gebhart/patrepeval huggingface dataset:
MicroRNAs and Esophageal Squamous Cell Carcinoma (2010)

Esophageal cancer is a common cause of cancer death worldwide. Esophageal squamous cell carcinoma (ESCC) is the most predominant type. Certain microRNAs (miRNAs) function in tumorgenesis involved in important biological and pathologic processes. To reveal miRNAs' signatures of ESCC, we analyzed miRNAs extracted from ESCC cell lines with the microRNA microarray. The significant alterations were confirmed by quantitative real-time PCR using miRNAs extracted from cell lines or patients' esophageal biopsy tissues. We found that miR-205 and miR-10a were significantly altered in cellular expression, and might be specific for ESCC with potential roles in the pathogenesis. As a result of function studies in miR-205, alterations in miR-205 expression could modulate the phenotype of epithelial cells towards epithelial-mesenchymal transition characterized by reduced abundance of E-cadherin, that is the ESCC-specific miRNA target and inhibit translationally a representative E-cadherin repressor, ZEB1 and ZEB2. Similarly, miR-10a is reported as a tumor suppressor by controlling cell migration/invasion, as it can target homeobox genes. These results provide insight into the potential mechanisms of ESCC in the pathogenesis. This review also includes a comprehensive overview of the relationship between miRNAs and ESCC.
Relation Classification via Recurrent Neural Network (2015)

Deep learning has gained much success in sentence-level relation classification. For example, convolutional neural networks (CNN) have delivered competitive performance without much effort on feature engineering as the conventional pattern-based methods. Thus a lot of works have been produced based on CNN structures. However, a key issue that has not been well addressed by the CNN-based method is the lack of capability to learn temporal features, especially long-distance dependency between nominal pairs. In this paper, we propose a simple framework based on recurrent neural networks (RNN) and compare it with CNN-based model. To show the limitation of popular used SemEval-2010 Task 8 dataset, we introduce another dataset refined from MIMLRE(Angeli et al., 2014). Experiments on two different datasets strongly indicates that the RNN-based model can deliver better performance on relation classification, and it is particularly capable of learning long-distance relation patterns. This makes it suitable for real-world applications where complicated expressions are often involved.
A multifunctional cell surface developmental stage-specific antigen in the cockroach embryo: involvement in pathfinding by CNS pioneer axons. (1992)

mAb DSS-8 binds to a 164-kD developmental stage-specific cell surface antigen in the nervous system of the cockroach, Periplaneta americana. The antigen is localized to different subsets of cells at various stages of development. The spatial and temporal distributions of DSS-8 binding were determined and are consistent with this antigen playing multiple roles in the development of the nervous system. Direct identification of some of these functions was made by perturbation experiments in which pioneer axon growth occurs in embryos that are cultured in vitro in the presence of mAb DSS-8 or its Fab fragment. Under these conditions the pioneer axons of the median fiber tract grow but follow altered pathways. In a smaller percentage of the ganglia, the immunoreagents additionally produce defasciculation of a subset of DSS-8 labeled axons. Therefore, direct roles for the DSS-8 antigen in both the guidance of pioneer axons and selective fasciculation have been demonstrated.
Gene expression in the chicken caecum in response to infections with non-typhoid Salmonella (2014)

