gebhart/patrepeval huggingface dataset:
Abstract 13455: Consecutive and Systematic Transcatheter Closure of Secundum Atrial Septal Defects with the Amplatzer Septal Occluder: a Single Center Study on Pediatric Patients (2011)

Introduction: Transcatheter closure of ostium secundum atrial septal defect (OSASD) has gradually replaced surgical closure. Most centers are selective for surgical versus percutaneous approach. In...
A new safe-point thinning algorithm based on the mid-crack code tracing (1995)

A new thinning algorithm for binary images, based on the safe-point testing and mid-crack code tracing, is presented. Thinning is treated as the deletion of nonsafe border pixels from the contour to the center of the object layer-by-layer. The deletion is determined by masking a 3/spl times/3 weighted template and by the use of lookup tables. The resulting skeleton does not require cleaning or pruning. The obtained skeleton possesses single-pixel thickness and preserves the object's connectivity. The algorithm is very simple and efficient since only boundary pixels are processed at each iteration and lookup tables are used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Loss of Function of <i>OsDCL1</i> Affects MicroRNA Accumulation and Causes Developmental Defects in Rice (2005)

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two types of noncoding RNAs involved in developmental regulation, genome maintenance, and defense in eukaryotes. The activity of Dicer or Dicer-like (DCL) proteins is required for the maturation of miRNAs and siRNAs. In this study, we cloned and sequenced 66 candidate rice (Oryza sativa) miRNAs out of 1,650 small RNA sequences (19 to approximately 25 nt), and they could be further grouped into 21 families, 12 of which are newly identified and three of which, OsmiR528, OsmiR529, and OsmiR530, have been confirmed by northern blot. To study the function of rice DCL proteins (OsDCLs) in the biogenesis of miRNAs and siRNAs, we searched genome databases and identified four OsDCLs. An RNA interference approach was applied to knock down two OsDCLs, OsDCL1 and OsDCL4, respectively. Strong loss of function of OsDCL1IR transformants that expressed inverted repeats of OsDCL1 resulted in developmental arrest at the seedling stage, and weak loss of function of OsDCL1IR transformants caused pleiotropic developmental defects. Moreover, all miRNAs tested were greatly reduced in OsDCL1IR but not OsDCL4IR transformants, indicating that OsDCL1 plays a critical role in miRNA processing in rice. In contrast, the production of siRNA from transgenic inverted repeats and endogenous CentO regions were not affected in either OsDCL1IR or OsDCL4IR transformants, suggesting that the production of miRNAs and siRNAs is via distinct OsDCLs.
Endnote: Leading, Learning, and Supporting Adult Development for All Educators. (2010)

The theme for this year’s journal is “Leading and Learning: Supporting Adult Development for All Educators.” The subject of adult learning has seen increased recognition during the past decade. Over twenty years ago, California established the New Teacher Project (NTP), a forerunner of the current Beginning Teacher Support and Assessment System (BTSA) which was developed to support new teachers in their journey in becoming an expert educator (Moir & Baron, 2002). Research on the NTP found that through intensive support, training, and assessment, teachers participating in the project provided better instruction for students (California Commission on Teacher Credentialing, 1992). Recently, organizations such as the Association for California School Administrators (ACSA) and the New Teacher Center have been offering training for those willing to coach and mentor school administrators (http://cust-65-98-140-199.static.o1.com/MainMenuCategories/ ProfessionalLearning/LeadershipCoaching.aspx). With this renewed interest in supporting adult learning, educational leadership programs are uniquely poised to provide opportunities for candidates to gain insight and knowledge into how adults learn and how to support adult learning in the K–12 community.
Charge-remote fragmentation of lithiated fatty acids on a TOF-TOF instrument using matrix-ionization (2007)

