gebhart/patrepeval huggingface dataset:
Pattern‐Based Quadrangulation for <i>N</i>‐Sided Patches (2014)

Abstract We propose an algorithm to quadrangulate an N‐sided patch (2 ≤ N ≤ 6) with prescribed numbers of edge subdivisions at its boundary. Our algorithm is guaranteed to succeed for arbitrary valid input, which is proved using a canonical simplification of the input and a small set of topological patterns that are sufficient for supporting all possible cases. Our algorithm produces solutions with minimal number of irregular vertices by default, but it also allows the user to choose other feasible solutions by solving a set of small integer linear programs. We demonstrate the effectiveness of our algorithm by integrating it into a sketch‐based quad remeshing system. A reference C++ implementation of our algorithm is provided as a supplementary material.
KNOWBEL: a hybrid expert system building tool (2002)

KNOWBEL is a tool offering the knowledge representation language Telos and the logic programming system MRS for the development of an expert system. Telos is a tightly integrated hybrid knowledge representation scheme, offering facilities for structuring a knowledge base as well as an assertional sublanguage for expressing deductive rules and integrity constraints. Unlike Prolog, MRS provides facilities for customizing an expert system inference engine. The KNOWBEL architecture clearly separates the knowledge and implementation levels for a knowledge base and its associated operations. KNOWBEL also supports temporal reasoning, extensive constraint enforcement, and a user-friendly window-based interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Visible Diode Laser-Induced Fluorescence Detection in Liquid Chromatography after Precolumn Derivatization of Amines (1995)

To fully exploit the attractive visible diode laser-induced fluorescence (LIF) detection technique in column liquid chromatography (LC), covalent labeling procedures need to be developed which are compatible with near-infrared fluorescence. For this purpose, several red-absorbing labels containing a single succinimidyl ester functionality were synthesized and used for the derivatization of primary and secondary amines. Oxazines/thiazines, squaraines, and dicarbocyanines were examined as redabsorbing fluorophores. The quality of the LC-diode LIF system for the analytes concerned is illustrated by the concentration detection limit of the labeled n-octylamine (a test compound), which was as low as 2 x 10
Survey of real-time processing systems for big data (2014)

In recent years, real-time processing and analytics systems for big data--in the context of Business Intelligence (BI)--have received a growing attention. The traditional BI platforms that perform regular updates on daily, weekly or monthly basis are no longer adequate to satisfy the fast-changing business environments. However, due to the nature of big data, it has become a challenge to achieve the real-time capability using the traditional technologies. The recent distributed computing technology, MapReduce, provides off-the-shelf high scalability that can significantly shorten the processing time for big data; Its open-source implementation such as Hadoop has become the de-facto standard for processing big data, however, Hadoop has the limitation of supporting real-time updates. The improvements in Hadoop for the real-time capability, and the other alternative real-time frameworks have been emerging in recent years. This paper presents a survey of the open source technologies that support big data processing in a real-time/near real-time fashion, including their system architectures and platforms.
Binding of apolipoprotein A-I model peptides to lipid bilayers. Measurement of binding isotherms and peptide-lipid headgroup interactions. (1994)

Amphiphatic alpha-helices are the lipid-binding motif in many apolipoproteins. Two model peptides, namely Asp-Trp-Leu-Lys-Ala-Phe-Tyr-Asp-Lys-Val-Ala-Glu-Lys-Leu-Lys-Glu-Ala-Phe (18A) and Lys-Trp-Leu-Asp-Ala-Phe-Tyr-Lys-Asp-Val-Ala-Lys-Glu-Leu-Glu-Lys-Ala- Phe (18R), have been synthesized previously to mimic the structural and functional properties of apolipoprotein A-1. Here a quantitative thermodynamic analysis of the binding process of 18A and 18R to neutral and negatively charged lipid membranes is provided. Peptide 18A has a higher lipid affinity than 18R, and both peptides bind better to mixed 1-palmitoyl-2-oleoyl-3-sn-glycero-phosphocholine-1- palmitoyl-2-oleoyl-3-sn-glycero-phosphoglycerol (POPC/POPG) bilayers than to pure POPC bilayers. At lipid-to-peptide ratios > 100, the binding of 18A and 18R to phospholipid bilayers can be described by an apparent surface partition equilibrium with binding constants in the range of 40-900 M-1. At high peptide concentrations, the membrane affinity of 18A and 18R increases dramatically. NMR studies provide evidence that peptide-peptide interactions make additional contributions to the binding energy. A cooperative binding model is developed to describe the binding process over the whole concentration range. The cooperativity parameter sigma is identical for 18A and 18R yielding a peptide-peptide interaction energy of about -2.4 kcal/mol. The free energy of membrane insertion is about -6.5 kcal/mol for 18A and -5.5 kcal/mol for 18R. The binding reaction is driven by the hydrophobic surface energy which is partially balanced by the loss in translational and rotational degrees of freedom. A molecular analysis of the free energy of binding predicts a 40-60% insertion of the peptides into the hydrophobic membrane environment. Deuterium and phosphorus solid state NMR were used to monitor the influence of 18A and 18R on the long range and short range order of the phospholipids. The spectra are characteristic of fluid-like lipid bilayers and provide no evidence for the formation of discoidal particles. However, both peptides change the conformation of the phosphocholine dipoles, moving the N+ end of the latter toward the water phase. The rotation of the -P-N+ dipoles is due to the interaction of the phospholipids with the positive charges on 18A and 18R, with 18A being more effective than 18R. For 18R the NMR data predict a pK shift and a partial charge neutralization of the carboxylate groups located at the edge of the polar/nonpolar interface.
Demonstration of Advanced Open WDM Operations and Analytics, based on an Application-Extensible, Declarative, Data Model Abstracted Instrumentation Platform (2019)

