gebhart/patrepeval huggingface dataset:
Automated Adherent Cell Elimination by a High-Speed Laser Mediated by a Light-Responsive Polymer (2018)

Abstract Conventional cell handling and sorting methods require manual dissociation, which decreases cell quality and quantity and is not well suited for monitoring applications. To purify adherent cultured cells, in situ cell purification technologies that are high throughput and can be utilized in an on-demand manner are expected. Previous demonstrations using direct laser-mediated cell elimination revealed only limited success in terms of their usability and throughput. Here, we developed a Laser-Induced, Light-responsive-polymer-Activated, Cell Killing (LILACK) system that enables high-speed and on-demand adherent cell sectioning and purification. This system employs a visible laser beam, which does not kill cells directly, but induces local heat production through the trans-cis-trans photo-isomerization of azobenzene moieties in only the irradiated area of a light-responsive thin layer. Using this system in each passage for sectioning, human induced pluripotent stem cells (hiPSCs) were maintained their pluripotency and self-renewal during long-term culture. Furthermore, combined with deep machine-learning analysis on fluorescent and phase contrast images, a label-free and automatic cell processing system was developed by eliminating unwanted spontaneously differentiated cells in undifferentiated hiPSC culture conditions.
Impaired JNK Signaling Cooperates with <i>KrasG12D</i> Expression to Accelerate Pancreatic Ductal Adenocarcinoma (2014)

The c-Jun N-terminal protein kinase (JNK) and its two direct activators, namely the mitogen-activated protein kinase (MAPK) kinase 4 (MKK4) and MKK7, constitute a signaling node frequently mutated in human pancreatic ductal adenocarcinoma (PDAC). Here we demonstrate the cooperative interaction of endogenous expression of Kras(G12D) with loss-of-function mutations in mkk4 or both, mkk4 and mkk7 genes in the pancreas. More specifically, impaired JNK signaling in a subpopulation of Pdx1-expressing cells dramatically accelerated the appearance of Kras(G12D)-induced acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasias, which rapidly progressed to invasive PDAC within 10 weeks of age. Furthermore, inactivation of mkk4/mkk7 compromised acinar regeneration following acute inflammatory stress by locking damaged exocrine cells in a permanently de-differentiated state. Therefore, we propose that JNK signaling exerts its tumor suppressive function in the pancreas by antagonizing the metaplastic conversion of acinar cells toward a ductal fate capable of responding to oncogenic stimulation.
Site-specific Recombination by the   Protein from the Streptococcal Plasmid pSM19035: Minimal Recombination Sequences and Crossing over Site (1996)

The beta recombinase from the broad host range Grampositive plasmid pSM19035 catalyzes intramolecular site-specific recombination between two directly or inversely oriented recombination sites in the presence of a chromatin-associated protein (Hbsu). The recombination site had been localized to a 447 bp DNA segment from pSM19035. This segment includes a 90 bp region that contains two adjacent binding sites (I and II) for beta protein dimers. Using in vitro recombination assays, we show that this 90 bp region is necessary and sufficient for beta protein-mediated recombination; this defines the six site as the region required for beta protein binding. The point of crossing over has been localized to the center of site I. Hbsu has a strong binding affinity for an unknown site located within the 447 bp segment containing the six site. We discuss the possibility that Hbsu recognizes an altered DNA structure, rather than a specific sequence, generated in the synaptic complex.
Effects of 2,4-Dinitrophenol on Respiration in the Dog (1958)

The intravenous administration of 2,4-dinitrophenol (DNP) to unanesthetized or anesthetized dogs produced an increase in arterial pH and decrease in arterial Pco 2 which preceded any significant rise in body temperature. Thus the hyperventilation associated with DNP-administration appears not to be solely the result of increased production of CO 2 . Although DNP in small amounts stimulated respiration via the carotid body, larger doses still produced increased ventilation and pH and decreased Pco 2 after denervation of the carotid bodies and bilateral vagotomy, thus demonstrating a stimulatory effect of DNP at some more central site as well. DNP increased the sensitivity of the respiratory center (or its afferent connections) to Pco 2 and/or concentration of hydrogen ion. The similarities of respiratory effects of DNP and salicylate are discussed. An unexplained increase in ‘buffer base’ of the blood occurred in association with the respiratory alkalosis induced by DNP.
Facies classification using machine learning (2016)