In numerous studies charge remote fragmentation (CRF) has been shown to be a powerful technique for determination of primary structure by allowing location of double bonds, various functional groups, and branching in a variety of compound types directly by mass spectrometry. Instrumentation and ionization methods traditionally used for CRF, however, are becoming rare, in large part because ESI and MALDI have to a significant extent replaced them. Here we demonstrate that by selecting a matrix that promotes rather than suppresses ionization of fatty acids (FA) by lithium ion adduction, and using a TOF-TOF mass spectrometer for high-energy collisional activation, CRF ions are produced that allow location of double-bond and branching positions. Further, we show that by using solvent-free MALDI sample preparation methods, thus eliminating the inherent segregation of the hydrophobic fatty acid from the hydrophilic LiCl that can occur during the evaporation of solvent, the desired [FA-H+2Li](+) ions are greatly enhanced. Because FAs can be vaporized using laser desorption, matrix assistance in desorption of the fatty acid may occur, but is not necessary. However, the matrix plays a crucial role in enhancing or suppressing ionization. For example, matrix materials with acid (e.g., 2,5-dihydroxybenzoic acid) or hydroxy groups (e.g., dithranol) compete with the FA for Li(+) and because of the high ratio of matrix to analyte, FA lithium adduction is minimized. However, highly electron-deficient matrix materials (e.g., TCNQ) readily donate Li(+) to FAs because of the instability associated with being positively charged.
The pro‐ or anti‐apoptotic function of NF‐κB is determined by the nature of the apoptotic stimulus (2000)

To test whether the behaviour of transcription factor NF-kappaB as a promoter or antagonist of apoptosis depends on the apoptotic stimulus, we determined the influence of NF-kappaB on cell killing elicited by a variety of inducers within a given cell type. Inhibition of NF-kappaB by genetic and pharmacological approaches rendered HeLa cells more susceptible to TNF-alpha-induced cell killing, but protected them almost completely from H2O2- and pervanadate-induced apoptosis. TNF-alpha was unable to protect HeLa from H2O2- and pervanadate-induced apoptosis and further enhanced the cytotoxicity induced by these two adverse agents. Supernatants from HeLa cells stably overexpressing a transdominant negative form of IkappaB-alpha selectively increased the cytotoxicity of TNF-alpha for HeLa cells, suggesting that the enhanced susceptibility of these cells can be attributed to one or more secretable factors. Supershift experiments showed that the various apoptotic stimuli induced the same subset of DNA-binding subunits. Therefore, the nature of the signals elicited by the respective death inducers determines whether NF-kappaB induction leads to apoptosis or survival, suggesting that the manipulation of NF-kappaB activity may provide a new approach to adjuvant therapy in cancer treatment.
NVO3 Data Plane Requirements (2014)

Several IETF drafts relate to the use of overlay networks to support
large scale virtual data centers. This draft provides a list of data
plane requirements for Network Virtualization over L3 (NVO3) that have
to be addressed in solutions documents.
Prototyping Energy Harvesting Active Networked Tags (EnHANTs) with MICA2 Motes (2010)

With the convergence of ultra-low-power communications and energy-harvesting technologies, networking self-sustainable ubiquitous devices is becoming feasible. Hence, we have been recently developing new devices, referred to as Energy Harvesting Active Networked Tags (EnHANTs). These small, flexible, and energetically self-reliant tags can be seen as a new class of devices in the domain between RFIDs and sensor networks. EnHANTs are made possible by advances in ultra-lowpower ultra-wideband (UWB) communications and in organic semiconductor-based energy harvesting materials. They will enable novel tracking applications, such as continuous monitoring of objects and locating misplaced items. In this demo, we present phase I EnHANT prototypes. These prototypes are much larger than the envisioned EnHANTs and do not include custom-made UWB and organic electronic components. Yet, they serve as platforms for preliminary experiments and allow demonstrating energy harvesting-adaptive EnHANT communications. Each prototype is based on a MICA2 mote and includes a custom-designed sensor board with a light sensor and a solar cell, which are used to determine the light energy received from the environment. We have also designed a monitoring system which is used in the demo to show how the EnHANT prototypes adjust their communications patterns based on their energy harvesting parameters.
T-Cell Activation by Antigen-Loaded pH-Sensitive Hydrogel Particles <i>in Vivo</i>: The Effect of Particle Size (2008)

