gebhart/patrepeval huggingface dataset:
Lossless Compression Algorithms for Hierarchical IC Layout (2008)

An important step in today's integrated circuit (IC) manufacturing is optical proximity correction (OPC). While OPC increases the fidelity of pattern transfer to the wafer, it also significantly increases IC layout file size. This has the undesirable side effect of increasing storage, processing, and I.O. times for subsequent steps of mask preparation. In this paper, we propose two techniques for compressing layout data, including OPC layout, while remaining compliant with existing industry standard formats such as OASIS and GDSII. Our approach is to eliminate redundancies in the representation of the geometrical data by finding repeating groups of geometries between multiple cells and within a cell. We refer to the former as ldquointercell subcell detection (InterSCD)rdquo and the latter as ldquointracell subcell detection (IntraSCD).rdquo We show both problems to be nondeterministic polynomial time hard (NP-hard), and propose two sets of heuristics to solve them. For OPC layout data, we also propose a fast compression method based on IntraSCD which utilizes the hierarchical information in the pre-OPC layout data. We show that the IntraSCD approach can also be effective in reconstructing hierarchy from flattened layout data. We demonstrate the results of our proposed algorithms on actual IC layouts for 90-nm, 130-nm, and 180-nm feature size circuit designs.
NG2 glia are required for maintaining microglia homeostatic state (2019)

Microglia play vital roles in the health and diseases of the central nervous system. Loss of microglia homeostatic state is a key feature of brain aging and neurodegeneration. However, the mechanisms underlying the maintenance of distinct microglia cellular states are largely unclear. Here, we show that NG2 glia, also known as oligodendrocyte precursor cells, are essential for maintaining the homeostatic microglia state. We developed a highly efficient and selective NG2 glia depletion method using small-molecule inhibitors of platelet-derived growth factor (PDGF) signaling in cultured brain slices. We found that loss of NG2 glia abolished the homeostatic microglia signature without affecting the disease-associated microglia profiles. Similar findings were also observed in vivo by genetically depleting NG2 glia or conditionally inhibiting NG2 glia PDGF signaling in the adult mouse brain. These data suggest that NG2 glia exert a crucial influence onto microglia cellular states that are relevant to brain aging and neurodegenerative diseases. In addition, our results provide a powerful, convenient, and selective tool for the investigation of NG2 glia function.
The Drosophila retinoid X receptor homolog ultraspiracle functions in both female reproduction and eye morphogenesis (1992)

Ultraspiracle (usp) encodes the Drosophila cognate of RXR, the human retinoid X receptor. To examine how RXR subfamily members function in development, we have undertaken a phenotypic analysis of usp mutants. usp is required at multiple stages of development for functions that occur in a wide variety of tissues. usp is required in the eye-antennal imaginal disc for normal eye morphogenesis and in the somatic and germline tissues of adult females for fertilization, eggshell morphogenesis and embryonic development. An unusual sunken eye phenotype with marked ventral-dorsal polarity appears to be caused by a lack of usp function in the imaginal disc cells that reside between the eye and antennal anlage. The usp functions include cell autonomous and non-cell autonomous components, suggesting that usp controls the production of factors important for both cell-cell communication and cellular differentiation. These usp signalling pathways have mechanistic parallels to steroid and retinoid action in developing vertebrate tissues.
Evidence for altered hepatic matrix degradation in genetic haemochromatosis (1998)

This study provides the first evidence of an alteration in matrix degradation in haemochromatosis that may be a contributing factor to hepatic fibrogenesis in this disease.
FHMA receiver over Rayleigh fading channels (1999)

A novel FH/MFSK receiver is proposed which utilises the side information of interfering signals for asynchronous frequency hopping multiple-access (FHMA) systems in the presence of Rayleigh fading. It is shown that the novel receiver performs much better than the conventional receiver for a wide range of signal to noise ratios.
Nucleosides. Part LXIII. Acetals as new 2′‐O‐protecting functions for the synthesis of oligoribonucleotides: Synthesis of uridine building blocks and evaluation of their relative acid stability (1998)

