gebhart/patrepeval huggingface dataset:
Rapid Purification of Plasmid DNAs by Hydroxyapatite Chromatography (1978)

A method is described for the rapid preparation of plasmid DNAs of molecular weight up to 14 X 10(6). This method involves the chromatography, at room temperature, of bacterial cleared lysates on hydroxyapatite in the presence of high concentrations of phosphate and urea. All detectable protein and RNA contamination of plasmid DNA is removed by this procedure and the conformation of the plasmid DNA is unaffected. Less than 0.5% chromosomal DNA is present in the purified preparation and even this can be removed if necessary by a simple extention of the procedure to include a heat-denaturation step. The method is extremely rapid and amenable to large-scale plasmid preparation; 5 mg ColE1 DNA have been purified within 40 min. The yield of plasmid DNA is similar to that obtained with the conventional dye-centrifugation technique, however the purity is greater.
An Analysis of English and Chinese Numerical Idioms Sharing the Equivalent Connotations (2014)

This paper, based on the analysis of English and Chinese numerical idioms which share the equivalent or similar connotative meaning, according to the different corresponding relationship between the expressive means and expressive forms, are divided into four groups. The expressive means are classified in terms of rhetorical device of English and Chinese numerical idioms and considered mainly from vehicle. Because the rhetorical device mainly used in number and numerical idiom is metaphor, and as the cultural backgrounds are different, the metaphorical image varies a lot. Sometimes, the same image is endowed different emotional colors in different countries and used in different occasions. Metaphorical images in English and Chinese numerical idioms are also reflections of the historical traditions, lifestyles, values, moral standards and customs in languages.
Analysis of the tissue-specific expression, developmental regulation, and linkage relationships of a rodent gene encoding heart fatty acid binding protein. (1987)

The rat contains at least three homologous cytosolic proteins that bind long chain fatty acids, termed liver (L-), intestinal (I-), and heart (H-) fatty acid binding protein (FABP). I-FABP mRNA is confined to the gastrointestinal tract while L-FABP mRNA is abundantly represented in hepatocytes as well as enterocytes. We have isolated a rat heart FABP cDNA clone and determined the pattern of H-FABP mRNA accumulation in a wide variety of tissues harvested from late fetal, suckling, weaning, and adult rats. RNA blot hybridizations and primer extension analysis disclosed that the distribution of H-FABP mRNA in adult rat tissues is different from that of I- or L-FABP mRNA. H-FABP mRNA is most abundant in adult heart. This mRNA was also present in an adult slow twitch (type I) skeletal muscle (soleus, 63% of the concentration in heart), testes (28%), a fast twitch skeletal muscle (psoas, 17%), brain (10%), kidney (5%), and adrenal gland (5%). H-FABP mRNA was not detected in adult small intestine, colon, spleen, lung, or liver RNA. Distinct patterns of developmental change in H-FABP mRNA accumulation were documented in heart, placenta, brain, kidney, and testes. Myocardial H-FABP mRNA levels rise rapidly during the 48 h prior to and after birth, reaching peak levels by the early weaning period. The postnatal increase in myocardial H-FABP mRNA concentration and its relative distribution in adult fast and slow twitch skeletal muscle are consistent with its previously proposed function in facilitating mitochondrial beta-oxidation of fatty acids. However, the presence of H-FABP mRNA in brain, a tissue which does not normally significantly oxidize fatty acids in late postnatal life, suggests that H-FABP may play a wider role in fatty acid metabolism than previously realized. Mouse-hamster somatic cell hybrids were utilized to map H-FABP. Using stringencies which did not produce cross-hybridization between L-, I-, and H-FABP DNA sequences, we found at least three loci in the mouse genome, each located on different chromosomes, which reacted with our cloned H-FABP cDNA. None of these H-FABP-related loci were linked to the gene which specifies a highly homologous adipocyte-specific protein termed aP2 or to genes encoding two other members of this protein family, cellular retinol binding protein and cellular retinol binding protein II.(ABSTRACT TRUNCATED AT 400 WORDS)
Phosphorylation of high mobility group protein 14 by casein kinase II. (1985)

