gebhart/patrepeval huggingface dataset:
Identification of Promoter Motifs Involved in the Network of Phytochrome A-Regulated Gene Expression by Combined Analysis of Genomic Sequence and Microarray Data (2003)

Several hundred Arabidopsis genes, transcriptionally regulated by phytochrome A (phyA), were previously identified using an oligonucleotide microarray. We have now identified, in silico, conserved sequence motifs in the promoters of these genes by comparing the promoter sequences to those of all the genes present on the microarray from which they were sampled. This was done using a Perl script (called Sift) that identifies over-represented motifs using an enumerative approach. The utility of Sift was verified by analysis of circadian-regulated promoters known to contain a biologically significant motif. Several elements were then identified in phyA-responsive promoters by their over-representation. Five previously undescribed motifs were detected in the promoters of phyA-induced genes. Four novel motifs were found in phyA-repressed promoters, plus a motif that strongly resembles the DE1 element. The G-box, CACGTG, was a prominent hit in both induced and repressed phyA-responsive promoters. Intriguingly, two distinct flanking consensus sequences were observed adjacent to the G-box core sequence: one predominating in phyA-induced promoters, the other in phyA-repressed promoters. Such different conserved flanking nucleotides around the core motif in these two sets of promoters may indicate that different members of the same family of DNA-binding proteins mediate phyA induction and repression. An increased abundance of G-box sequences was observed in the most rapidly phyA-responsive genes and in the promoters of phyA-regulated transcription factors, indicating that G-box-binding transcription factors are upstream components in a transcriptional cascade that mediates phyA-regulated development.
A New Sesquiterpene Ester from Celastrus orbiculatus Reversing Multidrug Resistance in Cancer Cells (1998)

In a search for revertants of multidrug-resistance in cancer cells, a novel (1) and two known (2,3) sesquiterpene esters were isolated from the root of Celastrus orbiculatus. The structure of 1 was elucidated as 1 beta,2 beta-diacetoxy-6 alpha,9 alpha-bis(benzoyloxy)dihydro-beta-agarofuran. Compounds 1-3 partially or completely reversed resistance to adriamycin, vinblastine, and paclitaxel of multidrug-resistant KB-V1 and MCF7/ADR cells.
SCROOGE:Perceptually‐Driven Polygon Reduction (1996)

Abstract Many real‐time 3D graphics renderers represent each object as a collection of simple polygons. The complexity of this polygon structure is of practical relevance because it can manifestly affect the performance of the graphics system. It is therefore common place to find techniques to reduce the polygonal complexity of a model with the ultimate aim of improving the interactivity of the application. In the past, many of these schemes have not been concerned with the perceptual side‐effects of this reduction and as a result a number of visual incongruities are often perceivable when these correspondingly‐reduced representations are employed. As an attempt to circumvent these problems, this paper presents a methodology for reducing the polygonal complexity of a model, whilst retaining a degree of perceptual predictability. This allows the visual consequences of the degradation to be quantified and accurately modelled.
Structure of human tankyrase 1 in complex with small-molecule inhibitors PJ34 and XAV939 (2012)

The crystal structures of tankyrase 1 (TNKS1) in complex with two small-molecule inhibitors, PJ34 and XAV939, both at 2.0 Å resolution, are reported. The structure of TNKS1 in complex with PJ34 reveals two molecules of PJ34 bound in the NAD(+) donor pocket. One molecule is in the nicotinamide portion of the pocket, as previously observed in other PARP structures, while the second molecule is bound in the adenosine portion of the pocket. Additionally, unlike the unliganded crystallization system, the TNKS1-PJ34 crystallization system has the NAD(+) donor site accessible to bulk solvent in the crystal, which allows displacement soaking. The TNKS1-PJ34 crystallization system was used to determine the structure of TNKS1 in complex with XAV939. These structures provide a basis for the start of a structure-based drug-design campaign for TNKS1.
A Targeted Inhibitor of the Alternative Complement Pathway Reduces Angiogenesis in a Mouse Model of Age-Related Macular Degeneration (2009)

