gebhart/patrepeval huggingface dataset:
The World Health Organization (WHO) classification of the myeloid neoplasms (2002)

A World Health Organization (WHO) classification of hematopoietic and lymphoid neoplasms has recently been published. This classification was developed through the collaborative efforts of the Society for Hematopathology, the European Association of Hematopathologists, and more than 100 clinical hematologists and scientists who are internationally recognized for their expertise in hematopoietic neoplasms. For the lymphoid neoplasms, this classification provides a refinement of the entities described in the Revised European-American Lymphoma (REAL) Classification-a system that is now used worldwide. To date, however, there has been no published explanation or rationale given for the WHO classification of the myeloid neoplasms. The purpose of this communication is to outline briefly the WHO classification of malignant myeloid diseases, to draw attention to major differences between it and antecedent classification schemes, and to provide the rationale for those differences.
Iron uptake from lactoferrin by intestinal brush-border membrane vesicles of human neonates. (1994)

It is uncertain to what extent the binding of human lactoferrin (LF) to its receptor in the intestinal brush-border membrane affects iron uptake in infants. The purpose of this study was to investigate iron uptake from human LF by brush-border membrane vesicles (BBMV) obtained from the small intestine of human neonates. LF was purified from pooled human colostrum. Uptake experiments were performed by incubation of 55Fe-citrate or 55Fe-LF with BBMV, followed by rapid filtration through microporous filters. 55Fe uptake from LF by BBMV was dependent on pH, with a maximum at 7.5, and increased with incubation time, reaching a maximum at 1 min. When 55Fe was bound to citrate, uptake was slower (maximum at 5 min) and not dependent on pH. In both experiments, the maximum uptake of iron bound to LF was about twice that of iron bound to citrate (230 pmol and 105 pmol/mg microvillus protein, respectively). Partial degradation of LF in two fragments resulted in the loss of its capacity to increase iron uptake by BBMV. From these preliminary results we conclude that LF may increase iron absorption during the neonatal period, contributing to the high bioavailability of this mineral in human milk.
CLONING AND SEQUENCING OF THE HEMAGGLUTININ GENEOF SWINE INFLUENZA VIRUS (1985)

Complete double-stranded DNA copies of the RNAs of swine influenza virus NJ/11/76(X53a) have been synthesized by using two synthetic oligodeoxynucleotide primers. The gene encoding the hemagglutinin, prepared with these primers, has been cloned and sequenced. A comparison is made on the predicted amino acid sequence of swine influenza hemagglutinin with those of two other human strains and the results are discussed.
Genotyping on a Complementary Metal Oxide Semiconductor Silicon Polymerase Chain Reaction Chip with Integrated DNA Microarray (2002)

A novel method for the fast identification of genetic material utilizing a micro-DNA amplification and analysis device (micro-DAAD) consisting of multiple PCR microreactors with integrated DNA microarrays was developed. The device was fabricated in Si-technology and used for the genotyping of Chinese medicinal plants on the basis of differences in the noncoding region of the 5S-rRNA gene. Successful amplification of the genetic material and the consecutive analysis of the fluorescent-labeled amplicons in the micro-DAAD by the integrated oligonucleotide probes were demonstrated. Parallel analysis was performed by loading the four PCR reactors of the micro-DAAD with different samples of 3-microL volume. Temperature sensors and heating elements of the micro-DAAD enable precise temperature control and fast cycling, allowing the rapid completion of a combined amplification and analysis (hybridization) experiment.
New features and enhancements in the X‐PLOR computer program (1999)

This article describes new methods for X-ray crystallographic refinement and nuclear magnetic resonance (NMR) structure determination that are available in the recent release of the X-PLOR software, X-PLOR 98.0. The major new features of the X-PLOR 98.0 software are: (i) the introduction of maximum likelihood methods (Pannu and Read, Acta Crystallogr 1996;A52:659–668) for X-ray crystallographic refinement with structure factor amplitude, intensity and phase probability targets, (ii) the addition of the Andersen thermal coupling method for temperature control during simulated annealing refinements, (iii) a new utility function for converting reflection data in to the X-PLOR format, (iv) validated scripts and performance enhancements for structure determination from NMR distance restraints using torsion angle dynamics, (v) fast code for direct nuclear Oberhauser effect (NOE) refinement using matrix doubling and gaussian quadratures, (vi) methodologies for using ambiguous restraint information to perform automated iterative peak assignment and structure determination (Nilges et al., J Mol Biol 1997;269:408–422). Additional developments in methodology for refining crystal structures from poor initial models include the implementation of a fast adaptive bulk solvent scattering correction and an energy minimization routine that makes use of second derivative information. Trial crystallographic refinements with an energy minimization protocol that includes these enhancements indicate significantly improved convergence. The quality of the resulting models appears comparable to models obtained from refinement protocols that incorporate torsion angle dynamics. Test applications of the new energy minimizer to NMR structure refinement with using NOE calculations also show improved convergence, leading to more optimized final models. Proteins 1999;35:25–33. © 1999 Wiley-Liss, Inc.
A Virtual Window on media space (1995)