Phosphorylation of chromosomal high mobility group (HMG) protein 14 by casein kinase II has been characterized. Two mol of 32P are incorporated per mol of bovine HMG 14. Kinetic analysis provided evidence for two distinct sites with apparent Km values of 14.5 and 134 microM and respective Vmax values of 0.17 and 0.68 mumol/min/mg casein kinase II. Tryptic peptide mapping identified two phosphorylated products, each with phosphoserine. Amino acid composition and sequence analysis demonstrate that the major high affinity phosphorylation site for casein kinase II is serine 89. This sequence located at the carboxyl-terminal of HMG 14 contains the primary sequence determinants for casein kinase II. On the basis of reverse-phase high performance liquid chromatography and amino acid analysis, HMG 14, serine 99 represents the low affinity phosphorylation site.
Automatic multidimensional deconvolution (1987)

A multiple convolution (e.g., an image formed by convolving several individual components) is automatically deconvolvable, provided that its dimension (i.e., the number of variables of which it is a function) is greater than unity. This follows because the Fourier transform of a K-dimensional function (having compact support) is zero on continuous surfaces (here called zero sheets) of dimension (2K − 2) in a space that effectively has 2K dimensions. A number of important practical applications are transfigured by the concept of the zero sheet. Image restoration can be effected without prior knowledge of the point-spread function, i.e., blind deconvolution is possible even when only a single blurred image is given. It is in principle possible to remove some of the additive noise when the form of the point-spread function is known. Fourier phase can be retrieved directly, and, unlike for readily implementable iterative techniques, complex images can be handled as straightforwardly as real images.
STK35L1 Associates with Nuclear Actin and Regulates Cell Cycle and Migration of Endothelial Cells (2011)

The results indicate that by regulating CDKN2A and inhibiting G1- to S-phase transition STK35L1 may act as a central kinase linking the cell cycle and migration of endothelial cells. The interaction of STK35L1 with nuclear actin might be critical in the regulation of these fundamental endothelial functions.
A novel diet‐induced murine model of steatohepatitis with fibrosis for screening and evaluation of drug candidates for nonalcoholic steatohepatitis (2016)

Many animal models of nonalcoholic steatohepatitis have been reported. While these models exhibit mild onset of hepatitis and fibrosis, induction is often slow. For faster screening of drug candidates, there is a compelling need for convenient animal models of steatohepatitis and nonalcoholic steatohepatitis in which fatty liver and hepatitis are stably induced within a short period. Here, we analyzed the hepatic lipid composition in nonalcoholic steatohepatitis, and used this information to successfully establish a murine model where steatohepatitis is induced within only 1 week using a novel diet (steatohepatitis-inducing high-fat diet, STHD-01) high in saturated fatty acids and cholesterol. After receiving STHD-01 for 1 week, normal mice (C57BL/6J) showed elevated markers of fatty liver and hepatitis, including hepatic triglycerides and plasma alanine aminotransferase; the administration of angiotensin receptor blockers reduced these symptoms. Furthermore, we confirmed that STHD-01 administration for 36 weeks induced not only sustained elevation of hepatic triglyceride and plasma alanine aminotransferase levels, but also fibrosis and tumor formation. Pretreatment with the carcinogen diethylnitrosamine accelerated tumor formation, and hepatic lesions were observed within 30 weeks of STHD-01 feeding following diethylnitrosamine pretreatment. Finally, branched-chain amino acids, known to reduce the risk for hepatocellular carcinoma in preclinical models, were effective in reducing the progression of liver fibrosis induced by STHD-01 feeding after diethylnitrosamine pretreatment. We concluded that STHD-01 administration successfully induces steatohepatitis within a short period of time. The proposed murine model is suitable for studying the long-term effects of pharmaceutical agents targeting steatohepatitis, fibrosis, and tumor formation.
Design of a peptide-based vector, PepFect6, for efficient delivery of siRNA in cell culture and systemically in vivo (2011)

