gebhart/patrepeval huggingface dataset:
Salt-Inducible Kinase Is Involved in the Regulation of Corticotropin-Releasing Hormone Transcription in Hypothalamic Neurons in Rats (2011)

Activation of CRH transcription requires phosphorylation of cAMP response element-binding protein (CREB) and translocation of the CREB coactivator, transducer of regulated CREB activity (TORC) from cytoplasm to nucleus. In basal conditions, transcription is low because TORC remains in the cytoplasm, inactivated by phosphorylation through Ser/Thr protein kinases of the AMP-dependent protein kinases (AMPK) family, including salt-inducible kinase (SIK). To determine which kinase is responsible for TORC phosphorylation in CRH neurons, we measured SIK1 and SIK2 mRNA in the hypothalamic paraventricular nucleus of rats by in situ hybridization. In basal conditions, low mRNA levels of the two kinases were found in the dorsomedial paraventricular nucleus, consistent with location in CRH neurons. One hour of restraint stress increased SIK1 mRNA levels, whereas SIK2 mRNA showed only minor increases. In 4B hypothalamic neurons, or primary cultures, SIK1 mRNA (but not SIK2 mRNA) was inducible by the cAMP stimulator, forskolin. Overexpression of either SIK1 or SIK2 in 4B cells reduced nuclear TORC2 levels (Western blot) and inhibited forskolin-stimulated CRH transcription (luciferase assay). Conversely, the nonselective SIK inhibitor, staurosporine, increased nuclear TORC2 content and stimulated CRH transcription in 4Bcells and primary neuronal cultures (heteronuclear RNA). Unexpectedly, in 4B cells specific short hairpin RNA knockdown of endogenous SIK2 but not SIK1 induced nuclear translocation of TORC2 and CRH transcription, suggesting that SIK2 mediates TORC inactivation in basal conditions, whereas induction of SIK1 limits transcriptional activation. The study provides evidence that SIK represses CRH transcription by inactivating TORC, providing a potential mechanism for rapid on/off control of CRH transcription.
Differential effects of parathyroid hormone and its analogues on cytosolic calcium ion and cAMP levels in cultured rat osteoblast-like cells. (1988)

While the stimulatory effect of parathyroid hormone (PTH) on osteoblast-like cell adenylate cyclase is well known, the effect of PTH on cytosolic calcium ion ([Ca2+]i) mobilization is controversial, one group finding no effect but others reporting various increases. We investigated the effects on [Ca2+]i of synthetic rat PTH fragment 1-34 (rPTH(1-34)) and two bovine PTH analogues that inhibit PTH's stimulation of adenylate cyclase (bovine 8,18Nle, 34Tyr-PTH(3-34) and 34Tyr-PTH(7-34]. [Ca2+]i was measured before, during, and after exposure to PTH analogues in perifused, attached osteoblast-like rat osteosarcoma cells (ROS 17/2.8) that had been scrape-loaded with the luminescent photoprotein aequorin. Resting [Ca2+]i was 0.094 +/- 0.056 microM (mean +/- S.D., n = 103) and rose in a time- and dose-specific way after exposure to rPTH(1-34). At 10(-10) M rPTH(1-34), [Ca2+]i rose 100% within 30 s to a plateau; higher concentrations of PTH yielded increasing initial peaks of [Ca2+]i followed by lower plateaus. At 10(-6) M, the initial peak was 5-fold basal, or 0.64 +/- 0.07 microM. Both analogues of PTH were at least partial agonists for [Ca2+]i mobilization and did not reduce peak [Ca2+]i when co-perifused with rPTH(1-34). However, the analogues did reduce significantly rPTH(1-34)-induced cAMP accumulation and did not increase cAMP accumulation by themselves. Thus, rPTH(1-34) strongly mobilizes [Ca2+]i in ROS 17/2.8 cells, at near-physiologic concentrations. Failure of the PTH analogues to block the effect of PTH on [Ca2+]i while inhibiting the effect on cAMP accumulation suggests separate pathways for PTH activation of adenylate cyclase and mobilization of calcium.
Avian retroviral RNA element promotes unspliced RNA accumulation in the cytoplasm (1996)