We demonstrate a novel application-flexible data-model-abstracted and declarative software instrumentation platform that advances open-WDM multivendor operations and analytics. We validate its functional extensibility by implementing software-agent-based service provisioning and monitoring, and leveraging multiple open-source technologies.
FDA-Approved Selective Estrogen Receptor Modulators Inhibit Ebola Virus Infection (2013)

Ebola viruses remain a substantial threat to both civilian and military populations as bioweapons, during sporadic outbreaks, and from the possibility of accidental importation from endemic regions by infected individuals. Currently, no approved therapeutics exist to treat or prevent infection by Ebola viruses. Therefore, we performed an in vitro screen of Food and Drug Administration (FDA)- and ex-US-approved drugs and selected molecular probes to identify drugs with antiviral activity against the type species Zaire ebolavirus (EBOV). From this screen, we identified a set of selective estrogen receptor modulators (SERMs), including clomiphene and toremifene, which act as potent inhibitors of EBOV infection. Anti-EBOV activity was confirmed for both of these SERMs in an in vivo mouse infection model. This anti-EBOV activity occurred even in the absence of detectable estrogen receptor expression, and both SERMs inhibited virus entry after internalization, suggesting that clomiphene and toremifene are not working through classical pathways associated with the estrogen receptor. Instead, the response appeared to be an off-target effect where the compounds interfere with a step late in viral entry and likely affect the triggering of fusion. These data support the screening of readily available approved drugs to identify therapeutics for the Ebola viruses and other infectious diseases. The SERM compounds described in this report are an immediately actionable class of approved drugs that can be repurposed for treatment of filovirus infections.
Modular Order-Preserving Encryption, Revisited (2015)

Order-preserving encryption (OPE) schemes, whose ciphertexts preserve the natural ordering of the plaintexts, allow efficient range query processing over outsourced encrypted databases without giving the server access to the decryption key. Such schemes have recently received increased interest in both the database and the cryptographic communities. In particular, modular order-preserving encryption (MOPE), due to Boldyreva et al., is a promising extension that increases the security of the basic OPE by introducing a secret modular offset to each data value prior to encrypting it. However, executing range queries via MOPE in a naive way allows the adversary to learn this offset, negating any potential security gains of this approach.
Generation of memory cells. III. Antibody class requirements for the generation of B-memory cells by antigen--antibody complexes. (1979)

Immunizing mice with preformed antigen--antibody complexes is a highly effective means of generating B-memory cells. In the present study we have compared the capacity of mouse anti-dinitrophenyl (DNP) IgM, IgG1, IgG2 and IgA antibodies to generate DNP-specific memory, when given in complex with antigen (DNP-KLH: keyhole limpet haemocyanin). Two monoclonal IgM antibodies exerted no adjuvant effect, whereas a monoclonal IgA antibody was effective, IgG2 antibodies were a more powerful adjuvant than IgG1, regardless of whether anti-DNP or anti-KLH antibodies were used. Furthermore, the capacity of DNP-KLH--antibody complexes to localize in splenic lymphoid follicles could be ranked IgG2 greater than IgG1 greater than IgA; IgM complexes did not localize in follicles. These results correlate well with data (presented elsewhere) on the capacity of these different antibodies to activate mouse complement, and confirm that C activation is an essential requirement for both follicular localization of immune complexes, and for the generation of B-memory cells. Although activation of the alternative complement pathway is sufficient to effect both processes, the results with IgG2 antibodies raise the possibility that classical pathway activation may be more effective.
Chaperone Function: The Assembly Of Ribulose Bisphosphate Carboxylase-Oxygenase (1990)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
High‐efficiency growth hormone releasing hormone plasmid vector administration into skeletal muscle mediated by electroporation in pigs (2003)

