gebhart/patrepeval huggingface dataset:
IPT: A novel iodinated ligand for the CNS dopamine transporter (1995)

An iodinated cocaine derivative, N-(3'-iodopropen-2'-yl)-2 beta-carbomethoxy-3 beta-(4-chlorophenyl) tropane (IPT), was evaluated as a probe for in vitro and in vivo labeling of dopamine (DA) and serotonin (5-HT) transporters in Sprague-Dawley rat brain. Saturation analysis of [125I]IPT in rat striatal homogenates, in two different buffer solutions, Tris-HCl and phosphate, demonstrated a one-site binding with affinities (Kd) of 0.25 +/- 0.02 and 0.16 +/- 0.02 nM and densities (Bmax) of 939 +/- 161 and 1,982 +/- 137 fmol/mg protein, respectively. Competition by known DA transporter ligands showed a rank order of RTI-55 > IPT > GBR12909 > mazindol > (-)cocaine. Binding to 5-HT transporter sites was evaluated in rat cortical homogenates. Saturation experiment results showed a single site with a Kd value of 1.2 +/- 0.2 nM and a Bmax value of 100 +/- 20 fmol/mg protein. The rank order of potency of several monoamine uptake inhibitors (paroxetine > fluoxetine > mazindol > R-nisoxetine > GBR12909) suggests that [125I] IPT labels 5-HT transporters in rat cortical homogenates. Both ex vivo and in vitro autoradiographic studies revealed high densities of [125I]IPT binding sites in the caudate nucleus, putamen, olfactory tubercle and nucleus accumbens, areas known to be rich in dopaminergic innervation. Moderate accumulation of activity was also observed in the substantia nigra. The dorsal raphe, a region with a high density of 5-HT innervation, was labeled using in vitro autoradiography with [125I]IPT, but the labeling using ex vivo autoradiography was less prominent at 30 min postinjection and not noticeable at 60 min postinjection.(ABSTRACT TRUNCATED AT 250 WORDS)
Photo-control of helix content in a short peptide (2000)

The alpha-helix is a key structural element in a wide range of peptides and proteins. We report here the design, synthesis, and characterization of a modified peptide in which the helix content can be reversibly photoregulated. The peptide contains two cysteine residues that are cross-linked by an azobenzene derivative in an intramolecular fashion. In accordance with the design, the photoisomerization of the azobenzene cross-linker from the trans to the cis form causes a large increase in the helix content of the peptide, in water.
Text document clustering and the space of concept on text document automatically generated (2002)

A method of automatically generating text document space is presented. Firstly, the paper considers text document clustering through the use of SOM and then fuzzy clustering to automatically generate and sum up the concept space for text document management. The result can be used to cluster Chinese documents and generates an index of the cluster automatically. SOM is an unsupervised learning neural network method that produces a mapping from text space into concept space. Some experiments and test results show that the concept space does well in arranging the classification of the text and is convenient for information retrieval.
3D Hand Shape and Pose Estimation from a Single RGB Image (2019)

This work addresses a novel and challenging problem of estimating the full 3D hand shape and pose from a single RGB image. Most current methods in 3D hand analysis from monocular RGB images only focus on estimating the 3D locations of hand keypoints, which cannot fully express the 3D shape of hand. In contrast, we propose a Graph Convolutional Neural Network (Graph CNN) based method to reconstruct a full 3D mesh of hand surface that contains richer information of both 3D hand shape and pose. To train networks with full supervision, we create a large-scale synthetic dataset containing both ground truth 3D meshes and 3D poses. When fine-tuning the networks on real-world datasets without 3D ground truth, we propose a weakly-supervised approach by leveraging the depth map as a weak supervision in training. Through extensive evaluations on our proposed new datasets and two public datasets, we show that our proposed method can produce accurate and reasonable 3D hand mesh, and can achieve superior 3D hand pose estimation accuracy when compared with state-of-the-art methods.
Acoustic radiation force analysis using finite difference time domain method (2012)