While small interfering RNAs (siRNAs) have been rapidly appreciated to silence genes, efficient and non-toxic vectors for primary cells and for systemic in vivo delivery are lacking. Several siRNA-delivery vehicles, including cell-penetrating peptides (CPPs), have been developed but their utility is often restricted by entrapment following endocytosis. Hence, developing CPPs that promote endosomal escape is a prerequisite for successful siRNA implementation. We here present a novel CPP, PepFect 6 (PF6), comprising the previously reported stearyl-TP10 peptide, having pH titratable trifluoromethylquinoline moieties covalently incorporated to facilitate endosomal release. Stable PF6/siRNA nanoparticles enter entire cell populations and rapidly promote endosomal escape, resulting in robust RNAi responses in various cell types (including primary cells), with minimal associated transcriptomic or proteomic changes. Furthermore, PF6-mediated delivery is independent of cell confluence and, in most cases, not significantly hampered by serum proteins. Finally, these nanoparticles promote strong RNAi responses in different organs following systemic delivery in mice without any associated toxicity. Strikingly, similar knockdown in liver is achieved by PF6/siRNA nanoparticles and siRNA injected by hydrodynamic infusion, a golden standard technique for liver transfection. These results imply that the peptide, in addition to having utility for RNAi screens in vitro, displays therapeutic potential.
Type structured file system (2002)

Describes the design of Nebula, a dynamic, object-based, typed file system. Nebula uses types to create well-structured files as well as to export existing files in the Internet environment. This allows for backward scalability. Files in Nebula are abstractions and are defined by objects. Nebula assumes a flat global namespace, and operations are provided to manipulate logical namespaces.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Performance analysis of RS-coded M-ary FSK for frequency-hopping spread spectrum mobile radios (1992)

Decoding performance of Reed-Solomon (RS) coded M-ary FSK with noncoherent detection in a frequency-hopping spread spectrum mobile radio channel is theoretically analyzed. Exact formulas and an approximate one for evaluating word error rates (WERs) of error correction and error-and-erasure correction schemes on decoding the RS codes are derived. It is shown that with K symbol erasure and C symbol error detection, RS coded M-ary FSK achieves the equivalent diversity order of (K+1)(C+1).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Receptors for the incretin glucagon-like peptide-1 are expressed on neurons in the central nervous system (2009)

Glucagon-like-peptide-1 is an incretin hormone that also has neuroprotective properties. Here we analyse where glucagon-like-peptide-1 receptors are expressed in the brain. The receptor is found only on neurons, not on glia cells. The pyramidal cell layer of the CA region and the granule cell layer of the dentate gyrus in the hippocampus show intense staining. In the neocortex, larger pyramidal neurons express the receptor. In the cerebellum, only Purkinje neurons express the receptor. Dendrites of larger neurons were stained; in particular, pyramidal cells in area CA and dendrites of Purkinje cells. The fact that the receptor is located on neurons and dendrites suggests that the neuroprotective action is caused by the modulation of neuronal excitation.
Simple Method for the Preparation of Esters from Grignard Reagents and Alkyl 1-Imidazolecarboxylates (2006)

The reaction of Grignard reagents with alkyl imidazolecarboxylates, which were prepared from alcohols with carbonyl diimidazole, gave the corresponding esters in good to excellent yields. This method conveniently provides esters from alkyl halides and alcohols by C1-carbon chain extension.
Intravascular Stents to Prevent Occlusion and Re-Stenosis after Transluminal Angioplasty (1987)

Occlusion and restenosis are the most common reasons that transluminal balloon angioplasty may fail to provide long-term benefit. An intravascular mechanical support was therefore developed with the aim of preventing restenosis and sudden closure of diseased arteries after angioplasty. The endoprosthesis consists of a self-expandable stainless-steel mesh that can be implanted nonsurgically in the coronary or peripheral arteries. Experiments in animals showed complete intimal coverage within weeks and no late thrombosis during a follow-up period of up to one year. We performed 10 implantations in 6 patients for iliac or femoral arterial disease; 24 coronary-artery stents were implanted in 19 patients who presented with coronary-artery restenoses (n = 17) or abrupt closure (n = 4) after transluminal angioplasty or deterioration of coronary-bypass grafts (n = 3). We observed three complications in the group with coronary disease. One thrombotic occlusion of a stent resulted in asymptomatic closure, a second acute thrombosis was managed successfully with thrombolysis, and one patient died after bypass surgery for a suspected but unfound occlusion. Follow-up in the patients has continued for nine months without evidence of any further restenoses within the stented segments. Our preliminary experience suggests that this vascular endoprosthesis may offer a useful way to prevent occlusion and restenosis after transluminal angioplasty. Long-term follow-up will be required to validate the early success of this procedure.
Structural and functional studies on a unique linear neutralizing antigenic site (G5) of the rabies virus glycoprotein (1993)