Abstract A broad variety of new acyclic vinyl ethers (see 6 – 41 ) have been synthesized via the vinyl‐interchange reaction of ethyl vinyl ether at room temperature using mercury(II) trifluoroacetate as a highly efficient catalyst. The appropriate vinyl ethers were reacted under acidic conditions with 3′,5′‐ O ‐silyl‐protected uridine 42 to the corresponding 2′‐ O ‐(1‐alkoxyethyl) derivatives 43 – 83 which gave, on desilylation of F − ions, in high yields the uridine‐2′‐ O ‐acetal derivatives 84 – 124 . The relative stabilities of the newly synthesized compounds under acidic and basic conditions were determined using TLC and HPLC techniques. Protected protecting groups offer the best properties for oligoribonucleotide syntheses. Interestingly, the very acid‐stable acetals of the β‐substituted ethyl‐type 118 – 121 and 123 can be cleaved by a β‐elimination process providing a series of base‐labile acetals of potential synthetic value.
Branch migration of Holliday junctions promoted by the Escherichia coli RuvA and RuvB proteins. II. Interaction of RuvB with DNA (1993)

Using recombination intermediates made by RecA protein, we have shown that the Escherichia coli RuvB protein can mediate the branch migration of Holliday junctions in vitro. The reaction is dependent on the presence of > or = 10 mM Mg2+ and stoichiometric amounts of RuvB. The presence of E. coli RuvA protein reduces the requirement for Mg2+ and also the stoichiometric requirement for RuvB (Müller, B., Tsaneva, I. R., and West, S. C. (1993) J. Biol. Chem. 268, 17179-17184). To determine the roles of the two proteins during branch migration, we have investigated the interaction of RuvB with DNA in the absence or presence of RuvA, by (i) gel retardation of protein-DNA complexes, (ii) stimulation of the RuvB ATPase, and (iii) protection of DNA from DNase I. The interaction of RuvB with duplex DNA was Mg(2+)-dependent and correlated with the Mg2+ requirement of the RuvB-mediated branch migration reaction. RuvB also interacted with ssDNA, but the affinity was significantly lower than for duplex DNA. In contrast to RuvB, the interaction of RuvA with duplex DNA occurred in the absence of Mg2+ and was inhibited by Mg2+ in a concentration-dependent manner. At 5 mM Mg2+, RuvA protein facilitated the interaction of RuvB with DNA, leading to the formation of a complex containing RuvA, RuvB, and duplex DNA.
Nanoscale Spatial Distribution of Thiolated DNA on Model Nucleic Acid Sensor Surfaces (2013)

The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determined the nanoscale spatial distribution of thiolated DNA that are attached to gold via different methods. We discovered significant heterogeneity in the probe density and limited stability for DNA monolayers prepared by the backfilling method, that is, first exposing the surface to thiolated DNA then "backfilling" with a passivating alkanethiol. On the other hand, the monolayers prepared by "inserting" thiolated DNA into a preformed alkanethiol monolayer lead to a more uniformly distributed layer of DNA. With high-resolution images of single DNA molecules on the surface, we have introduced spatial statistics to characterize the nanoscale arrangement of DNA probes. The randomness of the spatial distribution has been characterized. By determining the local densities surrounding individual molecules, we observed subpopulations of probes with dramatically different levels of "probe crowding". We anticipate that the novel application of spatial statistics to DNA monolayers can enable a framework to understand heterogeneity in probe spatial distributions, interprobe interactions, and ultimately probe activity on sensor surfaces.
3D puppetry (2012)

