gebhart/patrepeval huggingface dataset:
Growth-promoting effects of insulin-like growth factor-1 (IGF-1) on hematopoietic cells: overexpression of introduced IGF-1 receptor abrogates interleukin-3 dependency of murine factor-dependent cells by a ligand-dependent mechanism (1991)

Although insulin-like growth factor (IGF-1) stimulated 3H-thymidine incorporation upon addition to the interleukin-3 (IL-3)-dependent cell line FDC-P1, IGF-1 did not relieve IL-3 dependency for growth. To further examine the effects of IGF-1 on hematopoietic cells, FDC-P1 cells were infected with a retroviral construct (LISN) containing the human IGF-1 receptor (hIGF-1R) and neo genes. IL-3-independent cells were readily isolated after LISN infection when either IGF-1 or supraphysiologic concentrations of insulin were included in the culture medium. These cells were transformed to IL-3 independence by a ligand- dependent mechanism because their growth was dependent on the presence of either IGF-1 or insulin and growth factors capable of supporting autocrine growth were not detected. Furthermore, a monoclonal antibody (MoAb) directed against the human IGF-1R (alpha IR-3) inhibited IGF-1 but not IL-3-induced proliferation and these cells contained 20- to 200- fold more IGF-1 receptors than uninfected FDC-P1 cells. In contrast, when LISN-infected cells were plated in medium without exogenously supplied IGF-1 or insulin, factor-independent cells were rarely isolated. Growth of these cells was also inhibited by the alpha IR-3 MoAb and they expressed 100- to 400-fold more IGF-1 receptors than uninfected FDC-P1 cells. The endogenous IGF-1 and/or insulin present in the calf serum may have enabled their growth because these cells, unlike the parental cells, would proliferate in serum-free defined media and their growth was again inhibited by the alpha IR-3 MoAb. These results demonstrate that IGF-1 can replace IL-3 for growth when FDC-P1 cells overexpress the IGF-1R. Given the fairly ubiquitous expression of the IGF-1 receptor, these and additional experiments might help to determine whether increased expression of endogenous receptors by cells can lead to leukemogenesis and tumorigenesis. Moreover, hIGF-1R-infected cells will be useful in investigating the mechanisms of IGF1-mediated signal transduction because they are now known to proliferate in response to IGF-1.
Non-negative graph embedding (2008)

We introduce a general formulation, called non-negative graph embedding, for non-negative data decomposition by integrating the characteristics of both intrinsic and penalty graphs [17]. In the past, such a decomposition was obtained mostly in an unsupervised manner, such as Non-negative Matrix Factorization (NMF) and its variants, and hence unnecessary to be powerful at classification. In this work, the non-negative data decomposition is studied in a unified way applicable for both unsupervised and supervised/semi-supervised configurations. The ultimate data decomposition is separated into two parts, which separatively preserve the similarities measured by the intrinsic and penalty graphs, and together minimize the data reconstruction error. An iterative procedure is derived for such a purpose, and the algorithmic non-negativity is guaranteed by the non-negative property of the inverse of any M-matrix. Extensive experiments compared with NMF and conventional solutions for graph embedding demonstrate the algorithmic properties in sparsity, classification power, and robustness to image occlusions.
Explorable Volumetric Depth Images from Raycasting (2013)

View-dependent image-based rendering techniques have become increasingly popular as they combine the high quality of images with the explorability of interactive techniques. However, in the context of volume rendering, previous approaches suffer from various shortcomings, including the limitation to surfaces, expensive generation, and insufficient occlusion and motion parallax impairing depth perception. In this paper, we propose Volumetric Depth Images (VDI) to overcome these issues for view-dependent volume visualization by an extension of the Layered Depth Image (LDI) approach. Instead of only saving for each view ray of one camera configuration the depth and color values for a set of surfaces, as in LDIs, VDIs store so-called super segments, each consisting of a depth range as well as composited color and opacity. This compact representation is independent from the structure of the original data and can be generated by slight modification of ray casters with very low overhead. VDIs can be rendered efficiently at high quality with arbitrary camera configurations by means of proxy frustum geometry and an efficient depth ordering scheme. When viewing the scene from the initial view point, VDIs produce results identical to the original ray casting. As demonstrated by means of a prototype implementation and data from different fields, our approach can be useful for preview rendering and a-priori analysis in in-situ contexts among others.
Zinc Finger Nucleases as tools to understand and treat human diseases (2010)

