gebhart/patrepeval huggingface dataset:
Constitutive activation of the Janus kinase-STAT pathway in T lymphoma overexpressing the Lck protein tyrosine kinase (1997)

The Lck protein, a Src family tyrosine kinase, plays a critical role in T cell maturation and activation. Dysregulation of Lck expression or Lck kinase activity has been implicated in T cell leukemias from mice to humans, although the mechanism underlying Lck-mediated oncogenesis is still largely unclear. We report here that both DNA binding activities and tyrosine phosphorylation of STAT3 and STAT5, but not STAT1, are constitutively enhanced in the mouse T cell lymphoma LSTRA, which is a well-characterized cell line that overexpresses Lck protein and exhibits high levels of Lck kinase activity. Furthermore, Janus kinase 1 (jak1) and Jak2 protein tyrosine kinases are constantly activated in these cells, as determined by their autophosphorylation in an in vitro kinase assay and increased levels of tyrosine phosphorylation on immunoblots. Therefore, like Src-transformed cells, Lck-overexpressing LSTRA cells also exhibit constitutive activation of distinct Jak and STAT proteins.
Accurate three-dimensional wall thickness measurement from multi-slice short-axis MR imaging (2002)

In multiple slice, multiple phase short-axis MR images of the left ventricle the cardiac wall and imaging plane are often at an oblique angle. Planar wall thickness measurements will consequently not be measured perpendicular to the myocardial wall, and therefore overestimate true wall thickness. To correct for this deficiency a three-dimensional wall thickness calculation algorithm has been developed, based on the planar improved centerline method. Evaluation was carried out using software phantoms and MR imaging studies obtained from twenty healthy individuals. When applied to the software phantoms the 3D method demonstrated an error of only 1.6% at the mid to low slices and 10.6% at the apex, compared to errors of 8.1% and 28.6% with the planar method, respectively. In patient studies 3D wall thickness results at apical, low and mid slices were 11.2%, 8.7% and 2.6% smaller than the corresponding 2D values. In conclusion, this three-dimensional approach significantly improves the assessment of cardiac wall thickness measurements from short-axis MR studies.
NGF Activates Similar Intracellular Signaling Pathways in Vascular Smooth Muscle Cells as PDGF-BB But Elicits Different Biological Responses (1999)

The signaling pathways that regulate smooth muscle cell migration and proliferation are incompletely understood. Smooth muscle cells express at least 3 families of receptor tyrosine kinases that mediate cell migration: platelet-derived growth factor (PDGF) receptors, the trk family of neurotrophin receptors, and insulin-like growth factor 1 receptor. The neurotrophin, nerve growth factor (NGF), and insulin-like growth factor 1 induce the migration but not the proliferation of smooth muscle cells, whereas PDGF-BB stimulates both responses. To determine whether distinct signaling pathways downstream of receptor tyrosine kinases specifically mediate smooth muscle cell migration or proliferation, the ligand-induced activation of different signaling pathways in smooth muscle cells was examined. NGF induces prolonged activation of the Shc/MAP kinase pathway and phospholipase Cgamma compared with PDGF-BB. The activation of phosphatidylinositol-3 kinase, however, was 10-fold greater in response to PDGF-BB compared with NGF. Insulin-like growth factor 1 activates only phosphatidylinositol-3 kinase. Pharmacological inhibitors of phosphatidylinositol-3 kinase, Wortmannin and LY294002, inhibit PDGF-BB and NGF-induced migration, whereas an inhibitor of MAP kinase kinase, PD98059, has no effect. Our results suggest that (1) different receptor tyrosine kinases use similar patterns of activation of signaling pathways to mediate distinct biological outcomes of cell migration and proliferation, (2) NGF activates signaling proteins in smooth muscle cells similar to those activated during NGF-induced neuronal differentiation, and (3) the combinatorial effects of different signaling pathways are important for the regulation of smooth muscle cell migration and proliferation. Further studies using mutant trk receptors will help to define the signal transduction pathways mediating NGF-induced smooth muscle cell migration.
Complex Oncogenic Signaling Networks Regulate Brain Tumor‐Initiating Cells and Their Progenies: Pivotal Roles of Wild‐Type EGFR, EGFRvIII Mutant and Hedgehog Cascades and Novel Multitargeted Therapies (2011)