All retroviruses need mechanisms for nucleocytoplasmic export of their unspliced RNA and for maintenance of this RNA in the cytoplasm, where it is either translated to produce Gag and Pol proteins or packaged into viral particles. The complex retroviruses encode Rev or Rex regulatory proteins, which interact with cis-acting viral sequences to promote cytoplasmic expression of incompletely spliced viral RNAs. Since the simple retroviruses do not encode regulatory proteins, we proposed that they might contain cis-acting sequences that could interact with cellular Rev-like proteins. To test this possibility, we initially looked for a cis-acting sequence in avian retroviruses that could substitute for Rev and the Rev response element in human immunodeficiency virus type 1 expression constructs. A cis-acting element in the 3' untranslated region of Rous sarcoma virus (RSV) RNA was found to promote Rev-independent expression of human immunodeficiency virus type 1 Gag proteins. This element was mapped between RSV nucleotides 8770 and 8925 and includes one copy of the direct repeat (DR) sequences flanking the RSV src gene; similar activity was observed for the upstream DR. To address the function of this element in RSV, both copies of the DR sequence were deleted. Subsequently, each DR sequence was inserted separately back into this deleted construct. While the viral construct lacking both DR sequences failed to replicate, constructs containing either the upstream or downstream DR replicated well. In the absence of both DRs, Gag protein levels were severely diminished and cytoplasmic levels of unspliced viral RNA were significantly reduced; replacement of either DR sequence led to normal levels of Gag protein and cytoplasmic unspliced RNA.
Experimental System and Measurements of Transhorizon Signal Levels at 11GHz (1988)

The paper describes the experimental receiving system which operates at 11.6 and 10.7GHz to monitor transhorizon signa1 levels over two paths across the English Channel (La Manche). The structure of the receiver is described and the automatic/remote operation procedures are given. Estimated cumulative transmission losses are also given to permit the positioning of the 80dB dynamic rannge of the receivers. It is shown that considering the level of signals received for paths up to about 200km and antennas of less than 1 metre, X band voice and data communications can be contemplated.
Entropy-constrained halftoning using multipath tree coding (1997)

We suggest an optimization-based method for halftoning that involves looking ahead before a decision for each binary output pixel is made. We first define a mixture distortion criterion that is a combination of a frequency-weighted mean square error (MSE) and a measure depending on the distances between minority pixels in the halftone. A tree-coding approach with the ML-algorithm is used for minimizing the distortion criterion to generate a halftone. While this approach generates halftones of high quality, these halftones are not very amenable to lossless compression. We introduce an entropy constraint into the cost function of the tree-coding algorithm that optimally trades off between image quality and compression performance in the output halftones.
Reaction Pathways to CuInSe2 Formation from Electrodeposited Precursors (1995)

thin films have been obtained from different precursors prepared by direct or sequential electrodeposition processes. The nature of the as‐deposited layers and the evolution of the films during the heat‐treatment in an inert (vacuum) or a reactive (elemental Se vapor) atmosphere have been studied by x‐ray diffraction and x‐ray photoelectron spectroscopy analysis. The chemistry of the different phase transformations occurring as a function of the annealing temperature has been examined, and possible reaction pathways for the formation of are presented. The results show that high crystalline chalcopyrite films with the desired composition can be obtained after annealing either direct or sequentially electrodeposited precursors at 400°C. An improvement in film quality can be gained by using an electrodeposited Cu layer as growth surface for the formation. If elemental Se is also added during the heat‐treatment, then a higher recrystallization of the films is observed.
The Isolation and Characterization of cDNA Encoding the Mouse Bifunctional ATP Sulfurylase-Adenosine 5′-Phosphosulfate Kinase (1995)