There has been much excitement recently about big data and the dire need for data scientists who possess the ability to extract meaning from it. Geoscientists, meanwhile, have been doing science with voluminous data for years, without needing to brag about how big it is. But now that large, complex data sets are widely available, there has been a proliferation of tools and techniques for analyzing them. Many free and open-source packages now exist that provide powerful additions to the geoscientist's toolbox, much of which used to be only available in proprietary (and expensive) software platforms.
Aerobic and Anaerobic Storage of Single-pass, Chopped Corn Stover (2009)

Corn stover has great potential as a biomass feedstock due its widespread availability. However, storage characteristics of moist corn stover harvested from single-pass harvesters have not been well quantified. In 2007, moist whole-plant corn stover at 19.1 to 40.3 % (w.b.) moisture content was stored for 237 days in aerobic piles, one covered and one uncovered, as well an anaerobic silo bag. In 2008, two moist stover materials whole-plant and cob/husk from 31.7 to 58.1% (w.b.) moisture - were stored for 183 or 204 days in covered and uncovered anaerobic piles, ventilated bags, or anaerobic silo bags. Stover stored in uncovered piles was rehydrated from precipitation, which increased biological activity and produced DM losses from 8.2% to 39.1% with an average of 21.5%. Stover in covered piles was successfully conserved when the average moisture was less than 25% (w.b.) with DM losses of 3.3%. Stover above 36% (w.b.) and piled under a plastic cover had DM losses from 6.4% to 20.2% with an average of 11.9%. Localized heating to temperatures where spontaneous combustion might be a concern (i.e. > 70C) occurred in the aerobic piles when moisture was above 45% (w.b.). Ambient air blown through a center tube in the ventilated bag dried stover near the tube to an average of 24.2% (w.b.), but the remainder of the bag averaged 46.8% (w.b.) at removal. Loss of DM ranged from 7.4% to 22.0% with an average of 11.8%. Stover was most successfully conserved in the bags where anaerobic conditions were maintained. Under anaerobic conditions DM losses ranged from 0.2% to 0.9%. When anaerobic conditions were not maintained in the silo bag DM losses averaged 6.1% of DM. Anaerobic storage is the best solution for conserving the value of moist corn stover.
Binding of C1q and complement activation by vascular endothelium. (1981)

Exposure of intermediate filaments of cultured cells to serum leads to antibody-independent binding of complement (C) component C1q, C4, and C3. The apparent C-activating property of cytoskeletal intermediate filaments was examined on a tissue level in The present study by using frozen sections of human kidney and term placentas as targets. The assay used fresh human serum or isolated C1q as sources of C and the bound C components were demonstrated by fluorescent conjugates against C1q, C4, and C3. A consistent finding was that the endothelium of vessel walls had the capacity to bind both C1q and C components C4 and C3. Less intense binding of C to vascular smooth muscle was noted. Binding of C1q was very rapid, taking place within 10 sec. Subsequently, accumulation of C4 and C3 was seen. Subsequently, accumulation of C4 and C3 was seen. Upon prolonged incubation, a decrease in demonstrable C1q and C4 was observed. Unfixed vascular endothelium bound both isolated C1q and C1q of EDTA- or enzyme inhibitor-treated serum. However, if unfixed, the binding structures appeared to be destroyed in the process of C activation. They were also readily destroyed by trypsin. The described observations seem to suggest a possible mechanism whereby C components may become deposited in vessel walls independently of antibodies.
Synthesis and Electrochemical Properties of Vanadium Pentoxide Nanotube Arrays (2005)

Nanotube arrays of amorphous vanadium pentoxide (V(2)O(5)) were synthesized via template-based electrodeposition, and its electrochemical properties were investigated for Li-ion intercalation applications. The nanotubes have a length of 10 microm, outer diameter of 200 nm and inner diameter of 100 nm. Electrochemical analyses demonstrate that the V(2)O(5) nanotube array delivers a high initial capacity of 300 mAh/g, about twice that of the electrochemically prepared V(2)O(5) film. Although the V(2)O(5) nanotube array shows a more drastic degradation than the film under electrochemical redox cycles, the nanotube array reaches a stabilized capacity of 160 mAh/g, which remains about 1.3 times the stabilized capacity of the film.
Community Participation in Rural Tourism Development (2000)

