gebhart/patrepeval huggingface dataset:
Pathogenesis of hepatitis B and C‐induced hepatocellular carcinoma (1998)

Hepatocellular carcinoma (HCC) is estimated to have an annual worldwide incidence of 0.25 to 1.2 million new cases per year. Both the prevalence and incidence of HCC vary markedly as a function of geography and the local prevalence of chronic viral hepatitis. Both chronic hepatitis B and chronic hepatitis C are recognized as risk factors for HCC. The prevalence of cirrhosis in individuals with HCC and chronic hepatitis B or C is reported to be 80.9% and 75.8%, respectively. HCC occurs at a lower rate in chronic viral hepatitis in the absence of cirrhosis. Moreover, hepatitis C virus (HCV) rather than hepatitis B virus (HBV) is associated with the majority of non-cirrhotic cases of HCC. It is probable that the ongoing process of hepatocyte necrosis and liver cell renewal coupled with inflammation, which is characteristic of chronic viral hepatitis, causes not only nodular regeneration and cirrhosis but also progressive genomic errors in hepatocytes as well as unregulated growth and repair mechanisms leading to hepatocyte dysplasia and, in some cases, hepatic carcinoma. Current concepts concerning virus-induced HCC are reported and discussed in the following review.
Endoplasmic reticulum stress modulates the response of myelinating oligodendrocytes to the immune cytokine interferon-γ (2005)

Interferon-gamma (IFN-gamma) is believed to contribute to immune-mediated demyelinating disorders by targeting the myelin-producing oligodendrocyte, a cell known to be highly sensitive to the disruption of protein synthesis and to the perturbation of the secretory pathway. We found that apoptosis induced by IFN-gamma in cultured rat oligodendrocytes was associated with endoplasmic reticulum (ER) stress. ER stress also accompanied oligodendrocyte apoptosis and hypomyelination in transgenic mice that inappropriately expressed IFN-gamma in the central nervous system (CNS). Compared with a wild-type genetic background, the enforced expression of IFN-gamma in mice that were heterozygous for a loss of function mutation in pancreatic ER kinase (PERK) dramatically reduced animal survival, promoted CNS hypomyelination, and enhanced oligodendrocyte loss. PERK encodes an ER stress-inducible kinase that phosphorylates eukaryotic translation initiation factor 2alpha and specifically maintains client protein homeostasis in the stressed ER. Therefore, the hypersensitivity of PERK+/- mice to IFN-gamma implicates ER stress in demyelinating disorders that are induced by CNS inflammation.
A Biologically Inspired System for Action Recognition (2007)

We present a biologically-motivated system for the recognition of actions from video sequences. The approach builds on recent work on object recognition based on hierarchical feedforward architectures [25, 16, 20] and extends a neurobiological model of motion processing in the visual cortex [10]. The system consists of a hierarchy of spatio-temporal feature detectors of increasing complexity: an input sequence is first analyzed by an array of motion- direction sensitive units which, through a hierarchy of processing stages, lead to position-invariant spatio-temporal feature detectors. We experiment with different types of motion-direction sensitive units as well as different system architectures. As in [16], we find that sparse features in intermediate stages outperform dense ones and that using a simple feature selection approach leads to an efficient system that performs better with far fewer features. We test the approach on different publicly available action datasets, in all cases achieving the highest results reported to date.
Automatic rotating element ellipsometers: Calibration, operation, and real-time applications (1990)