Recent work has shown that it is possible to target regulatory elements to DNA sequences of an investigator's choosing, increasing the armamentarium for probing gene function. In this review, we discuss the development and use of designer zinc finger proteins (ZFPs) as sequence specific tools. While the main focus of this review is to discuss the attachment of the FokI nuclease to ZFPs and the ability of the resulting fusion protein (termed zinc finger nucleases (ZFNs)) to genomically manipulate a gene of interest, we will also cover the utility of other functional domains, such as transcriptional activators and repressors, and highlight how these are being used as discovery and therapeutic tools.
Is Congo Red an Amyloid-specific Dye? (2001)

Congo red (CR) binding, monitored by characteristic yellow-green birefringence under crossed polarization has been used as a diagnostic test for the presence of amyloid in tissue sections for several decades. This assay is also widely used for the characterization of in vitro amyloid fibrils. In order to probe the structural specificity of Congo red binding to amyloid fibrils we have used an induced circular dichroism (CD) assay. Amyloid fibrils from insulin and the variable domain of Ig light chain demonstrate induced CD spectra upon binding to Congo red. Surprisingly, the native conformations of insulin and Ig light chain also induced Congo red circular dichroism, but with different spectral shapes than those from fibrils. In fact, a wide variety of native proteins exhibited induced CR circular dichroism indicating that CR bound to representative proteins from different classes of secondary structure such as alpha (citrate synthase), alpha + beta (lysozyme), beta (concavalin A), and parallel beta-helical proteins (pectate lyase). Partially folded intermediates of apomyoglobin induced different Congo red CD bands than the corresponding native conformation, however, no induced CD bands were observed with unfolded protein. Congo red was also found to induce oligomerization of native proteins, as demonstrated by covalent cross-linking and small angle x-ray scattering. Our data suggest that Congo red is sandwiched between two protein molecules causing protein oligomerization. The fact that Congo red binds to native, partially folded conformations and amyloid fibrils of several proteins shows that it must be used with caution as a diagnostic test for the presence of amyloid fibrils in vitro.
Comparative studies of rat IgG to further delineate the Fc  :  FcRn interaction site (1998)

Recent data have indicated that the MHC class I-related receptor, FcRn, regulates the half-lives of serum IgG in addition to its known role in transferring IgG from mother to young. In the current study, the activity of rat IgG (rIgG) isotypes in FcRn-mediated functions has been analyzed. The serum half-life and maternofetal transfer in mice decreased in the order rIgG2a > rIgG1 > rIgG2c > rIgG2b. This decrease in activity correlates well with reduced binding affinity for soluble mouse FcRn, and site-directed mutagenesis of a recombinant Fc-hinge fragment has been used to investigate the molecular basis for the differences in activities of the rIgG. Analysis of the serum half-lives of the mutated Fc-hinge fragments demonstrated that, in addition to Ile253, His310, His435 and His436 that were identified in earlier studies, amino acids at positions 257, 307 and 309 play a role in building the FcRn interaction site of IgG. The study also excludes the involvement of amino acids in a fourth loop located at the CH2-CH3 domain interface that encompasses residues 386-387 in FcRn binding. Sequence differences at positions 257, 307 and 309 between rIgG most likely account for the reduced affinity of rIgG2b and IgG2c relative to rIgG1 and rIgG2a for binding to FcRn.
Beneficial Effects of Herbs, Spices and Medicinal Plants on the Metabolic Syndrome, Brain and Cognitive Function (2013)

