gebhart/patrepeval huggingface dataset:
G9a and Jhdm2a Regulate Embryonic Stem Cell Fusion-Induced Reprogramming of Adult Neural Stem Cells (2008)

Somatic nuclei can be reprogrammed to pluripotency through fusion with embryonic stem cells (ESCs). The underlying mechanism is largely unknown, primarily because of a lack of effective approaches to monitor and quantitatively analyze transient, early reprogramming events. The transcription factor Oct4 is expressed specifically in pluripotent stem cells, and its reactivation from somatic cell genome constitutes a hallmark for effective reprogramming. Here we developed a double fluorescent reporter system using engineered ESCs and adult neural stem cells/progenitors (NSCs) to simultaneously and independently monitor cell fusion and reprogramming-induced reactivation of transgenic Oct4-enhanced green fluorescent protein (EGFP) expression. We demonstrate that knockdown of a histone methyltransferase, G9a, or overexpression of a histone demethylase, Jhdm2a, promotes ESC fusion-induced Oct4-EGFP reactivation from adult NSCs. In addition, coexpression of Nanog and Jhdm2a further enhances the ESC-induced Oct4-EGFP reactivation. Interestingly, knockdown of G9a alone in adult NSCs leads to demethylation of the Oct4 promoter and partial reactivation of the endogenous Oct4 expression from adult NSCs. Our results suggest that ESC-induced reprogramming of somatic cells occurs with coordinated actions between erasure of somatic epigenome and transcriptional resetting to restore pluripotency. These mechanistic findings may guide more efficient reprogramming for future therapeutic applications of stem cells. Disclosure of potential conflicts of interest is found at the end of this article.
Secretion of thioredoxin by normal and neoplastic cells through a leaderless secretory pathway. (1992)

Thioredoxin, despite its function as an intracellular disulfide reducing enzyme and its lack of a signal sequence, has been found to play some roles extracellularly. Here we show that thioredoxin is actively secreted by a variety of normal and transformed cells, including fibroblasts, airway epithelial cells, and activated B and T lymphocytes. Neither brefeldin A nor dinitrophenol, two drugs that block transport through the exocytic pathway, inhibit secretion of thioredoxin, indicating that the latter does not follow the classical ER-Golgi route. The secretory mechanism for thioredoxin shares several features with the alternative pathway described for interleukin-1 beta, such as the potentiating effect on secretion of several unrelated drugs and the sensitivity to methylamine. However, unlike interleukin-1 beta, thioredoxin is not detected in membrane-bound compartments of secreting cells. In addition, when COS7 are transfected with plasmids encoding pro-interleukin-1 beta or thioredoxin, only the latter is detectable extracellularly.
Neuronal Deletion of Caspase 8 Protects against Brain Injury in Mouse Models of Controlled Cortical Impact and Kainic Acid-Induced Excitotoxicity (2011)

Background: Acute brain injury is an important health problem. Given the critical position of caspase 8 at the crossroads of cell death pathways, we generated a new viable mouse line (Ncasp8 2/2 ), in which the gene encoding caspase 8 was selectively deleted in neurons by cre-lox system.
A Transcriptionally Active State Is Required for Post-Transcriptional Silencing (Cosuppression) of Nitrate Reductase Host Genes and Transgenes (1997)

, Laurent Nussaume, Jean-Christophe Palauqui, , Taline Elmayan, A Transcriptionally Active State Is Required for Post-Transcriptional Silencing (Cosuppression) of Nitrate Reductase Host Genes and Transgenes, The Plant Cell, Vol. 9, No. 8 (Aug., 1997), pp. 1495-1504
Body mass index and body energy stores in developing countries. (1990)

Body mass index (BMI) is used widely as an index of fatness (the proportion of the body as fat) but its application to the low weight and stature populations in developing countries has not been established. As BMI is an indicator of size (the amounts of fat and fat free masses) as well as fatness, its relation to fatness and interpretation as a measure of energy stores may vary in different groups. Very low BMI reflects low fat and fat free mass, a state for greater concern than low fat mass alone, and possibly more typical of chronic energy deficiency.
Antisense oligodeoxynucleotides and antisense RNA : novel pharmacological and therapeutic agents (1997)