Biosynthesis of the activated sulfate donor, adenosine 3'-phosphate 5'-phosphosulfate, involves the sequential action of two enzyme activities: ATP sulfurylase, which catalyzes the formation of adenosine 5'-phosphosulfate (APS) from ATP and free sulfate, and APS kinase, which subsequently phosphorylates APS to produce adenosine 3'-phosphate 5'-phosphosulfate. Oligonucleotide primers were derived from a human infant brain-expressed sequence tag putatively encoding a portion of APS kinase. Using these primers, reverse transcriptase-polymerase chain reaction was performed on mRNA from neonatal normal mice resulting in amplification of a 127-bp DNA fragment. This fragment was subsequently used to screen a mouse brain lambda gt11 cDNA library, yielding a 2.2-kb clone. Primers were designed from the 5'-end of the 2.2-kb clone, and 5'-rapid amplification of cDNA ends was used to obtain the translation start site. Sequence from the overlapping clones was assembled into a 2475-bp composite sequence, which contains a single open reading frame that translates into a 624-deduced amino acid sequence. Northern blots of total RNA from neonatal mice yielded a single message species at approximately 3.3 kb. Southern blot of genomic DNA digested with several restriction enzymes suggested the gene is present as a single copy. Comparison against sequence data bases suggested the composite sequence was a fused sulfurylase-kinase product, since the deduced amino acid sequence showed extensive homology to known separate sequences of both ATP sulfurylase and APS kinase from several sources. The first 199 amino acids corresponded to APS kinase sequence, followed by 37 distinct amino acids, which did not match any known sequence, followed by 388 amino acids that are highly homologous to known ATP sulfurylase sequences. Finally, recombinant enzyme expressed in COS-1 cells exhibited both ATP sulfurylase and APS kinase activity.
Strategies for Safer Liver Surgery and Partial Liver Transplantation (2007)

The liver possesses the unique ability to regenerate within a short period of time, a feature that has led to the development of innovative strategies in liver surgery and transplantation. This review presents both established and novel methods for manipulating liver volume to attain improved liver surgery and transplantation.
Transfer and expression of the human multiple drug resistance gene into live mice. (1992)

The human multiple drug resistance (MDR) gene has been used as a selectable marker to increase the proportion of bone marrow cells that contain and express this gene by drug selection. By constructing retroviral vectors containing and expressing the MDR gene and a nonselectable gene such as the beta-globin gene, enrichment for cells containing both of these genes can be achieved. A retroviral construct containing MDR cDNA in a Harvey virus-based vector has been used to transfect our ecotropic 3T3 retroviral packaging line GP+E86. Clones have been isolated by exposure of the retrovirally transfected cells (MDR producer cells) to colchicine (60 ng/ml), a selective agent that kills MDR-negative cells. Flow cytometry analysis (fluorescence-activated cell sorting) with an antibody to MDR demonstrates expression of human MDR protein on the surface of these colchicine-resistant producer clones. Untransfected GP+E86 cells are negative. Colchicine-resistant clones were titered using clone supernatants and the highest titer clone (4 x 10(4) viral particles per ml) was cocultured with 10(6) donor mouse bone marrow cells for 24-48 hr. The donor cells were then injected into congenic irradiated mice, and the presence of the MDR gene was assayed by the polymerase chain reaction (PCR) analysis using MDR-specific primers. In one experiment eight of nine transduced mice were positive for MDR by PCR of peripheral blood 14 and 50 days posttransplantation; after 240 days three of nine transduced mice were positive. Bone marrow obtained from one of these positive animals was stained with the MDR monoclonal antibody and the granulocyte population was analyzed by FACS. Approximately 14% of the total granulocyte pool contain increased levels of MDR protein. In addition, the bone marrow cells of several mice initially positive for MDR gene by PCR, and subsequently negative, were exposed to taxol, a drug whose detoxification depends on MDR gene expression; a positive signal was obtained in all of these mice, indicating drug selection of MDR-positive marrow cells. Cell sorting studies of these mice also show an increased number of high-MDR-expressing marrow cells, selected after exposure to taxol. Thus, in this live animal model MDR transduction is effective in selecting a human MDR-expressing population of marrow cells resistant to taxol chemotherapy. This strategy may, thus, be useful in humans to prevent the marrow toxicity induced by anticancer agents such as taxol and as a selectable marker to enrich for cells simultaneously transduced with a nonselectable gene.
Turbulence Slope After Atrial Premature Complexes Is an Independent Predictor of Mortality in Survivors of Acute Myocardial Infarction (2004)

TSA is a significant and independent predictor of all-cause mortality in postinfarction patients with left ventricular dysfunction.
Ultrathin Composite Films Incorporating the Nanoporous Isopolyoxomolybdate “Keplerate” (NH4)42[Mo132O372(CH3COO)30(H2O)72] (2000)