Acoustic radiation force exerted by standing waves on particles is analyzed using a finite difference time domain Lagrangian method. This method allows the acoustic radiation force to be obtained directly from the solution of nonlinear fluid equations, without any assumptions on size or geometry of the particles, boundary conditions, or acoustic field amplitude. The model converges to analytical results in the limit of small particle radii and low field amplitudes, where assumptions within the analytical models apply. Good agreement with analytical and numerical models based on solutions of linear scattering problems is observed for compressible particles, whereas some disagreement is detected when the compressibility of the particles decreases.
Best practices for producing quality digital audio files (2006)

http://deepblue.lib.umich.edu/bitstream/2027.42/40248/1/Audio-Best_Practice.pdf
In Vivo Fluorescence of Human Skin (1988)

Fluorescence is a feature of elastin and collagen, both major compounds of human dermis that are altered by age and photoexposure. We studied the intrinsic fluorescence of skin in vivo in 28 human volunteers to determine whether photoaging and chronologic aging of the skin could be evaluated by this noninvasive technique. We demonstrate that the excitation of skin autofluorescence by laser ultraviolet radiation yields characteristic tissue fluorescence spectra that are unrelated to age, pigmentation, or skin thickness. The differences in skin autofluorescence appear to be related to photoexposure. Thus, laser-induced fluorimetry, a noninvasive technique, may be adaptable as a marker of photoaging.
Genetic analysis of the atrial natriuretic peptide gene in essential hypertension (2000)

Atrial natriuretic peptide (ANP) plays an important role in the regulation of blood pressure through sodium–water homoeostasis. Accordingly, several investigators have raised the question of whether the gene encoding ANP is involved in the aetiology of essential hypertension or related phenotypes such as salt sensitivity. Most of the studies have used anonymous polymorphic markers of the gene, and made inconclusive claims about the disease relevance of ANP. Therefore, in order to find sequence variations with potential functional significance and to characterize the pattern of linkage disequilibrium between polymorphisms, we screened a 3368-bp genomic fragment of ANP. Subsequently we tested the association of detected polymorphisms with plasma ANP levels and with hypertension status. Two new polymorphisms were identified, in the 5′-untranslated region and exon 1 respectively, as well as three previously reported polymorphisms in intron 2 and exon 3. When analysed in 102 healthy normotensive subjects, none of the polymorphisms appeared to significantly affect plasma ANP levels. A case–control study in a Japanese population (255 hypertensive and 225 normotensive individuals) revealed a marginally significant association (P = 0.026) between an ANP polymorphism located in the 5′-untranslated region (C-664G) and hypertension, but no association for the other polymorphisms. Each of the uncommon variants has an allele frequency of less than 10% in Japanese people, which may have hampered our detection of a significant association between ANP variants and hypertension status (and plasma ANP levels). The pathophysiological relevance of ANP, however, needs to be further defined in relation to hypertension-associated phenotypes, and also should be examined in different ethnic groups.
Mechanism of mRNA capping by vaccinia virus guanylyltransferase: characterization of an enzyme--guanylate intermediate. (1981)

Vaccinia virus RNA guanylyltransferase catalyzes the transfer of GMP from GTP to the 5'-triphosphate or diphosphate terminus of RNA to generate the cap structure G(5')ppp(5')N-. The guanylylation reaction consists of a series of at least two partial reactions: (i) GTP + E in equilibrium E-pG + PPi, (ii) E-pG + (p)ppNpNpN- leads to GpppNpNpN- + E. Inthe first of these, GTP reacts with capping enzyme in the absence of an RNA acceptor to form a covalent enzyme-guanylate intermediate. The GMP is linked to the Mr 95,000 subunit of the capping enzyme via a phosphoamide bond, as judged by the acid-labile, alkali-stable nature of the bond and by the susceptibility of the linkage to cleavage by hydroxylamine at pH 4.75. The isolated enzyme-guanylate complex is able to transfer the guanylate moiety to triphosphate-terminated poly(A) to yield the 5' cap structure GpppA or to pyrophosphate to regenerate GTP. Both partial reactions of transguanylylation require a divalent cation.
Velocity estimation by beam stack (1992)

