gebhart/patrepeval huggingface dataset:
Characterization of Euglenaformis gen. nov. and the chloroplast genome of Euglenaformis [Euglena] proxima (Euglenophyta) (2014)

:Euglena proxima is a common, globally dispersed, and easily identified photosynthetic euglenoid. Previous phylogenetic analyses using nuclear-encoded small subunit (SSU) and large subunit (LSU) rRNA genes revealed that this taxon was paraphyletic with other Euglena species and was positioned as sister to all Euglenaceae. Despite this, authors were reluctant to remove this taxon from Euglena until additional data, or taxa pairing with E. proxima, were obtained because it created a monotypic genus. To clarify the taxonomy, the chloroplast genome of E. proxima was sequenced and compared with those of other photosynthetic euglenoids. Phylogenomic analyses were performed comparing 79 chloroplast-encoded genes from E. proxima with those found in seven photosynthetic euglenoids and three prasinophytes, the group from which the euglenoid chloroplast was probably derived. These analyses resulted in highly supported phylogenomic trees with topologies that were consistent with all previous phylogenetic analyses, i.e. they positioned E. proxima as sister to all of the Euglenaceae. In addition, a syntenic comparison was conducted between E. proxima and the chloroplast genomes of two Euglena taxa in order to determine their similarities. This analysis showed that the construction of the E. proxima chloroplast genome was very different from that of the two Euglena chloroplast genomes, which were extremely similar to each other. Based on these data, E. proxima was removed from Euglena, and a new genus, Euglenaformis, was erected to clarify the true relationship of this taxon to the rest of the photosynthetic euglenoids.
Excess of methyl donors in maternal diet affects postnatal down regulation of Igf2, Igf2r and H19 genes in liver (2014)

Excess of methyl donors in maternal diet affects postnatal down regulation of Igf2, Igf2r and H19 genes in liver. Congrès SF DOHAD
Strong in Vitro Synergy Between the Fusion Inhibitor T-20 and the CXCR4 Blocker AMD-3100 (2000)

Attachment and entry of HIV-1 into CD4 cells involve a series of events in which different viral envelope proteins interact with specific cell receptors, culminating in fusion of viral and cell membranes. AMD-3100 is a small molecule inhibitor of HIV-1 attachment to the CXCR4 chemokine receptor, and T-20 is a synthetic peptide corresponding to a region of HIV-1 gp41 that blocks fusion to cell membranes. To evaluate the interaction between agents acting at two different steps of the entry process, we conducted in vitro studies of the combination of T-20 and AMD-3100 against an X4 HIV-1 isolate. Single drugs or multiply diluted fixed ratio combinations of drugs were added to peripheral blood mononuclear cells infected with a clinical isolate, 14aPre. Drug interactions were evaluated using the median-effect principle and the combination index technique. The 50% inhibitory concentration (IC50) for T-20 was 0.10 μg/ml and for AMD-3100 was 0.19 μg/ml. Synergy was observed between T-20 and AMD-3100 and this increased with higher inhibitory concentrations, with combination indices ranging from 0.62 at IC50 to 0.02 at IC95. Whether these synergistic interactions translate into clinical benefit will need to be addressed in the context of clinical trials.
Terrain visualization and data discovery using lunar high-resolution laser altimeter data sets (2012)

NASA's latest space mission on the Lunar Reconnaissance Orbiter (LRO) has produced some of the largest publicly accessible Laser Altimeter data products available to date. The spatial density of these new data products are up to four times greater than laser altimeter data produced from previous space missions. However, partially due to the size, volume and density of the new altimeter data, current software tools provide only limited or no support for real-time cartographical projects, slope analysis, distance measurements or other analyses method critical to physiographic study of planetary systems. We discuss a novel software tool called mVTK, which facilitates the physiographic analysis of the Lunar surface using the newly acquired high resolution altimeter data products. Some of the features provided by m VTK include realtime cartographic projects, slope analysis, distance measurement and visual data discovery.
Temporal subtraction of thorax CR images using statistical deformation model (2003)