In a typical reflection ellipsometry experiment, one characterizes the polarization state change that a polarized light beam undergoes upon reflection from a specular surface. This measurement provides ρ≡rp/rs, where rp and rs are the complex amplitude reflection coefficients of the surface for p- and s-polarized waves. Nearly 15 years have passed since the development of automatic ellipsometers along with the detailed calibration, error analysis, and data reduction procedures to be used with them. More specifically, these powerful instruments permit (1) determination of bulk dielectric functions and nondestructive depth profiling of static multilayered materials through measurements as a function of photon energy and (2) characterization of dynamic surfaces in adverse environments through measurements as a function of time at fixed photon energy. In the 15 intervening years, the major research thrusts in ellipsometry have been the exploitation of these instruments in materials and process characterization in diverse areas of materials science and electrochemistry. One of the simplest and most popular automatic ellipsometers is a photometric instrument in which one or more of the optical elements (polarizer, compensator, and/or analyzer) is designed to rotate continuously. In this article, the major developments in rotating element ellipsometry are reviewed since the first report of an automatic rotating analyzer instrument by Cahan and Spanier in 1969. The topics covered include rotating element configurations, calibration, characterization of errors and imperfections, absolute accuracy, data reduction, precision, and a review of the real-time applications accessible to these instruments. The sections on calibration, errors, and data reduction include new material and are written from a practical standpoint to assist in instrumentation setup and troubleshooting. The development and improvement of next-generation rotating element instruments that employ optical multichannel detectors to collect spectroscopic data on dynamic surfaces with time resolution as short as 5 ms now defines the forefront of research in this field.
Cytoplasmic control of nuclear DNA synthesis during early development of Xenopus laevis: a cell-free assay. (1975)

Nuclei isolated from nondividing cells were induced to synthesize DNA by incubation with cytoplasm from early embryos of Xenopus laevis. Numerous replication eyes were formed in the nuclear DNA molecules, and high levels of [3-H]dTTP were incorporated. With this assay a protein(s) which appears to initiate DNA synthesis was found at high levels in the cytoplasm of eggs, blastulae, or gastrulae, but only at low levels in the cytoplasm of oocytes, hatched embryos, or adult tissues.
Lambert-Eaton myasthenic syndrome: Clinical diagnosis, immune-mediated mechanisms, and update on therapies (1995)

The Lambert-Eaton myasthenic syndrome (LEMS) is a rare condition in which weakness results from a presynaptic abnormality of acetylcholine release at the neuromuscular junction. It was first described as a paraneoplastic syndrome in patients with lung cancer but we now know about half of the patients with LEMS do not have cancer. The diagnosis is made on the basis of the clinical findings and characteristic electromyographic patterns. Recent evidence indicates that LEMS results from an autoimmune attack directed against the voltage-gated calcium channels on the presynaptic motor nerve terminal. In patients with LEMS who have cancer, effective treatment of the underlying tumor frequently produces marked improvement of weakness as well. Otherwise, treatment involves the use of agents that improve neuromuscular transmission by increasing the release of neurotransmitter, and immunosuppression.
Selective changes in expression of HLA class I polymorphic determinants in human solid tumors. (1989)

Analysis of surgical biopsies with monoclonal antibodies (mAbs) to framework determinants of major histocompatibility complex class I antigens has shown that malignant transformation is frequently associated with a marked loss of these cell surface molecules. The present study sought to determine whether more selective losses of major histocompatibility complex class I expression occur. Multiple specimens from 13 different types of primary and metastatic tumors were tested utilizing mAb BB7.2, which recognizes a polymorphic HLA-A2 epitope. In each case, expression of HLA-A,B,C molecules was determined by testing with mAb W6/32 directed to a framework HLA class I determinant. We have found that in HLA-A2-positive patients (identified by reactivity of their normal tissues with mAb BB7.2), HLA-A2 products are not detectable or are reduced in their expression in 70-80% of endometrial, colorectal, mammary, and renal tumors; in 40-60% of soft-tissue, skin, ovary, urinary bladder, prostate, and stomach tumors; and in 25-30% of melanomas and lung carcinomas tested. All tumors expressed the framework HLA-A,B,C determinant. The HLA-A2 epitope recognized by mAb BB7.2 is located in a portion of the HLA-A2 molecule postulated to react with the T-cell receptor. Immune surveillance to tumors is thought to depend on cytotoxic T cells, which require corecognition of polymorphic HLA class I epitopes, and on natural killer cells, which are, on the contrary, activated by the absence of HLA class I antigens. The selective loss of an HLA class I polymorphic epitope shown in this study may explain the mechanism by which tumor cells escape both T-cell recognition and natural killer cell surveillance.
Diarrhea or colorectal cancer: Can bacterial toxins serve as a treatment for colon cancer? (2003)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The NMDA Receptor/Ion Channel Complex: A Drug Target for Modulating Synaptic Plasticity and Excitotoxicity (2007)