Complex signaling cross-talks between different growth factor cascades orchestrate the primary brain cancer development. Among the frequent deregulated oncogenic pathways, the ligand-activated wild-type epidermal growth factor receptor (EGFR), constitutively activated EGFRvIII mutant and sonic hedgehog pathways have attracted much attention because of their pivotal roles in pediatric medulloblastomas and adult glioblastoma multiformes (GBM) brain tumors. The enhanced expression levels and activation of EGFR, EGFRvIII mutant and hedgehog signaling elements can provide key roles for the sustained growth, migration and local invasion of brain tumor-initiating cells (BTICs) and their progenies, resistance to current therapies and disease relapse. These tumorigenic cascades also can cooperate with Wnt/β-catenin, Notch, platelet-derived growth factor (PDGF)/PDGF receptors (PDGFRs), hepatocyte growth factor (HGF)/c-Met receptor and vascular endothelial growth factor (VEGF)/VEGF receptors (VEGFRs) for the acquisition of a more malignant behavior and survival advantages by brain tumor cells during disease progression. Therefore, the simultaneous targeting of these oncogenic signaling components including wild-type EGFR, EGFRvIII mutant and hedgehog pathways may constitute a potential therapeutic approach of great clinical interest to eradicate BTICs and improve the efficacy of current clinical treatments by radiation and/or chemotherapy against aggressive and recurrent medulloblastomas and GBMs.
Anti-L-selectin oligonucleotide ligands recognize CD62L-positive leukocytes: Binding affinity and specificity of univalent and bivalent ligands (1998)

Oligonucleotide aptamers generated against purified LS-Rg, a human L-selectin/IgG fusion protein, bound human CD62L-positive leukocytes. FACS analysis of lymphocytes or neutrophils stained with fluorescently labeled aptamers indicated specificity and sensitivity for cellular L-selectin similar to that observed with anti-L-selectin antibody. Univalent aptamers were compared to bivalent aptamers as well as to the anti-adhesion, anti-L-selectin antibody DREG56. Equilibrium and kinetic binding experiments were performed to examine the affinity and kinetic binding parameters of L-selectin aptamers to evaluate their binding to CD62L-positive leukocytes and to test their potential as L-selectin antagonists. Binding experiments indicated that bivalent aptamers approached the affinity and the dissociation rate of bivalent antibody, and preferentially recognized cellular compared to soluble L-selectin, a potentially useful distinction in vivo. Anti-L-selectin aptamers also inhibited L-selectin dependent self-adhesion of neutrophils suggesting that in vitro univalent and bivalent aptamers provided anti-adhesion activity similar to that observed with blocking antibody and indicated a direct blocking mechanism of action during inhibition of L-selectin-dependent trafficking of lymphocytes observed in vivo.
BMP Signaling Pathways in Cartilage and Bone Formation (2001)

This review focuses on the molecular aspects of osteogenesis and chondrogenesis as they relate to cellular and developmental levels. We discuss BMP (bone morphogenetic protein)-mediated signaling pathways for the patterning of skeletal elements and mechanisms for the induction of cartilage and bone formation. We emphasize BMP-mediated initiation of chondrogenesis and osteogenesis and consider BMP-dependent signaling cascades in mesenchymal progenitor cells during the development of the axial and appendicular skeleton and during growth plate and joint formation. In particular, we discuss BMP-signaling mediators of the Smad and TAK family and the modulation of these signals by cross-talk and integration with other signaling pathways.
Structural and electronic properties of pentagon-heptagon pair defects in carbon nanotubes (1996)