The giant, nanoporous Keplerate (NH4)42[Mo132O372(CH3COO)30(H2O)72] was incorporated into a permeable ultrathin film using a stepwise self-assembly strategy. Alternating adsorption of the Keplerate anions and PAH results in single layers with an apparent surface coverage of ≈50%. Such permeable composite coatings may lead into a practical approach to utilize nanoporous polyoxometalate clusters in sensors or heterogeneous catalysts.
Convex non-negative matrix factorization for automatic music structure identification (2013)

We propose a novel and fast approach to discover structure in western popular music by using a specific type of matrix factorization that adds a convex constrain to obtain a decomposition that can be interpreted as a set of weighted cluster centroids. We show that these centroids capture the different sections of a musical piece (e.g. verse, chorus) in a more consistent and efficient way than classic non-negative matrix factorization. This technique is capable of identifying the boundaries of the sections and then grouping them into different clusters. Additionally, we evaluate this method on two different datasets and show that it is competitive compared to other music segmentation techniques, outperforming other matrix factorization methods.
TOLERANCE OF ALLOGENEIC HEART GRAFTS IN MICE SIMULTANEOUSLY RECONSTITUTED WITH PURIFIED ALLOGENEIC HEMATOPOIETIC STEM CELLS1 (1998)

These data indicate that tolerance to concurrently or subsequently placed solid organ grafts can be reliably achieved with limited numbers of purified HSCs in a model where immunocompetence to third-party major histocompatibility complex antigens is delayed but intact.
Biological effects of γ‐interferon on human tumor cells: Quantity and affinity of cell membrane receptors for γ‐IFN in relation to growth inhibition and induction of HLA‐DR expression (1985)

A large difference in the number of gamma-IFN receptors was found on a variety of human tumor cell lines with a range of 0.4 to 15 X 10(3) binding sites/cell. The receptor number did not correlate with the potential responsiveness of the cells to gamma-IFN, in regard to either growth inhibition or induction of HLA-DR expression, two independently regulated gamma-IFN effects. However, with respect to HLA-DR expression it was found that the gamma-IFN sensitivity of inducible cell lines depended on the number of receptors, so that with increasing number of receptors present on these cells lower doses of gamma-IFN were required for induction of the gamma-IFN effect.
Genome-Wide Association Mapping for Tomato Volatiles Positively Contributing to Tomato Flavor (2015)

Tomato volatiles, mainly derived from essential nutrients and health-promoting precursors, affect tomato flavor. Taste volatiles present a major challenge for flavor improvement and quality breeding. In this study, we performed genome-wide association studies (GWAS) to investigate potential chromosome regions associated with the tomato flavor volatiles. We observed significant variation (1200x) among the selected 28 most important volatiles in tomato based on their concentration and odor threshold importance across our sampled accessions. Using 174 tomato accessions, GWAS identified 125 significant associations (P < 0.005) among 182 SSR markers and 28 volatiles (27 volatiles with at least one significant association). Several significant associations were co-localized in previously identified quantitative trait loci (QTL). This result provides new potential candidate loci affecting the metabolism of several volatiles.
Rapid Determination of Transferrin Isoforms by Immunoaffinity Liquid Chromatography and Electrospray Mass Spectrometry (2001)

Advantages of the LC-MS method include improved sensitivity, minimal sample preparation, and an analysis time of <10 min. The method was automated, which allowed high throughput, with >100 samples analyzed in a single day. Moreover, the nature of the oligosaccharide defect in CDG is accurately reflected by mass resolution, and subtle oligosaccharide truncations may also be detected by this method.
The inhibition of oligodendrocytic differentiation of O‐2A progenitors caused by basic fibroblast growth factor is overridden by astrocytes (1993)