The Virtual Window system uses iiead movements in a local office to control camera movement in a remote office. The result is like a window allowing exploration of remote scenes rather than a flat screen showing moving pictures. Our analysis of the system, experience implementing a prototype, and observations of people using it, combine to suggest that it may help overcome the limitations of typical media space configurations. In particular, it seems useful in offering an expanded field of view, reducing visual discontinuities, allowing mutual negotiation of orientation, providing depth information, and supporting camera awareness. The prototype we built is too large, noisy, slow and inaccurate for extended use, but it is valuable in opening a space of possibilities for the design of systems that allow richer access to remote colleagues.
Is Infliximab Effective for Induction of Remission in Patients with Ulcerative Colitis? (2001)

Crohn's disease (CD) and ulcerative colitis (UC) constitute distinct yet somewhat similar idiopathic inflammatory disorders of the gastrointestinal tract. Manifestations of these diseases can be quite severe and often require treatment with long-term therapy mandating a variety of medications and/or surgery. Standard medical therapy is classically guided towards antiinflammatory treatment, antimicrobial treatment, and immune modulation. Laboratory-based research has helped identify many specific chemokine and cytokine-effector molecules that comprise the end effect of immune system activation resulting in the promotion of intestinal inflammation. These bench-based laboratory investigations have led to experimental clinical trials with specific cytokine agonists and antagonists. Inhibition of one such cytokine, tumor necrosis factor alpha (TNF), with a monoclonal chimeric antibody, infliximab, has demonstrated significant clinical efficacy in the treatment of patients with CD. This observed clinical efficacy is consistent with scientific observations that suggest a central role for TNF in the inflammatory cascade.
Meniscal regeneration using tissue engineering with a scaffold derived from a rat meniscus and mesenchymal stromal cells derived from rat bone marrow (2005)

The purpose of this study was to regenerate a meniscus using a scaffold from a normal meniscus and mesenchymal stromal cells derived from bone marrow (BM-MSCs). Thirty Sprague-Dawley rat menisci were excised and freeze-thawed three times with liquid nitrogen to kill the original meniscal cells. Bone marrow was aspirated from enhanced green fluorescent protein transgenic Sprague-Dawley rats. BM-MSCs were isolated, cultured for 2 weeks, and 2 x 10(5) cells were then seeded onto the meniscal scaffolds. Using a fluorescent microscope and immunohistochemical staining, repopulation of enhanced green fluorescent protein positive cells was observed in the superficial zone of the scaffold after 1 week of culture, and then in the deep zone after 2 weeks. At 4 weeks, expression of extracellular matrices was detected histologically and expression of mRNA for aggrecan and type X collagen was detected. Stiffness of the cultured tissue, assessed by the indentation stiffness test, had increased significantly after 2 weeks in culture, and approximated the stiffness of a normal meniscus. From this study, we conclude that a scaffold derived from a normal meniscus seeded with BM-MSCs can form a meniscus approximating a normal meniscus.
A Novel Bioinformatics Approach Identifies Candidate Genes for the Synthesis and Feruloylation of Arabinoxylan (2007)

Arabinoxylans (AXs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. Despite some recent advances in identifying the genes encoding biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of AX synthesis have not been identified. We have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous genes between taxonomic divisions of species. Over 3 million public domain cereal and dicot expressed sequence tags were mapped onto the complete sets of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes, respectively. It was assumed that genes in cereals involved in AX biosynthesis would be expressed at high levels and that their orthologs in dicotyledonous plants would be expressed at much lower levels. Considering all rice genes encoding putative glycosyl transferases (GTs) predicted to be integral membrane proteins, genes in the GT43, GT47, and GT61 families emerged as much the strongest candidates. When the search was widened to all other rice or Arabidopsis genes predicted to encode integral membrane proteins, cereal genes in Pfam family PF02458 emerged as candidates for the feruloylation of AX. Our analysis, known activities, and recent findings elsewhere are most consistent with genes in the GT43 families encoding beta-1,4-xylan synthases, genes in the GT47 family encoding xylan alpha-1,2- or alpha-1,3-arabinosyl transferases, and genes in the GT61 family encoding feruloyl-AX beta-1,2-xylosyl transferases.
The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses (1997)