General features of the energetics and electronic states of carbon nanotubes, containing pentagon-heptagon pair (5/7) topological defects in the hexagonal network of the zigzag configuration, are investigated within simple tight-binding models. This 5/7 pair defect on the nanotube structure is not only responsible for a change in nanotube diameter, but also governs the electronic behavior around the Fermi level. Furthermore, nanotubes having different helicities and different electronic properties can be connected using such a pair. Various configurations including one, two, and three 5/7 pairs are explored in order to understand the influence of several defects on the electronic properties of the system. Topological aspects associated with the presence of 5/7 pair defects in armchair and chiral nanotubes are also discussed. \textcopyright{} 1996 The American Physical Society.
Histamine and the Response to IFN-α in Chronic Hepatitis C (1998)

Whole blood concentrations of histamine were examined in 20 patients with chronic hepatitis C after longterm treatment with interferon-alpha (IFN-alpha). In 13 of these patients, a transient (n = 5) or sustained (n = 8) normalization of liver enzymes and elimination of viral RNA were noted at the end of therapy. Seven patients did not respond to IFN-alpha. Nonresponding patients had significantly lower histamine levels in blood than transient (p = 0.0005) or sustained (p = 0.04) responders. Histamine levels were not different in patients with a sustained vs. a transient IFN response. Confounding factors, such as ongoing viral replication or liver cirrhosis, did not account for the differences in histamine levels. Our data suggest that hypohistaminism in peripheral blood may determine a poor response to IFN-alpha in chronic hepatitis C.
ACCNT—A Metallic-CNT-Tolerant Design Methodology for Carbon-Nanotube VLSI: Concepts and Experimental Demonstration (2009)

We demonstrate ACCNT (pronounced as ldquoaccentrdquo), a solution to the metallic-nanotube problem that does not require any metallic-nanotube removal of any kind. ACCNT uses asymmetrically correlated carbon nanotubes to achieve metallic-nanotube tolerance, delivering high on-off ratios (10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> -10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> ) while preserving the current drive. In addition, this metallic-nanotube tolerance can be engineered arbitrarily close to 100%. We present the ACCNT concepts in detail, verifying the concepts and underlying assumptions via experimental results. We further demonstrate inverters using ACCNT and ACCNT scalability to a wafer scale. ACCNT marks the first demonstration of a VLSI-compatible metallic-nanotube-tolerant design methodology.
Specific Lymphocyte Subsets Predict Response to Adoptive Cell Therapy Using Expanded Autologous Tumor-Infiltrating Lymphocytes in Metastatic Melanoma Patients (2012)

These results indicate that the immunotherapy with expanded autologous TIL is capable of achieving durable clinical responses in patients with metastatic melanoma and that CD8(+) T cells in the infused TIL, particularly differentiated effectors cells and cells expressing BTLA, are associated with tumor regression.
Five unique open reading frames of infectious laryngotracheitis virus are expressed during infection but are dispensable for virus replication in cell culture (2003)

The chicken alphaherpesvirus infectious laryngotracheitis virus (ILTV) exhibits several unique genetic features including an internal inversion of a conserved part of the unique long genome region. At one end, this inversion is preceded by a cluster of five open reading frames (ORFs) of 335-411 codons, designated ORF A to ORF E, that are not present in any other known herpesvirus genome. In this report we analysed expression of these genes and identified the corresponding viral RNA and protein products. Northern blot analyses showed 3'-coterminal transcripts of ORFs A and B, and monocistronic mRNAs of ORFs C and D. ORF E is part of a 3'-coterminal transcription unit that includes the conserved glycoprotein H and thymidine kinase genes. Monospecific antisera obtained after immunization of rabbits with bacterial fusion proteins allowed detection of the protein products of ORF A (40 kDa), ORF B (34 kDa), ORF C (38 and 30 kDa), ORF D (41 kDa) and ORF E (44 kDa) in ILTV-infected cells. For functional analyses, five virus recombinants possessing deletions within the individual ORFs and concomitant insertions of a reporter gene cassette encoding green fluorescent protein were generated. All virus mutants were replication competent in cell culture, but exhibited reduced virus titres or plaque sizes when compared to wild-type ILTV. These findings indicate that the ILTV-specific ORF A to ORF E genes might be important for virus replication in the natural host organism.
IL-15 Promotes the Survival of Naive and Memory Phenotype CD8+ T Cells (2003)