Herbs and spices have been used since ancient times to not only improve the flavor of edible food but also to prevent and treat chronic health maladies. While the scientific evidence for the use of such common herbs and medicinal plants then had been scarce or lacking, the beneficial effects observed from such use were generally encouraging. It is, therefore, not surprising that the tradition of using such herbs, perhaps even after the advent of modern medicine, has continued. More recently, due to an increased interest in understanding the nutritional effects of herbs/spices more comprehensively, several studies have examined the cellular and molecular modes of action of the active chemical components in herbs and their biological properties. Beneficial actions of herbs/spices include anti-inflammatory, antioxidant, anti-hypertensive, gluco-regulatory, and anti-thrombotic effects. One major component of herbs and spices is the polyphenols. Some of the aforementioned properties are attributed to the polyphenols and they are associated with attenuating the metabolic syndrome. Detrimental changes associated with the metabolic syndrome over time affect brain and cognitive function. Metabolic syndrome and type-2 diabetes are also risk factors for Alzheimer's disease and stroke. In addition, the neuroprotective effects of herbs and spices have been demonstrated and, whether directly or indirectly, such beneficial effects may also contribute to an improvement in cognitive function. This review evaluates the current evidence available for herbs/spices in potentially improving the metabolic syndrome, as well as their neuroprotective effects on the brain, and cognitive function in animal and human studies.
Validation Procedures in Radiologic Diagnostic Models (1999)

The NN classifier performs better than the one based on LR. This advantage is well detected by three-fold cross-validation but remains unnoticed when leave-one-out or bootstrap algorithms are used.
Effect of human umbilical cord blood‐derived mesenchymal stem cells in a cirrhotic rat model (2009)

Our results showed that HMSCs infusion could improve liver fibrosis in rats with CCl4-induced cirrhosis, raising the possibility for clinical use of HMSCs in the treatment of cirrhosis.
Anaplasma phagocytophilum p44 mRNA Expression Is Differentially Regulated in Mammalian and Tick Host Cells: Involvement of the DNA Binding Protein ApxR (2007)

The natural life cycle of Anaplasma phagocytophilum, an obligatory intracellular bacterium that causes human granulocytic anaplasmosis, consists of alternate infection of two distinct hosts, ticks and mammals, in which bacterial surface proteins are expected to have a critical role. The present study investigated regulation of A. phagocytophilum p44 genes, which encode the P44 major surface proteins. Quantitative real-time reverse transcription-PCR analysis revealed that the amount of p44 mRNA obtained from spleens of A. phagocytophilum-infected SCID mice was approximately 10-fold greater than the amount obtained from salivary glands of A. phagocytophilum-infected Ixodes scapularis nymphs. Similarly, the amount of p44 mRNA obtained from A. phagocytophilum-infected HL-60 cells per bacterium was significantly greater than the amount obtained from infected ISE6 tick cells. The relative amount of p44 mRNA was approximately threefold higher in A. phagocytophilum-infected HL-60 cells cultured at 37 degrees C than in A. phagocytophilum-infected HL-60 cells cultured at 28 degrees C. Although there are more than 100 p44 paralogs, we observed expression mainly from the p44 expression locus (p44E) in various host environments. Interestingly, transcription of the A. phagocytophilum gene encoding the DNA binding protein ApxR was also significantly greater in A. phagocytophilum-infected HL-60 cells than in infected ISE6 tick cells. Gel mobility shift and DNase I protection assays revealed recombinant ApxR binding to the promoter regions of p44E and apxR. ApxR also transactivated the p44E and apxR promoter regions in a lacZ reporter assay. These results indicate that p44 genes and apxR are specifically up-regulated in the mammalian host environment and suggest that ApxR not only is positively autoregulated but also acts as a transcriptional regulator of p44E.
RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases (1995)

