gebhart/patrepeval huggingface dataset:
Complexity of the cytokine and antibody response elicited by immunizing mice with Plasmodium yoelii circumsporozoite protein plasmid DNA (1995)

The number, type, and location of cytokine- and Ab-secreting cells activated in mice immunized and boosted with plasmid DNA encoding the circumsporozoite protein of the malarial parasite Plasmodium yoelii (PyCSP) were monitored. The initial humoral response was localized to the draining lymph nodes and was characterized by production of IgG1 anti-PyCSP Abs and the Th2 cytokine IL-4. In contrast, the secondary response was dominated by IFN-gamma production (a Th1 cytokine) and the secretion of IgG2a anti-PyCSP Abs in the spleen. PyCSP DNA and mRNA were detected only in the quadriceps muscles (sites of plasmid injection), yet these sites lacked either cytokine- or Ab-secreting cells. These findings indicate that circulating lymphocytes encounter plasmid-encoded Ag in the muscle bed, initiate a humoral response in the draining lymph nodes, and then seed distal lymphoid organs. Profound differences were observed between the primary and secondary immune responses induced by plasmid immunization, which may influence vaccine efficacy.
Providing precise indoor location information to mobile devices (2001)

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.
A trace-driven analysis of the UNIX 4.2 BSD file system (1985)

Article Free Access Share on A trace-driven analysis of the UNIX 4.2 BSD file system Authors: John K. Ousterhout Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CA Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CAView Profile , Hervé Da Costa Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CA Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CAView Profile , David Harrison Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CA Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CAView Profile , John A. Kunze Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CA Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CAView Profile , Mike Kupfer Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CA Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CAView Profile , James G. Thompson Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CA Computer Science Division, Electrical Engineering and Computer Sciences, University of California, Berkeley, CAView Profile Authors Info & Claims SOSP '85: Proceedings of the tenth ACM symposium on Operating systems principlesDecember 1985 Pages 15–24https://doi.org/10.1145/323647.323631Published:01 December 1985Publication History 390citation1,640DownloadsMetricsTotal Citations390Total Downloads1,640Last 12 Months127Last 6 weeks18 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Picquot Ware - delayed deco (2003)

The story of the Picquot Ware range is an interesting example of the effect the Second World War had on business and the availability of household goods. It is also a story of how good design can overcome long delays in production and still be a success. Firstly though, I'd like to explain how I became interested in these charming but very functional items.
Retinoic Acid Is a Potent Regulator of Growth Plate Chondrogenesis (2000)

Vitamin A deficiency and excess both cause abnormalities in mammalian longitudinal bone growth. Because all-trans retinoic acid (RA) is synthesized from vitamin A, we hypothesized that RA regulates growth plate chondrogenesis. Consistent with this hypothesis, a single oral dose of RA reduced the height of the rat proximal tibial growth plate. To determine whether RA acts directly on growth plate, fetal rat metatarsal bones were cultured in the presence of RA. In this system, RA inhibited longitudinal bone growth by three mechanisms: 1) decreased chondrocyte proliferation, (assessed by 3H-thymidine incorporation), particularly in the proliferative zone of the growth plate; 2) decreased matrix synthesis (assessed by 35SO4 incorporation into glycosaminoglycans); and 3) decreased cell hypertrophy (determined histologically). The growth-inhibiting effects of RA were completely reversed by a retinoic acid receptor (RAR) antagonist. In the absence of exogenous RA, this antagonist accelerated bone growth, as did an RA-specific neutralizing antibody, suggesting that endogenous RA negatively regulates growth plate chondrogenesis. We conclude that RA, acting through RARs, negatively regulates longitudinal bone growth by inhibiting growth plate chondrocyte proliferation, chondrocyte hypertrophy, and matrix synthesis.
Mapping Change in Large Networks (2010)

Change is a fundamental ingredient of interaction patterns in biology, technology, the economy, and science itself: Interactions within and between organisms change; transportation patterns by air, land, and sea all change; the global financial flow changes; and the frontiers of scientific research change. Networks and clustering methods have become important tools to comprehend instances of these large-scale structures, but without methods to distinguish between real trends and noisy data, these approaches are not useful for studying how networks change. Only if we can assign significance to the partitioning of single networks can we distinguish meaningful structural changes from random fluctuations. Here we show that bootstrap resampling accompanied by significance clustering provides a solution to this problem. To connect changing structures with the changing function of networks, we highlight and summarize the significant structural changes with alluvial diagrams and realize de Solla Price's vision of mapping change in science: studying the citation pattern between about 7000 scientific journals over the past decade, we find that neuroscience has transformed from an interdisciplinary specialty to a mature and stand-alone discipline.
Penh is not a measure of airway resistance! (2007)