Specific inhibition of the AP reduces angiogenesis in mouse CNV. Of note, intravenous injection of C3d-targeted CR2-fH is protective even though endogenous fH is present in serum at a higher relative concentration, and serum fH contains native C3d and cell surface binding domains that target it to cell surfaces. The most common AMD-associated variant of fH resides within a native cell-binding region of fH (Tyr402His). These data may open new avenues for AMD treatment strategies.
Energy efficient data transfer and storage organization for a MAP turbo decoder module (1999)

Turbo codes are the most recent breakthrough in coding theory. Although their decoding algorithm is highly data dominated, no systematic memory optimization study has been performed yet. We have applied the IMEC Data Transfer and Storage Exploration (DTSE) methodology to the MAP (Maximum A Posteriori) class of turbo decoding algorithms. We present an extensive overview of our optimizations and tradeoffs, which result in a parametric family of new optimized algorithms. The optimal choice of parameters depends on the specific turbo code and on the implementation target, which can be either hardware or software.
Sinusoidal Voltammetry for the Analysis of Carbohydrates at Copper Electrodes (1997)

A digital approach for the collection and analysis of electrochemical frequency domain spectra is presented for the oxidation of carbohydrates at a copper electrode using a continuous, large-amplitude sine wave as an excitation waveform. The background charging current response is a phase-shifted sine wave with the major frequency component concentrated at the fundamental frequency. A nonlinear faradaic response due to the oxidation of sugars produces significant signal intensities at the higher harmonics as well as the fundamental frequency. Examination of the frequency spectra of glucose and maltose leads to selective and sensitive detection of these sugars at a copper electrode. The selectivity of this measurement relies on the inherent difference in the frequency domain spectra (i.e., magnitude and phase of each harmonic) of sugars of different sizes. This frequency distribution is dramatically affected by temperature, indicating the effect of kinetics in the mechanism for the oxidation of sugars. The sensitivity of the measurement of glucose and maltose is demonstrated with flow injection analysis and postprocessing the data with the digitial equivalent of a lock-in amplifier. A limit of detection of 8 nM is obtained for glucose when the isolated faradaic current is optimized for phase and frequency.
Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene (1997)

The Bacillus subtilis araC locus, mapped at about 294 degrees on the genetic map, was defined by mutations conferring an Ara- phenotype to strains bearing the metabolic araA, araB, and araD wild-type alleles (located at about 256 degrees on the genetic map) and by mutants showing constitutive expression of the three genes. In previous work, it has been postulated that the gene in which these mutations lie exerts its effect on the ara metabolic operon in trans, and this locus was named araC by analogy to the Escherichia coli regulatory gene. Here, we report the cloning and sequencing of the araC locus. This region comprises two open reading frames with divergently arranged promoters, the regulatory gene, araC, encoding a 41-kDa polypeptide, and a partially cloned gene, termed araE, which most probably codes for a permease involved in the transport of L-arabinose. The DNA sequence of araC revealed that its putative product is very similar to a number of bacterial negative regulators (the GalR-LacI family). However, a helix-turn-helix motif was identified in the N-terminal region by its identity to the consensus signature sequence of another group of repressors, the GntR family. The lack of similarity between the predicted primary structure of the product encoded by the B. subtilis regulatory gene and the AraC regulator from E. coli and the apparently different modes of action of these two proteins lead us to propose a new name, araR, for this gene. The araR gene is monocistronic, and the promoter region contains -10 and -35 regions (as determined by primer extension analysis) similar to those recognized by RNA polymerase containing the major vegetative cell sigma factor sigmaA. An insertion-deletion mutation in the araR gene leads to constitutive expression of the L-arabinose metabolic operon. We demonstrate that the araR gene codes for a negative regulator of the ara operon and that the expression of araR is repressed by its own product.
Paracrystalline Structure of Polymer-Crystal Lattice Distortion Induced by Electron Irradiation (1970)

The melting temperature of polyethylene crystals decreases and the lattice constants (both a and b) and lattice distortion increase, but the macroscopic volume of the specimen does not change with electron irradiation. From these results a model of a deformed lattice structure with point defects produced by irradiation is proposed. Calculations indicate that the anisotropy of a polymer crystal (difference between the elastic modulus along the molecular axis and perpendicular to the axis) increases the range of the distortion in a crystal caused by a defect. The presence of lattice distortion in electron irradiated polymer single crystals produces observable features in the Moiré patterns obtained from the crystals.
The AG Dinucleotide Terminating Introns Is Important but Not Always Required for Pre-mRNA Splicing in the Maize Endosperm1 (1999)

