gebhart/patrepeval huggingface dataset:
AVERAGE MUTUAL INFORMATION OF CODING AND NONCODING DNA (1999)

One basic problem in the analysis of DNA sequences is the recognition of protein-coding genes. Computer algorithms to facilitate gene identification have become important as genome sequencing projects have turned from mapping to large-scale sequencing, resulting in an exponentially growing number of sequenced nucleotides that await their annotation. Many statistical patterns have been discovered that are different in coding and noncoding DNA, but most of them vary from species to species, and hence require prior training on organism-specific data sets. Here, we investigate if there exist species-independent statistical patterns that are different in coding and noncoding DNA. We introduce an information-theoretic quantity, the average mutual information (AMI), and we find that the probability distribution functions of the AMI are significantly different in coding and noncoding DNA, while they are almost identical for different species. This finding suggests that the AMI might be useful for the recognition of protein-coding regions in genomes for which training sets do not exist.
Dietary Taurine Decreases Hepatic Secretion of Cholesterol Ester in Rats Fed a High-Cholesterol Diet (2000)

The effects of dietary taurine on lipid secretion and ketone body production were examined in the livers of Wistar and Sprague-Dawley rats fed high-cholesterol diets. The weight gain of the Sprague-Dawley rats tended to be higher than that of the Wistar rats, although food intake was comparable between the strains. The concentration of hepatic triglyceride was significantly higher but that of phospholipid was significantly lower in the Sprague-Dawley rats. Ketone body production by livers of Sprague-Dawley rats was significantly higher than that by the livers of Wistar rats. Dietary taurine repressed the weight gain of Wistar rats, perhaps due to decreased food intake, but it had no apparent effect on these growth parameters in Sprague-Dawley rats. There was a significant reduction in the hepatic concentration of cholesterol ester, but not other lipid components following feeding of taurine. Taurine feeding resulted in a stimulation of hepatic ketogenesis, whereas it markedly reduced the hepatic secretion of cholesterol ester in both strains of rats. The effect of dietary taurine on the hepatic secretion of triglyceride, phospholipid and free-cholesterol was marginal in either strain. These results suggest that taurine feeding significantly ameliorated the dietary cholesterol-dependent increase in hepatic accumulation and secretion of cholesterol ester, regardless of strain differences, and the decrease in the hepatic secretion of this cholesterol ester appeared to be partly responsible for the observed reduction in the concentration of serum cholesterol following feeding of taurine in these cholesterol-fed rats.
Sequential structures provide insights into the fidelity of RNA replication (2007)

RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.
Bone Marrow‐Derived Stem Cells Can Differentiate into Retinal Cells in Injured Rat Retina (2002)

It has recently been shown that bone marrow cells can differentiate into various lineage cells including neural cells in vitro and in vivo. We therefore examined whether bone marrow stem cells can differentiate into retinal neural cells in adult rats. PKH-67-labeled stem cell-enriched bone marrow cells (BMCs) were injected into the vitreous space of eyes in which the retinas had been mechanically injured using a hooked needle. Two weeks after the injection of these cells, immunohistochemical examinations were carried out. The stem cell-enriched BMCs had been incorporated and had differentiated into retinal neural cells in the injured retina. The stem cell-enriched BMCs had accumulated mainly in the outer nuclear layer around the injured sites. The incorporated cells expressed glial fibrillary acidic protein, calbindin, rhodopsin, and vimentin. These results raise the possibility that stem cell-enriched BMCs have the ability to differentiate into retinal neural cells, and that the injection of stem cell-enriched BMCs into the retina would help repair damaged retinal cells.
Regulation of Alternative Splicing by snoRNAs (2006)

The SNURF-SNRPN locus located on chromosome 15 is maternally imprinted and generates a large transcript containing at least 148 exons. Loss of the paternal allele causes Prader-Willi syndrome (PWS). The 3' end of the transcript harbors several evolutionarily conserved C/D box small nucleolar RNAs (snoRNAs) that are tissue-specifically expressed. With the exception of 47 copies of HBII-52 snoRNAs, none of the snoRNAs exhibit complementarity to known RNAs. Due to an 18-nucleotide sequence complementarity, HBII-52 can bind to the alternatively spliced exon Vb of the serotonin receptor 2C pre-mRNA, where it masks a splicing silencer, which results in alternative exon usage. This silencer can also be destroyed by RNA editing, which changes the amino acid sequence and appears to be independent of HBII-52. Lack of HBII-52 expression in individuals with PWS causes most likely a lack of the high-efficacy serotonin receptor, which could contribute to the disease. It is therefore possible that snoRNAs could act as versatile modulators of gene expression by modulating alternative splicing.
Glutamine attenuates obstructive cholestasis in rats via farnesoid X receptor–mediated regulation of Bsep and Mrp2 (2016)