We report here a very efficient method for the in vivo transfer of therapeutic plasmid DNA into porcine muscle fibers by using electric pulses of low field intensity. We evaluated delivery of 0.1-3 mg of plasmid vectors that encode reporter secreted-embryonic alkaline phosphatase (SEAP) or therapeutic growth hormone releasing hormone (GHRH). Reporter gene studies showed that internal needle electrodes give a 25-fold increase in expression levels compared with caliper electrodes in skeletal muscle in swine. Dose and time courses were performed. Pigs injected with 0.1 mg plasmid had significantly greater weight gain than controls over 53 days (22.4 +/- 0.8 kg vs. 19.7 +/- 0.03 kg, respectively; P<0.01). The group treated with GHRH-expressing plasmid at 14 days of age demonstrated greater weight gain than controls at every time point (25.8 +/- 1.5 kg vs. 19.7 +/- 0.03 kg; P<0.01). Body composition studies by dual X-ray absorbitometry showed a 22% decrease in fat deposition (P<0.05) and a 10% increase in bone mineral density (P<0.004). Our studies demonstrate that by optimizing the electroporation method, favorable physiological changes, such as enhanced weight gain and improved body composition, can be obtained at extremely low plasmid doses in a large mammal.
劳动积极性(概念、本质、结构) (1987)

“劳动积极性”概念的定义同“社会积极性”概念是分不开的。最近,斯米尔诺夫指出:社会积极性就是“社会活动过程的规模和性质(社会意义)所表现的社会活动的尺度,以及由于这些活动所引起的个人(群体)周围的自然和社会环境改变的尺度,也包括个人(群体)本身改变的尺度。既然社会积极性是全部社会活动的尺度,那末,把它仅仅视为创造性活动就是错误的。这一结论可以
Malware Clearance for Secure Commitment of OS-Level Virtual Machines (2012)

A virtual machine(VM) can be simply created upon use and disposed upon the completion of the tasks or the detection of error. The disadvantage of this approach is that if there is no malicious activity, the user has to redo all of the work in her actual workspace since there is no easy way to commit (i.e., merge) only the benign updates within the VM back to the host environment. In this work, we develop a VM commitment system called Secom to automatically eliminate malicious state changes when merging the contents of an OS-level VM to the host. Secom consists of three steps: grouping state changes into clusters, distinguishing between benign and malicious clusters, and committing benign clusters. Secom has three novel features. First, instead of relying on a huge volume of log data, it leverages OS-level information flow and malware behavior information to recognize malicious changes. As a result, the approach imposes a smaller performance overhead. Second, different from existing intrusion detection and recovery systems that detect compromised OS objects one by one, Secom classifies objects into clusters and then identifies malicious objects on a cluster by cluster basis. Third, to reduce the false-positive rate when identifying malicious clusters, it simultaneously considers two malware behaviors that are of different types and the origin of the processes that exhibit these behaviors, rather than considers a single behavior alone as done by existing malware detection methods. We have successfully implemented Secom on the feather-weight virtual machine system, a Windows-based OS-level virtualization system. Experiments show that the prototype can effectively eliminate malicious state changes while committing a VM with small performance degradation. Moreover, compared with the commercial antimalware tools, the Secom prototype has a smaller number of false negatives and thus can more thoroughly clean up malware side effects. In addition, the number of false positives of the Secom prototype is also lower than that achieved by the online behavior-based approach of the commercial tools.
Vascular Indications for Integrin αv Antagonists (1997)