Chickens can be infected with Salmonella enterica at any time during their life. However, infections within the first hours and days of their life are epidemiologically the most important, as newly hatched chickens are highly sensitive to Salmonella infection. Salmonella is initially recognized in the chicken caecum by TLR receptors and this recognition is followed by induction of chemokines, cytokines and many effector genes. This results in infiltration of heterophils, macrophages, B- and T-lymphocytes and changes in total gene expression in the caecal lamina propria. The highest induction in expression is observed for matrix metalloproteinase 7 (MMP7). Expression of this gene is increased in the chicken caecum over 4000 fold during the first 10 days after the infection of newly hatched chickens. Additional highly inducible genes in the caecum following S. Enteritidis infection include immune responsive gene 1 (IRG1), serum amyloid A (SAA), extracellular fatty acid binding protein (ExFABP), serine protease inhibitor (SERPINB10), trappin 6-like (TRAP6), calprotectin (MRP126), mitochondrial ES1 protein homolog (ES1), interferon-induced protein with tetratricopeptide repeats 5 (IFIT5), avidin (AVD) and transglutaminase 4 (TGM4). The induction of expression of these proteins exceeds a factor of 50. Similar induction rates are also observed for chemokines and cytokines such as IL1β, IL6, IL8, IL17, IL18, IL22, IFNγ, AH221 or iNOS. Once the infection is under control, which happens approx. 2 weeks after infection, expression of IgY and IgA increases to facilitate Salmonella elimination from the gut lumen. This review outlines the function of individual proteins expressed in chickens after infection with non-typhoid Salmonella serovars.
Alterations on peripheral blood B-cell subpopulations in very early arthritis patients (2010)

In very early polyarthritis patients, there is a reduction in circulating pre-switch memory B cells. The reasons that may account for this effect are still unknown. Short-term corticosteroids and MTX do not seem to have a direct effect on circulating B-cell subpopulations in VERA patients.
Reproducibility of the determination of caffeine in coffee by micellar electrokinetic capillary chromatography (1994)

Abstract Samples of regular and decaffeinated varieties of green coffee beans, instant coffee, and “roast &amp; grind” coffee have been examined by micellar electrokinetic capillary chromatography (MECC). The separation conditions affecting the reproducibility of the determination of caffeine in these samples are presented. Sodium dodecyl sulfate (SDS) and cetyltrimethylammonium chloride (CTAC) Were employed to demonstrate the role of the surfactant system in reproducibility. The use of NaOH and HCl was explored for column rinsing to enhance the stability of the electroosmotic flow. The levels of caffeine ranged from 3.95% (by weight) for regular coffee to 0.07% for decaffeinated coffee. The relative standard deviation (RSD) for the migration time of the peak corresponding to caffeine in coffee samples was 0.74%. The RSDs for the peak areas and heights were 1.04 and 2.07%, respectively. The results of the quantitation of caffeine by MECC are compared to levels determined by high‐performance liquid chromatography (HPLC).
A novel gene delivery system using EGF receptor‐mediated endocytosis (1994)

A monoclonal antibody to the human epidermal growth factor (EGF) receptor was conjugated with polylysine and the resulting conjugate was affinity-linked with DNA (gene). This novel gene delivery system utilizes receptor-mediated endocytosis and would be especially suitable for gene therapy for EGF receptor-overproducing squamous cell carcinomas.
Toxin-Antitoxin Genes of the Gram-Positive Pathogen Streptococcus pneumoniae: So Few and Yet So Many (2012)

Pneumococcal infections cause up to 2 million deaths annually and raise a large economic burden and thus constitute an important threat to mankind. Because of the increase in the antibiotic resistance of Streptococcus pneumoniae clinical isolates, there is an urgent need to find new antimicrobial approaches to triumph over pneumococcal infections. Toxin-antitoxin (TA) systems (TAS), which are present in most living bacteria but not in eukaryotes, have been proposed as an effective strategy to combat bacterial infections. Type II TAS comprise a stable toxin and a labile antitoxin that form an innocuous TA complex under normal conditions. Under stress conditions, TA synthesis will be triggered, resulting in the degradation of the labile antitoxin and the release of the toxin protein, which would poison the host cells. The three functional chromosomal TAS from S. pneumoniae that have been studied as well as their molecular characteristics are discussed in detail in this review. Furthermore, a meticulous bioinformatics search has been performed for 48 pneumococcal genomes that are found in public databases, and more putative TAS, homologous to well-characterized ones, have been revealed. Strikingly, several unusual putative TAS, in terms of components and genetic organizations previously not envisaged, have been discovered and are further discussed. Previously, we reported a novel finding in which a unique pneumococcal DNA signature, the BOX element, affected the regulation of the pneumococcal yefM-yoeB TAS. This BOX element has also been found in some of the other pneumococcal TAS. In this review, we also discuss possible relationships between some of the pneumococcal TAS with pathogenicity, competence, biofilm formation, persistence, and an interesting phenomenon called bistability.
Evaluation of Automated Cell Culture Incubators (2003)