We present a system for producing 3D animations using physical objects (i.e., puppets) as input. Puppeteers can load 3D models of familiar rigid objects, including toys, into our system and use them as puppets for an animation. During a performance, the puppeteer physically manipulates these puppets in front of a Kinect depth sensor. Our system uses a combination of image-feature matching and 3D shape matching to identify and track the physical puppets. It then renders the corresponding 3D models into a virtual set. Our system operates in real time so that the puppeteer can immediately see the resulting animation and make adjustments on the fly. It also provides 6D virtual camera \\rev{and lighting} controls, which the puppeteer can adjust before, during, or after a performance. Finally our system supports layered animations to help puppeteers produce animations in which several characters move at the same time. We demonstrate the accessibility of our system with a variety of animations created by puppeteers with no prior animation experience.
QTL for Fatty Acid Composition of Maize Kernel Oil in Illinois High Oil × B73 Backcross‐Derived Lines (2008)

Maize ( Zea mays L.) produces high‐quality oil valued for oxidative stability and low concentrations of saturated fatty acids. The nutritional value of maize oil could be improved by increasing the concentration of oleic acid, a “heart‐friendly” monounsaturated fatty acid. To identify quantitative trait loci (QTL) for the major fatty acids constituting oil from maize kernels, we produced 150 backcross1‐derived S 1 (BC 1 S 1 ) lines from donor parent, Illinois High Oil (IHO), and recurrent parent, B73. There was a positive phenotypic correlation between oil and oleic acid (r p = 0.47**, α ≤ 0.01) and negative correlations between oil and linoleic acid (r p = −0.46**), and between oleic and linoleic acids (r p = −0.99**). Multiple regression models with QTL detected by composite interval mapping (CIM) on a genetic map with length = 1486 cM, explained 15.4, 41.6, 51.0, 59.6, and 47.9% of the phenotypic variation for palmitic, stearic, oleic, linoleic, and linolenic acids, respectively. A 6‐cM interval on chromosome 6 (bin 6.04) includes QTL for stearic, oleic, linoleic, and linolenic acids, explains 10.9 to 39.6% of the variation for these fatty acids, and is 10 to 16 cM from QTL for oil. Another region on chromosome 6 (bin 6.01) includes QTL for oleic and linoleic acids and was epistatic with the QTL in bin 6.04. One or both of these two QTL regions on chromosome 6 may be responsible for fatty acid variation previously attributed to linoleic acid1
ChemInform Abstract: Synthesis of N‐Chloroacetyl‐β‐glycopyranosylamines ‐ Derivatives of Monosaccharides and Lactose. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Fabrication of Submicrometer Features on Curved Substrates by Microcontact Printing (1995)

Microcontact printing (mu CP) has been used to produce patterned self-assembled monolayers (SAMs) with submicrometer features on curved substrates with radii of curvature as small as 25 micrometers. Wet-chemical etching that uses the patterned SAMs as resists transfers the patterns formed by mu CP into gold. At present, there is no comparable method for microfabrication on curved surfaces.
Video on Demand: Architecture, Systems, and Applications (1994)

This article describes video on demand (VOD) and near video on demand (NVOD) and explains the differences between the various types of VOD systems as they relate to telephone company (Telco), commmunity antenna or cable television (CATV), cellular TV, and hotel applications. System similarities of the various carriers are described, with the intent to identify as much common equipment as possible that will be compatible across the various applications. Basic VOD functional requirements are also discussed. Hotel VOD systems are really small CATV or Telco systems that can be expanded into full-size, commercially viable VOD systems easily because of their scalable architecture. The roles of image compression, video-friendly disk-storage systems, video servers, encryption, switching, transmission, and control-system elements in this VOD application are also discussed.
A Mutant of Mycobacterium tuberculosis H37Rv That Lacks Expression of Antigen 85A Is Attenuated in Mice but Retains Vaccinogenic Potential (2004)