Previous RNA analysis of lesions within the 15 intron-containing Sh2 (shrunken2) gene of maize (Zea mays) revealed that the majority of these mutants affect RNA splicing. Here we decipher further two of these mutants, sh2-i (shrunken2 intermediate phenotype) and sh2-7460. Each harbors a G-to-A transition in the terminal nucleotide of an intron, hence destroying the invariant AG found at the terminus of virtually all nuclear introns. Consequences of the mutations, however, differ dramatically. In sh2-i the mutant site is recognized as an authentic splice site in approximately 10% of the primary transcripts processed in the maize endosperm. The other transcripts exhibited exon skipping and lacked exon 3. A G-to-A transition in the terminus of an intron was also found in the mutant sh2-7460, in this case intron 12. The lesion activates a cryptic acceptor site downstream 22 bp within exon 13. In addition, approximately 50% of sh2-7460 transcripts contain intron 2 and 3 sequences.
Transcriptional activation of the human papillomavirus-16 P97 promoter by an 88-nucleotide enhancer containing distinct cell-dependent and AP-1-responsive modules. (1990)

The P97 promoter upstream of the oncogenic early genes of human papillomavirus (HPV)-16 is active in keratinocytes and in cervical carcinoma cells due to a 5' keratinocyte-dependent cis enhancer. In this study, we have mapped the main enhancer activity to an 88-nucleotide (nt) fragment composed of multiple cis elements. A 63-nt promoter-proximal enhancer core was sufficient for P97 activation in a human keratinocytic cell line, HaCaT, and in cervical carcinoma cells. Although the enhancer functioned poorly in hepatoma cells or in fibroblasts, nuclear extracts from different cells protected similar cis elements from DNase I digestion. Two protected half-palindromic NF-I/CTF sites within the 63-nt core were necessary for its function; one represents a "cytokeratin element" (CK), a previously described 8-nt sequence shared with cytokeratin gene promoters. Both sites formed complexes of the same apparent size and relative binding affinity with NF-I/CTF-like factor(s) present in all cells tested. Although cell-dependent P97 activation could be determined by similar, yet distinct NF-I/CTF-like proteins, adjacent cis elements in the enhancer core were also required for function, and may thus interact with additional transcription factors. A 25-nt distal module with two AP-1 sites increased enhancer activity and cooperated with cis elements of the proximal core. Each AP-1 site as well as a third AP-1 site near the promoter bound c-Jun and Jun/Fos in vitro, and was activated by c-Jun and c-Fos in transfections. In addition to cell type-dependent activation, HPV-16 P97 transcription may therefore respond to growth factors and oncogene products via the AP-1 pathway.
Potency estimation of recombinant factor VIII: effect of assay method and standard (2001)

Large potency discrepancies between the chromogenic and one-stage clotting methods have been reported for patients' plasma samples following the infusion of recombinant factor VIII (rFVIII) concentrates. We have investigated the potency estimation of two different full-length rFVIII concentrates using both assay methods relative to both plasma and concentrate standards. Potencies by the chromogenic method were significantly higher (53% and 45%) than potencies by the one-stage clotting method when a plasma standard was used. In contrast, there was no significant potency difference between methods when a concentrate standard was used. Time-course studies into thrombin and activated factor X (FXa) generation, in modified clotting and chromogenic methods, respectively, revealed that the two rFVIII concentrates behaved very similarly to the concentrate standard, whereas the plasma standard showed slightly more rapid thrombin generation and markedly slower FXa generation. The different behaviour of rFVIII and plasma FVIII in the chromogenic method is proposed as the main cause of the methods-based potency discrepancy. The results support the use of a concentrate standard to measure rFVIII in post-infusion plasma.
The use of multicast delivery to provide a scalable and interactive video-on-demand service (1996)