To investigate the protective effect of glutamine (Gln) against obstructive cholestasis in association with farnesoid X receptor (FXR) activation, an obstructive cholestasis model was established in male Sprague-Dawley rats by bile duct ligation (BDL). Serum biomarkers and hematoxylin plus eosin staining were used to identify the degree of hepatic injury in the rats with obstructive cholestasis after Gln treatment. Immunohistochemistry, real-time PCR, Western blot, cultured primary rat hepatocytes with FXR knockdown, and dual-luciferase reporter assay were performed to elucidate the mechanisms underlying Gln hepatoprotection. We found that Gln treatment protected against obstructive cholestasis induced by BDL through reducing hepatocyte injury. Upregulation of the hepatic efflux transporters small heterodimer partner (Shp), bile salt export pump (Bsep), and multidrug resistance-associated protein 2 (Mrp2), and inhibition of the hepatic uptake transporter Na<sup>+</sup>/taurocholate cotransporting polypeptide (Ntcp) and the bile acid synthesis enzyme cholesterol 7α-hydroxylase (Cyp7a1) expression were observed in rats with BDL treated with Gln in vivo. Furthermore, the regulatory effect of Gln on Bsep and Mrp2 expression was abrogated after FXR knockdown in rat primary cultured hepatocytes. Luciferase assay HepG2 cells also illustrated FXR was a direct target for Gln treatment. In conclusion, the regulation of Bsep and Mrp2 expression mediated by FXR might be an important mechanism for Gln against obstructive cholestasis.
A programmable ENG amplifier with passive EMG neutralization for FES applications (2008)

An integrated amplifier for electroneurogram (ENG) recordings from tripolar cuff electrodes is described. The amplifier is dedicated to urinary incontinence and other functional electrical stimulation (FES) applications. To remove myoelectric (EMG) interference a parallel RC network is used to balance the electrode impedances in the quasi-tripole amplifier configuration. The various ENG amplifier settings, such as resistance and capacitance trimming for the neutralization RC network, amplifier gain and filter cut-off frequencies, are controlled by an external microcontroller which communicates with the embedded SPI (Serial Port Interface) block in the amplifier. By this topology control of the ENG amplifier is executed in software allowing for the system parameters to be re-configured after implantation. The analog system blocks and details of the SPI logic are described. The amplifier was fabricated in a 3-V 0.35-mum BiCMOS process technology and preliminary measured results are reported. Input signals as low as 1muV can be reliably detected. The amplifier occupies an area of 1.5mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and consumes about 1.4mW when configured to detect sub-microvolt neural signals.
Functional genomics-based studies of the microbial ecology of hyperthermophilic micro-organisms (2004)

Although much attention has been paid to the genetic, biochemical and physiological aspects of individual hyperthermophiles, how these unique micro-organisms relate to each other and to their natural habitats must be addressed in order to develop a comprehensive understanding of life at high temperatures. Phylogenetic 16 S rRNA-based profiling of samples from various geothermal sites has provided insights into community structure, but this must be complemented with efforts to relate metabolic strategies to biotic and abiotic characteristics in high-temperature habitats. Described here are functional genomics-based approaches, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well as to determine what genes or sets of genes may be tied to environmental functionality.
Locating and Tracking BLE Beacons with Smartphones (2017)

We present a smartphone-based application, called LocBLE, for enabling users to estimate the location of nearby Bluetooth low energy (BLE) beacons. In contrast to existing BLE beacon-based proximity applications that can only show coarse-grained (immediate, near, and far) distance estimation, LocBLE's fine-grained estimation can enhance human-environment interactions.
The human survivin promoter: a novel transcriptional targeting strategy for treatment of glioma (2006)

Together these data indicate that the survivin promoter is a promising tumor-specific promoter for transcriptional targeting of adenovirus-based vectors and CRAds for malignant gliomas. The strategy of using survivin-CRAds may thus translate into an experimental therapeutic approach that can be used in human clinical trials.
Improved microbial gene identification with GLIMMER (1999)

The GLIMMER system for microbial gene identification finds approximately 97-98% of all genes in a genome when compared with published annotation. This paper reports on two new results: (i) significant technical improvements to GLIMMER that improve its accuracy still further, and (ii) a comprehensive evaluation that demonstrates that the accuracy of the system is likely to be higher than previously recognized. A significant proportion of the genes missed by the system appear to be hypothetical proteins whose existence is only supported by the predictions of other programs. When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes.
An assessment of tag presentation techniques (2007)

