gebhart/patrepeval huggingface dataset:
Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock (2016)

The circadian clock is a biological timekeeping system that provides organisms with the ability to adapt to day-night cycles. Timing of the expression of four members of the Arabidopsis thaliana PSEUDO-RESPONSE REGULATOR(PRR) family is crucial for proper clock function, and transcriptional control of PRRs remains incompletely defined. Here, we demonstrate that direct regulation of PRR5 by CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) determines the repression state of PRR5 in the morning. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analyses indicated that CCA1 associates with three separate regions upstream of PRR5 CCA1 and its homolog LATE ELONGATED HYPOCOTYL (LHY) suppressed PRR5 promoter activity in a transient assay. The regions bound by CCA1 in the PRR5 promoter gave rhythmic patterns with troughs in the morning, when CCA1 and LHY are at high levels. Furthermore,ChIP-seq revealed that CCA1 associates with at least 449 loci with 863 adjacent genes. Importantly, this gene set contains genes that are repressed but upregulated incca1 lhy double mutants in the morning. This study shows that direct binding by CCA1 in the morning provides strong repression of PRR5, and repression by CCA1 also temporally regulates an evening-expressed gene set that includes PRR5.
Epitope Mapping of the Outer Membrane Protein P5-Homologous Fimbrin Adhesin of Nontypeable Haemophilus influenzae (2000)

To identify potential immunodominant and/or adhesin binding domains of the outer membrane protein P5-homologous fimbrin adhesin of nontypeable Haemophilus influenzae (NTHI), three sets of synthetic peptides were synthesized and assayed in an adherence inhibition assay, by Western blotting, and in a biomolecular interaction analysis (BIA) system. The first series of 34 8- to 10-mer peptides represented the entire mature protein sequentially. The second set of four peptides (each 19 to 28 residues) represented the four predicted major surface-exposed regions (or loops) of this adhesin. The third series of seven peptides (each 27 to 34 residues) were specifically designed to map the third surface-exposed region. Data obtained by BIA indicated limited reactivity of a panel of high-titered immune chinchilla sera to the 8- to 10-mer peptides representing the mature protein, likely because these linear peptides did not represent continuous epitopes. However, several of these short peptides did inhibit adherence of multiple NTHI strains to a human respiratory epithelial cell. Overall, greatest relative reactivity in both BIA and adherence inhibition assays was demonstrated against, or shown by, peptides mapping to the third and fourth predicted surface-exposed regions of this adhesin, thereby indicating the presence of immunodominant and adhesin binding domains at these sites. Middle ear fluids sequentially recovered from a chinchilla with an ongoing NTHI-induced otitis media (OM) as well as sera from children with OM due to NTHI also reacted exclusively with peptides representing the third and fourth surface-exposed regions of the P5-fimbrin adhesin, indicating a similarity in immune recognition of this bacterial protein by these two hosts. Collectively, these data together with the previously demonstrated protective efficacy of immunogens derived from this adhesin in chinchilla models support the continued development of P5-fimbrin based vaccine components.
Use of green fluorescent protein for visualization of cell-specific gene expression and subcellular protein localization during sporulation in Bacillus subtilis (1995)

We report the use of the green fluorescent protein (GFP) of Aequorea victoria to visualize cell-specific gene expression and protein subcellular localization during sporulation in Bacillus subtilis. Sporangia bearing the gene (gfp) for the green fluorescent protein fused to genes under the control of the sporulation transcription factor sigma F exhibited a forespore-specific pattern of fluorescence. Forespore-specific fluorescence could be detected with fusions to promoters that are utilized with low (csfB) and high (sspE-2G) efficiency by sigma F-containing RNA polymerase. Conversely, a mother cell-specific pattern of fluorescence was observed in sporangia bearing a transcriptional fusion of gfp to a spore coat protein gene (cotE) under the control of sigma E and an in-frame fusion to a regulatory gene (gerE) under the control of sigma K. An in-frame fusion of gfp to cotE demonstrated that GFP can also be used to visualize protein subcellular localization. In sporangia producing the CotE-GFP fusion protein, fluorescence was found to localize around the developing spore, and this localization was dependent upon SpoIVA, a morphogenetic protein known to determine proper localization of CotE.
Enantioselective Synthesis of Natural Polyoxygenated Cyclohexanes and Cyclohexenes from [(p‐Tolylsulfinyl)methyl]‐p‐quinols (2006)