The Arabidopsis gai mutant allele confers a reduction in gibberellin (GA) responsiveness. Here we report the molecular cloning of GAI and a closely related gene GRS. The predicted GAI (wild-type) and gai (mutant) proteins differ only by the deletion of a 17-amino-acid segment from within the amino-terminal region. GAI and GRS contain nuclear localization signals, a region of homology to a putative transcription factor, and motifs characteristic of transcriptional coactivators. Genetic analysis indicates that GAI is a repressor of GA responses, that GA can release this repression, and that gai is a mutant repressor that is relatively resistant to the effects of GA. Mutations at SPY and GAR2 suppress the gai phenotype, indicating the involvement of GAI, SPY, and GAR2 in a signaling pathway that regulates GA responses negatively. The existence of this pathway suggests that GA modulates plant growth through derepression rather than through simple stimulation.
Synthesis and characterization of metallo and metal-free octaalkylphthalocyanines and uranyl decaalkylsuperphthalocyaninates (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of metallo and metal-free octaalkylphthalocyanines and uranyl decaalkylsuperphthalocyaninatesEdward A. Cuellar and Tobin J. MarksCite this: Inorg. Chem. 1981, 20, 11, 3766–3770Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/ic50225a039https://doi.org/10.1021/ic50225a039research-articleACS PublicationsRequest reuse permissionsArticle Views611Altmetric-Citations96LEARN 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
Deep Survival: A Deep Cox Proportional Hazards Network. (2016)

Previous research has shown that neural networks can model survival data in situations in which some patients' death times are unknown, e.g. right-censored. However, neural networks have rarely been shown to outperform their linear counterparts such as the Cox proportional hazards model. In this paper, we run simulated experiments and use real survival data to build upon the risk-regression architecture proposed by Faraggi and Simon. We demonstrate that our model, DeepSurv, not only works as well as other survival models but actually outperforms in predictive ability on survival data with linear and nonlinear risk functions. We then show that the neural network can also serve as a recommender system by including a categorical variable representing a treatment group. This can be used to provide personalized treatment recommendations based on an individual's calculated risk. We provide an open source Python module that implements these methods in order to advance research on deep learning and survival analysis.
Controlled plasmon resonance in closed metal/insulator/metal nanocavities (2006)

The controlled plasmon resonance in nanometer-sized optical cavities with a closed end has been demonstrated. A nanosheet plasmon cavity is a metal/insulator/metal waveguide with a finite length. Its lowest-order transverse-magnetic guided mode is reflected at the ends and exhibits the Fabry-Pérot resonance. In this study, one of the ends was closed by an obliquely evaporated Au film, and the so-called organ pipe resonances were observed as reflection dips. Since such closed configurations offer a higher field enhancement and higher detection efficiency of the scattered light, they are promising as fundamental structures for Raman enhancement.
Learning Depth From Single Images With Deep Neural Network Embedding Focal Length (2018)

Learning depth from a single image, as an important issue in scene understanding, has attracted a lot of attention in the past decade. The accuracy of the depth estimation has been improved from conditional Markov random fields, non-parametric methods, to deep convolutional neural networks most recently. However, there exist inherent ambiguities in recovering 3D from a single 2D image. In this paper, we first prove the ambiguity between the focal length and monocular depth learning, and verify the result using experiments, showing that the focal length has a great influence on accurate depth recovery. In order to learn monocular depth by embedding the focal length, we propose a method to generate synthetic varying-focal-length dataset from fixed-focal-length datasets, and a simple and effective method is implemented to fill the holes in the newly generated images. For the sake of accurate depth recovery, we propose a novel deep neural network to infer depth through effectively fusing the middle-level information on the fixed-focal-length dataset, which outperforms the state-of-the-art methods built on pretrained VGG. Furthermore, the newly generated varying-focallength dataset is taken as input to the proposed network in both learning and inference phases. Extensive experiments on the fixed- and varying-focal-length datasets demonstrate that the learned monocular depth with embedded focal length is significantly improved compared to that without embedding the focal length information.
Ovol2 Suppresses Cell Cycling and Terminal Differentiation of Keratinocytes by Directly Repressing c-Myc and Notch1 (2009)