Automated cell culture incubators generally are considered primary components of fully automated cell culture systems, which are able to monitor cell growth without human interaction. This tutorial is focused on automated cell culture incubators. It emphasizes the impact of automation on throughput and environmental controls (temperature, humidity, and CO 2 ) and proposes some basic protocols to check these functions. In addition, it details practical aspects for switching from manual to automated cell culture incubators.
BMP Sustains Embryonic Stem Cell Self-Renewal through Distinct Functions of Different Krüppel-like Factors (2016)

Bone morphogenetic protein (BMP) signaling exerts paradoxical roles in pluripotent stem cells (PSCs); it sustains self-renewal of mouse embryonic stem cells (ESCs), while it induces differentiation in other PSCs, including human ESCs. Here, we revisit the roles of BMP-4 using mouse ESCs (mESCs) in naive and primed states. SMAD1 and SMAD5, which transduce BMP signals, recognize enhancer regions together with KLF4 and KLF5 in naive mESCs. KLF4 physically interacts with SMAD1 and suppresses its activity. Consistently, a subpopulation of cells with active BMP-SMAD can be ablated without disturbing the naive state of the culture. Moreover, Smad1/5 double-knockout mESCs stay in the naive state, indicating that the BMP-SMAD pathway is dispensable for it. In contrast, the MEK5-ERK5 pathway mediates BMP-4-induced self-renewal of mESCs by inducing Klf2, a critical factor for the ground state pluripotency. Our study illustrates that BMP exerts its self-renewing effect through distinct functions of different Krüppel-like factors.
Structure and specificity of lamprey monoclonal antibodies (2008)

Adaptive immunity in jawless vertebrates (lamprey and hagfish) is mediated by lymphocytes that undergo combinatorial assembly of leucine-rich repeat (LRR) gene segments to create a diverse repertoire of variable lymphocyte receptor (VLR) genes. Immunization with particulate antigens induces VLR-B-bearing lymphocytes to secrete antigen-specific VLR-B antibodies. Here, we describe the production of recombinant VLR-B antibodies specific for BclA, a major coat protein of Bacillus anthracis spores. The recombinant VLR-B antibodies possess 8-10 uniform subunits that collectively bind antigen with high avidity. Sequence analysis, mutagenesis, and modeling studies show that antigen binding involves residues in the beta-sheets lining the VLR-B concave surface. EM visualization reveals tetrameric and pentameric molecules having a central core and highly flexible pairs of stalk-region "arms" with antigen-binding "hands." Remarkable antigen-binding specificity, avidity, and stability predict that these unusual LRR-based monoclonal antibodies will find many biomedical uses.
Transcriptional up-regulation of intracellular adhesion molecule-1 in human endothelial cells by the antioxidant pyrrolidine dithiocarbamate involves the activation of activating protein-1 (1996)