Exploitation of the beta-hydroxysulfoxide fragment present in a number of enantiomerically pure (SR)- and (SS)-[(p-tolylsulfinyl)methyl]-p-quinols allowed chemo- and stereocontrolled conjugate additions of different organoaluminium reagents to the cyclohexadienone moiety. The same fragment was also shown to act as an efficient chiral masking carbonyl group, after oxidation to sulfone and retroaddition in basic medium, with elimination of methyl p-tolyl sulfone. Through the use of both transformations as key steps, enantiocontrolled syntheses of different natural products-such as the two enantiomers of dihydroepiepoformin, (-)-gabosine O, (+)-epiepoformin, (-)-theobroxide and (+)-4-epigabosine A (an epimer of the natural product gabosine A)-has been achieved. The presence of the beta-hydroxy sulfone moiety makes the cyclic structures rigid, allowing a number of stereoselective transformations such as carbonyl reductions, enone epoxidations or cis-dihydroxylations, en route to the natural structures. The observed selectivities were dependent on the particular substitution in each substrate, providing evidence of a strong influence of remote groups on the preferred approach of the reactants to the reactive conformations. An advanced precursor of natural (+)-harveynone was also synthesized, but the isolation of the natural product was not possible because of the instability of the corresponding enone, containing a triple bond, under the basic conditions necessary to eliminate the beta-hydroxy sulfone. This demonstrated that the limitations of the use of the beta-hydroxy sulfoxide as a chiral protecting carbonyl group were dependent on the relative stabilities of the final targets in the presence of the required base.
Sequence preferences of DNA interstrand crosslinking agents: quantitation of interstrand crosslink locations in DNA duplex fragments containing multiple crosslinkable sites (1991)

A general approach to the quantitative study of the sequence specificity of DNA interstrand crosslinking agents in synthetic duplex DNA fragments is described. In the first step, a DNA fragment previously treated with an interstrand crosslinking agent is subjected to denaturing PAGE. Not only does this distinguish crosslinked from native or monoadducted DNA, it is shown herein that isomeric crosslinked DNAs differing in position of the crosslink can in some cases be separated. In the second stage, the now fractionated crosslinked DNAs isolated from denaturing PAGE are subjected to fragmentation using iron(II)/EDTA. For those fractions which are structurally homogeneous, analysis of the resulting fragment distribution has previously been shown to reveal the crosslink position at nucleotide resolution. It is shown herein that in fractions which are structurally heterogeneous due to differences in position of crosslink, this analysis quantifies the relative extent of crosslinking at distinct sites. Using this method it is shown that reductively activated mitomycin C crosslinks the duplex sequences 5'-GCGC and 5'-TCGA with 3 +/- 1:1 relative efficiency.
Model-based self-adaptive resource allocation in virtualized environments (2011)

The adoption of virtualization and Cloud Computing technologies promises a number of benefits such as increased flexibility, better energy efficiency and lower operating costs for IT systems. However, highly variable workloads make it challenging to provide quality-of-service guarantees while at the same time ensuring efficient resource utilization. To avoid violations of service-level agreements (SLAs) or inefficient resource usage, resource allocations have to be adapted continuously during operation to reflect changes in application workloads. In this paper, we present a novel approach to self-adaptive resource allocation in virtualized environments based on online architecture-level performance models. We present a detailed case study of a representative enterprise application, the new SPECjEnterprise2010 benchmark, deployed in a virtualized cluster environment. The case study serves as a proof-of-concept demonstrating the effectiveness and practical applicability of our approach.
Hoeffding Races: Accelerating Model Selection Search for Classification and Function Approximation (2018)