Ovol2 belongs to the Ovo family of evolutionarily conserved zinc finger transcription factors that act downstream of key developmental signaling pathways including Wg/Wnt and BMP/TGF-beta. We previously reported Ovol2 expression in the basal layer of epidermis, where epidermal stem/progenitor cells reside. In this work, we use HaCaT human keratinocytes to investigate the cellular and molecular functions of Ovol2. We show that depletion of Ovol2 leads to transient cell expansion but a loss of cells with long term proliferation potential. Mathematical modeling and experimental findings suggest that both faster cycling and precocious withdrawal from the cell cycle underlie this phenotype. Ovol2 depletion also accelerates extracellular signal-induced terminal differentiation in two- and three-dimensional culture models. By chromatin immunoprecipitation, luciferase reporter, and functional rescue assays, we demonstrate that Ovol2 directly represses two critical downstream targets, c-Myc and Notch1, thereby suppressing keratinocyte transient proliferation and terminal differentiation, respectively. These findings shed light on how an epidermal cell maintains a proliferation-competent and differentiation-resistant state.
Cyclometalated Z-Selective Ruthenium Metathesis Catalysts with Modified N-Chelating Groups (2015)

In order to design improved ruthenium catalysts for Z-selective olefin metathesis reactions, four cyclometalated catalysts with new chelated architectures were synthesized, structurally characterized, and tested in metathesis assays. The mechanism of formation of each was explored using DFT calculations. Of note, two complexes are derived from activation of a tertiary C–H bond, and one features a four-membered chelating architecture. In addition, two dipivalate complexes that did not undergo further C–H activation were isolated and studied to elucidate information about the factors affecting cyclometalation.
Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals (2014)

Translational readthrough gives rise to low abundance proteins with C-terminal extensions beyond the stop codon. To identify functional translational readthrough, we estimated the readthrough propensity (RTP) of all stop codon contexts of the human genome by a new regression model in silico, identified a nucleotide consensus motif for high RTP by using this model, and analyzed all readthrough extensions in silico with a new predictor for peroxisomal targeting signal type 1 (PTS1). Lactate dehydrogenase B (LDHB) showed the highest combined RTP and PTS1 probability. Experimentally we show that at least 1.6% of the total cellular LDHB is targeted to the peroxisome by a conserved hidden PTS1. The readthrough-extended lactate dehydrogenase subunit LDHBx can also co-import LDHA, the other LDH subunit, into peroxisomes. Peroxisomal LDH is conserved in mammals and likely contributes to redox equivalent regeneration in peroxisomes.
Functional arginyl residues in carboxypeptidase A. Modification with butanedione (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFunctional arginyl residues in carboxypeptidase A. Modification with butanedioneJames F. RiordanCite this: Biochemistry 1973, 12, 20, 3915–3923Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/bi00744a020https://doi.org/10.1021/bi00744a020research-articleACS PublicationsRequest reuse permissionsArticle Views201Altmetric-Citations276LEARN 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
Halichondrins - antitumor polyether macrolides from a marine sponge (1986)

Abstract
Effect of 3-Hydroxyproline Residues on Collagen Stability (2003)

Collagen is an integral part of many types of connective tissue in animals, especially skin, bones, cartilage, and basement membranes. A fibrous protein, collagen has a triple-helical structure, which is comprised of strands with a repeating Xaa-Yaa-Gly sequence. l-Proline (Pro) and 4(R)-hydroxy-l-proline (4-Hyp) residues occur most often in the Xaa and Yaa positions. The 4-Hyp residue is known to increase markedly the conformational stability of a collagen triple helix. In natural collagen, a 3(S)-hydroxy-l-proline (3-Hyp) residue occurs in the sequence: 3-Hyp-4-Hyp-Gly. Its effect on collagen stability is unknown. Here, two host-guest peptides containing 3-Hyp are synthesized: (Pro-4-Hyp-Gly)(3)-3-Hyp-4-Hyp-Gly-(Pro-4-Hyp-Gly)(3) (peptide 1) and (Pro-4-Hyp-Gly)(3)-Pro-3-Hyp-Gly-(Pro-4-Hyp-Gly)(3) (peptide 2). The 3-Hyp residues in these two peptides diminish triple-helical stability in comparison to Pro. This destabilization is small when 3-Hyp is in the natural Xaa position (peptide 1). There, the inductive effect of its 3-hydroxyl group diminishes slightly the strength of the interstrand 3-HypC=O.H-NGly hydrogen bond. The destabilization is large when 3-Hyp is in the nonnatural Yaa position (peptide 2). There, its pyrrolidine ring pucker leads to inappropriate mainchain dihedral angles and interstrand steric clashes. Thus, the natural regioisomeric residues 3-Hyp and 4-Hyp have distinct effects on the conformational stability of the collagen triple helix.
Two new all-organic complexes with electrical bistable states (1995)

Two all-organic complexes, MC+TCNQ and BBDN+TCNQ, with electrical bistable states at room temperature have been discovered. The resistivity of these thin films prepared in vacuum can be transferred from high to low under a voltage of few volts. The transition time is &amp;lt;100 ns. Therefore, both materials are suitable for making write-once read-only memories.