Historical Aspects of Antisense Oligodeoxynucleotides, J.-J. Toulme Advances in Understanding the Pharmacological Properties of Antisense Oligonucleotides, S. Crooke Pharmacokinetics of Phosphorothioate Oligonucleotides and its Novel Analogs, S. Agrawal and R. Zhang Non-Antisense Effects of Antisense Oligonucleotides, L.M. Neckers and K. Iyer Use of Antisense Oligodeoxynucleotides to Modulate Reproductive Behavior, M.M. McCarthy Establishing the Molecular Biology of Opioid Behavior through Antisense Approaches, G.C. Rossi and G.W. Pasternak Antisense Oligodeoxynucleotides Targeted to the Angiotensin System as a Novel Strategy to Treat Hypertension, M.I. Philips and R. Gyurko Antisense DNA Therapy of Burkitt's Lymphoma in Em-myc Transgenic Mice, E. Wickstrom Regulating Genes with Antisense RNA, J. Oberstrass and W. Nellen Development of Retroviral Vectors Expressing Antisense RNA to Inhibit Replication of the Human Immunodeficiency Virus, B.A. Bunnell and R. Morgan Use of Plasmid Antisense RNA Expression Vectors to Alter Neurobiological Effects, G. Davidkova, S.-P. Zhang, L.-W. Zhou, R.A. Nichols, and B. Weiss Index
Engagement of the signaling lymphocytic activation molecule (SLAM) on activated T cells results in IL-2-independent, cyclosporin A-sensitive T cell proliferation and IFN-gamma production (1997)

The expression and function of the novel signaling lymphocytic activation molecule (SLAM) are described. SLAM is present on immature thymocytes, CD45R0(high) memory T cells, T cell clones, CD56+ T cells, EBV-transformed B-cell lines and on a proportion of B cells. SLAM is rapidly induced on naive T cells, TCR gammadelta+ T cells, and B cells following activation. Engagement of SLAM by the agonistic anti-SLAM mAb A12 resulted in proliferation of T cell clones and Ag- or PHA-activated peripheral blood T cells. mAb A12-induced T cell proliferation is independent of IL-2 and sensitive to inhibition by cyclosporin A. The extent of the anti-SLAM-induced proliferation was related to the activation state of the T cells, since fully rested T cell clones failed to proliferate in response to mAb A12 stimulation, despite unchanged SLAM expression on their surface. Ligation of SLAM on activated peripheral T cells or T cell clones by mAb A12 induced IFN-gamma production in the absence of other exogenous stimuli, even in allergen-specific Th2 clones. These data indicate that stimulation via SLAM reverses the cytokine production profile of Th2 clones to a Th0 phenotype, whereas it further polarizes cytokine production by Th1 clones. Thus, SLAM is a novel receptor that mediates IL-2-independent expansion of activated T cells during immune responses, while concomitantly directing these proliferating cells to a Th0/Th1 pathway.
Endosomolysis by Masking of a Membrane-Active Agent (EMMA) for Cytoplasmic Release of Macromolecules (2002)

Endosomolysis, a critical barrier to efficient delivery of macromolecules such as nucleic acids, has been breached using a novel approach: endosomolysis by masking of a membrane-active agent (EMMA). To demonstrate the concept of EMMA, a cationic membrane-active peptide, melittin, was reversibly inhibited using a maleic anhydride derivative. At neutral pH, the lysines of melittin are covalently acylated with the anhydride, thereby inhibiting melittin's membrane disruption activity. Under acidic conditions such as those present within endosomes, the amide bond of the maleamate is cleaved, thus unmasking melittin. The active melittin can then disrupt the endosomal membrane resulting in release of biologically active molecules into the cytoplasm. This approach avoids cellular toxicity by restricting melittin's activity until it reaches the endosomal compartment. The utility of this approach was demonstrated by delivery phosphorodiamidate morpholino oligonucleotides (PMOs).
A role for fungal β-glucans and their receptor Dectin-1 in the induction of autoimmune arthritis in genetically susceptible mice (2005)