mRNA capping entails GMP transfer from GTP to a 5' diphosphate RNA end to form the structure G(5')ppp(5')N. A similar reaction involving AMP transfer to the 5' monophosphate end of DNA or RNA occurs during strand joining by polynucleotide ligases. In both cases, nucleotidyl transfer occurs through a covalent lysyl-NMP intermediate. Sequence conservation among capping enzymes and ATP-dependent ligases in the vicinity of the active site lysine (KxDG) and at five other co-linear motifs suggests a common structural basis for covalent catalysis. Mutational studies support this view. We propose that the cellular and DNA virus capping enzymes and ATP-dependent ligases constitute a protein superfamily evolved from a common ancestral enzyme. Within this superfamily, the cellular capping enzymes display more extensive similarity to the ligases than they do to the poxvirus capping enzymes. Recent studies suggest that eukaryotic RNA viruses have evolved alternative pathways of cap metabolism catalysed by structurally unrelated enzymes that nonetheless employ a phosphoramidate intermediate. Comparative analysis of these enzymes, particularly at the structural level, should illuminate the shared reaction mechanism while clarifying the basis for nucleotide specificity and end recognition. The capping enzymes merit close attention as potential targets for antiviral therapy.
Similarity-based search and evaluation of environmentally relevant properties for organic compounds in combination with the group contribution approach (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSimilarity-based search and evaluation of environmentally relevant properties for organic compounds in combination with the group contribution approachAxel Drefahl and Martin ReinhardCite this: J. Chem. Inf. Comput. Sci. 1993, 33, 6, 886–895Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ci00016a011https://doi.org/10.1021/ci00016a011research-articleACS PublicationsRequest reuse permissionsArticle Views68Altmetric-Citations8LEARN 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 options Get e-Alerts
Photobiomodulation Improves Cutaneous Wound Healing in an Animal Model of Type II Diabetes (2004)

The results demonstrate that PBM at an energy density of 4 J/cm(2) is effective in improving the healing of cutaneous wounds in an animal model of type II diabetes, suggesting that PBM (632 nm, 4 J/cm(2)) would be effective in treating chronic cutaneous wounds in diabetic patients.
Virtualization of cellular network EPC gateways based on a scalable SDN architecture (2014)

The gateways in mobile cellular networks are capable to handle the traffic from millions of subscribers at the same time, while providing high availability guarantee. Such entities are not only expensive, but also inflexible in terms of system deployment and maintenance. In this work, we investigate the feasibilities to virtualize gateway entities used in the Long Term Evolution (LTE) Evolved Packet Core (EPC). We propose a novel PDN Gateway (PGW) architecture, which decouples the control plane from the user plane by using Software Defined Network (SDN) technology. Moreover, we propose to run the user plane forwarding function on low cost IT hardware. The major advantages of our proposal are two-fold. First, our proposal lowers down the expenditure of operating services in LTE networks. Second, fine-grained resource management policies can be implemented in our virtualized gateway, which brings agility and reliability for the mobile cellular network.
Molecular Cloning and Sequencing of Three GranulocyticEhrlichiaGenes Encoding High-Molecular-Weight Immunoreactive Proteins (1998)

Granulocytic Ehrlichia was isolated from canine blood obtained from animals challenged with field-collected Ixodes scapularis and propagated in HL60 cells. PCR primers specific for the 16S ribosomal DNA (rDNA) of the Ehrlichia genogroup comprising E. equi, E. phagocytophila, and the agent of human granulocytic ehrlichiosis (HGE) amplified DNA from extracts of these cells. Sequence analysis of this amplified DNA revealed that it is identical to the 16S rDNA sequence of the HGE agent. A genomic library was constructed with DNA from granulocytic Ehrlichia and screened with pooled sera from tick-challenged, granulocytic Ehrlichia-infected dogs. Several clones were isolated and sequenced. Three complete genes encoding proteins with apparent molecular masses of 100, 130, and 160 kDa were found. The recombinant proteins reacted with convalescent-phase sera from dogs and human patients recovering from HGE. This approach will be useful for identifying candidate diagnostic and vaccine antigens for granulocytic ehrlichiosis and aid in the classification of genogroup members.
The in vitro and in vivo phosphotyrosine map of activated MuSK (2000)