Polymeric carriers designed to encapsulate protein antigens have great potential for improving the efficacy of vaccines and immunotherapeutics for diseases such as cancer. We recently developed a carrier system based on polyacrylamide hydrogel microparticles cross-linked with acid-labile moieties. After being phagocytosed by antigen-presenting cells, the protein encapsulated within the carrier is released and processed for subsequent presentation of antigenic epitopes. To understand the impact of particle size on the activation of T-cells following uptake by antigen-presenting cells, particles with mean diameters of 3.5 microm and 35 nm encapsulating a model protein antigen were synthesized by emulsion and microemulsion based polymerization techniques, respectively. In vivo tests demonstrated that both sizes of particles were effective at stimulating the proliferation of T-cells and were capable of generating an antigen-specific cytotoxic T-cell response when coadministered with immunostimulatory DNA. Contrary to previous reports in the literature, our results suggest that there is no significant difference in the magnitude of T-cell activation for the two sizes of particles used in these experiments. This disparity in findings may be related to fundamental differences in material properties of the carriers used in these studies, such as the hydrophilicity of the polyacrylamide particles described here versus the hydrophobic nature of carriers investigated by other groups.
Epitope-specific enhancement of antigen presentation by invariant chain. (1993)

The MHC class II-associated invariant chain (Ii) is involved in the intracellular sorting of class II molecules to the endocytic pathway where peptides from processed exogenous antigens are bound, and thereby Ii is thought to enhance antigen presentation. Here we demonstrate that presentation of only one out of five epitopes of a given antigen is augmented by Ii. We have compared the presentation of five different epitopes derived from hen egg white lysozyme (HEL) to Ak-restricted T hybridomas by rat-2 fibroblasts transfected with A alpha k and A beta k (RKK) and RKK cells supertransfected with the mouse invariant chain (RKKI). Only the presentation of the HEL epitope 46-61 was enhanced whereas the presentation of the HEL epitopes 25-43, 34-45, 112-124, and 116-129 was unchanged or even slightly diminished in RKKI cells. The presentation of the epitopes 25-43 and 34-45 was virtually insensitive to the lysosomotropic reagent chloroquine. Brefeldin A (BFA), which inhibits protein egress from the endoplasmic reticulum, blocked the presentation of all epitopes tested in RKKI cells. In contrast, in Ii-negative RKK cells only the presentation of the epitope HEL(46-61) was inhibited by BFA and the presentation of the epitopes 25-43 and 34-45 was only slightly impaired. These findings suggest that Ii may target class II molecules to selected endosomal subcompartments involved in the processing of different peptides derived from an endocytosed antigen. As a result, the enhancement of the class II-restricted presentation in Ii expressing cells appears to be epitope specific rather than antigen specific.
Modeling the reversible addition–fragmentation chain transfer process in cumyl dithiobenzoate‐mediated styrene homopolymerizations: Assessing rate coefficients for the addition–fragmentation equilibrium (2001)

Abstract A full kinetic scheme for the free‐radical reversible addition–fragmentation chain transfer (RAFT) process is presented and implemented into the program package PREDICI®. With the cumyl dithiobenzoate‐mediated bulk polymerization of styrene at 60 °C as an example, the rate coefficients associated with the addition–fragmentation equilibrium are deduced by the careful modeling of the time‐dependent evolution of experimental molecular weight distributions. The rate coefficient for the addition reaction of a free macroradical to a polymeric RAFT species ( k β ) is approximately 5 · 10 5 L mol −1 s −1 , whereas the fragmentation rate coefficient of the formed macroradical RAFT species is close to 3 · 10 −2 s −1 . These values give an equilibrium constant of K = k β / k −β = 1.6 · 10 7 L mol −1 . Conclusive evidence is given that the equilibrium lies well on the side of the macroradical RAFT species. The high value of k β is comparable in size to the propagation rate coefficients reported for acrylates. The transfer rate coefficient to cumyl dithiobenzoate is close to 3.5 · 10 5 L mol −1 s −1 . A careful sensitivity analysis was performed, which indicated that the reported rate coefficients are accurate to a factor of 2. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1353–1365, 2001
The DCC Gene: Structural Analysis and Mutations in Colorectal Carcinomas (1994)