IL-15 stimulates the proliferation of memory phenotype CD44(high)CD8(+) T cells and is thought to play a key role in regulating the turnover of these cells in vivo. We have investigated whether IL-15 also has the capacity to affect the life span of naive phenotype (CD44(low)) CD8(+) T cells. We report that IL-15 promotes the survival of both CD44(low) and CD44(high) CD8(+) T cells, doing so at much lower concentrations than required to induce proliferation of CD44(high) cells. Rescue from apoptosis was associated with the up-regulation of Bcl-2 in both cell types, whereas elevated expression of Bcl-x(L) was observed among CD44(high) but not CD44(low) CD8(+) cells. An investigation into the role of IL-15R subunits in mediating the effects of IL-15 revealed distinct contributions of the alpha- and beta- and gamma-chains. Most strikingly, IL-15R alpha was not essential for either induction of proliferation or promotion of survival by IL-15, but did greatly enhance the sensitivity of cells to low concentrations of IL-15. By contrast, the beta- and gamma-chains of the IL-15R were absolutely required for the proliferative and pro-survival effects of IL-15, although it was not necessary for CD44(high)CD8(+) cells to express higher levels of IL-15R beta than CD44(low) cells to proliferate in response to IL-15. These results show that IL-15 has multiple effects on CD8 T cells and possesses the potential to regulate the life span of naive as well as memory CD8(+) T cells.
MARTX, Multifunctional Autoprocessing Repeats-in-Toxin Toxins (2007)

The repeats-in-toxin (RTX) exoproteins are a diverse collection of proteins exported via type I secretion by gram-negative bacteria. These proteins include the pore-forming RTX toxins typified by α-hemolysin of Escherichia coli and Bordetella pertussis adenylate cyclase toxin (ACT) and also
Early-life stress impacts the developing hippocampus and primes seizure occurrence: cellular, molecular, and epigenetic mechanisms (2014)

Early-life stress includes prenatal, postnatal, and adolescence stress. Early-life stress can affect the development of the hypothalamic-pituitary-adrenal (HPA) axis, and cause cellular and molecular changes in the developing hippocampus that can result in neurobehavioral changes later in life. Epidemiological data implicate stress as a cause of seizures in both children and adults. Emerging evidence indicates that both prenatal and postnatal stress can prime the developing brain for seizures and an increase in epileptogenesis. This article reviews the cellular and molecular changes encountered during prenatal and postnatal stress, and assesses the possible link between these changes and increases in seizure occurrence and epileptogenesis in the developing hippocampus. In addititon, the priming effect of prenatal and postnatal stress for seizures and epileptogenesis is discussed. Finally, the roles of epigenetic modifications in hippocampus and HPA axis programming, early-life stress, and epilepsy are discussed.
Peripheral blood progenitor cell grafts contain high levels of platelet‐secreted mediators (2001)

The cytokine network of PBPC autografts includes increased levels of TPO and several platelet-derived mediators.
Neurodegenerative Diseases of the Retina and Potential for Protection and Recovery (2008)

Recent advances in our understanding of the mechanisms in the cascade of events resulting in retinal cell death in ocular pathologies like glaucoma, diabetic retinopathy and age-related macular degeneration led to the common descriptive term of neurodegenerative diseases of the retina. The final common pathophysiologic pathway of these diseases includes a particular form of metabolic stress, resulting in an insufficient supply of nutrients to the respective target structures (optic nerve head, retina). During metabolic stress, glutamate is released initiating the death of neurones containing ionotropic glutamate (N-methyl-D-aspartat, NMDA) receptors present on ganglion cells and a specific type of amacrine cells. Experimental studies demonstrate that several drugs reduce or prevent the death of retinal neurones deficient of nutrients. These agents generally block NMDA receptors to prevent the action of glutamate or halt the subsequent pathophysiologic cycle resulting in cell death. The major causes for cell death following activation of NMDA receptors are the influx of calcium and sodium into cells, the generation of free radicals linked to the formation of advanced glycation endproducts (AGEs) and/or advanced lipoxidation endproducts (ALEs) as well as defects in the mitochondrial respiratory chain. Substances preventing these cytotoxic events are considered to be potentially neuroprotective.
The anhydride content of some commercial PP-g-MA: FTIR and titration (1996)