Penh is not a measure of airway resistance!
Aryl Piperazinyl Ureas as Inhibitors of Fatty Acid Amide Hydrolase (FAAH) in Rat, Dog, and Primate (2012)

A series of aryl piperazinyl ureas that act as covalent inhibitors of fatty acid amide hydrolase (FAAH) is described. A potent and selective (does not inhibit FAAH-2) member of this class, JNJ-40355003, was found to elevate the plasma levels of three fatty acid amides: anandamide, oleoyl ethanolamide, and palmitoyl ethanolamide, in the rat, dog, and cynomolgous monkey. The elevation of the levels of these lipids in the plasma of monkeys suggests that FAAH-2 may not play a significant role in regulating plasma levels of fatty acid ethanolamides in primates.
IMG/M: a data management and analysis system for metagenomes (2007)

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m.
Curcumin ameliorates ethanol and nonethanol experimental pancreatitis (2003)

Treatments for pancreatitis are limited. Activation of transcription factor NF-kappaB, a key regulator of inflammatory molecule expression, is an early event in experimental pancreatitis and correlates with the inflammatory response. We report here that curcumin, a natural phytochemical known to inhibit NF-kappaB and activator protein (AP)-1, another important proinflammatory transcription factor, ameliorates pancreatitis in two rat models. In both cerulein pancreatitis and pancreatitis induced by a combination of ethanol diet and low-dose CCK, curcumin improved the severity of the disease as measured by a number of parameters (histology, serum amylase, pancreatic trypsin, and neutrophil infiltration). Curcumin markedly inhibited NF-kappaB and AP-1 activation, assessed by DNA binding and degradation of inhibitory IkappaB proteins, and the induction of mRNAs for cytokines IL-6 and TNF-alpha, the chemokine KC, and inducible nitric oxide synthase in pancreas. Curcumin also blocked CCK-induced NF-kappaB and AP-1 activation in isolated pancreatic acini. Our findings indicate that blocking key signals of the inflammatory response ameliorates pancreatitis in both ethanol and nonethanol models. They suggest that curcumin, which is currently in clinical trials for cancer prevention, may be useful for treatment of pancreatitis.
Molecular ordering of organosulfur compounds on Au(111) and Au(100): Adsorption from solution and in ultrahigh vacuum (1993)

Low-energy electron diffraction and reflection-absorption infrared spectroscopy were used to study the monolayers formed by the adsorption of n-alkane thiols [HS(CH2)mCH3] on both (111) and (100) single-crystal gold substrates. Samples were prepared by dosing either from solution (m=15, 17, 18, and 21) or in ultrahigh vacuum (m=0–9). On Au(111), ordered surface structures are obtained which can be indexed as (n√3×√3)R30°, where n varies from 1 to 6. On Au(100), the adsorption of short chain thiols leads to the formation of a c(2×2) overlayer while the longer chain homologs show additional diffraction spot splittings. It is also found that chain length influences both the character of the diffraction seen and perturbs the reactive sticking probability of molecules dosed in UHV. Infrared studies reveal that the polymethylene chains of the monolayers formed on Au(100) are comprised of nearly all-trans conformations and are less canted than the comparable structures formed on Au(111). A simple model is proposed to account for the differences seen on the two surfaces and a mechanism for the adsorption and assembly of organic thiols into ordered monolayer phases on gold is presented.
Heart induction by Wnt antagonists depends on the homeodomain transcription factor Hex (2005)

