gebhart/patrepeval huggingface dataset:
Cloning and characterisation of the glyceraldehyde 3-phosphate dehydrogenase gene of Candida bombicola and use of its promoter (2008)

The glyceraldehyde-3-phosphate dehydrogenase gene (GPD) of the sophorolipid producing yeast Candida bombicola was isolated using degenerated PCR and genome walking. The obtained 3,740 bp contain the 1,008 bases of the coding sequence and 1,613 and 783 bp of the upstream and downstream regions, respectively. The corresponding protein shows high homology to the other known GPD genes and is 74% identical to the gyceraldehyde-3-phosphate dehydrogenase of Yarrowia lipolytica. The particular interest in the C. bombicola GPD gene sequence originates from the potential use of its promoter for high and constitutive expression of homologous and heterologous genes. Southern blot analysis did not give any indication for the presence of multiple GPD genes and it can therefore be expected that the promoter can be used for efficient and high expression. This hypothesis was further confirmed by the biased codon usage in the GPD gene. GDP promoter fragments of different lengths were used to construct hygromycin resistance cassettes. The constructs were used for the transformation of C. bombicola and all of them, even the ones with only 190 bp of the GPD promoter, were able to render the cells resistant to hygromycin. The efficacy of a short GPD promoter can be a convenient characteristic for the construction of compact expression cassettes or vectors for C. bombicola. The GenBank accession number of the sequence described in this article is EU315245.
Pharmacotherapy for prevention of post-traumatic stress disorder (2006)

This is the protocol for a review and there is no abstract. The objectives are as follows: 1) To provide an estimate of the efficacy of medication in preventing the development of post-traumatic stress disorder following exposure to a traumatic event. The efficacy of medication in reducing symptom severity for those individuals who subsequently develop PTSD will also be considered. 2) To determine whether particular classes of medication are more effective and/or acceptable than others in the prevention of PTSD. 3) To assess whether depression is a predictor of treatment response in the prevention of PTSD. Copyright © 2006 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd.
Intramolecular PhIO Mediated Copper-Catalyzed Aziridination of Unsaturated Sulfamates: A New Direct Access to Polysubstituted Amines from Simple Homoallylic Alcohols (2002)

[reaction: see text] Olefinic sulfamates derived from primary and secondary alcohols undergo intramolecular copper-catalyzed aziridination in the presence of iodosylbenzene to afford novel bicyclic fused aziridines. The latter were opened by various nucleophiles to give the corresponding substituted cyclic sulfamates, which in turn reacted, after nitrogen activation, with a second nucleophile at the carbon atom bearing the oxygen atom. Concomitant removal of the sulfonyloxy moiety thus gave access to polysubstituted amines.
Least-Squares Luma–Chroma Demultiplexing Algorithm for Bayer Demosaicking (2011)

This paper addresses the problem of interpolating missing color components at the output of a Bayer color filter array (CFA), a process known as demosaicking. A luma-chroma demultiplexing algorithm is presented in detail, using a least-squares design methodology for the required bandpass filters. A systematic study of objective demosaicking performance and system complexity is carried out, and several system configurations are recommended. The method is compared with other benchmark algorithms in terms of CPSNR and S-CIELAB ∆E∗ objective quality measures and demosaicking speed. It was found to provide excellent performance and the best quality-speed tradeoff among the methods studied.
Striatocortical pathway dysfunction in addiction and obesity: differences and similarities (2012)

Neuroimaging techniques are starting to reveal significant overlap in the brain circuitry underlying addiction and disorders of dyscontrol over rewarding behaviors (such as binge eating disorder and obesity). Positron emission tomography (PET) has demonstrated impaired striatal dopamine (DA) signaling (decreased D2 receptors) in drug addiction and obesity that is associated with reduced baseline glucose metabolism in medial and ventral prefrontal brain regions. Functional magnetic resonance imaging (fMRI) has documented brain activation abnormalities that also implicate DA-modulated striato-cortical pathways. In this review we map findings from recent neuroimaging studies that differentiate brain activation in drug/food addiction from those in controls within brain networks functionally connected with ventral and dorsal striatum. We show that regions found to be abnormal in addiction and obesity frequently emerge at the overlap of the dorsal and the ventral striatal networks. Medial temporal and superior frontal regions functionally connected with dorsal striatum display greater vulnerability in obesity and eating disorders than in drug addictions, indicating more widespread abnormalities for obesity and eating disorders than for addictions. This corroborates involvement of both ventral striatal (predominantly associated with reward and motivation) and dorsal striatal networks (associated with habits or stimulus response learning) in addiction and obesity but also identify distinct patterns between these two disorders.
Paired gang scheduling (2003)