Abstract Imaging seismic data requires detailed knowledge of the propagation velocity of compressional waves in the subsurface. In conventional seismic processing, the interval velocity model is usually derived from stacking velocities. Stacking velocities are determined by measuring the coherency of the reflections along hyperbolic moveout trajectories in offset. This conventional method becomes inaccurate in geologically complex areas because the conversion of stacking velocities to interval velocities assumes a horizontally stratified medium and mild lateral variations in velocity.The tomographic velocity estimation proposed in this paper can be applied when there are dipping reflectors and strong lateral variations. The method is based on the measurements of moveouts by beam stacks. A beam stack measures local coherency of reflections along hyperbolic trajectories. Because it is a local operator, the beam stack can provide information on nonhyperbolic moveouts in the data. This information is more reliable than traveltimes of reflec-tions picked directly from the data because many seismic traces are used for computing beam stacks.To estimate interval velocity, I iteratively search for the velocity model that best predicts the events in beam-stacked data. My estimation method does not require a preliminary picking of the data because it directly maximizes the beam-stack's energy at the traveltimes and surface locations predicted by ray tracing. The advantage of this formulation is that detection of the events in the beam-stacked data can be guided by the imposition of smoothness constraints on the velocity model. The optimization problem of maximizing beam-stack energy is solved by a gradient algorithm. To compute the derivatives of the objective function with respect to the velocity model, I derive a linear operator that relates perturbations in velocity to the observed changes in the beam-stack kinematics.The method has been successfully applied to a marine survey for estimating a low-velocity anomaly. The estimated velocity function correctly predicts the nonhyperbolic moveouts in the data caused by the velocity anomaly.
Flexor Tendon Blood Vessels (2000)

The aim of this study was to assess rabbit long flexor tendon vascularity in a qualitative and quantitative manner using immunohistochemistry. The endothelial cell surface marker CD31 was targeted with a specific monoclonal mouse-anti-human antibody with good species cross-reactivity. Subsequent signal amplification and chromogen labelling allowed vessel visualization. Computer image analysis was performed. Values for vessel number and total vessel area per section, as well as the sections' cross-sectional tendon areas, were obtained. There was a consistent deep tendon avascular zone between the A2 and A4 pulley in the rabbit forepaw. This was not the case in the hindpaw, with dorsally orientated longitudinal vessels coursing the length of the intrasynovial tendon. The area of least vascularity in the hindpaw was around the metacarpophalangeal joint. We therefore recommend the use of hindpaw tendons when using the rabbit as a flexor tendon experimental model. This is because its vascular pattern is similar to that of the human flexor digitorum profundus.
The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes (2008)

Genetics aims to understand the relation between genotype and phenotype. However, because complete deletion of most yeast genes ( approximately 80%) has no obvious phenotypic consequence in rich medium, it is difficult to study their functions. To uncover phenotypes for this nonessential fraction of the genome, we performed 1144 chemical genomic assays on the yeast whole-genome heterozygous and homozygous deletion collections and quantified the growth fitness of each deletion strain in the presence of chemical or environmental stress conditions. We found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.
A retinoic acid-inducible mRNA from human erythroleukemia cells encodes a novel tissue transglutaminase homologue. (1992)

A 1.9-kilobase (kb) cDNA for a new transglutaminase protein has been cloned and sequenced from retinoic acid-induced human erythroleukemia (HEL) cells. Full-length cDNA analysis reveals an open reading frame coding for a polypeptide of 548 amino acid residues with a molecular weight of 61,740. The deduced amino acid sequence exhibited 98% identity to the human cellular transglutaminase sequence. The cysteine at position 277 in the active site and the putative Ca(2+)-binding pocket at residues 446-453 of cellular transglutaminase are conserved. Such evidence predicts that the encoded protein product is likely to be a transglutaminase homologue (TGase-H). Immunoprecipitation of the in vitro translation products from a synthetic TGase-H mRNA and from total protein of cultured erythroleukemia HEL cells revealed a protein with a molecular weight of 63,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Northern blot analysis of HEL cells and normal human fibroblast cells WI-38 using a cellular TGase probe detected the 1.9- and 4.0-kb RNA species at a relative abundance of 1:3 and 1:7, respectively. The 3'-end of the human cellular transglutaminase mRNA was also cloned and sequenced to allow comparison to the 3'-end of TGase-H reported here. This new piece gives a full length of 4012 nucleotides (4.0 kb) for human cellular transglutaminase. Comparison of the 5'-end (bases 1-1747) of the 1.9- and 4.0-kb cDNA sequences revealed a very high degree of identity. Beginning with base 1748, the sequences diverge showing no homology. The divergence point correlates with known intron-exon consensus boundaries indicative of alternative splicing.
Direct demonstration of rapid insulin-like growth factor II Receptor internalization and recycling in rat adipocytes. Insulin stimulates 125I-insulin-like growth factor II degradation by modulating the IGF-II receptor recycling process. (1985)