The muscle-specific receptor tyrosine kinase MuSK plays a crucial role in neuromuscular synapse formation. Activation of MuSK is induced by agrin leading to clustering of several proteins, including acetylcholine receptors, at synaptic sites. In a first step to elucidate the signal transduction cascade following MuSK activation and leading to clustering of synaptic proteins, we sought to identify the tyrosine residues that are phosphorylated in activated MuSK. We mapped the tyrosine residues that are phosphorylated in vitro and in vivo using methods that provide high sensitivity and do not require radioactive tracers. We expressed MuSK in insect cells by using a baculovirus expression vector and mapped the tyrosines that are phosphorylated in MuSK in an in vitro kinase assay using matrix-assisted laser desorption ionization MS to sequence tryptic peptides fractionated by HPLC. In addition, we isolated MuSK from Torpedo electric organ and used nanoelectrospray tandem mass spectrometry and parent ion scanning to identify the tyrosine residues that are phosphorylated in activated, endogenous MuSK in vivo. We found that six of the nineteen intracellular tyrosine residues in MuSK are phosphorylated in activated MuSK: the juxtamembrane tyrosine (Y553), the tyrosines within the activation loop (Y750, Y754, and Y755), a tyrosine near the beginning of the kinase domain (Y576), and a tyrosine (Y812) within the C-terminal lobe of the kinase domain. Our biochemical data are consistent with results from functional experiments and establish a good correlation between tyrosine residues that are phosphorylated in activated MuSK and tyrosines that are required for MuSK signaling.
Hip Fracture (1996)

Hip fractures, particularly in older persons, result in problems that extend far beyond the orthopedic injury, with repercussions in the areas of medicine, rehabilitation, psychiatry, social work, and health care economics. There are over 250,000 hip fractures in the United States each year, with 90 percent occurring in patients over the age of 50 years.1 With the aging of the population, the annual number of hip fractures is projected to double by the year 2040.1,2 It is unlikely that efforts to prevent these injuries will have a substantial effect in the foreseeable future. Therefore, it is imperative that we . . .
Atomic resolution STM imaging of a twisted single-wall carbon nanotube (1998)

We present atomically resolved scanning tunneling microscopy images of single-wall carbon nanotubes (SWNT's) embedded in a crystalline nanotube rope. Although they may be interpreted as of a chiral nanotube, the images are more consistently explained as an achiral armchair tube with a quenched twist distortion. The existence of quenched twists in SWNT's in ropes might explain the fact that both as-grown bulk nanotube material and individual ropes have insulatorlike conductivity at low temperature.
Diastereospecific Photochemical Dimerization of a Stilbene‐Containing Daisy Chain Monomer in Solution as well as in the Solid State (2003)

A crown ether/dialkylammonium ion hybrid containing a stilbene group self-assembles into a [c2]daisy chain-like pseudorotaxane, the solid-state superstructure of which was confirmed by X-ray crystallography. Upon irradiation, the pseudorotaxane undergoes an efficient photochemical [2+2] dimerization, both in solution as well as in the solid state, to yield one cyclobutane diastereoisomer with syn-anti-syn stereochemistry and head-to-tail regiochemistry (see scheme).
‘Don’t Touch My Holocaust’: Responding to Life is Beautiful (2000)

This article uses a study of Life is Beautiful (dir. Benigni, 1998) to interrogate the intimate relation between the Holocaust and film. It discusses the appropriateness of the cinematic medium for handling the Holocaust, and the use of humour to negotiate atrocity. It is suggested that many criticisms of Benigni’s film are inappropriate. However, the article closes by proposing an alternative, further-reaching basis for criticism. Drawing on Rose’s suggestion that fascism and representation are inseparable, the resonances between film and the Nazi project are explored, raising profound questions not just for Benigni’s work but for all cinematic treatments of the topic.