Conventional gang scheduling has the disadvantage that when processes perform I/O or blocking communication, their processors remain idle because alternative processes cannot be run independently of their own gangs. To alleviate this problem, we suggest a slight relaxation of this rule: match gangs that make heavy use of the CPU with gangs that make light use of the CPU (presumably due to I/O or communication activity), and schedule such pairs together, allowing the local scheduler on each node to select either of the two processes at any instant. As I/O-intensive gangs make light use of the CPU, this only causes a minor degradation in the service to compute-bound jobs. This degradation is more than offset by the overall improvement in system performance due to the better utilization of the resources.
XeF2 Etching of Silicon for the Release of Micro-Cantilever Based Sensors (2008)

The release of microstructures from a Si substrate depends directly on the underetching (isotropic) characteristics of the etchant used. For the purpose of this study, XeF2 gas was selected as the etchant medium. Etching by XeF2 is primarily a function of pressure, which determines the rate of interaction between the Si surface and the etchant gas. However, other factors play a large role in XeF2 etching characteristics. Testing was conducted to determine the etch rate and profile of XeF2 etching when various parameters of the structure design are changed (Si exposure area, size and dimension of structures, spacing of structures). The gas was introduced at a pressure cycle of approximately 4.0 Torr for 180 s. Uniformity of the etched surface is improved by increasing the number of etch cycles, or by increasing the gas pressure of the surrounding XeF2.
T‐DNA tagging of a pathogen inducible promoter in <i>Arabidopsis thaliana</i> (2002)

Summary Many events associated with the plant defence responses are regulated on the transcriptional level. Here we report the results of a promoter tagging approach to identify promoters that are induced upon pathogen attack in Arabidopsis thaliana. A line was identified in a T-DNA UidA tagged Arabidopsis library with induced GUS expression after Botrytis cinerea infection around the site of fungal infection. The upstream sequence was isolated and fused to the UidA gene and tested in transgenic Arabidopsis thaliana and Brassica napus plants. Promoter function was very similar to the expression pattern found in the original promoter tagged line. We found that the promoter sequence was located on Arabidopsis chromosome III and linked to a predicted open reading frame in the reverse orientation. The predicted gene codes for a putative receptor serine threonine protein kinase of 383 amino acids in size. The clone contains a protein kinase ATP binding region, a protein kinase active site, a region with similarity to motifs found in Alpha Isopropylmalate/homocitrate synthase enzymes and a putative leucine zipper motif. Analysis of the expression pattern of the gene using RT-PCR demonstrated that the putative receptor serine threonine protein kinase is up-regulated after Salicylic acid treatment and Botrytis infection.
Phosphazene-Based Host Materials for the Use in Blue Phosphorescent Organic Light-Emitting Diodes (2011)

We present a series of low-molecular-weight materials based on cyclic phosphazenes for the use as host materials in blue phosphorescent organic light-emitting diodes. Substituted phenyl rings are attached to the central phosphazene ring either via phosphorus–oxygen bonds to yield phenoxy-substituted derivatives or via direct phosphorus–carbon bonds to yield phenyl-substituted derivatives. The phenoxy substituted cyclic phosphazenes were prepared by nucleophilic substitution of the six chlorine atoms in hexachlorocyclotriphosphazene with phenoxy groups, whereas the phenyl substituted cyclic phosphazenes were formed in a cyclocondensation reaction of three equivalents of substituted phosphinic amides. The phenyl substitution leads to materials with superior thermal properties compared to the phenoxy substitution. Because of the nonconjugated linkage to the phosphazene core, the host materials have very high triplet energies of more than 3 eV. In an OLED device using one compound as host for the saturated blue phosphorescent emitter Ir(dbfmi), a peak power efficiency of 7.6 lm W–1 and a peak luminance of 5000 cd m–2 were achieved.
Suppression of Phytophthora Root Rot in Red Raspberries with Cultural Practices and Soil Amendments (2005)

Various soil amendments and cultural practices were examined in both a phytophthora-infested ( Phytophthora fragariae var. rubi ) (+PFR) and uninfested field (–PFR) planted to `Heritage' red raspberries. Although plants in the +PFR field did not exhibit typical disease symptoms due to unseasonably dry weather, their growth was less than those in the –PFR field. After 2 years, plants in the +PFR site had the highest yields in plots treated with phosphorous acid or amended with gypsum, whereas compost-amended plots had the lowest yields in both +PFR and –PFR sites. A second field study confirmed the positive effect of gypsum on growth and yield of raspberries in an infested site. In a third study, `Titan' raspberries grown under greenhouse conditions in pots containing unamended soil from the infested site, then flooded, exhibited severe disease symptoms; however, pasteurization of the soil, treatment with phosphorous acid and metalaxyl fungicide, or gypsum amendment mostly prevented symptoms from developing. These three studies suggest that a preplant soil amendment containing certain readily available forms of calcium, such as found in gypsum, can help suppress phytophthora root rot and increase survival, growth and yield of raspberries in sites where the pathogen is present.
Studies on the Synthesis of Casein Messenger RNA during Pregnancy in the Rabbit (1976)