Abstract This paper examines rural tourism development at the community level. Research was undertaken in four rural communities in Ontario, Canada which identified outcomes and impacts of unplanned tourism development. The research indicated that critical problems arise as development increases. Frustration sets in after years of the community's inability to solve the issues. Members of the research communities identified the development of a tourism plan as the solution to these problems, however, this paper suggests that unless vital preplanning activities are established in the community, a plan may only produce increased frustration. The preplanning activity needs to focus on process issues including capacity building, trust and creating procedures for dialogue.
Asthma and the role of inflammation. (1986)

Asthma has been defined as variable airflow obstruction. The symptoms of asthma are not specific for the condition and, therefore, the presence of variable airflow obstruction needs to be objectively confirmed. When airflow obstruction is present and when it can be completely reversed with treatment, confirmation of the diagnosis is easy. When spirometry is normal or when there is chronic airflow limitation, however, other methods of investigation are required. These methods include inhalation tests with histamine or methacholine, diurnal variation of peak flow rates and tests with exercise or hyperventilation. When spirometry is normal, methacholine or histamine tests appear to be the most sensitive method but, if results are normal, they do not exclude past or future asthma. However, when there is chronic airflow limitation neither variable airflow obstruction nor methacholine or histamine hyperresponsiveness are specific for asthma; tests with hyperventilation (and probably others that act through mediator release) may be more specific. The presence of asthma probably requires the release of chemical mediators, from mast cells and other cells, which can produce inflammation. This has been particularly studied after inhalation of allergens or chemical sensitizers which can trigger both early and late asthmatic responses. The late responses are associated with prolonged increases in airway responsiveness and are considered to be a result of the cellular phase of inflammation. It is possible that persistent or recurrent inflammation, due to these and other stimuli, is the cause of the persisting airway hyperresponsiveness and variable airflow obstruction in asthma, as well as the other features of cough and sputum, but this requires further investigation.(ABSTRACT TRUNCATED AT 250 WORDS)
Functional specialization of gut CD103 <b>+</b> dendritic cells in the regulation of tissue-selective T cell homing (2005)

Gut-associated lymphoid tissue (GALT) dendritic cells (DCs) display a unique ability to generate CCR9+alpha4beta7+ gut-tropic CD8+ effector T cells. We demonstrate efficient induction of CCR9 and alpha4beta7 on CD8+ T cells in mesenteric lymph nodes (MLNs) after oral but not intraperitoneal (i.p.) antigen administration indicating differential targeting of DCs via the oral route. In vitro, lamina propria (LP)-derived DCs were more potent than MLN or Peyer's patch DCs in their ability to generate CCR9+alpha4beta7+ CD8+ T cells. The integrin alpha chain CD103 (alphaE) was expressed on almost all LP DCs, a subset of MLN DCs, but on few splenic DCs. CD103+ MLN DCs were reduced in number in CCR7-/- mice and, although CD8+ T cells proliferated in the MLNs of CCR7-/- mice after i.p. but not oral antigen administration, they failed to express CCR9 and had reduced levels of alpha4beta7. Strikingly, although CD103+ and CD103- MLN DCs were equally potent at inducing CD8+ T cell proliferation and IFN-gamma production, only CD103+ DCs were capable of generating gut-tropic CD8+ effector T cells in vitro. Collectively, these results demonstrate a unique function for LP-derived CD103+ MLN DCs in the generation of gut-tropic effector T cells.
Lymphoid Organs as a Major Reservoir for Human T-Cell Leukemia Virus Type 1 in Experimentally Infected Squirrel Monkeys (<i>Saimiri sciureus</i>): Provirus Expression, Persistence, and Humoral and Cellular Immune Responses (2000)