A recent search on PubMed for the phrase NMDA receptor results in 2,190 hits on this topic for review articles and 20,100 hits for experimental papers. This is a direct reflection of the intensiveness, significance, and complexity associated with the research on this key receptor protein over the last several decades. In this review, we briefly describe the NMDA receptor structure, discuss the role of NMDA receptors in modulating synaptic plasticity and excitotoxicity, explore age-dependent changes in NMDA receptor functioning, and survey interesting NMDA receptor blockers. Given the huge existing literature on the subject, an exhaustive review has not been endeavored. Instead, an attempt was made to point out those studies that have been instrumental in the field or that are of special interest.
[Porphyrias and drugs]. (1995)

The porphyrias are a metabolic disorders of heme biosynthesis characterized by the excessive production and excretion of porphyrins and porphyrin precursors. They are caused by defects in specific enzyme activities and classified into 7 subtypes. Some of them present with photosensitivity of skin and intermittent acute attacks related to nervous system disturbance. Especially in acute intermittent porphyria, patients have recurrent acute attacks of abdominal, neurologic, and psychiatric symptoms. Some precipitating factors; including drugs, hormonal factors, starvation, and stress; induces acute attacks. In this article, pathophysiology of the neurologic symptoms and relation between precipitating factors, especially focused in drugs, and acute attacks may be reviewed.
GdN Nanoisland-Based GaN Tunnel Junctions (2013)

Tunnel junctions could have a great impact on gallium nitride and aluminum nitride-based devices such as light-emitting diodes and lasers by overcoming critical challenges related to hole injection and p-contacts. This paper demonstrates the use of GdN nanoislands to enhance interband tunneling and hole injection into GaN p-n junctions by several orders of magnitude, resulting in low tunnel junction specific resistivity (1.3 × 10(-3) Ω-cm(2)) compared to the previous results in wide band gap semiconductors. Tunnel injection of holes was confirmed by low-temperature operation of GaN p-n junction with a tunneling contact layer, and strong electroluminescence down to 20 K. The low tunnel junction resistance combined with low optical absorption loss in GdN is very promising for incorporation in GaN-based light emitters.
Aqueous coordination chemistry of vanadocene dichloride with nucleotides and phosphoesters. Mechanistic implications for a new class of antitumor agents (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAqueous coordination chemistry of vanadocene dichloride with nucleotides and phosphoesters. Mechanistic implications for a new class of antitumor agentsJeffrey H. Toney, Carolyn P. Brock, and Tobin J. MarksCite this: J. Am. Chem. Soc. 1986, 108, 23, 7263–7274Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://doi.org/10.1021/ja00283a022RIGHTS & PERMISSIONSArticle Views244Altmetric-Citations88LEARN 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 InReddit PDF (1 MB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
In vivo selection of basic region-leucine zipper proteins with altered DNA-binding specificities. (1996)