With the growth of social bookmarking a new approach for metadata creation called tagging has emerged. In this paper we evaluate the use of tag presentation techniques. The main goal of our evaluation is to investigate the effect of some of the different properties that can be utilized in presenting tags e.g. alphabetization, using larger fonts etc. We show that a number of these factors can affect the ease with which users can find tags and use the tools for presenting tags to users.
A Polyepitope DNA Vaccine Targeted to Her-2/ErbB-2 Elicits a Broad Range of Human and Murine CTL Effectors to Protect against Tumor Challenge (2007)

A cDNA vaccine (pVax1/pet-neu) was designed to encode 12 different Her-2/ErbB-2-derived, HLA-A*0201-restricted dominant and high-affinity heteroclitic cryptic epitopes. Vaccination with pVax1/pet-neu triggered multiple and ErbB-2-specific CTL responses in HLA-A*0201 transgenic HHD mice and in HLA-A*0201 healthy donors in vitro. Human and murine CTL specific for each one of the 12 ErbB-2 peptides recognized in vitro both human and murine tumor cells overexpressing endogenous ErbB-2. Furthermore, vaccination of HHD mice with pVax1/pet-neu significantly delayed the in vivo growth of challenged ErbB-2-expressing tumor (EL4/HHD/neu murine thymoma) more actively when compared with vaccination with the empty vector (pVax1) or vehicle alone. These data indicate that the pVax1/pet-neu cDNA vaccine coding for a poly-ErbB-2 epitope is able to generate simultaneous ErbB-2-specific antitumor responses against dominant and cryptic multiple epitopes.
Electroless Silver and Silver with Tungsten Thin Films for Microelectronics and Microelectromechanical System Applications (2000)

In this study we present the results of electroless deposition of silver (Ag) and silver tungsten [Ag(W)] layers on Si, intended for application in microelectronics and microelectromechanical systems (MEMS) technology. Silver has excellent resistivity but its thin‐film properties and its vulnerability to corrosion may cause a problem. In this work we present a novel Ag(W) type of layer that has improved thin‐film properties, such as resistivity and surface roughness, and can serve as both barrier layer and capping layer for corrosion protection of the Ag thin films. The thin‐film composition was studied as a function of the deposition parameters. We found the presence of tungsten, up to 3.1 atom %, and oxygen, up to 8 atom %, in addition to the silver atoms. We also studied the thin‐film morphology using atomic force microscopy and scanning tunneling microscopy imaging of the surface after each process step. Finally, we discuss the possible mechanisms for the deposition of Ag(W). © 2000 The Electrochemical Society. All rights reserved.
Lysine-specific histone demethylase 1 (LSD1): A potential molecular target for tumor therapy (2012)

Lysine-specific demethylase 1 (LSD1), the first identified histone demethylase, was belonged to the superfamily of the flavin adenine dinucleotide (FAD)-dependent amine oxidases. LSD1 specifically demethylates mono- or dimethylated dimethylated histone H3 lysine4 (H3K4) and H3 lysine 9 (H3K9) via a redox process. Recently evidences showed that LSD1 played an important role in a broad spectrum of biological processes, including cell proliferation, adipogenesis, spermatogenesis, chromosome segregation and embryonic development. Furthermore, LSD1 also could promote progress of tumor by inhibiting the tumor suppressor activity of p53. To date, as a potential drug for discovering anti-tumor drugs, the medical significance of LSD1 inhibitors have been greatly appreciated. Here, we reviewed the remarkable progress being made in understanding of LSD1, mainly on its structure, basic function and medical application in tumor therapy.
비가시광선을 이용한 범죄사진 연구 (2004)

This article `The research on forensic photography by using invisible spectrum` has made progress by Korea Research Foundation support for join research. We have studied with cooperation of National Institute of Scientific Investigation. The research focused on two subjects. 1. Examination of questioned documents by IR photography. 2. Finding ways of taking pictures of fingerprints, sperms, bloodstains and so on. Digital camera is a useful tool for crime scene investigation and questioned documents analysis.
Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology (2000)

Saturated BLAST is a package that performs ISS in an efficient and automated manner. It was developed using Perl and Perl/Tk and implemented on the LINUX operating system. Starting with a protein sequence, Saturated BLAST runs a BLAST search and identifies representative sequences for the next generation of searches. The procedure is run until convergence or until some predefined criteria are met. Saturated BLAST has a friendly graphic user interface, a built-in BLAST result parser, several multiple alignment tools, clustering algorithms and various filters for the elimination of false positives, thereby providing an easy way to edit, visualize, analyze, monitor and control the search. Besides detecting remote homologies, Saturated BLAST can be used to maintain protein family databases and to search for new genes in genomic databases.
Construction of C1-symmetric zirconium complexes by the design of new Salan ligands. Coordination chemistry and preliminary polymerisation catalysis studies (2008)