The core of a unique linear neutralization epitope (G5) on the glycoprotein of rabies virus, recognized by a virus-neutralizing mouse monoclonal antibody (MAb 6-15C4), was determined by Pepscan analysis. The G5 epitope was defined as an octapeptide (LHDFRSDE). The contribution of the individual amino acids of the G5 epitope to the binding of MAb 6-15C4 was analysed with a set of synthetic peptides in which the individual amino acids had been replaced in turn by each of the other 19 naturally occurring amino acids. Five amino acids of the octapeptide proved to be essential for the binding of MAb 6-15C4. The conservation of the G5 epitope within the glycoprotein of the different rabies virus strains sequenced to date proved to be absolute at the amino acid level. Studies concerning the immunodominance of the G5 epitope were carried out by determining the presence of G5 epitope-specific serum antibodies in vaccinated human and mice, and by determining the frequency of G5 epitope-specific B lymphocytes in the blood of vaccinated humans. These studies indicated that antibodies to the G5 epitope constitute a minor population of the rabies virus-specific serum antibodies induced by rabies vaccination.
qPrimerDepot: a primer database for quantitative real time PCR (2006)

Gene expression studies employing high throughput real time PCR methods require finding uniform conditions for optimal amplification of multiple targets, often a daunting task. We developed a primer database, qPrimerDepot, which provides optimized primers for all human and mouse RefSeq genes. These primers are designed to amplify desired templates under unified annealing temperature. For most intron-bearing genes, primers flank one of the largest introns thus minimizing background noise due to genomic DNA contamination. The qPrimerDepot database can be accessed at http://primerdepot.nci.nih.gov/ and http://mouseprimerdepot.nci.nih.gov/.
Conjugative Transposons and the Dissemination of Antibiotic Resistance in Streptococci (1986)

INTRODUCTION 636 IDENTIFICATION AND PROPERTIES OF Tn916 636 MECHANISM OF Tn916 MOVEMENT 642 OTHER CONJUGATIVE TRANSPOSONS 644 Tn918 and Tn919 ......... ...... 644 Nonplasmid Multiple Resistance Transfer in Various Species of Streptococci........ 645 COMMON ASSOCIATION OF Tc RESISTANCE WITH CONJUGATIVE TRANSPOSONS 650 SOME COMMON EFFECTS OF CONJUGATED TRANSPOSONS ON HEMOLYSIN GENES IN STREPTOCOCCUS FAECALlS 65 I HOST RANGE OF CONJUGATIVE TRANSPOSONS 652 POTENTIAL USES FOR CONJUGATIVE TRANSPOSONS IN GENETIC STUDIES.. . . . . . . ... . . . . . . . . . . . . . . .. . . . . . . . . .. . . . . . . . . . . . . . . . .. .. . . . .. . . . . ..... 652 CONCLUDING REMARKS 653
Condon usage tabulated from the international DNA sequence databases (1996)

CUTG (codon usage tabulated from GenBank) is a comprehensive database for codon usage. The codon usage for each full-length protein gene has been calculated using the nucleotide sequence obtained from GenBank sequence database. The sum of the codon use of each organism has been also calculated. The data files can be obtained from anonymous ftp sites of DDBJ, DISC and EBI. The list of codonusage of genes in organisms was made searchableby name of organism through a web site http://www.dna.affrc.go.jp/ approximately nakamura/CUTG.html The compilation is synchronized with major release of GenBank.
Digital chaotic coding and modulation in CDMA (2003)