Abstract: During early investigations into the biology associated with the platelet integrin αlIbβ3, monoclonal antibodies to αllbβ3 indicated that an αllbβ3-like integrin was expressed on endothelial cells, smooth muscle cells and on a variety of cancer cell lines. That integrin became known as the vitronectin receptor. It was shown to contain the same β3 subunit as αllbβ3, but it contained a different alpha subunit, named αv. Instead of a large family of β3 integrins, a large family of av integrins was discovered. To date, the family includes αvβI, αvβ3, αvβ5, αvβ6 and αvβ8. Two members of the family, αvβ3 and αvβ5, have received the most attention, showing potential in therapeutic targets as diverse as osteoporosis, restenosis and angiogenesis. This paper focuses on the potential vascular indications for av antagonists. It reviews the role of αvβ3 and αvβ5 as smooth muscle cell and endothelial cell adhesion receptors, as well as their capacity to mediate cell spreading and migration as signaling receptors. The current evidence for the role of αvβ3 and αvβ5 in restenosis and angiogenesis is reviewed. Endothelial cells, smooth muscle cells, and macrophages (mΦ) express either integrin, depending upon the cytokine that drives the migratory phenotype. Accessory membrane-bound molecules and matrix-degrading proteinases, as well as subcellular second messengers are reviewed. A model for the involvement of Integrin Associated Protein (IAP), and its ligation by thrombospondin is also proposed. A number of αv antagonists that inhibit cell adhesion to αvβ3 and αvβ5 have succeeded in proof of concept experiments in animal disease models. Nonpeptide av antagonists with high selectivity and adequate oral bioavailability have also been discovered. Thus, the field of av antagonists is poised to move into clinical development in the areas of restenosis, cancer, and ocular angiogenesis. Other areas that could blossom with potential for av antagonists include rheumatoid arthritis and atherosclerosis.
Magnetic and microstructure studies of boron-enriched (Nd/sub 0.95/La/sub 0.05/)/sub 11/Fe/sub 76.5$/ -/sub x/Co/sub x/Ti/sub 2/B/sub 10.5/ (x=0-15) melt-spun ribbons (2000)

The magnetic properties and microstructures of rare earth lean and boron-rich (Nd/sub 0.95/La/sub 0.05/)/sub 11/ Fe/sub 76.5-x/CoxTi/sub 2/B/sub 10.5/ (x=0-15) melt-spun ribbons have been investigated. Two magnetic phases, namely /spl alpha/-Fe and R/sub 2/Fe/sub 14/B, were found, by thermal magnetic analysis (TMA), in all the ribbons studied. High intrinsic coercivity (iHc) and maximum energy product [(BH)max] values in the range of 14-18.7 kOe and 13.9-18.3 MGOe, respectively, have been achieved in these nanocomposites. Among compositions studied, the Co-substitutions, x/spl les/10, were found to be effective in increasing the Br and (BH)max, while keeping a high value of iHc. It was evidenced from transmission electron microscopy that the homogeneity, fine grain size, and high volume fraction of the R/sub 2/Fe/sub 14/B phase led to an increase in the iHc and maximum energy product of nanocomposites studied. The optimum magnetic properties of Br=9.4 kG, iHc=16.1 kOe and (BH)max=18.3 MGOe have been obtained on (Nd/sub 0.95/La/sub 0.05/)/sub 11/Fe/sub bal./Co/sub 10/Ti/sub 2/B/sub 10.5/ ribbons after an optimum treatment.
Threshold Voltage Distribution in MLC NAND Flash Memory: Characterization, Analysis and Modeling (2013)

With continued scaling of NAND flash memory process technology and multiple bits programmed per cell, NAND flash reliability and endurance are degrading. Understanding, characterizing, and modeling the distribution of the threshold voltages across different cells in a modern multi-level cell (MLC) flash memory can enable the design of more effective and efficient error correction mechanisms to combat this degradation. We show the first published experimental measurement-based characterization of the threshold voltage distribution of flash memory. To accomplish this, we develop a testing infrastructure that uses the read retry feature present in some 2Y-nm (i.e., 20–24nm) flash chips. We devise a model of the threshold voltage distributions taking into account program/erase (P/E) cycle effects, analyze the noise in the distributions, and evaluate the accuracy of our model. A key result is that the threshold voltage distribution can be modeled, with more than 95% accuracy, as a Gaussian distribution with additive white noise, which shifts to the right and widens as P/E cycles increase. The novel characterization and models provided in this paper can enable the design of more effective error tolerance mechanisms for future flash memories.
A Novel Approach of Direct Ex Vivo Epitope Mapping Identifies Dominant and Subdominant CD4 and CD8 T Cell Epitopes from <i>Listeria monocytogenes</i> (2001)