A combination of genetic and environmental factors can cause autoimmune disease in animals. SKG mice, which are genetically prone to develop autoimmune arthritis, fail to develop the disease under a microbially clean condition, despite active thymic production of arthritogenic autoimmune T cells and their persistence in the periphery. However, in the clean environment, a single intraperitoneal injection of zymosan, a crude fungal beta-glucan, or purified beta-glucans such as curdlan and laminarin can trigger severe chronic arthritis in SKG mice, but only transient arthritis in normal mice. Blockade of Dectin-1, a major beta-glucan receptor, can prevent SKG arthritis triggered by beta-glucans, which strongly activate dendritic cells in vitro in a Dectin-1-dependent but Toll-like receptor-independent manner. Furthermore, antibiotic treatment against fungi can prevent SKG arthritis in an arthritis-prone microbial environment. Multiple injections of polyinosinic-polycytidylic acid double-stranded RNA also elicit mild arthritis in SKG mice. Thus, specific microbes, including fungi and viruses, may evoke autoimmune arthritis such as rheumatoid arthritis by stimulating innate immunity in individuals who harbor potentially arthritogenic autoimmune T cells as a result of genetic anomalies or variations.
Incidence and prevalence studies in epilepsy and their methodological problems: a review. (1987)

Epidemiological studies in epilepsy have a number of specific problems, discussed here with reference to the published literature. Case ascertainment may pose difficulties because of deficiencies in patients reporting and in the diagnosis of seizures, and inherent methodological problems; the classification of epilepsy is often arbitrary and definitions variable; unsuspected selection bias may markedly influence incidence and prevalence rates. The major published incidence and prevalence studies are reviewed and the factors influencing these rates discussed.
Sporicidal activity of ceragenin CSA-13 against Bacillus subtilis (2017)

Spore-forming bacteria are a class of microorganisms that possess the ability to survive in extreme environmental conditions. Morphological features of spores assure their resistance to stress factors such as high temperature, radiation, disinfectants, and drying. Consequently, spore elimination in industrial and medical environments is very challenging. Ceragenins are a new class of cationic lipids characterized by a broad spectrum of bactericidal activity resulting from amphipathic nature and membrane-permeabilizing properties. To assess the impact of ceragenin CSA-13 on spores formed by Bacillus subtilis (ATCC 6051), we performed the series of experiments confirming that amphipathic and membrane-permeabilizing properties of CSA-13 are sufficient to disrupt the structure of B. subtilis spores resulting in decreased viability. Raman spectroscopy analysis provided evidence that upon CSA-13 treatment the number of CaDPA-positive spores was clearly diminished. As a consequence, a loss of impermeability of the inner membranes of spores, accompanied by a decrease in spore resistance and killing take place. In addition to their broad antimicrobial spectrum, ceragenins possess great potential for development as new sporicidal agents.
Green Fluorescent Protein (GFP)-tagged Cysteine-rich Domains from Protein Kinase C as Fluorescent Indicators for Diacylglycerol Signaling in Living Cells (1998)

Cysteine-rich domains (Cys-domains) are approximately 50-amino acid-long protein domains that complex two zinc ions and include a consensus sequence with six cysteine and two histidine residues. In vitro studies have shown that Cys-domains from several protein kinase C (PKC) isoforms and a number of other signaling proteins bind lipid membranes in the presence of diacylglycerol or phorbol ester. Here we examine the second messenger functions of diacylglycerol in living cells by monitoring the membrane translocation of the green fluorescent protein (GFP)-tagged first Cys-domain of PKC-gamma (Cys1-GFP). Strikingly, stimulation of G-protein or tyrosine kinase-coupled receptors induced a transient translocation of cytosolic Cys1-GFP to the plasma membrane. The plasma membrane translocation was mimicked by addition of the diacylglycerol analogue DiC8 or the phorbol ester, phorbol myristate acetate (PMA). Photobleaching recovery studies showed that PMA nearly immobilized Cys1-GFP in the membrane, whereas DiC8 left Cys1-GFP diffusible within the membrane. Addition of a smaller and more hydrophilic phorbol ester, phorbol dibuterate (PDBu), localized Cys1-GFP preferentially to the plasma and nuclear membranes. This selective membrane localization was lost in the presence of arachidonic acid. GFP-tagged Cys1Cys2-domains and full-length PKC-gamma also translocated from the cytosol to the plasma membrane in response to receptor or PMA stimuli, whereas significant plasma membrane translocation of Cys2-GFP was only observed in response to PMA addition. These studies introduce GFP-tagged Cys-domains as fluorescent diacylglycerol indicators and show that in living cells the individual Cys-domains can trigger a diacylglycerol or phorbol ester-mediated translocation of proteins to selective lipid membranes.
CpG Island Methylator Phenotype Predicts Progression of Malignant Melanoma (2009)