Selecting a good model of a set of input points by cross validation is a computationally intensive process, especially if the number of possible models or the number of training points is high. Techniques such as gradient descent are helpful in searching through the space of models, but problems such as local minima, and more importantly, lack of a distance metric between various models reduce the applicability of these search methods. Hoeffding Races is a technique for finding a good model for the data by quickly discarding bad models, and concentrating the computational effort at differentiating between the better ones. This paper focuses on the special case of leave-one-out cross validation applied to memory-based learning algorithms, but we also argue that it is applicable to any class of model selection problems.
Highly Sensitive and Specific Fluorescence Reverse Transcription-PCR Assay for the Pseudogene-free Detection of β-Actin Transcripts as Quantitative Reference (1999)

The use of common reverse transcription (RT)-PCR reference target sequences can produce false-positive results by amplification of either contaminating DNA or processed pseudogenes. Furthermore, qualitative RT-PCR alone cannot distinguish between high- and poor-quality cDNA preparations, which again may be crucial for the interpretation of low-abundance transcripts. We have developed a highly sensitive quantitative RT-PCR for β-actin, using the TaqManTM chemistry. Through this technique, we were able to quantitatively detect 10 β-actin molecules per 100 ng of cDNA without coamplification of pseudogenes or genomic DNA. Thus, the presented method may be advantageous for the interpretation of quantitative RT-PCR results.

PCR analysis may be difficult to interpret unless a reference target sequence is amplified in parallel. This control reaction is necessary to evaluate whether a sufficient amount of amplifiable material is present in the sample investigated. Thus, negative PCR can be defined as such only when amplification of a reference gene reveals a positive result. Amplifying a reference is especially important in RT-PCR because RNA can be degraded rapidly before or during cDNA synthesis.

As reference sequences for RT-PCR, so called “housekeeping” genes are preferred because they are constitutionally expressed by all cell types. β-Actin is an attractive candidate for reference coamplification because it exhibits only minor intraindividual kinetic changes and is not primarily affected by any human disease (1). However, a major concern with β-actin and other commonly used references such as glyceraldehyde-3-phosphate dehydrogenase is that processed pseudogenes can be coamplified by primers that are originally restricted to cDNA. This problem is difficult to circumvent because sequence homologies of >90% exist between mRNA and the respective pseudogenes (2); thus, the pseudogenes usually cannot be distinguished in gel electrophoresis. Furthermore, as long as genomic DNA contamination cannot safely be excluded, DNA may be coamplified together with cDNA. Thus, positive analysis of …
Reversing established sepsis with antagonists of endogenous high-mobility group box 1 (2003)

Despite significant advances in intensive care therapy and antibiotics, severe sepsis accounts for 9% of all deaths in the United States annually. The pathological sequelae of sepsis are characterized by a systemic inflammatory response, but experimental therapeutics that target specific early inflammatory mediators [tumor necrosis factor (TNF) and IL-1beta] have not proven efficacious in the clinic. We recently identified high mobility group box 1 (HMGB1) as a late mediator of endotoxin-induced lethality that exhibits significantly delayed kinetics relative to TNF and IL-1beta. Here, we report that serum HMGB1 levels are increased significantly in a standardized model of murine sepsis, beginning 18 h after surgical induction of peritonitis. Specific inhibition of HMGB1 activity [with either anti-HMGB1 antibody (600 microg per mouse) or the DNA-binding A box (600 microg per mouse)] beginning as late as 24 h after surgical induction of peritonitis significantly increased survival (nonimmune IgG-treated controls = 28% vs. anti-HMGB1 antibody group = 72%, P < 0.03; GST control protein = 28% vs. A box = 68%, P < 0.03). Animals treated with either HMGB1 antagonist were protected against the development of organ injury, as evidenced by improved levels of serum creatinine and blood urea nitrogen. These observations demonstrate that specific inhibition of endogenous HMGB1 therapeutically reverses lethality of established sepsis indicating that HMGB1 inhibitors can be administered in a clinically relevant time frame.
Untersuchungen über das Zustandekommen der Diphtherie-Immunität bei Thieren (1890)