The aim of this study was to investigate the distribution of human T-cell leukemia virus type 1 (HTLV-1) in various organs of serially sacrificed squirrel monkeys (Saimiri sciureus) in order to localize the reservoir of the virus and to evaluate the relationship between viral expression and the humoral or cellular immune response during infection. Six squirrel monkeys infected with HTLV-1 were sacrificed 6, 12, and 35 days and 3, 6, and 26 months after inoculation, and 20 organs and tissues were collected from each animal. PCR and reverse transcription-PCR (RT-PCR) were performed with gag and tax primers. Proviral DNA was detected by PCR in peripheral blood mononuclear cells (PBMCs) of monkeys sacrificed 6 days after inoculation and in PBMCs, spleens, and lymph nodes of monkeys sacrificed 12 and 35 days and 3, 6, and 26 months after inoculation. Furthermore, tax/rex mRNA was detected by RT-PCR in the PBMCs of two monkeys 8 to 12 days after inoculation and in the spleens and lymph nodes of the monkey sacrificed on day 12. In this animal, scattered HTLV-1 tax/rex mRNA-positive lymphocytes were detected by in situ hybridization in frozen sections of the spleen, around the germinal centers and close to the arterial capillaries. Anti-HTLV-1 cell-mediated immunity was evaluated at various times after inoculation. Anti-p40(Tax) and anti-Env cytolytic T-cell responses were detected 2 months after infection and remained detectable thereafter. When Tax peptides were used, this response appeared to be directed against various Tax epitopes. Our results indicate that squirrel monkeys represent a promising animal model for studying the early events of HTLV-1 infection and for evaluating candidate vaccines against HTLV-1.
Isolation and Characterization of Specialized φ80 Transducing Phages Carrying Regions of the <i>Salmonella typhimurium trp</i> Operon (1974)

We have isolated a series of nondefective phi80 specialized transducing phage which carry segments of the Salmonella typhimurium trp operon. These phage were obtained from a lysogenic derivative of a merozygote constructed by transferring an S. typhimurium trp episome into an Escherichia coli strain which lacks the normal phi80 attachment site. The deoxyribonucleic acid (DNA) from one such phage was purified and employed in DNA-ribonucleic acid (RNA) hybridization studies. The results obtained show that, under our hybridization conditions, heterologous hybridization is less efficient than homologous hybridization. It was also observed that not all S. typhimurium trp messenger RNA can readily anneal to E. coli trp operon DNA. Heterologous hybrids consisting of S. typhimurium trp messenger RNA and E. coli trp operon DNA were estimated to have a dissociation constant 10-fold larger than that of homologous hybrids.
Early response gene signalling in bryostatin-stimulated primary B chronic lymphocytic leukaemia cells in vitro (1996)

The protein kinase C activator bryostatin induces differentiation and antagonizes the effects of tumour-promoting phorbol esters in a number of different cell types. We show here that bryostatin preferentially inhibits phorbol 12-myristate 13-acetate (PMA)-induced proliferation compared with differentiation in a number of different B chronic lymphocytic leukaemia (BCLL) cell populations examined. By using a panel of 11 early-response gene probes in Northern hybridization analysis, we found that the profile of genes induced in response to bryostatin and PMA was qualitatively similar and displayed comparable sensitivities to inhibition with the serine-threonine kinase inhibitor 1-(5-isoquinolinylsulphonyl)-2-methylpiperazine hydrochloride (H7), consistent with common signalling through protein kinase C. However, the nuclear oncogene. c-myc, which was induced strongly in response to PMA treatment, was only marginally up-regulated by bryostatin. In addition, bryostatin selectively inhibited the magnitude of PMA-responsive induction of c-myc, to a degree commensurate with its antagonistic effects seen at the biological level. Finally, an anti-sense oligonucleotide blockade of c-myc inhibited PMA-induced proliferation but not the differentiation of BCLL cells, implicating this nuclear oncogene as an important determinant distinguishing PMA from bryostatin-coupled biological responses and also as a candidate third-messenger effector target for the anti-tumour effects of bryostatin.
Toward natural language computation (1980)

A computer programming system called the Natural Language Computer (NLC) is described which allows a user to type English commands while watching them executed on sample data appearing on a display screen. Direct visual feedback enables the user to detect most misinterpretation errors as they are made so that incorrect or ambiguous commands can be retyped or clarified immediately. A sequence of correctly executed commands may be given a name and used as a subroutine, thus extending the set of available operations and allowing larger English-language programs to be constructed hierarchically. In addition to discussing the transition network syntax and procedural semantics of the system, special attention is devoted to the following topics: the nature of imperative sentences in the matrix domain; the processing of non-trivial noun phrases; conjunction; pronominals; and programming constructs such as if, repeat, and procedure definition.
Steady-state kinetics of malonyl-CoA synthetase from <i>Bradyrhizobium japonicum</i> and evidence for malonyl-AMP formation in the reaction (1994)