The fbpA and fbpB genes encoding the 85A and 85B proteins of Mycobacterium tuberculosis H37Rv, respectively, were disrupted, the mutants were examined for their ability to survive, and the strain lacking 85A (DeltafbpA) was tested for its ability to immunize mice. The DeltafbpA mutant was attenuated in mice after intravenous or aerosol infection, while replication of the DeltafbpB mutant was similar to that of the wild type. Complementation of the fbpA gene in DeltafbpA restored its ability to grow in the lungs of mice. The DeltafbpA mutant induced a stronger expression of pulmonary mRNA messages in mice for tumor necrosis factor alpha, interleukin-1 beta (IL-1beta), gamma interferon, IL-6, IL-2, and inducible nitric oxide (NO) synthase, which led to its decline, while H37Rv persisted despite strong immune responses. H37Rv and DeltafbpA both induced NO in macrophages and were equally susceptible to NO donors, although DeltafbpA was more susceptible in vitro to peroxynitrite and its growth was enhanced by NO inhibitors in mice and macrophages. Aerosol-infected mice, which cleared a low-dose DeltafbpA infection, resisted a challenge with virulent M. tuberculosis. Mice subcutaneously immunized with DeltafbpA or Mycobacterium bovis BCG and challenged with M. tuberculosis also showed similar levels of protection, marked by a reduction in the growth of challenged M. tuberculosis. The DeltafbpA mutant was thus attenuated, unlike DeltafbpB, but was also vaccinogenic against tuberculosis. Attenuation was incomplete, however, since DeltafbpA revived in normal mice after 370 days, suggesting that revival was due to immunosenescence but not compensation by the fbpB or fbpC gene. Antigen 85A thus affects susceptibility to peroxynitrite in M. tuberculosis and appears to be necessary for its optimal growth in mice.
Isolation, characterization and localization of annexin V from chicken liver (1993)

Annexin V has been purified from chicken liver; 40 mg of annexin V was obtained per kg of tissue. In contrast with mammalian liver, very little annexin VI was obtained. Surprisingly, chicken liver annexin V resembles mammalian annexin IV in its M(r) (32,500) and its isoelectric point (5.6), but amino-acid-sequence analysis demonstrates identity with chicken annexin V (anchorin CII). It binds to phospholipids in a Ca(2+)-dependent manner with free-Ca2+ concentrations for half-maximal binding to phosphatidylserine and phosphatidic acid of 10 microM; phosphatidylethanolamine of 32 microM and phosphatidylinositol of 90 microM. No binding to phosphatidylcholine was observed at Ca2+ concentrations up to 300 microM. In isolated liver membranes a significant proportion of annexin V was not extractable with EGTA but could only be extracted with Triton X-100, suggesting the existence of a tightly membrane-associated form of annexin V. A specific antiserum to chicken annexin V was used to localize the protein in adult and embryonic chicken liver. In the adult, annexin V was highly concentrated in epithelial cells lining the bile ducts, and along the bile canaliculi. In embryonic liver, strong staining of the bile-duct epithelial cells was again evident, and in addition, endothelial cells were strongly immunoreactive.
Copper azide as a new reagent for syn-SN2 displacement of .gamma.-sulfonyloxy-.alpha.,.beta.-unsaturated esters (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCopper azide as a new reagent for syn-SN2 displacement of .gamma.-sulfonyloxy-.alpha.,.beta.-unsaturated estersYoshinori Yamamoto and Naoki AsaoCite this: J. Org. Chem. 1990, 55, 19, 5303–5304Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/jo00306a001https://doi.org/10.1021/jo00306a001research-articleACS PublicationsRequest reuse permissionsArticle Views337Altmetric-Citations11LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
[Helping people is beautiful: an inquiry into the aesthetic consciousness of the helping profession]. (2013)

This article addresses the helping profession as an art. The author uses an art philosophy perspective to review the phenomenon and meaning of the helping profession as "art" and addresses several questions. These questions include: What category or categories of art best define the helping profession? Can the process and / or results of helping be appreciated as works of art? What is the value of treating the helping profession as an art form? The purpose of this article is to expand knowledge regarding the aesthetic nature of the helping profession.
Interpolating view and scene motion by dynamic view morphing (2003)