A set of anhydride-grafted polypropylenes was collected from various companies. They were studied in light of our recent results on polypropylene melt grafted with maleic an-hydride.1 This work confirmed that an important decrease of the anhydride content is recorded on heating or washing, due to the elimination of free, ungrafted products, re-spectively, by sublimation of maleic anhydride and by polymaleic anhydride solubilization. The deconvolution of the infrared spectra of washed anhydride-grafted polypropylenes (PP-g-MA) revealed two types of grafted anhydride: succinic anhydride form and polymaleic anhydride form. All in all, four forms of anhydride functions were detected: two grafted and two free, each being either on monomeric or polymeric forms. Nevertheless, one PP-g-MA (Hercoprime) can be distinguished by its very high grafting level. This polymer is therefore discussed in more detail. Finally, all the present results are discussed with regard to the principal applications of the PP-g-MA as a blend compatiblizer or as an adhesion promoter. © 1996 John Wiley & Sons, Inc.
Comparison of EORTC Criteria and PERCIST for PET/CT Response Evaluation of Patients with Metastatic Colorectal Cancer Treated with Irinotecan and Cetuximab (2013)

Response evaluation with EORTC criteria and PERCIST gave similar responses and OS outcomes with good agreement on BOmR (κ-coefficient, 0.76) and similar significant differences in median OS between response groups. Compared with EORTC criteria, we find PERCIST unambiguous because of clear definitions and therefore more straightforward to use.
Small RNAs Make Big Splash (2002)

Just when scientists thought they had deciphered the roles played by the cell9s leading actors, a familiar performer has turned up in a stunning variety of guises. RNA, long upstaged by its more glamorous sibling, DNA, is turning out to have star qualities of its own.
 Science
 hails these electrifying discoveries, which are prompting biologists to overhaul their vision of the cell and its evolution, as 20029s Breakthrough of the Year. The online version of the Breakthrough of the Year section contains references and links not found in the print edition (see
 www.sciencemag.org/content/vol298/issue5602/#special).
Use of Placebo Surgery in Controlled Trials of a Cellular-Based Therapy for Parkinson's Disease (1999)

Surgical procedures are frequently introduced into general practice on the basis of uncontrolled studies that are less rigorous than those required for the approval of medical interventions.1 The standard for the evaluation of surgical therapy is lower because of the complexity of designing and conducting scientifically valid and ethically acceptable clinical trials of surgical procedures.2 As a result, many surgical trials fail to control for investigator bias or placebo effects.3,4 The list of inadequately studied invasive or surgical procedures that became part of standard medical practice only to be abandoned after closer scrutiny includes bloodletting, routine tonsillectomy, routine circumcision, . . .
The keratin proteins and genes of wool and hair. (1996)

This review has endeavoured to outline the state of knowledge of the wool keratin proteins and their genes from structural viewpoints. The acquisition of sequence information over the last decade through molecular techniques, combined with the protein data derived in the '70s and '80s, now represents a database of significant proportions describing the proteins and genes of wool. The challenge is now to determine where these proteins are located in the keratin IF/matrix complex and how they interact. Gene mapping programs are revealing interesting links between keratin genes that have ramifications for the mechanisms of keratin gene regulation. While the study of keratin gene regulation is in its infancy it will be an active field for years to come. The recent discovery of a transcription factor that not only regulates hair keratin gene expression but also hair follicle initiation shows how different fields of research can come together in exciting and unexpected ways.
Multiplex-Ready PCR: A new method for multiplexed SSR and SNP genotyping (2008)

Multiplex-ready PCR provides several technological advantages that can facilitate fluorescence-based SSR genotyping and the multiplexed preparation of DNA templates for SNP assays. These advantages can be captured at several points in the genotyping process, and offer considerable cost and labour savings. Multiplex-ready PCR is broadly applicable to plant genomics and marker assisted breeding, and should be transferable to any animal or plant species.