Inhibition of canonical Wnt/beta-catenin signaling by Dickkopf-1 (Dkk-1) or Crescent initiates cardiogenesis in vertebrate embryos. However, nearly nothing is known about the downstream effectors of these secreted Wnt antagonists or the mechanism by which they activate heart formation. Here we show that Wnt antagonists in Xenopus stimulate cardiogenesis non-cell-autonomously, up to several cells away from those in which canonical Wnt/beta-catenin signaling is blocked, indicative of an indirect role in heart induction. A screen for downstream mediators revealed that Dkk-1 and other inhibitors of the canonical Wnt pathway induce the homeodomain transcription factor Hex, which is normally expressed in endoderm underlying the presumptive cardiac mesoderm in amphibian, bird, and mammalian embryos. Loss of Hex function blocks both endogenous heart development and ectopic heart induction by Dkk-1. As with the canonical Wnt pathway antagonists, ectopic Hex induces expression of cardiac markers non-cell-autonomously. Thus, to initiate cardiogenesis, Wnt antagonists act on endoderm to up-regulate Hex, which, in turn, controls production of a diffusible heart-inducing factor. This novel function for Hex suggests an etiology for the cardiac malformations in Hex mutant mice and will make possible the isolation of factors that induce heart directly in the mesoderm.
Role of microRNAs in cardiac hypertrophy and heart failure (2009)

MicroRNAs (miRNAs) are a class of endogenous, highly conserved, small noncoding RNAs that regulate gene expression post-transcriptionally. Recent studies have demonstrated that miRNAs are aberrantly expressed in the cardiovascular system. The implications of miRNAs in cardiovascular disease have recently been recognized, representing the most rapidly evolving research field. Gain- and loss-of-function studies in mice models have identified distinct roles for specific miRNAs during cardiac hypertrophy, heart failing, and myocardial infarction. In the present article, the currently relevant findings on the role of miRNAs in cardiac hypertrophy and heart failure will be summarized and the target genes and signaling pathways linking these miRNAs will be discussed. Furthermore, we focus on the use of miRNA mimics and antagonists (antagomirs) as tools for disease therapy in the cardiovascular system in the future. Taken together, the recent studies showed that miRNAs are key regulators of gene expression in cardiovascular biology and suggested the potential importance of miRNAs as diagnostic markers and therapeutic targets for cardiovascular disease.
Adult Mammalian Forebrain Ependymal and Subependymal Cells Demonstrate Proliferative Potential, but only Subependymal Cells Have Neural Stem Cell Characteristics (1999)

The adult derivatives of the embryonic forebrain germinal zones consist of two morphologically distinct cell layers surrounding the lateral ventricles: the ependyma and the subependyma. Cell cycle analyses have revealed that at least two proliferating populations exist in this region, one that is constitutively proliferating and one that is relatively quiescent and thought to include the endogenous adult neural stem cells. Earlier studies demonstrated that specific dissection of the region surrounding the lateral ventricles was necessary for the in vitro isolation of multipotent, self-renewing neural stem cells. However, in these studies, the ependymal layer was not physically separated from the subependymal layer to identify the specific adult laminar localization of the neural stem cells around the lateral ventricles. To determine which cellular compartment in the adult forebrain contained the neural stem cells, we isolated and cultured the ependyma separately from the subependyma and tested for the presence of neural stem cells using the in vitro neurosphere assay. We demonstrate that the ependymal cells can proliferate in vitro to form sphere-like structures. However, the ependymal cells generating spheres do not have the ability to self-renew (proliferate to form secondary spheres after dissociation) nor to produce neurons, but rather only seem to generate glial fibrillary acidic protein-positive ependymal cells when plated under differentiation conditions in culture. On the other hand, a subpopulation of subependymal cells do possess the self-renewing and multipotential characteristics of neural stem cells. Therefore, the adult forebrain neural stem cell resides within the subependymal compartment.
The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG). (1989)

The structure of d(CGCGCG) crystallized in the presence of magnesium and sodium ions alone is compared to that of the spermine form of the molecule. The very high resolution nature of these structure determinations allows the first true examination of an oligonucleotide structure in fine detail. The values of bond distances and angles are compared to those derived from small molecule crystal structures. In addition, the interactions of cations and polyamines with the Z-DNA helix are analyzed. In particular, multiple cationic charges appear to offer enhanced stabilization for the Z-DNA conformation. The location of spermine molecules along the edge of the deep groove and also spanning the entrance to the groove emphasizes the importance of polyamines for stabilizing this left-handed structure. On averaging, we obtained very similar structural parameters for the two different structures with standard deviations generally smaller than the deviations of the crystallographic model from ideal values. This indicates a high degree of accuracy of the two structures, which have been refined using different data and different refinement methods. The derived bond lengths and angles may thus be more representative of this polymeric DNA structure than those derived from mono- and dinucleotide structures at a similar accuracy.
Post-translational control of genetic circuits usingPotyvirusproteases (2016)

Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.
c-Jun N-terminal kinases as potential therapeutic targets (2007)

One principal aim of research in the signal transduction field is to identify targets for therapeutic intervention, in an attempt to modify disease and curtail human suffering. Diseases such as chronic inflammation, atherosclerosis, diabetes and cancer exact a huge toll on health, in physical, social and financial terms. Defective signaling mechanisms are central to their pathogenesis. One candidate signaling molecule that is presently undergoing intense investigation is the c-Jun N-terminal kinase. With roles described in almost all classes of disease, the main questions are what type of inhibitor to use and when exactly to use it during the disease course?
Transcriptional enhancement of the Listeria monocytogenes PCR and simple immunoenzymatic assay of the product using anti-RNA:DNA antibodies (1994)

A method was developed to enhance the sensitivity of a Listeria monocytogenes PCR detection system by in vitro transcription of amplicons incorporating bacteriophage T7 RNA polymerase promoter sequences in one of the priming oligonucleotides. The resulting transcript can be detected by hybridization with a DNA probe immobilized in the wells of a microtiter plate, followed by immunoenzymatic assay of the RNA-DNA hybrids with an anti-RNA-DNA hybrid antibody. This highly sensitive method was reactive in the assay of various L. monocytogenes isolates but not with other Listeria or non-Listeria species.
Spermless males elicit large-scale female responses to mating in the malaria mosquito Anopheles gambiae (2011)

Anopheles gambiae sensu stricto is the major vector of malaria, a disease with devastating consequences for human health. Given the constant spread of the disease, alternative approaches to the use of insecticides are urgently needed to control vector populations. Females of this species undergo large behavioral changes after mating, which include a life-long refractoriness to further insemination and the induction of egg laying in blood-fed individuals. Genetic control strategies aimed at impacting Anopheles fertility through the release of sterile males are being advocated to reduce the size of mosquito field populations. Such strategies depend on the ability of the released sterile males to mate successfully with wild females and to switch off the female receptivity to further copulation. Here we evaluate the role of sperm in regulating female behavioral responses after mating in An. gambiae. We developed spermless males by RNAi silencing of a germ cell differentiation gene. These males mated successfully and preserved standard accessory gland functions. Females mated to spermless males exhibited normal postcopulatory responses, which included laying large numbers of eggs upon blood feeding and becoming refractory to subsequent insemination. Moreover, spermless males induced transcriptional changes in female reproductive genes comparable to those elicited by fertile males. Our data demonstrate that, in contrast to Drosophila, targeting sperm in An. gambiae preserves normal male and female reproductive behavior for the traits and time frame analyzed and validate the use of approaches based on incapacitation or elimination of sperm for genetic control of vector populations to block malaria transmission.
Characteristics of Elastomeric Nanofiber Membranes Produced by Electrospinning (2007)

This study examines the feasibility of co-electrospinning vapor grown carbon nanofibers (VGNF) within thermoplastic elastomer. The reinforcement effect was studied. The diameter of the thermoplastic elastomer was found to range from 0.5 to 3 μm. The mechanical properties of the electrospun fibrous structure were found to be similar to that of cast elastomeric films. However, the electrospun fibrous membranes have superior tactile properties. The addition of VGNF significantly increases the bulkiness of the fibrous elastomeric membranes.
Control of Translation of Masked mRNAs in Clam Oocytes (1990)

The pattern of protein synthesis changes soon after fertilization of clam oocytes. The most abundant of the mRNAs whose translation increases at this time encode ribonucleotide reductase and the A- and B-type cyclins. These mRNAs have been cloned and sequenced, yet their sequences do not show regions of similarity that could explain the masking mechanism. However, these mRNAs retain their 'masked' state in cell-free translation assays and their translation can be activated by gel filtration in high salt, which probably removes repressor proteins. A 'competitive unmasking' assay was used to identify the protein-binding regions of each mRNA. This involved adding short segments of antisense RNA that annealed to the mRNA and displaced the repressors. The unmasking regions in ribonucleotide reductase and cyclin A mRNAs revealed by this assay are 120-140 nt long and are located in the central portions of the 3' non-coding regions.