The quantity of casein mRNA in the rabbit mammary gland was assayed during the course of pregnancy, by translation of casein mRNA in a reticulocyte lysate and by hybridization to DNA complementary to purified casein mRNA. Both methods indicated that the major increases in the concentration of casein mRNA in both polysomal and total cellular RNA occurred between the 18th and 25th day of pregnancy. The change in casein mRNA concentration during this period coincided with a sharp rise in casein synthesis in mammary gland explants suggesting that the levels of casein mRNA determine the rate of casein synthesis in the mammary gland. The sensitivity of the hybridization assay made it possible to detect the presence of casein mRNA in virgin animals and during the very early stages of pregnancy. At day 5, casein mRNA was found associated with polysomes indication that there was probably some casein synthesis at this early stage of gestation. These results suggest that the hormones controlling lactogenesis in the rabbit may function by augmenting the rate of casein mRNA synthesis rather that initiating transcription of previously inactive genes.
Dehydroepiandrosterone Induces a Neuroendocrine Phenotype in Nerve Growth Factor-Stimulated Chromaffin Pheochromocytoma PC12 Cells (2007)

The adrenal androgen dehydroepiandrosterone (DHEA) is produced in the inner zone of the adrenal cortex, which is in direct contact to adrenal medullary cells. Due to their close anatomical proximity and tightly intermingled cell borders, a direct interaction of adrenal cortex and medulla has been postulated. In humans congenital adrenal hyperplasia due to 21-hydroxylase deficiency results in androgen excess accompanied by severe adrenomedullary dysplasia and chromaffin cell dysfunction. Therefore, to define the mechanisms of DHEA action on chromaffin cell function, we investigated its effect on cell survival and differentiation processes on a molecular level in the chromaffin cell line PC12. DHEA lessened the positive effect of NGF on cell survival and neuronal differentiation. Nerve growth factor (NGF)-mediated induction of a neuronal phenotype was inhibited by DHEA as indicated by reduced neurite outgrowth and decreased expression of neuronal marker proteins such as synaptosome-associated protein of 25 kDa and vesicle-associated membrane protein-2. We examined whether DHEA may stimulate the cells toward a neuroendocrine phenotype. DHEA significantly elevated catecholamine release from unstimulated PC12 cells in the presence but not absence of NGF. Accordingly, DHEA enhanced the expression of the neuroendocrine marker protein chromogranin A. Next, we explored the possible molecular mechanisms of DHEA and NGF interaction. We demonstrate that NGF-induced ERK1/2 phosphorylation was reduced by DHEA. In summary, our data show that DHEA influences cell survival and differentiation processes in PC12 cells, possibly by interacting with the ERK1/2 MAPK pathway. DHEA drives NGF-stimulated cells toward a neuroendocrine phenotype, suggesting that the interaction of intraadrenal steroids and growth factors is required for the maintenance of an intact adrenal medulla.
San Diego's streetlights get smart (2018)

None of the people walking around San Diego's East Village neighborhood one recent afternoon were looking up at the streetlights (except me). And if they had, they likely wouldn't have noticed that some of these lights were a little thicker around the middle than others, or that some lanterns topping old-style lampposts had a clear glass panel here and there. But unbeknownst to the people below, those streetlights were looking- and listening-all around them, while also monitoring temperature, humidity, and other characteristics of the air.
Linking single-cell measurements of mass, growth rate, and gene expression (2018)

Abstract We introduce a microfluidic platform that enables single-cell mass and growth rate measurements upstream of single-cell RNA-sequencing (scRNA-seq) to generate paired single-cell biophysical and transcriptional data sets. Biophysical measurements are collected with a serial suspended microchannel resonator platform (sSMR) that utilizes automated fluidic state switching to load individual cells at fixed intervals, achieving a throughput of 120 cells per hour. Each single-cell is subsequently captured downstream for linked molecular analysis using an automated collection system. From linked measurements of a murine leukemia (L1210) and pro-B cell line (FL5.12), we identify gene expression signatures that correlate significantly with cell mass and growth rate. In particular, we find that both cell lines display a cell-cycle signature that correlates with cell mass, with early and late cell-cycle signatures significantly enriched amongst genes with negative and positive correlations with mass, respectively. FL5.12 cells also show a significant correlation between single-cell growth efficiency and a G1-S transition signature, providing additional transcriptional evidence for a phenomenon previously observed through biophysical measurements alone. Importantly, the throughput and speed of our platform allows for the characterization of phenotypes in dynamic cellular systems. As a proof-of-principle, we apply our system to characterize activated murine CD8+ T cells and uncover two unique features of CD8+ T cells as they become proliferative in response to activation: i) the level of coordination between cell cycle gene expression and cell mass increases, and ii) translation-related gene expression increases and shows a correlation with single-cell growth efficiency. Overall, our approach provides a new means of characterizing the transcriptional mechanisms of normal and dysfunctional cellular mass and growth rate regulation across a range of biological contexts.
Aberrations and adaptive optics in super-resolution microscopy (2015)