DCC is a candidate tumor-suppressor gene encoding a protein with sequence similarity to cell adhesion molecules such as N-CAM. A set of overlapping YAC clones that contains the entire DCC coding region was isolated. Studies of this YAC contig showed that the DCC gene spans approximately 1.4 Mb. For elucidation of exon-intron structure, lambda phage clones containing all known coding sequences were isolated from a genomic library. These clones were used to demonstrate the existence of 29 DCC exons, and the sequences of the exon-intron boundaries were determined for each. Twenty-three polymorphic markers from chromosome 18 were then studied in a panel of primary colorectal tumors that had lost some, but not all, of chromosome 18. In most of these tumors, the region that was lost included DCC. Finally, Southern blot and PCR-based approaches were used to search for subtle mutations in several DCC exons. One tumor that had a point mutation in exon 28 was found, resulting in a proline to histidine substitution. A second tumor with a point mutation in intron 13 was also found. The regional map and genomic structure of DCC should provide the means to more extensively study DCC gene alterations and protein function in normal and neoplastic cells.
“There Was So Much” (2018)

Anthropologists debate the usefulness of an “Ontological Turn” in theory and practice as a way to confront the social and ecological disjuncture at the heart of the Anthropocene. Is it possible, scholars wonder, to validate rather than rationalize the idea that mountains, rivers, and trees are social interlocutors as well as arbiters of justice, resource access, and societal well-being? In a twist of monumental irony, previously market-independent Cambodians are facing, in an odious confluence of fear, need, and desire, an ontological turn toward the rationalized notion that trees, mountains, rivers and all their inhabitants are important primarily as commodities that can be converted to money. This paper explores part of that nexus of fear, need, and desire through accounts of social relationships with the “owner of the water and the land,” whose permission is sought for territorial access and resource use. Successful navigation of relationships with the original owner of the territory require respect, solidarity, conservation, and offerings of gratitude. In return people enjoy resource abundance, ritual/technical knowledge, and good health. Improper comportment results in illness, loss of access to forest and water resources, and knowledge loss. In yet another ironic twist, the Development State (defined within) promises poverty alleviation, education, and health care for all those who master the extractive market economy. The paper explores how different ontologies give rise to particular social, political, and economic possibilities, and demonstrates that the punishments of the Original owner of the water and the land are visited upon those who either will not or cannot successfully navigate the extractive market system.
Origin and Differentiation of Human and Murine Stroma (2002)

Stromal cells generated in long-term cultures appear to follow a vascular smooth muscle differentiation pathway. Such a pathway, comprising several steps hallmarked by the expression of cytoskeletal and extracellular matrix markers, is found not only for bone marrow stromal cells, but also for stromal cells generated from the different developmental sites of hematopoiesis (yolk sac, aorta-gonad-mesonephros region, fetal liver, and spleen). Factors responsible for this differentiation pathway and its functional significance are discussed. The mesenchymal founder cell might be, at least for bone marrow, a mesenchymal stem cell (MSC), giving rise to stromal cells, endothelial cells, adipocytes, osteoblasts, and chondrocytes. A feature that distinguishes the MSC lineage from that of the hematopoietic stem cell lineage is that differentiation pathways are not strictly delineated, since even apparently fully differentiated cells from a given lineage have the potential to convert into another lineage (phenotype "plasticity") and intermediate cell phenotypes are observed. A stochastic Repression/Induction model that would account for this plasticity is proposed.
Hedges in the Warehouse: The Banks Get Trimmed (2008)