The photoactive insulin-like growth factor (IGF)-II analogue 4-azidobenzoyl-125I-IGF-II was synthesized and used to label specifically and covalently the Mr = 250,000 Type II IGF receptor. When rat adipocytes are irradiated after a 10-min incubation with 4-azidobenzoyl-125I-IGF-II at 10 degrees C and immediately homogenized, most of the labeled IGF-II receptors are associated with the plasma membrane fraction, indicating that receptors accessible to the labeling reagent at low temperature are on the cell surface. However, when the photolabeled cells are incubated at 37 degrees C for various times before homogenization, labeled IGF-II receptors are rapidly internalized with a half-time of 3.5 min as evidenced by a loss from the plasma membrane fraction and a concomitant appearance in the low density microsome fraction. The low density microsomes were previously shown to contain intracellular membranes (Oka, Y., and Czech, M.P. (1984) J. Biol. Chem. 259, 8125-8133). The steady state level of cell surface IGF-II receptors in the presence or absence of IGF-II, measured by the binding of anti-IGF-II receptor antibody to cells, remains constant under these conditions, demonstrating that IGF-II receptors rapidly recycle back to the cell surface at the same rate as receptor internalization. Using the above methodology, it is shown that acute insulin action: 1) increases the steady state number of cell surface IGF-II receptors; 2) increases the number of ligand-bound IGF-II receptors that are internalized per unit of time, as evidenced by a large increase in the photolabeling of intracellular membrane IGF-II receptors when cells are incubated at 37 degrees C with insulin and 4-azidobenzoyl-125I-IGF-II prior to photoactivation; and 3) increases the rate of cellular 125I-IGF-II degradation by a process that is blocked by anti-IGF-II receptor antibody. The results indicate that the action of insulin to elevate the steady state number of cell surface IGF-II receptors leads to an increased internalization flux of IGF-II-bound receptors, mediating increased IGF-II uptake and degradation.
Characterization of the Tautomycetin Biosynthetic Gene Cluster from Streptomyces griseochromogenes Provides New Insight into Dialkylmaleic Anhydride Biosynthesis (2009)

Tautomycetin (TTN) is a highly potent and specific protein phosphatase inhibitor isolated from Streptomyces griseochromogenes. The biological activity of TTN makes it an important lead for drug discovery, whereas its rare dialkylmaleic anhydride moiety and structural similarity to tautomycin (TTM), another potent phosphatase inhibitor with tremendous medicinal potential, draws attention to novel biosynthetic chemistries responsible for its production. To elucidate the biosynthetic machinery associated with TTN production, the ttn biosynthetic gene cluster from S. griseochromogenes was isolated and characterized, and its involvement in TTN biosynthesis confirmed by gene inactivation and complementation experiments. The ttn cluster was localized to a 79 kb DNA region, consisting of 19 open reading frames that encode two modular type I polyketide synthases (TtnAB), one type II thioesterase (TtnH), eight proteins for dialkylmaleic anhydride biosynthesis (TtnKLMNOPRS), four tailoring enzymes (TtnCDFI), two regulatory proteins (TtnGQ), and one resistance protein (TtnJ). A model for TTN biosynthesis is proposed on the basis of functional assignments from sequence analysis, which agrees well with previous feeding experiments, has been supported by in vivo gene inactivation experiments, and is supported by analogy to the recently reported ttm cluster. These findings set the stage to fully investigate TTN biosynthesis and to biosynthetically engineer new TTN analogues.
The Group Domain of Interpretation (2003)

This document presents an ISAMKP Domain of Interpretation (DOI) for group key management to support secure group communications. The GDOI manages group security associations, which are used by IPSEC and potentially other data security protocols running at the IP or application layers. These security associations protect one or more key-encrypting keys, traffic-encrypting keys, or data shared by group members.
Body Mass Index as a Predictor of Mortality in Elderly People in Taiwan (2011)