In typical proposals for video-on-demand (VoD) systems, customers are serviced individually by allocating and dedicating a transmission channel and a set of server resources to each customer. This approach leads to an expensive to operate, nonscalable system. We consider a VoD system that uses multicast delivery to service multiple customers with a single set of resources. The use of multicast communication requires that part of the on-demand nature of the system be sacrificed to achieve scalability and cost-effectiveness. One drawback to using multicast communication is that it complicates the provision or interactive VCR-style functions. Interactivity can be provided by either increasing the complexity of the customer set-top box (STB) or by modifying the semantics of the interactive functions to make them easier to provide. We describe a framework and mechanisms by which such interactive functions can be incorporated into a multicast delivery VoD system. Through the use of simulation, we evaluate and compare the performance of a unicast VoD system and multicast VoD systems offering various levels of interactivity.
Prophylactic Effect of Low Doses of Human Leukocyte Interferon Against Infection with Rhinovirus (1982)

The prophylactic effect of low doses of human leukocyte interferon (HuIFN-alpha) against infection with rhinovirus was measured in double-blind, placebo-controlled studies with volunteer subjects. An antihistamine (chlorpheniramine) was given before administration of single or multiple doses of HuIFN-alpha but saturated cotton pledget or by aerosol; volunteers were then challenged with rhinovirus. When the results for all groups were combined, a lower frequency of respiratory illness was demonstrated in the HuIFN-alpha-treated volunteers (20 of 39 vs. 11 of 38, P less than 0.05). A significant improvement in mean symptom scores was found only in the volunteers who received HuIFN-alpha by cotton pledget. The total numbers of isolates of rhinovirus and seroconversions were similar for HuIFN-alpha-treated and control volunteers. No significant side effects were noted in the HuIFN-alpha-treated volunteers. Higher concentrations or improved methods of delivery of HuIFN-alpha will be necessary for improving the clinical efficacy of HuIFN-alpha against viral infections in the respiratory system.
Properties of the Etiologic Agent of Infectious Hepatitis. (1945)

An experiment on the transmission of the naturally occurring disease, injectious hepatitis, to human volunteers has demonstrated certain properties of the etiologic agent. As in homologous serum jaundice and post-vaccinal jaundice the icterogenic agent of infectious hepatitis is filtrable and withstands heating to 56°C for 30 minutes. The icterogenic agent of infectious hepatitis can be transmit ted in serial passage in human volunteers.
Biodistribution of ellagic acid and dose‐related inhibition of lung tumorigenesis in A/J mice (1992)

Ellagic acid (EA), derived from fruit ellagitannins, is known to be antimutagenic and anticarcinogenic in various animal tumor models. In this study, EA at a dose of 4 g/kg diet inhibited multiplicity of tumors induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in A/J mice by 54%. This inhibition was dose related between 0.06 and 4.0 g/kg diet. In contrast, two related compounds, esculin and esculetin, had no effect on lung tumorigenesis. The biodistribution of EA was studied as a function of dose and time after gavage of EA. The levels of EA in the lung were directly proportional to the dose of EA between 0.2 and 2.0 mmol. The maximum level of EA, corresponding to 21.3 nmol/g, was observed 30 minutes after gavage with 2.0 mmol of EA/kg body wt, which corresponds to only 70 ppm of the administered dose. The levels in liver tissues were 10-fold lower and reached a maximum 30 minutes after gavage. At this interval, the blood level of EA was 1 nmol/ml. The inclusion of EA in cyclodextrin doubles the level of EA in lung tissues. These results demonstrate that EA localizes preferentially in lung tissues and confirm that EA administered orally can inhibit lung tumorigenesis.
Deep Reinforcement Learning with Knowledge Transfer for Online Rides Order Dispatching (2018)

Ride dispatching is a central operation task on a ride-sharing platform to continuously match drivers to trip-requesting passengers. In this work, we model the ride dispatching problem as a Markov Decision Process and propose learning solutions based on deep Q-networks with action search to optimize the dispatching policy for drivers on ride-sharing platforms. We train and evaluate dispatching agents for this challenging decision task using real-world spatio-temporal trip data from the DiDi ride-sharing platform. A large-scale dispatching system typically supports many geographical locations with diverse demand-supply settings. To increase learning adaptability and efficiency, we propose a new transfer learning method Correlated Feature Progressive Transfer, along with two existing methods, enabling knowledge transfer in both spatial and temporal spaces. Through an extensive set of experiments, we demonstrate the learning and optimization capabilities of our deep reinforcement learning algorithms. We further show that dispatching policies learned by transferring knowledge from a source city to target cities or across temporal space within the same city significantly outperform those without transfer learning.
Isolation of Ethylene-Insensitive Soybean Mutants That Are Altered in Pathogen Susceptibility and Gene-for-Gene Disease Resistance1 (1999)