Malonyl-CoA synthetase catalyses the formation of malonyl-CoA directly from malonate and CoA with hydrolysis of ATP into AMP and PP1. The catalytic mechanism of malonyl-CoA synthetase from Bradyrhizobium japonicum was investigated by steady-state kinetics. Initial-velocity studies and the product-inhibition studies with AMP and PPi strongly suggested ordered Bi Uni Uni Bi Ping Pong Ter Ter system as the most probable steady-state kinetic mechanism of malonyl-CoA synthetase. Michaelis constants were 61 microM, 260 microM and 42 microM for ATP, malonate and CoA respectively, and the value for Vmax, was 11.2 microM/min. The t.l.c. analysis of the 32P-labelled products in a reaction mixture containing [gamma-32P]ATP in the absence of CoA showed that PPi was produced after the sequential addition of ATP and malonate. Formation of malonyl-AMP, suggested as an intermediate in the kinetically deduced mechanism, was confirmed by the analysis of 31P-n.m.r. spectra of an AMP product isolated from the 18O-transfer experiment using [18O]malonate. The 31P-n.m.r. signal of the AMP product appeared at 0.024 p.p.m. apart from that of [16O4]AMP, indicating that one atom of 18O transferred from [18O]malonate to AMP through the formation of malonyl-AMP. Formation of malonyl-AMP was also confirmed through the t.l.c. analysis of reaction mixture containing [alpha-32P]ATP. These results strongly support the ordered Bi Uni Uni Bi Pin Pong Ter Ter mechanism deduced from initial-velocity and product-inhibition studies.
past changes & future uncertainties Climate (2008)

Climate has varied significantly over periods of thousands to millions of years, and will change over the next century as it responds to human activities.
A self-testable SiGe LNA and Built-in-Self-Test methodology for multiple performance specifications of RF amplifiers (2012)

In this paper, a self-testable SiGe low noise amplifier (LNA) is designed and a Built-in-Self-Test (BIST) methodology is proposed for amplifiers embedded in RF systems. In this BIST methodology, the RF amplifier has the capability to simultaneously test multiple performance specifications on-chip, including Gain and PldB. The self-testable LNA can be placed in a testing mode, in which it self generates a signature of its health using oscillation principles. It eliminates the requirement of any external test stimulus for testing purposes, thus enables the possibility of self-testable RF designs. For the proof of concept, the presented SiGe LNA is designed to operate in the X-band (9.0 GHz) in a commercially-available 6 metal layer, 0.18 μm, 120 GHz SiGe BiCMOS platform. This self-testing design concept can be extended to CMOS amplifiers as well. Furthermore, in this paper, the built-in-self-test methodology is demonstrated using board-level as well as chip-level prototypes.
Man of Independence (1952)

Journal Article Man of Independence Get access Man of Independence. By Jonathan Daniels. London, Gollancz, 1951. 384 pp. Bibliog. Index. 834′​′×512′​′⁠. 18s. Martin Wight Martin Wight Search for other works by this author on: Oxford Academic Google Scholar International Affairs, Volume 28, Issue 3, July 1952, Page 403, https://doi.org/10.2307/2607498 Published: 01 July 1952
Conserved expression and functions of PDE4 in rodent and human heart (2010)

PDE4 isoenzymes are critical in the control of cAMP signaling in rodent cardiac myocytes. Ablation of PDE4 affects multiple key players in excitation–contraction coupling and predisposes mice to the development of heart failure. As little is known about PDE4 in human heart, we explored to what extent cardiac expression and functions of PDE4 are conserved between rodents and humans. We find considerable similarities including comparable amounts of PDE4 activity expressed, expression of the same PDE4 subtypes and splicing variants, anchoring of PDE4 to the same subcellular compartments and macromolecular signaling complexes, and downregulation of PDE4 activity and protein in heart failure. The major difference between the species is a fivefold higher amount of non-PDE4 activity in human hearts compared to rodents. As a consequence, the effect of PDE4 inactivation is different in rodents and humans. PDE4 inhibition leads to increased phosphorylation of virtually all PKA substrates in mouse cardiomyocytes, but increased phosphorylation of only a restricted number of proteins in human cardiomyocytes. Our findings suggest that PDE4s have a similar role in the local regulation of cAMP signaling in rodent and human heart. However, inhibition of PDE4 has ‘global’ effects on cAMP signaling only in rodent hearts, as PDE4 comprises a large fraction of the total cardiac PDE activity in rodents but not in humans. These differences may explain the distinct pharmacological effects of PDE4 inhibition in rodent and human hearts.