Conventional CDMA system uses PN sequences to spread user information. The number of shift registers used to generate them limit the lengths of these sequences. Good correlation properties can be achieved by Walsh codes and time-shifted version of PN sequences. The ability to predict future sequence is nevertheless possible, though difficult. Transmission therefore is not completely secured. Several other codes (Gold codes, Kasami etc) perform equally well as PN sequences, however it has been reported that these do not improve the security aspect of the system. Hence there is a need for a highly secure code that can be regenerated at the receiver and that can mimic PN sequences for spreading. In this paper, chaotic codes are investigated and their performance compared with the conventional PN sequences in an AWGN and Raleigh fading channel. The other type of spreading code which is the Walsh code uses its orthogonal property for user separation in the channel. This paper also investigates the behaviour of chaotic code in a multi-user situation. The auto and cross correlation properties of the spreading codes are also investigated. Chaotic codes are dependent on initial conditions and are continuous in nature. The undeterministic property of its amplitude from past sequences yields better security. Common modulation techniques (BPSK, QPSK) require higher SNRs to give similar performance in a multi-user environment. The use of QAM in order to improve BER whilst simultaneously inheriting secure property of chaotic codes is also investigated.
Geometry images (2002)

Surface geometry is often modeled with irregular triangle meshes. The process of remeshing refers to approximating such geometry using a mesh with (semi)-regular connectivity, which has advantages for many graphics applications. However, current techniques for remeshing arbitrary surfaces create only semi-regular meshes. The original mesh is typically decomposed into a set of disk-like charts, onto which the geometry is parametrized and sampled. In this paper, we propose to remesh an arbitrary surface onto a completely regular structure we call a geometry image. It captures geometry as a simple 2D array of quantized points. Surface signals like normals and colors are stored in similar 2D arrays using the same implicit surface parametrization --- texture coordinates are absent. To create a geometry image, we cut an arbitrary mesh along a network of edge paths, and parametrize the resulting single chart onto a square. Geometry images can be encoded using traditional image compression algorithms, such as wavelet-based coders.
Current Methods of Adipogenic Differentiation of Mesenchymal Stem Cells (2011)

There has been a recent increase in our understanding in the isolation, culture, and differentiation of mesenchymal stem cells (MSCs). Concomitantly, the availability of MSCs has increased, with cells now commercially available, including human MSCs from adipose tissue and bone marrow. Despite an increased understanding of MSC biology and an increase in their availability, standardization of techniques for adipogenic differentiation of MSCs is lacking. The following review will explore the variability in adipogenic differentiation in vitro, specifically in 3T3-L1 and primary MSCs derived from both adipose tissue and bone marrow. A review of alternative methods of adipogenic induction is also presented, including the use of specific peroxisome proliferator-activated receptor-gamma agonists as well as bone morphogenetic proteins. Finally, we define a standard, commonly used adipogenic differentiation medium in the hopes that this will be adopted for the future standardization of laboratory techniques--however, we also highlight the essentially arbitrary nature of this decision. With the current, rapid pace of electronic publications, it becomes imperative for standardization of such basic techniques so that interlaboratory results may be easily compared and interpreted.
Identification of multiple structural domains regulating viroid pathogenicity. (1992)

To investigate the role of individual structural domains in viroid pathogenicity and replication, a series of interspecific chimeras was constructed by exchanging the terminal left (TL) and/or pathogenicity (P) domains between tomato apical stunt (TASVd) and citrus exocortis (CEVd) viroids. All six chimeras tested were replicated stably in tomato, and the symptoms exhibited by infected plants were intermediate between those induced by the parental viroids. Quantitative comparisons of symptom development and progeny accumulation revealed that: (i) the TL domain of TASVd contains a determinant required for appearance of severe veinal necrosis in tomato, (ii) the severe epinasty and stunting characteristic of TASVd requires the presence of its TL and P domains, and (iii) the variable (V) and terminal right (TR) domains comprising the right side of the native structure also play an important role in viroid pathogenicity. Chimeras containing the right side of TASVd accumulated to higher levels early in infection, and infected plants developed more severe symptoms than those whose right halves were derived from CEVd. Although the individual contributions of the TL and P domains to symptom induction could not be completely separated from that of viroid titer, the TL domain appears to exert a greater effect upon symptom severity than does the P domain. The TL, P, V, and TR domains of TASVd and CEVd contain three discrete regions of sequence and/or structural variability that may correspond to the pathogenicity determinants uncovered by our genetic analysis.