We introduce the problem of view interpolation for dynamic scenes. Our solution to this problem extends the concept of view morphing and retains the practical advantages of that method. We are specifically concerned with interpolating between two reference views captured at different times, so that there is a missing interval of time between when the views were taken. The synthetic interpolations produced by our algorithm portray one possible physically-valid version of what transpired in the scene during the missing time. It is assumed that each object in the original scene underwent a series of rigid translations. Dynamic view morphing can work with widely-spaced reference views, sparse point correspondences, and uncalibrated cameras. When the camera-to-camera transformation can be determined, the synthetic interpolation will portray scene objects moving along straight-line, constant-velocity trajectories in world space.
Anaplasma phagocytophilum induces Ixodes scapularis ticks to express an antifreeze glycoprotein gene that enhances their survival in the cold (2010)

In the United States, Ixodes scapularis ticks overwinter in the Northeast and Upper Midwest and transmit the agent of human granulocytic anaplasmosis, Anaplasma phagocytophilum, among other pathogens. We now show that the presence of A. phagocytophilum in I. scapularis ticks increases their ability to survive in the cold. We identified an I. scapularis antifreeze glycoprotein, designated IAFGP, and demonstrated via RNAi knockdown studies the importance of IAFGP for the survival of I. scapularis ticks in a cold environment. Transfection studies also show that IAFGP increased the viability of yeast cells subjected to cold temperature. Remarkably, A. phagocytophilum induced the expression of iafgp, thereby increasing the cold tolerance and survival of I. scapularis. These data define a molecular basis for symbiosis between a human pathogenic bacterium and its arthropod vector and delineate what we believe to be a new pathway that may be targeted to alter the life cycle of this microbe and its invertebrate host.
Preservation of the Structure of Enzymatically-Degraded Bovine Vitreous Using Synthetic Proteoglycan Mimics (2014)

Proteoglycan mimics preserved bovine vitreous physical properties after enzymatic degradation. These compounds may be useful in delaying or preventing the pathological effects of age-related, or enzymatically-induced, degradation of the vitreous body.
Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler (2009)

These algorithms extend the utility of short read only assemblies into large complex genomes. They have been implemented and made available within the open-source Velvet short-read de novo assembler.
Phylogenetic Analysis of the Human Gut Microbiota Using 16S rDNA Clone Libraries and Strictly Anaerobic Culture‐Based Methods (2002)

The human gut microbiota from three healthy subjects were compared by the use of a sequence analysis of 16S rDNA libraries and a culture-based method. Direct counts ranged from 1.9 X 10" to 4.0 X 10" cells/g (wet weight), and plate counts totaled 6.6 X 10(10) to 1.2 X 10(11) CFU/g (wet weight). Sixty to seventy percent of the bacteria in the human intestinal tract cannot be cultured with currently available methods. The 16S rDNA libraries from three subjects were generated from total community DNA in the intestinal tract with universal primer sets. Randomly selected clones were partially sequenced. All purified colonies detected from the surface of the agar plate were used for a partial sequencing of 16S rDNA. On the basis of sequence similarities, the clones and colonies were classified into several clusters corresponding to the major phylum of the domain Bacteria. Among a total of 744 clones obtained, approximately 25% of them belonged to 31 known species. About 75% of the remaining clones were novel "phylotypes" (at least 98% similarity of clone sequence). The predominant intestinal microbial community consisted of 130 species or phylotypes according to the sequence data in this study. The 16S rDNA libraries and colonies included the Bacteroides group, Streptococcus group, Bifidobacterium group, and Clostridium rRNA clusters IV, IX, XIVa, and XVIII. Moreover, several previously uncharacterized and uncultured microorganisms were recognized in clone libraries and colonies. Our results also showed marked individual differences in the composition of intestinal microbiota.
Endothelial Lipase Is Increased In Vivo by Inflammation in Humans (2008)

In humans, plasma inflammatory markers are directly correlated with plasma EL concentrations, and experimental endotoxemia significantly increases plasma EL concentrations, proving that EL is upregulated by inflammation in humans. This mechanism may partially explain the low high-density lipoprotein cholesterol levels seen in obesity and metabolic syndrome.