A transcription interference assay was used to generate mutant basic region-leucine zipper proteins with altered DNA-binding specificities. A library of mutants of a CCAAT/enhancer binding protein was constructed by randomizing five DNA-contacting amino acids in the basic region Asn-18, Ala-15, Val-14, Ser-11, and Arg-10. These mutants were then selected for their ability to bind mutant recognition sequences containing substitutions at the 2 and 3 positions of the wild-type sequence 5'-A5T4T3G2C1G1'C2'A3A4'T5'-3'. Mutants containing the sequence Leu-18Tyr-15Xaa-14Tyr-11Arg-10, in which four of the five contact residues are altered, were identified that recognize the palindromic sequence 5'-ATCYCGY'GAT-3' (Xaa = asparagine when Y = G; Xaa = methionine when Y = A). Moreover, in a selection against the sequence 5'-ATTACGTAAT-3', mutants were obtained containing substitutions not only in the basic region but also in the hinge region between the basic and leucine zipper regions. The mutant proteins showed high specificity in a functional transcription interference assay. A model for the interaction of these mutants with the target DNA sequences is discussed.
Characterization of Pit, a Streptococcus pneumoniae Iron Uptake ABC Transporter (2002)

Bacteria frequently have multiple mechanisms for acquiring iron, an essential micronutrient, from the environment. We have identified a four-gene Streptococcus pneumoniae operon, named pit, encoding proteins with similarity to components of a putative Brachyspira hyodysenteriae iron uptake ABC transporter, Bit. An S. pneumoniae strain containing a defined mutation in pit has impaired growth in medium containing the iron chelator ethylenediamine di-o-hydroxyphenylacetic acid, reduced sensitivity to the iron-dependent antibiotic streptonigrin, and impaired virulence in a mouse model of S. pneumoniae systemic infection. Furthermore, addition of a mutation in pit to a strain containing mutations in the two previously described S. pneumoniae iron uptake ABC transporters, piu and pia, resulted in a strain with impaired growth in two types of iron-deficient medium, a high degree of resistance to streptonigrin, and a reduced rate of iron uptake. Comparison of the susceptibilities to streptonigrin of the individual pit, piu, and pia mutant strains and comparison of the growth in iron-deficient medium and virulence of single and double mutant strains suggest that pia is the dominant iron transporter during in vitro and in vivo growth.
Metabolism of 15-hydroxy-5,8,11,13-eicosatetraenoic acid by MOLT-4 cells and blood T-lymphocytes. (1990)

MOLT-4 lymphocytes metabolize 15-hydroxy-5,8,11,13-eicosatetraenoic acid (15-HETE) via beta-oxidation with retention of the hydroxyl group at the omega 6-carbon atom. 15-HETE oxidation is accompanied by the time-dependent accumulation of both beta-hydroxy acids and metabolites produced by repetitive cycles of the beta-oxidation spiral. Detection of 7-hydroxy-5-dodecenoic acid shows that these cells continue to beta-oxidize the substrate when the conjugated diene is allylic to a hydroxyl group. When 15-HETE was the substrate, it was also possible to detect 12-hydroxy-5,8,10-heptadecatrien-1-al and 3,15-dihydroxy-8,11,13-eicosatrienoic acid. The former product may be produced by alpha-oxidation of 13-hydroxy-6,9,11-octadecatrienoic acid followed by its decarboxylation. Detection of a 20-carbon metabolite, lacking a double bond at position 5, suggests that an intermediate of beta-oxidation was used as a substrate for chain elongation. When 13-hydroxy-6,9,11-octadecatrienoic acid was used as a substrate, it was indeed possible to detect 3,15-dihydroxy-8,11,13-eicosatrienoic acid as well as 15-hydroxy-8,11,13-eicosatrienoic acid. In addition, 13-hydroxy-6,9,11-octadecatrienoic acid was a precursor for the biosynthesis of both 14-hydroxy-7,10,12-nonadecatrien-1-al and 1,14-dihydroxy-7,10,12-nonadecatriene. These studies with MOLT-4 cells as well as with T-lymphocytes isolated from blood show that products of the 15-lipoxygenase pathway are metabolized with the accumulation of a variety of compounds. Since 15-HETE has been implicated as a modulator of T-cell function, these findings raise the possibility that the newly described metabolites may be involved in regulating lymphocyte function.
Electroholographic neurons implemented on potassium lithium tantalate niobate crystals (1996)