An interesting original article was reported by Hwang et al.1 recently. The authors found that body mass index (BMI) was a predictor of elderly mortality in Taiwan. Their conclusion was that obesity (BMI> 25 kg/m2) was a significant independent predictor of all-cause mortality, whereas being overweight (BMI> 23 kg/m2) increased the risk of mortality from cancer, cardiovascular diseases, and diabetes. That was a cohort study. The researchers measured the BMI values of the participants at baseline and followed up for 23 years. They excluded subjects who died during the first 3 years of followup. However, they did not consider to evaluate weight changes according to their baseline BMI values of the participants during the follow-up period; in other words, they did not have the premortality BMI values of the participants. Thus, we thought there was a question about the causal relationship between BMI value and mortality. Because the body weight dynamically changed over time2,3, could the baseline BMI values of the participants represent the BMI values during the follow-up, especially 3 years later? In addition, body weight loss of 5% or more in a 3-year period was an independent risk factor of mortality in older adults3. In Hwanget al.’s study,we found that beingoverweight increased the risk of mortality from cancer, cardiovascular diseases, and diabetes, but not from respiratory diseases. Mortality factors of being underweight (BMI < 18.5 kg/m2) 1 increased mortality from cancer and respiratory diseases but not from cardiovascular diseases and diabetes in the elderly review of IJGE. Both over and under BMI changes increase the risks from cancers. It is interesting to consider whether the abnormal BMI value leads to different preexisting chronic disease mortalities or whether different preexisting chronic
Fluoride content of infant formulae in Australia (1996)

The prevalence of dental fluorosis in Australia and the United States of America has increased in both optimally fluoridated and non-fluoridated areas. This has been attributed to an increase in the fluoride level of food and beverages through processing with fluoridated water, inadvertent ingestion of fluoride toothpaste, and the inappropriate use of dietary supplements. A major source of fluoride in infancy is considered to be infant formula which has been implicated as a risk factor for fluorosis in a number of studies. In this study the fluoride content of the infant formulae commonly used in Australia was determined. The acid diffusible fluoride of each powdered formula was isolated by microdiffusion and measured using a fluoride ion-specific electrode. The fluoride content of milk-based formulae ranged from 0.23 to 3.71 micrograms F/g and for soy-based formulae from 1.08 to 2.86 micrograms F/g. When reconstituted, according to the manufacturer's directions, with water not containing fluoride, the formulae ranged in fluoride content from 0.031 to 0.532 ppm, with the average fluoride content 0.240 ppm. Using average infant body masses and suggested volumes of formula consumption for infants 1-12 months of age, possible fluoride ingestion per kg body mass was estimated. None of the formulae, if reconstituted using water containing up to 0.1 ppm F, should provide a daily fluoride intake above the suggested threshold for fluorosis of 0.1 mg F/kg body mass. However, if reconstituted with water containing 1.0 ppm F they should all provide a daily fluoride intake of above the suggested threshold for fluorosis with intakes up to 2-3 times the recommended upper 'optimal' limit of 0.07 mg/kg body mass. Under these conditions the water used to reconstitute the formulae would provide 65-97 percent of the fluoride ingested. These figures are likely to be overestimates due to the intake of nutrients from other sources reducing formulae consumption and also due to the lower bioavailability of fluoride from milk-based formulae. Further, it is generally believed that the maturation stage of enamel formation is the critical period for fluorosis development by chronic, above-threshold fluoride exposure. The maturation stage for the anterior permanent teeth, however, is after the first twelve months of life where fluoride intake from infant formula consumption per kg body mass is highest. The level of fluoride in the commonly used Australian formulae would suggest that infant formula consumption alone is unlikely to be a risk factor for dental fluorosis in a non-fluoridated community, but could make a major contribution to an infant's daily fluoride intake. However, prolonged consumption (beyond 12 months of age) of infant formula reconstituted with optimally-fluoridated water could result in excessive amounts of fluoride being ingested during enamel development of the anterior permanent teeth and therefore may be a risk factor for fluorosis of these teeth.