Drug Prescribing for Patients with Chronic Kidney Disease in General Practice: a Cross-Sectional Study
Fingerprint Spectroscopic SRS Imaging of Single Living Cells and Whole Brain by Ultrafast Tuning and Spatial-Spectral Learning (2020)

Label-free vibrational imaging by stimulated Raman scattering (SRS) provides unprecedented insight into real-time chemical distributions in living systems. Specifically, SRS in the fingerprint region can resolve multiple chemicals in a complex bio-environment using specific and well-separated Raman signatures. Yet, fingerprint SRS imaging with microsecond spectral acquisition has not been achieved due to the small fingerprint Raman cross-sections and the lack of ultrafast acquisition scheme with high spectral resolution and high fidelity. Here, we report a fingerprint spectroscopic SRS platform that acquires a distortion-free SRS spectrum with 10 cm-1 spectral resolution in 20 microseconds using a lab-built ultrafast delay-line tuning system. Meanwhile, we significantly improve the signal-to-noise ratio by employing a spatial-spectral residual learning network, reaching comparable quality to images taken with two orders of magnitude longer pixel dwell times. Collectively, our system achieves reliable fingerprint spectroscopic SRS with microsecond spectral acquisition speed, enabling imaging and tracking of multiple biomolecules in samples ranging from a live single microbe to a tissue slice, which was not previously possible with SRS imaging in the highly congested carbon-hydrogen region. To show the broad utility of the approach, we have demonstrated high-speed compositional imaging of lipid metabolism in living pancreatic cancer Mia PaCa-2 cells. We then performed high-resolution mapping of cholesterol, fatty acid, and protein in the mouse whole brain. Finally, we mapped the production of two biofuels in microbial samples by harnessing the superior spectral and temporal resolutions of our system.
Human interleukin 6 is a direct promoter of maturation of megakaryocytes in vitro. (1989)

The response of cells of the murine megakaryocytic lineage to human interleukin 6 (IL-6) was assessed in serum-depleted cultures using a variety of biological assays. IL-6 alone had no influence on megakaryocytic colony formation but augmented the numbers of these colonies induced by the multipotent colony-stimulating factor interleukin 3. However, in liquid marrow cultures, IL-6 alone promoted marked increments in megakaryocytic size and the activity of acetyl-cholinesterase, a marker enzyme of the lineage. Moreover, IL-6 induced a significant shift toward higher ploidy classes when megakaryocytic DNA was quantitated by flow cytometry. To determine whether the influence of IL-6 on megakaryocytic maturation was direct, the factor was added to cultures of single megakaryocytes isolated from megakaryocytic colonies. Fifty-four percent of these cells increased in size compared with 19% of those grown without IL-6. The data show that human IL-6 is a potent direct-acting growth factor for murine megakaryocytes with activity promoting maturation of that lineage.
Wake-up-word spotting for mobile systems (2014)