The redox status of the cell plays an essential role in regulating signal transduction, transcription factor activity, and expression of cell surface molecules. In this study, we show that pyrrolidine dithiocarbamate (PDTC), a potent antioxidant agent, upregulated the cell surface expression of intercellular adhesion molecule-1 (ICAM-1) in human endothelial cells (EC). Further analysis of PDTC-mediated ICAM-1 up-regulation revealed that PDTC increased ICAM-1 mRNA levels and augmented its gene promoter activity. Transfection experiments in EC with reporter constructs harboring nested deletion fragments of the ICAM-1 promoter indicated the presence of a functional PDTC-responsive region located between positions -136 to -353 of the promoter. Gel retardation assays together with supershift analysis revealed that PDTC induced the binding of c-fos and c-jun to a consensus activating protein-1 (AP-1) binding site located at position -284. PDTC alone or in combination with TNF-alpha enhanced AP-1-dependent transactivation in HUVEC, as determined by DNA binding assays. The functional implication of AP-1 in the transcription of the ICAM-1 gene was further demonstrated by cotransfection experiments in which a c-jun expression vector induced the promoter activity of the PDTC-responsive element of the ICAM-1 promoter. Taken together, these results indicate that the antioxidant PDTC induces transcriptional activation of ICAM-1 and that this induction is mediated at least in part by the transcription factor AP-1. This mechanism might be operative in pathologic conditions in which a redox imbalance plays a key role, such as ischemia/reperfusion injury or arteriosclerosis.
Magnetic resonance imaging guided and monitored ultrasound surgery. (1996)

During the past few years there has been an interest in using magnetic resonance imaging (MRI) to guide focused ultrasound beams during noninvasive surgery. MRI offers good soft tissue contrast, allowing the beam to be accurately aimed. Temperature sensitive MRI sequences can be used during low power test pulses to visualize the temperature elevation in the focal zone at temperature levels that do not cause tissue damage. This allows the beam to be aimed, eliminating all potential image or ultrasound propagation distortions. It may even be possible to calibrate the MRI signal to give the temperature elevation and use it as a feedback to modify the power output to assure adequate thermal exposure during every therapy sonication. Finally, MRI allows tissue changes induced by the sonication to be detected. This may be useful after the treatment to establish the boundaries of the thermal damage and is also very useful when experiments are conducted. All of these aspects of MRI guided ultrasound surgery have been investigated using in vivo experiments and the results will be reviewed here. The future technical developments and potential clinical applications will be discussed. [Work supported by NIH and General Electric Medical Systems.]
Interleukin-4 is Required for the Induction of Lung Th2 Mucosal Immunity (1995)

Aerosol antigen challenge of ovalbumin-sensitized mice induced an eosinophilic airway inflammation that was dependent on interleukin (IL)-5 and CD4+, but not CD8+, T lymphocytes. The involvement of the Th2 phenotype of CD4+ T cells was supported by demonstrating that FACS-sorted purified lung T cells from sensitized, but not control, mice produced IL-4, IL-5, and IL-10 after activation of the CD3/TCR complex. To determine the role of IL-4 in this process, we used mice in which the gene for IL-4 was deleted by homologous recombination. Antigen challenge of IL-4 gene-targeted mice resulted in a marked attenuation of eosinophilic inflammation and IL-5 secretion. To more fully understand the time when IL-4 was involved, we administered a neutralizing anti-IL-4 antibody (11B11) either immediately before antigen challenge or during immunization. Inhibition of IL-4 before antigen challenge had little effect on antigen-induced eosinophil infiltration. However, when 11B11 was administered during immunization, there was a marked reduction in eosinophil infiltration. Cross-linking of the CD3/TCR complex of FACS-sorted lung T cells revealed that only when anti-IL-4 was administered during immunization was there an inhibition of T cell-derived IL-5 and IgE production. These results suggest that IL-4 is central both to the induction of a local Th2 response and to the development of eosinophilic inflammation of the lung. Moreover, we suggest a sequential involvement of IL-4 and IL-5, with IL-4 committing naive T cells to a Th2 phenotype which upon activation by aerosol provocation secrete IL-5, resulting in eosinophil accumulation.
クズネツォーヴォ1遺跡（1979―2001年の調査結果） (2003)

The Kuznetsovo 1 is a multi strata site and situates at the Nevel'sk district in Sakhalin region. Kimura S. and Ito N. investigated this site first, and since 1979 until now the staff of the Laboratory of Archaeological Research of Sakhalin State University have studied it. Golubev V. and Vasilevski A. have excavated total area of 450 m2. Two main layers were distinguished: the lower belonged to the Epi-Jomon,the Susuya, and the Towada cultures (2,750 ± 150 ; 2,384 ± 270 ; 1,640 ± 340BP), and the upper was of the Enoura and the Minami Kaiduka periods of the Okhotsk culture (VII-XIII cal AD). The Ainu cemetery of XVI-XVII cal AD was found in the upper layer of the site.
Role of octanoic and decanoic acids in the control of seizures. (1986)