As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy - or rather nanoscopy - to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem.
Recent progress in wafer-fused VECSELs emitting in the 1310nm and 1550nm bands (2013)

Recent developments of wafer-fused long-wavelength VECSELs resulted in reaching record high CW output power of 6.6 W at 1300 nm and a coherence length longer than 5 km in fiber and 1 Watt of output power in single frequency regime at 1550 nm. First wafer-fused electrically pumped VECSELs emitting at 1470 nm demonstrate maximum CW output power of 6.5 mW which represents more than 10-times improvement compared with previously published results.
A systematic review of software process tailoring (2007)

Although software process proposals appear continuously, it is difficult to fit any of them into a given company as they are. Thus, some kind of adaptation or tailoring is always necessary. The goal of software process tailoring is to adapt an "off-the-shelf" software process to meet the needs of a specific organization or project. Although process tailoring is a mandatory activity in most software process proposals, it is usually carried out by following an ad-hoc approach, and the amount of research done on this topic to date can be considered small. This paper presents a systematic review of software process tailoring, analyzing the existing approaches towards this activity, discussing the main issues related to the problem, and providing an up-to-date and complete framework in which to position new research activities.
Empirical Regioselectivity Models for Human Cytochromes P450 3A4, 2D6, and 2C9 (2007)

Cytochromes P450 3A4, 2D6, and 2C9 metabolize a large fraction of drugs. Knowing where these enzymes will preferentially oxidize a molecule, the regioselectivity, allows medicinal chemists to plan how best to block its metabolism. We present QSAR-based regioselectivity models for these enzymes calibrated against compiled literature data of drugs and drug-like compounds. These models are purely empirical and use only the structures of the substrates, in contrast to those models that simulate a specific mechanism like hydrogen radical abstraction, and/or use explicit models of active sites. Our most predictive models use three substructure descriptors and two physical property descriptors. Descriptor importances from the random forest QSAR method show that other factors than the immediate chemical environment and the accessibility of the hydrogen affect regioselectivity in all three isoforms. The cross-validated predictions of the models are compared to predictions from our earlier mechanistic model (Singh et al. J. Med. Chem. 2003, 46, 1330-1336) and predictions from MetaSite (Cruciani et al. J. Med. Chem. 2005, 48, 6970-6979).
Ceramide-induced inhibition of T lymphocyte voltage-gated potassium channel is mediated by tyrosine kinases (1997)

The n-type K+ channel (n-K+, Kv1.3) in lymphocytes has been recently implicated in the regulation of Fas-induced programmed cell death. Here, we demonstrate that ceramide, a lipid metabolite synthesized upon Fas receptor ligation, inhibits n-K+ channel activity and induces a tyrosine phosphorylation of the Kv1.3 protein in Jurkat T lymphocytes. Tyrosine phosphorylation of the n-K+ channel correlated with an activation of the Src-like tyrosine kinase p56lck upon cellular treatment with the ceramide analog C6-ceramide. Because genetic deficiency of p56lck or inhibition of Src-like tyrosine kinases by herbimycin A prevented ceramide-mediated n-K+ channel inhibition and tyrosine phosphorylation, we propose a ceramide-initiated activation of p56lck resulting in tyrosine phosphorylation and inhibition of the n-K+ channel protein.
Temozolomide for the Treatment of Metastatic Melanoma: A Systematic Review (2007)

Our review of the available literature suggests that temozolomide demonstrates comparable activity to the current standard treatment, dacarbazine, with the additional benefit of being a convenient oral treatment that penetrates the blood-brain barrier.
Permanganate oxidation of 4-thiouracil derivatives. Isolation and properties of I-substituted 2-pyrimidone 4-sulfonates. (1970)

Abstract A mild permanganate oxidation of 4-thiouridine brought about the formation of uridine 4-sulfonate (1-(β- d -ribofuranosyl)-2-pyrimidone-4-sulfonate). When 1-methyl analog of 4-thiouridine was subjected to the identical treatment, crystalline potassium 1-methyluracil 4-sulfonate was isolated. Structures of these new compounds were established. The uracil-4-sulfonate derivatives were found to be very reactive toward nucleophiles such as OH−, SH−, primary and secondary alkyl amines, and imidazole. Since 4-thiouridine disulfide was resistant to the permanganate oxidation, an intermediate formation of the disulfide in the oxidation of 4-thiouridine was considered to be improbable.