The first synthesis of achiral and chiral [ONNO']-type Salan ligands featuring two different phenol arms, and the diastereoselective formation of the corresponding octahedral C1-symmetric zirconium complexes is described; the activity and isospecificity induction of the [ONNO']Zr(bn)2 complexes in 1-hexene polymerisation reflected those of the parent symmetric compounds.
Fusion of lidar data and optical imagery for building modeling (2004)

This paper presents a scheme for building detection and building reconstruction from LIDAR data and optical imagery. The proposed scheme comprises two major parts: (1) detection of building regions, and (2) reconstruction of building models. Spatial registration of LIDAR data and optical images is performed as data preprocessing. Then, at the first stage, a region-based segmentation and knowledge-based classification are integrated to detect building regions. Once the building regions are detected, we analyze the coplanarity of the LIDAR raw data to shape the roof. The accurate position of walls of the building is determined by the integration of the edges extracted from optical imagery. Thus the three dimensional building edges can be used for the reconstruction. A patented method SMS (Split-Merge-Shape) is employed to generated building models in the last step. Having the advantages of high reliability and flexibility, the SMS method provides stable reconstruction even when those 3D building lines are broken. LIDAR data acquired by Leica ALS 40, QuickBird multispectral satellite images and aerial images were used in the validation. * Corresponding author. 1.
Bile acids as regulatory molecules (2009)

In the past, bile acids were considered to be just detergent molecules derived from cholesterol in the liver. They were known to be important for the solubilization of cholesterol in the gallbladder and for stimulating the absorption of cholesterol, fat-soluble vitamins, and lipids from the intestines. However, during the last two decades, it has been discovered that bile acids are regulatory molecules. Bile acids have been discovered to activate specific nuclear receptors (farnesoid X receptor, preganane X receptor, and vitamin D receptor), G protein coupled receptor TGR5 (TGR5), and cell signaling pathways (c-jun N-terminal kinase 1/2, AKT, and ERK 1/2) in cells in the liver and gastrointestinal tract. Activation of nuclear receptors and cell signaling pathways alter the expression of numerous genes encoding enzyme/proteins involved in the regulation of bile acid, glucose, fatty acid, lipoprotein synthesis, metabolism, transport, and energy metabolism. They also play a role in the regulation of serum triglyceride levels in humans and rodents. Bile acids appear to function as nutrient signaling molecules primarily during the feed/fast cycle as there is a flux of these molecules returning from the intestines to the liver following a meal. In this review, we will summarize the current knowledge of how bile acids regulate hepatic lipid and glucose metabolism through the activation of specific nuclear receptors and cell signaling pathways.
End-Functionalized Phosphorylcholine Methacrylates and their Use in Protein Conjugation (2008)

Polymer-protein conjugation was performed using N-hydroxysuccinimide and aldehyde-terminated zwitterionic polymers, and the resulting polymer-protein conjugates were characterized by gel electrophoresis and fast protein liquid chromatography. Methacryloyloxyethyl phosphorylcholine (MPC) polymers were prepared by atom transfer radical polymerization in which the requisite functional end-groups for protein conjugation were embedded within the polymerization initiators. These phosphorylcholine polymers were conjugated to lysozyme as a model protein, as well as two therapeutic proteins, granulocyte colony stimulating factor (G-CSF) and erythropoietin (EPO). These MPC polymer-protein conjugates represent alternatives to PEGylated proteins, with the potential to provide improved efficacy in a therapeutic treatment relative to the protein itself.
Genomic subtraction for cloning DNA corresponding to deletion mutations. (1990)

We have developed a technique, called genomic subtraction, for isolating the DNA that is absent in deletion mutants. The method removes from wild-type DNA the sequences that are present in both the wild-type and the deletion mutant genomes. The DNA that corresponds to the deleted region remains. Enrichment for the deleted sequences is achieved by allowing a mixture of denatured wild-type and biotinylated mutant DNA to reassociate. After reassociation, the biotinylated sequences are removed by binding to avidin-coated beads. This subtraction process is then repeated several times. In each cycle we hybridize the unbound wild-type DNA from the previous round with fresh biotinylated deletion mutant DNA. The unbound DNA from the final cycle is ligated to adaptors and amplified by using one strand of the adaptor as a primer in the polymerase chain reaction. The amplified sequences can then be used to probe a genomic library. We applied genomic subtraction to a yeast strain that has a 5-kilobase deletion, corresponding to 1/4000th of the genome. In the experiment reported here, three rounds of subtraction were sufficient to accurately identify genomic clones containing sequences that are missing in the deletion mutant. We discuss the limitations and some potential applications of the method.