These findings show the significance of a CIMP pattern that is associated with advancing clinical stage of malignant melanoma. Future prospective large-scale studies may determine if CIMP-positive primary melanomas are at high risk of metastasis or recurrence.
Molecular dynamics of spermine-DNA 1nteractioas sequence specificity and DNA bending for a simple ligand (1989)

We used molecular dynamics to model interactions between the physiologically important polyamine spermine and two B-DNA oligomers, the homopolymer (dG)10-(dC)10 and the heteropolymer (dGdC)5-(dGdC)5. Water and counterions were included in the simulation. Starting coordinates for spermine-DNA complexes were structures obtained by molecular mechanics modeling of spermine with the two oligomers; in these models, spermine binding induced a bend in the heteropolymer but not in the homopolymer. During approximately 40 psec of molecular dynamics simulation, spermine moves away from the floor of the major groove and interacts nospecifically with d(G)10-d(C)10. In contrast, a spermine-induced bend in the helix of (dGdC)5-(dGdC)5 is maintained throughout the simulation and spermine remains closely associated with the major groove. These results provide further evidence that the binding of spermine to nucleic acids can be sequence specific and that bending of alternating purine-pyrimidine sequences may be a physiologically important result of spermine binding.
Induction of a Mucosal Antitoxin Response and Its Role in Immunity to Experimental Canine Cholera (1978)

The induction of a jejunal antitoxin response was studied in dogs immunized with cholera toxin or toxoid. Single doses of toxoid given subcutaneously (s.c.) or of toxin given intraluminally (i.l.) were each effective in priming the mucosal immune system, whereas toxoid given i.l. was much less effective. In contrast, toxin and toxoid given i.l. were each effective as booster antigens. The local secondary response was rapid and brief, the peak occurring at about 7 days after i.l. boosting and declining by 90% after 2 more weeks. After s.c. priming and i.l. boosting with toxoid, antitoxin-containing plasma cells appeared predominantly in the portion of jejunum exposed to the i.l. booster. The appearance of antitoxin-containing plasma cells in jejunal lamina propria correlated with the amount of antitoxin recovered in jejunal washings which, in turn, correlated with protection against challenge with cholera toxin. Thus, lamina propria antitoxin-containing plasma cells appeared to be the source of protective antitoxin. However, after sequential s.c.-oral immunization with toxoid, protection against challenge with Vibrio cholerae far outlasted the major systemic and local antitoxin responses and was not obviously explained by either. These studies reveal methods for induction of a mucosal antitoxin response, but leave in question the mechanism of prolonged protection induced by s.c.-oral immunization of dogs.
PACS: Basic Principles and Applications (1999)

1.4.1 Background 1.4.2Four Methods of PACS Implementation 1.4.3PACS Evolution 1.4.4Large-Scale PACS and Some Examples 1.5 Organization of This Book 2. Digital Radiologic Image Fundamentals of Imaging 2.1 Terminology 2.2 Density Resolution, Spatial Resolution, and Signal-to-Noise Ratio 2.3 Radiologic Test Objects and Patterns 2.4 Spatial Domain and Frequency Domain 2.4.1 Frequency Components of an Image 2.4.2The Fourier Transform Pair 2.4.3The Discrete Fourier Transform 2.5 Measurement of Image Quality 2.5.1 Measurement of Sharpness 2.5.2Measurement of Noise 3. Projection Radiography 3.1 Principles of Conventional Projection Radiography VII
An electrochemical P-N junction etch-stop for the formation of silicon microstructures (1981)

An electrochemical technique allowing the protection of selected areas of silicon in ethylene diamine-based etchants is reported, and its application to the formation of silicon microstructures is described. Dissolution rates for passivated samples are less than 5 Å/minute, a factor of over 3000 times less than for unpassivated silicon.
Polymorphism in the tumor necrosis factor-? promotor region and in the heat shock protein 70 genes associated with malignant tumors (1997)

Tunisian persons carrying the TNF2 allele may have an increased risk of cancer. In this study, non-Hodgkin's lymphoma and breast carcinoma were significantly associated with polymorphism in hsp70 genes.
Migration and granulomatous reaction after periurethral injection of polytef (Teflon) (1984)

