properties, power consumption during programming and read operations, thermal cross-talk between memory cells, and failure mechanisms. We then discuss experiments that directly address the scaling properties of the phase-change materials themselves, including studies of phase transitions in both nanoparticles and ultrathin films as a function of particle size and film thickness. This work in materials directly motivated the successful creation of a series of prototype PCRAM devices, which have been fabricated and tested at phase-change material cross-sections with extremely small dimensions as low as 3 nm × 20 nm. These device measurements provide a clear demonstration of the excellent scaling potential offered by this technology, and they are also consistent with the scaling behavior predicted by extensive device simulations. Finally, we discuss issues of device integration and cell design, manufacturability, and reliability.
Distance browsing in spatial databases (1999)

We compare two different techniques for browsing through a collection of spatial objects stored in an R-tree spatial data structure on the basis of their distances from an arbitrary spatial query object. The conventional approach is one that makes use of a k -nearest neighbor algorithm where k is known prior to the invocation of the algorithm. Thus if m &lt; k neighbors are needed, the k -nearest neighbor algorithm has to be reinvoked for m neighbors, thereby possibly performing some redundant computations. The second approach is incremental in the sense that having obtained the k nearest neighbors, the k + 1 st neighbor can be obtained without having to calculate the k + 1 nearest neighbors from scratch. The incremental approach is useful when processing complex queries where one of the conditions involves spatial proximity (e.g., the nearest city to Chicago with population greater than a million), in which case a query engine can make use of a pipelined strategy. We present a general incremental nearest neighbor algorithm that is applicable to a large class of hierarchical spatial data structures. This algorithm is adapted to the R-tree and its performance is compared to an existing k -nearest neighbor algorithm for R-trees [Rousseopoulos et al. 1995]. Experiments show that the incremental nearest neighbor algorithm significantly outperforms the k -nearest neighbor algorithm for distance browsing queries in a spatial database that uses the R-tree as a spatial index. Moreover, the incremental nearest neighbor algorithm usually outperforms the k -nearest neighber algorithm when applied to the k -nearest neighbor problem for the R-tree, although the improvement is not nearly as large as for distance browsing queries. In fact, we prove informally that at any step in its execution the incremental nearest neighbor algorithm is optimal with respect to the spatial data structure that is employed. Furthermore, based on some simplifying assumptions, we prove that in two dimensions the number of distance computations and leaf nodes accesses made by the algorithm for finding k neighbors is O ( k + k ).
Phosphodiesterase‐Iα/autotaxin (PD‐Iα/ATX): A multifunctional protein involved in central nervous system development and disease (2005)

Phosphodiesterase-Ialpha/autotaxin (PD-Ialpha/ATX) was originally identified as a cell-motility-stimulating factor secreted by a variety of tumor cells. Thus, studies related to its potential functional roles have traditionally focused on tumorigenesis. PD-Ialpha/ATX's catalytic activity, initially defined as nucleotide pyrophosphatase/phosphodiesterase, was soon recognized as being necessary for its tumor cell-motility-stimulating activity. However, only the discovery of PD-Ialpha/ATX's identity with lysophospholipase D, an extracellular enzyme that converts lysophosphatidylcholine into lysophosphatidic acid (LPA) and potentially sphingosylphosphoryl choline into sphingosine 1-phosphate (S1P), revealed the actual effectors responsible for PD-Ialpha/ATX's ascribed motogenic functions, i.e., its catalytic products. PD-Ialpha/ATX has also been detected during normal development in a number of tissues, in particular, the central nervous system (CNS), where expression levels are high. Similar to tumor cells, PD-Ialpha/ATX-expressing CNS cells secrete catalytically active PD-Ialpha/ATX into the extracellular environment. Thus, it appears reasonable to assume that PD-Ialpha/ATX's CNS-related functions are mediated via lysophospholipid, LPA and potentially S1P, signaling. However, recent studies identified PD-Ialpha/ATX as a matricellular protein involved in the modulation of oligodendrocyte-extracellular matrix interactions and oligodendrocyte remodeling. This property of PD-Ialpha/ATX was found to be independent of its catalytic activity and to be mediated by a novel functionally active domain. These findings, therefore, uncover PD-Ialpha/ATX, at least in the CNS, as a multifunctional protein able to induce complex signaling cascades via distinct structure-function domains. This Mini-Review describes PD-Ialpha/ATX's multifunctional roles in the CNS and discusses their potential contributions to CNS development and pathology.