Octanoic and decanoic acid, the major constituents of the Medium Chain Triglyceride (MCT) Emulsion diet, have been detected in appreciable quantities in the peripheral blood of children with intractable seizures treated with the MCT diet. Serum concentrations of these acids as well as beta hydroxybutyrate and acetoacetate rose as the diet was introduced and on full diet showed pronounced diurnal variation and low concentrations in the morning. No correlation between octanoic and decanoic acid concentrations and control of seizures was established, but further studies with octanoic and decanoic acid using animal models are necessary to assess the role of these acids and of control of seizures.
127. Adenovirus Type 5 Vectors Pseudotyped with Fibers from Subgroup D (19p and 37) Show Detargeting from Hepatocytes In Vitro and In Vivo (2004)

Use of adenoviral gene therapy vectors based on different non-cross reacting serotypes is being investigated by several groups as a means to administer adenoviral vectors, either in a re-administration setting, or in subjects with circulating antibodies against the common serotypes such as Ad2 or Ad5. We have previously developed GFP expressing vectors using the chimpanzee adenoviruses Pan 6 (C6-GFP) and Pan 7 (C7-GFP). We have determined that administration of either one of the two chimpanzee adenovirus vectors does not affect the transduction efficiency of the other vector while re-administration of the same vector is severely compromised. Adenoviruses have three major capsid proteins, hexon, penton base, and fiber, which elicit the production of circulating antibodies. We wished to elucidate the relative importance of each of the three capsid components in preventing transduction in a gene therapy setting. In order to do this we have generated a panel of GFP expressing vectors that are chimeric between Pan 6 and Pan 7 where the hexon protein or the fiber protein or both hexon and fiber proteins of the Pan 7 vector have been replaced by those from Pan 6. Balb/C mice were immunized with either Pan 6 or Pan 7 and re-administration (by tail vein injection) was attempted 3 weeks later using each of the five GFP expressing vectors (C6-GFP, C7-GFP, and the three chimeric vectors). Three days later the level of liver transduction was estimated qualitatively by examining liver sections for the presence of GFP expression and quantitatively by estimating copies of GFP DNA by Taqman analysis. The data showed that antibodies to both hexon and fiber are important in preventing re-administration of adenoviral vectors.
An approach to the study of structure-function relationships of MHC class I molecules: isolation and serologic characterization of H-2Kb somatic cell variants. (1986)

Somatic cell variants expressing an altered antigenic form of the H-2Kb molecule were isolated for the purpose of performing structure-function analysis of a class I MHC molecule. Over 25 independently isolated variants were derived from an Abelson virus transformed pre- B cell line (R8) by mutagenesis with ethyl methane sulfonate or ethyl nitrosourea. Negative selection was performed by complement-dependent cytotoxicity with anti-H-2Kb monoclonal antibodies subsequently followed by positive selection to separate the H-2Kb surface negative variants from structural variants. Biochemical characterization of a random selection of three independent variants indicated that the variant H-2Kb molecule was present in normal amounts in lysates, and was unchanged in size. Cytofluorometric analysis with the use of a panel of seven monoclonal antibodies against H-2Kb indicated that all of the variants had lost one or more alloantigenic determinants (monoclonal antibody binding sites). For these variants, the pattern of monoclonal antibody loss of recognition suggested that antibody defined alloantigenic determinants appear to be discretely localized to a single domain, either the alpha 1 or the alpha 2 domain, of the H-2Kb molecule. In contrast, CTL recognition of the Kb molecule of these variants depends on involvement of both alpha 1 and alpha 2 domains as shown in the companion paper.