Although patients with urinary incontinence have been treated successfully by periurethral injection of polytef paste, this study in continent animals demonstrates migration of polytef particles from the injection site. We injected polytef paste periurethrally into female dogs and male monkeys. Particles were found at 50 to 70 days in pelvic nodes in six of seven animals and lungs in four of seven (the kidneys and brain were not studied); and at 10 1/2 months in pelvic nodes, lungs, and brain in seven of seven; kidneys in four of seven; and spleen in two of seven. X-ray microanalysis confirmed that the particles were polytef. At 10% months, polytef granulomas were found at all injection sites and some sites of distant migration. Since these granulomas signify chronic foreign-body reaction, we believe that until the long-term effects in humans are known, polytef paste should not be used in children or young adults with normal life expectancy. (<i>JAMA</i>1984;251:3277-3281)
Inactivation of bacteria by Purogene (1988)

The bacteriocidal efficacy of Purogene, a stabilized aqueous solution of chlorine dioxide (ClO2) was examined using bacteria of concern to public health. The organisms tested were: Escherichia coli, Pseudomonas aeruginosa, Yersinia enterocolitica, Klebsiella pneumoniae, Streptococcus pyogenes Group A, Salmonella typhimurium and Bacillus subtilis. The test organisms responded differently to inactivation by Purogene. At least a 4 log reduction in bacterial counts was noted when Purogene was applied at a concentration of 0.75 mg/l. Since Purogene is a stabilized complex, it was necessary to provide a chemical environment suitable for the release of ClO2 in this solution. This was done by varying the pH of Purogene from 3.5 to 8.6 (pH of Purogene is 8.6) while keeping the pH of the experimental medium constant (pH 7.0). The results showed that Purogene was most efficacious at the lowest pH tested (pH 3.5). This indicates that as chlorine dioxide solutions were reduced to chlorite (which predominates at pH 8.6), their bacteriocidal efficacy was reduced, suggesting free chlorine dioxide as the active disinfecting species.
Design of the First‐in‐Class, Highly Potent Irreversible Inhibitor Targeting the Menin‐MLL Protein–Protein Interaction (2017)

The structure-based design of M-525 as the first-in-class, highly potent, irreversible small-molecule inhibitor of the menin-MLL interaction is presented. M-525 targets cellular menin protein at sub-nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition and in the suppression of MLL-regulated gene expression in MLL leukemia cells. M-525 demonstrates high cellular specificity over non-MLL leukemia cells and is more than 30 times more potent than its corresponding reversible inhibitors. Mass spectrometric analysis and co-crystal structure of M-525 in complex with menin firmly establish its mode of action. A single administration of M-525 effectively suppresses MLL-regulated gene expression in tumor tissue. An efficient procedure was developed to synthesize M-525. This study demonstrates that irreversible inhibition of menin may be a promising therapeutic strategy for MLL leukemia.
Toward a Fully Autonomous UAV: Research Platform for Indoor and Outdoor Urban Search and Rescue (2012)

Urban search and rescue missions raise special requirements on robotic systems. Small aerial systems provide essential support to human task forces in situation assessment and surveillance. As external infrastructure for navigation and communication is usually not available, robotic systems must be able to operate autonomously. A limited payload of small aerial systems poses a great challenge to the system design. The optimal tradeoff between flight performance, sensors, and computing resources has to be found. Communication to external computers cannot be guaranteed; therefore, all processing and decision making has to be done on board. In this article, we present an unmanned aircraft system design fulfilling these requirements. The components of our system are structured into groups to encapsulate their functionality and interfaces. We use both laser and stereo vision odometry to enable seamless indoor and outdoor navigation. The odometry is fused with an inertial measurement unit in an extended Kalman filter. Navigation is supported by a module that recognizes known objects in the environment. A distributed computation approach is adopted to address the computational requirements of the used algorithms. The capabilities of the system are validated in flight experiments, using a quadrotor.
Characterization of Viral Agents Causing Acute Respiratory Infection in a San Francisco University Medical Center Clinic during the Influenza Season (2005)

Our findings demonstrate that, even during the influenza season, rhinovirus and RSV are prevalent and must be considered in the differential diagnosis of adult acute respiratory infection before prescribing antiviral medication. Human coronavirus and human metapneumovirus did not play a substantial role. PCR was an especially useful tool in the identification of influenza and other viral pathogens not easily detected by traditional testing methods.