Plants commonly respond to pathogen infection by increasing ethylene production, but it is not clear if this ethylene does more to promote disease susceptibility or disease resistance. Ethylene production and/or responsiveness can be altered by genetic manipulation. The present study used mutagenesis to identify soybean (Glycine max L. Merr.) lines with reduced sensitivity to ethylene. Two new genetic loci were identified, Etr1 and Etr2. Mutants were compared with isogenic wild-type parents for their response to different soybean pathogens. Plant lines with reduced ethylene sensitivity developed similar or less-severe disease symptoms in response to virulent Pseudomonas syringae pv glycinea and Phytophthora sojae, but some of the mutants developed similar or more-severe symptoms in response to Septoria glycines and Rhizoctonia solani. Gene-for-gene resistance against P. syringae expressing avrRpt2 remained effective, but Rps1-k-mediated resistance against P. sojae races 4 and 7 was disrupted in the strong ethylene-insensitive etr1-1 mutant. Rps1-k-mediated resistance against P. sojae race 1 remained effective, suggesting that the Rps1-k locus may encode more than one gene for disease resistance. Overall, our results suggest that reduced ethylene sensitivity can be beneficial against some pathogens but deleterious to resistance against other pathogens.
Preparation and properties of organic polymer sub-micrometer function films (2002)

Two methods for preparing organic polymer sub-micrometer thin films, electropolymerization and low pressure chemical vapor deposition, are discussed. The influences of the mononer concentration, the electrolytic concentration, the current density and the electrolytic time on polypyrrole sub-micrometer thin films are studied. In addition, the influences of the driving voltage, oxide concentration and solvent are discussed for LPCVD polypyrrole films. The NH/sub 3/-sensing properties of films of different thickness are tested and studied. The molecular structure of polypyrrole and microstructure of films are analysed by elemental analysis and FT-IR. The NH/sub 3/-sensing mechanism is discussed.
Shivering and rewarming after cardiac surgery: comparison of ventilator circuits with humidifier and heated wires to heat and moisture exchangers (1995)

These data suggest that use of heated wire humidified ventilator circuits with heated water blankets in adult cardiac surgery patients significantly reduces the incidence of shivering and results in a more rapid return to normothermia.
Bile Salt Transporters (2002)

Bile salts are the major organic solutes in bile and undergo extensive enterohepatic circulation. Hepatocellular bile salt uptake is mediated predominantly by the Na(+)-taurocholate cotransport proteins Ntcp (rodents) and NTCP (humans) and by the Na(+)-independent organic anion-transporting polypeptides Oatp1, Oatp2, and Oatp4 (rodents) and OATP-C (humans). After diffusion (bound by intracellular bile salt-binding proteins) to the canalicular membrane, monoanionic bile salts are secreted into bile canaliculi by the bile salt export pump Bsep (rodents) or BSEP (humans). Both belong to the ATP-binding cassette (ABC) transporter superfamily. Dianionic conjugated bile salts are secreted into bile by the multidrug-resistance-associated proteins Mrp2/MRP2. In bile ductules, a minor portion of protonated bile acids and monomeric bile salts are reabsorbed by non-ionic diffusion and the apical sodium-dependent bile salt transporter Asbt/ASBT, transported back into the periductular capillary plexus by Mrp3/MRP3 [and/or a truncated form of Asbt (tAsbt)], and subjected to cholehepatic shunting. The major portion of biliary bile salts is aggregated into mixed micelles and transported into the intestine, where they are reabsorbed by apical Oatp3, the apical sodium-dependent bile salt transporter (ASBT), cytosolic intestinal bile acid-binding protein (IBABP), and basolateral Mrp3/MRP3 and tAsbt. Transcriptional and posttranscriptional regulation of these enterohepatic bile salt transporters is closely related to the regulation of lipid and cholesterol homeostasis. Furthermore, defective expression and function of bile salt transporters have been recognized as important causes for various cholestatic liver diseases.