Wake-up-word (WUW) spotting for mobile devices has at-tracted much attention recently. The aim is to detect the oc-currence of very few or only one personalized keyword in a continuous potentially noisy audio signal. The application in personal mobile devices is to activate the device or to trigger an alarm in hazardous situations by voice. In this paper, we present a low-resource approach and results for WUW spot-ting based on template matching using dynamic time warp-ing and other measures. The recognition of the WUW is per-formed by a combination of distance measures based on a simple background noise level classification. For evaluation we recorded a WUW spotting database with three different background noise levels, four different speaker distances to the microphone, and ten different speakers. It consists of 480 keywords embedded in continuous audio data.
Comparison of various K-nearest neighbor voting schemes with the self-training interpretive and retrieval system for identifying molecular substructures from mass spectral data (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparison of various K-nearest neighbor voting schemes with the self-training interpretive and retrieval system for identifying molecular substructures from mass spectral dataS. R. Lowry, T. L. Isenhour, J. B. Justice, F. W. McLafferty, H. E. Dayringer, and Rengachari. VenkataraghavanCite this: Anal. Chem. 1977, 49, 12, 1720–1722Publication Date (Print):October 1, 1977Publication History Published online1 May 2002Published inissue 1 October 1977https://doi.org/10.1021/ac50020a022RIGHTS & PERMISSIONSArticle Views82Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (348 KB) Get e-Alerts Get e-Alerts
GLP‐1 and Appetite Responses to a Meal in Lean and Overweight Adolescents Following Exercise (2008)

Lower concentrations of GLP-1, a satiety hormone, in OW compared to NW male adolescents support the theory that GLP-1 plays a role in the etiology of overweight. Whether the greater meal-induced, 0-30 min GLP-1 response following exercise is associated with increased satiety, a potentially beneficial effect of exercise, needs to be evaluated in larger studies. Obesity (2008) 16, 202-204. doi:10.1038/oby.2007.39.
5'-UTR G-quadruplex structures acting as translational repressors (2010)

Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experiments permitting an in-depth evaluation of the impact of G-quadruplexes as translational repressors. Sequences including potential G-quadruplexes were selected within nine distinct genes encoding proteins involved in various biological processes. Their abilities to fold into G-quadruplex structures in vitro were evaluated using circular dichroism, thermal denaturation and the novel use of in-line probing. Six sequences were observed to fold into G-quadruplex structures in vitro, all of which exhibited translational inhibition in cellulo when linked to a reporter gene. Sequence analysis, direct mutagenesis and subsequent experiments were performed in order to define the rules governing the folding of G-quadruplexes. In addition, the impact of single-nucleotide polymorphism was shown to be important in the formation of G-quadruplexes located within the 5'-untranslated region of an mRNA. In light of these results, clearly the 5'-UTR G-quadruplexes represent a class of translational repressors that is broadly distributed in the cell.
From Data Distributions to Regularization in Invariant Learning (1995)

Ideally pattern recognition machines provide constant output when the inputs are transformed under a group G of desired invariances. These invariances can be achieved by enhancing the training data to include examples of inputs transformed by elements of G, while leaving the corresponding targets unchanged. Alternatively the cost function for training can include a regularization term that penalizes changes in the output when the input is transformed under the group. This paper relates the two approaches, showing precisely the sense in which the regularized cost function approximates the result of adding transformed examples to the training data. We introduce the notion of a probability distribution over the group transformations, and use this to rewrite the cost function for the enhanced training data. Under certain conditions, the new cost function is equivalent to the sum of the original cost function plus a regularizer. For unbiased models, the regularizer reduces to the intuitively obvious choice—a term that penalizes changes in the output when the inputs are transformed under the group. For infinitesimal transformations, the coefficient of the regularization term reduces to the variance of the distortions introduced into the training data. This correspondence provides a simple bridge between the two approaches.
InGaAsP/InGaAs tandem cells for a solar cell configuration with more than three junctions (2008)

Abstract Currently, triple‐junction solar cells realized from III–V semiconductor compounds hold the solar energy conversion efficiency world record. To improve the efficiency significantly, it is necessary to increase the number of junctions and to involve a sub‐cell with an absorber layer in the band gap range of 1 eV. For the realization of a stacked four‐junction device with optimised band gaps, we have grown InGaAsP/InGaAs tandem cells lattice matched to InP substrates, and investigated properties of the absorber bulk material. Time‐resolved photoluminescence of the low band gap In 0.53 Ga 0.47 As absorber embedded between InP barriers was measured. The InGaAs/GaAsSb tunnel diode structure used in the tandem has been processed into a separate device and I – V curves were measured. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)