When banks “warehouse” loans, that is, hold them temporarily before selling them through securitizations, how do they protect themselves against credit risk? This article examines the effectiveness of hedging strategies in the context of the recent heavy losses in financial markets.
Fast and sensitive read mapping with approximate seeds and multiple backtracking (2012)

We present Masai, a read mapper representing the state of the art in terms of speed and sensitivity. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2--3 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared to exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic datasets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai.
An Efficient and Practical N-Methylation of Amino Acid Derivatives (2002)

[reaction: see text] An efficient and practical N-methylation of amino acid derivatives with dimethyl sulfate in the presence of sodium hydride and a catalytic amount of water is described. Reaction of water with sodium hydride generated highly reactive dry sodium hydroxide, which led to much faster reaction rates than powdered sodium hydroxide itself.
Generic ontology of datatypes (2015)

We present OntoDT, a generic ontology for the representation of scientific knowledge about datatypes. OntoDT defines basic entities, such as datatype, properties of datatypes, specifications, characterizing operations, and a datatype taxonomy. We demonstrate the utility of OntoDT on several use cases. OntoDT was used within an Ontology of core data mining entities for constructing taxonomies of datasets, data mining tasks, generalizations and data mining algorithms. Furthermore, we show how OntoDT can be used to annotate and query dataset repositories. We also show how OntoDT can improve the representation of datatypes in the BioXSD exchange format for basic bio-informatics types of data. The generic nature of OntoDT enables it to support a wide range of other applications, especially in combination with other domain specific ontologies: the construction of data mining workflows, annotation of software and algorithms, semantic annotation of scientific articles, etc. OntoDT is open source and is available at http://www.ontodt.com.
Germline polymorphisms in an enhancer of <i>PSIP1</i> are associated with progression-free survival in epithelial ovarian cancer (2016)

Women with epithelial ovarian cancer (EOC) are usually treated with platinum/taxane therapy after cytoreductive surgery but there is considerable inter-individual variation in response. To identify germline single-nucleotide polymorphisms (SNPs) that contribute to variations in individual responses to chemotherapy, we carried out a multi-phase genome-wide association study (GWAS) in 1,244 women diagnosed with serous EOC who were treated with the same first-line chemotherapy, carboplatin and paclitaxel. We identified two SNPs (rs7874043 and rs72700653) in TTC39B (best P=7x10-5, HR=1.90, for rs7874043) associated with progression-free survival (PFS). Functional analyses show that both SNPs lie in a putative regulatory element (PRE) that physically interacts with the promoters of PSIP1, CCDC171 and an alternative promoter of TTC39B. The C allele of rs7874043 is associated with poor PFS and showed increased binding of the Sp1 transcription factor, which is critical for chromatin interactions with PSIP1. Silencing of PSIP1 significantly impaired DNA damage-induced Rad51 nuclear foci and reduced cell viability in ovarian cancer lines. PSIP1 (PC4 and SFRS1 Interacting Protein 1) is known to protect cells from stress-induced apoptosis, and high expression is associated with poor PFS in EOC patients. We therefore suggest that the minor allele of rs7874043 confers poor PFS by increasing PSIP1 expression.
879. A polarographic investigation into the redox behaviour of quinones: the roles of electron affinity and solvent (1962)

M. E. Peover, J. Chem. Soc., 1962, 4540 DOI: 10.1039/JR9620004540
Leaky mode directional coupler for prism coupling interconnection (2005)

A leaky mode directional coupler was fabricated with its beam shaped into a Gaussian-like profile and was experimentally demonstrated for suppressing the diffraction of an out-coupled beam. The demonstrated coupler consists of a multilayered waveguide with six layers that are embedded in a symmetric slab waveguide. The out-coupled beam profile was measured to be shaped into a Gaussian function by using the prism coupling method. There was an excellent agreement between the measured and theoretically predicted coupling angles, and it was also confirmed that the diffraction was suppressed.