We describe a new approach for constructing large-scale artificial neural networks. The novelty of our approach is based on the concept of electroholography (EH), which permits interconnecting of electronic neurons by minute-volume holograms, using the voltage-controlled photorefractive effect in paraelectric crystals. Crystals of potassium lithium tantalate niobate (KLTN) in the paraelectric phase are shown to be suitable for implementing this concept. A small network composed of two KLTN crystals on which holographic connections are recorded is presented to demonstrate the EH approach.
Ab initio Simulation of the Grafting of Phenylacetylene on Hydrogenated Surfaces of Crystalline Silicon Catalyzed by a Lewis Acid (2006)

Car-Parrinello simulations have been carried out to identify the grafting mechanism of phenylacetylene, a prototypical alkyne, on the hydrogenated surfaces of crystalline silicon, catalyzed by a Lewis acid (AlCl3). To this purpose, we have made use of a new technique, metadynamics, devised recently to deal with complex chemical reactions in first principles simulations. The reaction mechanism, leading to a styrenyl-terminated surface, turns out to be equivalent to the corresponding gas-phase hydrosilylation reaction by silanes that we have identified in a previous work. The activation energies for the surface reactions (0.43, 0.42, 0.35 eV, for H-Si(111), H-Si(100)2 x 1, and H-Si(100)1 x 1, respectively) are very close to that of the corresponding gas-phase reaction (0.37 eV). The estimated activation free energy at room temperature is sufficiently low for the grafting reaction to be viable at normal conditions and at low coverage on the crystalline silicon surfaces, as already well documented to occur on the surface of porous silicon. However, the conformation of the transition state shadows a large area of the surface, which might contribute to making the grafting process self-limiting.
Encapsulation for Somatic Gene Therapy (1999)

With the human genome project approaching its completion date of 2005, gene-based technology will play an increasingly important role in health-care delivery. Non-autologous somatic gene therapy is a novel application in which non-autologous cell lines engineered to secrete a recombinant protein are enclosed within immunoisolation devices and implanted into all patients requiring the same product for therapy. The development of this technology requires a multi-disciplinary effort towards optimization of the biomaterial used to manufacture the implantable devices and selection of the appropriate cell lines for enclosure. The efficacy of this technology is illustrated in the treatment of dwarfism and lysosomal storage disease in murine models. The potential of a safe and cost-effective gene-based delivery method should have wide applications in treating both classical genetic disorders and non-Mendelian diseases.
Combating HER2-overexpressing breast cancer through induction of calreticulin exposure by Tras-Permut CrossMab (2015)

Although trastuzumab has succeeded in breast cancer treatment, acquired resistance is one of the prime obstacles for breast cancer therapies. There is an urgent need to develop novel HER2 antibodies against trastuzumab resistance. Here, we first rational designed avidity-imporved trastuzumab and pertuzumab variants, and explored the correlation between the binding avidity improvement and their antitumor activities. After characterization of a pertuzumab variant L56TY with potent antitumor activities, a bispecific immunoglobulin G-like CrossMab (Tras-Permut CrossMab) was generated from trastuzumab and binding avidity-improved pertuzumab variant L56TY. Although, the antitumor efficacy of trastuzumab was not enhanced by improving its binding avidity, binding avidity improvement could significantly increase the anti-proliferative and antibody-dependent cellular cytotoxicity (ADCC) activities of pertuzumab. Further studies showed that Tras-Permut CrossMab exhibited exceptional high efficiency to inhibit the progression of trastuzumab-resistant breast cancer. Notably, we found that calreticulin (CRT) exposure induced by Tras-Permut CrossMab was essential for induction of tumor-specific T cell immunity against tumor recurrence. These data indicated that simultaneous blockade of HER2 protein by Tras-Permut CrossMab could trigger CRT exposure and subsequently induce potent tumor-specific T cell immunity, suggesting it could be a promising therapeutic strategy against trastuzumab resistance.