We used a novel approach for the direct ex vivo identification and characterization of T cell epitopes based on the screening of peptide spot libraries with freshly isolated splenocytes in a sensitive enzyme-linked immunospot (ELISPOT) assay. This technique was applied for the analysis of splenocytes from Listeria monocytogenes-infected BALB/c and C57BL/6 mice. The screening of peptide spot libraries covering the whole listeriolysin O and p60 of L. monocytogenes confirmed all known CD4 and CD8 T cell epitopes of these proteins and additionally revealed six new H-2(d) and six new H-2(b)-restricted T cell epitopes. New epitopes were categorized into CD4 and CD8 T cell epitopes by ex vivo ELISPOT analysis with separated T cell populations. The quantitative analysis of cells reactive with these CD4 and CD8 T cell epitopes revealed the existence of dominant and subdominant CD4 and CD8 T cell populations during L. monocytogenes infection. As a consequence of these data we suggest that ELISPOT-based screening of peptide spot libraries could be a general approach for the rapid identification and characterization of pathogen-specific T cell populations during various infectious diseases.
Prevention of Swine Stillbirth with Attenuated S- Strain Japanese Encephalitis Virus Vaccine (1974)

When inoculated with attenuated S- strain Japanese encephalitis virus vaccine, SPF pigs 1 month old presented no abnormal clinical signs, but retained antibody for a long time and resisted challenge with the high virulent AS-6 field strain. When inoculated with the same vaccine, pregnant SPF sows exhibited no clinical symptoms either. Autopsy on them revealed no abnormal fetuses and no virus was recovered from them.In a field trial of this vaccine, the frequencies of occurrence of dead fetuses and sows giving birth to abnormal fetuses were lower in sows inoculated once or twice with this vaccine than in those inoculated with no vaccine. In conclusion, this vaccine is safe and well immunogenic for piglets and pregnant sows, and effective for the prevention of stillbirth to be caused by Japanese encephalitis virus in swine.
Studies on Canine Parvovirus Isolation, Experimental Infection and Serologic Survey (1981)

出血性腸炎で斃死, または臨床的にイヌ・パルボウイルス感染症を疑われた犬52頭のうち19頭から, イヌ・パルボウイルスがネコ腎継代細胞(CRFK細胞)および同初代細胞培養で分離された. 本ウイルスは糞便および種々の臓器から分離され, 年齢的には必ずしも幼犬に限らず, 成・老犬からも分離され, 犬は本ウイルスに対して年齢に関わりなく感受性を有するものと考えられた. 本ウイルスは血清学的にはネコ・パルボウイルスと全く区別できなかった. また健康な犬3頭における感染実験では, 抗体陰性であった犬の1頭が, 自然感染における重症斃死例と極めて類似した症状を呈し, 6日目に斃死した. 剖検所見では, 腸管のほぼ全長にわたる激しい漿膜・粘膜の出血が認められ, 病理組織学的には, 小腸粘膜上皮の広汎な剥脱・絨毛萎縮・陰窩の拡張と上皮の剥脱および核内封入体が見られた. 369頭の犬血清について本ウイルスのHI抗体調査(一部は中和抗体)を実施した結果, 1978年以前のものは陰性であり, 1979年以降の例では, 本ウイルス感染症を疑わせるもの, およびそれとの接触があったものでは極めて高率に陽性であるのみならず, このような経歴のないものにおいても陽性例が認められた.
The Thrombopoietin Receptor: Structural Basis of Traffic and Activation by Ligand, Mutations, Agonists, and Mutated Calreticulin (2017)

A well-functioning hematopoietic system requires a certain robustness and flexibility to maintain appropriate quantities of functional mature blood cells, such as red blood cells and platelets. This review focuses on the cytokine receptor that plays a significant role in thrombopoiesis: the receptor for thrombopoietin (TPO-R; also known as MPL). Here, we survey the work to date to understand how this receptor functions at a molecular level throughout its lifecycle, from traffic to the cell surface, dimerization and binding cognate cytokine <i>via</i> its extracellular domain, through to its subsequent activation of associated Janus kinases and initiation of downstream signaling pathways, as well as the regulation of these processes. Atomic level resolution structures of TPO-R have remained elusive. The identification of disease-causing mutations in the receptor has, however, offered some insight into structure and function relationships, as has artificial means of receptor activation, through TPO mimetics, transmembrane-targeting receptor agonists, and engineering in dimerization domains. More recently, a novel activation mechanism was identified whereby mutated forms of calreticulin form complexes with TPO-R <i>via</i> its extracellular N-glycosylated domain. Such complexes traffic pathologically in the cell and persistently activate JAK2, downstream signal transducers and activators of transcription (STATs), and other pathways. This pathologic TPO-R activation is associated with a large fraction of human myeloproliferative neoplasms.