The inhibition of differentiation of oligodendrocyte-type-2 astrocyte (O-2A) progenitors into oligodendrocytes caused by basic fibroblast growth factor (bFGF) can be overcome by non-O-2A lineage cells present in the optic nerve and by astrocytes purified from cerebral cortices. Although purified O-2A progenitors grown in the presence of bFGF for up to 6 days were inhibited from differentiating into oligodendrocytes, O-2A progenitors growing in heterogeneous optic nerve cultures did not show a similar inhibition of differentiation. The factor(s) responsible for overriding the inhibitory effects of bFGF appeared to be secreted by astrocytes, as extensive generation of oligodendrocytes was seen in cultures of purified O-2A progenitors exposed to bFGF+ medium conditioned by purified astrocytes (ACM). In addition, purified O-2A progenitors displayed a remarkable sensitivity to bFGF, which extended at least down to concentrations of 0.03 ng/ml, a concentration of < 2 x 10(-12) M. At a bFGF concentration of just 0.1 ng/ml, this mitogen still promoted DNA synthesis in as many O-2A progenitors as in cultures exposed to 1-30 ng/ml of this growth factor, but exhibited a reduced ability to promote DNA synthesis in oligodendrocytes. In addition, although concentrations of bFGF as low as 0.03 ng/ml were a potent stimulator of DNA synthesis in O-2A progenitors, application of this amount of bFGF no longer inhibited the differentiation of progenitors into oligodendrocytes as effectively as application of higher bFGF concentrations. Thus, the induction of DNA synthesis by bFGF can be uncoupled from the inhibition of differentiation.(ABSTRACT TRUNCATED AT 250 WORDS)
Optical spectrum analyzer using cascaded AWGs with different channel spacings (1999)

A new type of optical spectrum analyzer is proposed that features the cascade connection of different arrayed-waveguide gratings (AWGs) with different channel spacings through optical switches. The spectral resolution of our system is determined by the narrowest channel spacing and its available channels are ten times the original channels of the AWG with the spacing. We demonstrate the analyzer using 100- and 10-GHz spaced AWGs.
Seasonal Synechococcus and Thaumarchaeal population dynamics examined with high resolution with remote in situ instrumentation (2011)

Monterey Bay, CA is an Eastern boundary upwelling system that is nitrogen limited much of the year. In order to resolve population dynamics of microorganisms important for nutrient cycling in this region, we deployed the Environmental Sample Processor with quantitative PCR assays targeting both ribosomal RNA genes and functional genes for subclades of cyanobacteria (Synechococcus) and ammonia-oxidizing Archaea (Thaumarchaeota) populations. Results showed a strong correlation between Thaumarchaea abundances and nitrate during the spring upwelling but not the fall sampling period. In relatively stratified fall waters, the Thaumarchaeota community reached higher numbers than in the spring, and an unexpected positive correlation with chlorophyll concentration was observed. Further, we detected drops in Synechococcus abundance that occurred on short (that is, daily) time scales. Upwelling intensity and blooms of eukaryotic phytoplankton strongly influenced Synechococcus distributions in the spring and fall, revealing what appear to be the environmental limitations of Synechococcus populations in this region. Each of these findings has implications for Monterey Bay biogeochemistry. High-resolution sampling provides a better-resolved framework within which to observe changes in the plankton community. We conclude that controls on these ecosystems change on smaller scales than are routinely assessed, and that more predictable trends will be uncovered if they are evaluated within seasonal (monthly), rather than on annual or interannual scales.
Delayed Leaf Senescence in Tobacco Plants Transformed with tmr, a Gene for Cytokinin Production in Agrobacterium. (1991)

The aim of this study was to investigate whether enhanced levels of endogenous cytokinins could influence plant development, particularly leaf senescence. Tobacco plants were transformed with the Agrobacterium tumefaciens gene tmr, under the control of the soybean heat shock promoter HS6871. This gene encodes the enzyme isopentenyl transferase, which catalyzes the initial step in cytokinin biosynthesis. After heat shock, the cytokinin level increased greatly and the level of tmr mRNA, undetectable at 20[deg]C, rose and remained high for up to 8 hours. The levels of cytokinin and tmr mRNA were substantially lower by 24 hours. Transformed plants grown at 20[deg]C were shorter, had larger side shoots, and remained green for longer than untransformed plants. The differences were more pronounced after several heat shocks of whole plants or defined areas of leaves. Our results demonstrated that plant morphology and leaf senescence can be manipulated by changing the endogenous level of cytokinins.