We propose a voxel-based nonrigid registration algorithm for temporal subtraction of two-dimensional thorax X-ray computed radiography images of the same subject. The deformation field is represented by a B-spline with a limited number of degrees of freedom, that allows global rib alignment to minimize subtraction artifacts within the lung field without obliterating interval changes of clinically relevant soft-tissue abnormalities. The spline parameters are constrained by a statistical deformation model that is learned from a training set of manually aligned image pairs using principal component analysis. Optimization proceeds along the transformation components rather then along the individual spline coefficients, using pattern intensity of the subtraction image within the automatically segmented lung field region as the criterion to be minimized and applying a simulated annealing strategy for global optimization in the presence of multiple local optima. The impact of different transformation models with varying number of deformation modes is evaluated on a training set of 26 images using a leave-one-out strategy and compared to the manual registration result in terms of criterion value and deformation error. Registration quality is assessed on a second set of validation images by a human expert rating each subtraction image on screen. In 85% of the cases, the registration is subjectively rated to be adequate for clinical use.
Human G protein-coupled receptor 30 is N-glycosylated and N-terminal domain asparagine 44 is required for receptor structure and activity (2019)

G protein-coupled receptor 30 (GPR30), or G protein-coupled estrogen receptor (GPER), is a G protein-coupled receptor (GPCR) that is currently attracting considerable attention in breast cancer and cardiometabolic regulation. The receptor was reported to be a novel membrane estrogen receptor mediating rapid non-genomic responses. However, questions remain about both the cognate ligand and the subcellular localization of receptor activity. Here, we used human embryonic kidney (HEK) 293 (HEK293) cells ectopically expressing N-terminally FLAG-tagged human GPR30 and three unique antibodies (Ab) specifically targetting the receptor N-terminal domain (N-domain) to investigate the role of <i>N</i>-glycosylation in receptor maturation and activity, the latter assayed by constitutive receptor-stimulated extracellular-regulated protein kinase (ERK) 1/2 (ERK1/2) activity. GPR30 expression was complex with receptor species spanning from approximately 40 kDa to higher molecular masses and localized in the endoplasmatic reticulum (ER), the plasma membrane (PM), and endocytic vesicles. The receptor contains three conserved asparagines, Asn<sup>25</sup>, Asn<sup>32</sup>, and Asn<sup>44</sup>, in consensus <i>N</i>-glycosylation motifs, all in the N-domain, and PNGase F treatment showed that at least one of them is <i>N</i>-glycosylated. Mutating Asn<sup>44</sup> to isoleucine inactivated the receptor, yielding a unique receptor species at approximately 20 kDa that was recognized by Ab only in a denatured state. On the other hand, mutating Asn<sup>25</sup> or Asn<sup>32</sup> either individually or in combination, or truncating successively N-domain residues 1-42, had no significant effect either on receptor structure, maturation, or activity. Thus, Asn<sup>44</sup> in the GPR30 N-domain is required for receptor structure and activity, whereas N-domain residues 1-42, including specifically Asn<sup>25</sup> and Asn<sup>32</sup>, do not play any major structural or functional role(s).
Substituted 2-Azabicyclo[2.1.1]hexanes as Constrained Proline Analogues:  Implications for Collagen Stability (2004)

Among the proteinogenic amino acids, only proline is a secondary amine and only proline has a saturated ring. Electronegative substituents on C-4 (that is, C(gamma)) have a substantial effect on the trans/cis ratio of the prolyl peptide bond and the pucker of the pyrrolidine ring. 2-Azabicyclo[2.1.1]hexane is, in essence, a proline analogue with two C(gamma) atoms, one in each of the two prevalent ring puckers of proline. Here, 2-azabicyclo[2.1.1]hexane analogues of 2S-proline, (2S,4S)-4-hydroxyproline, and (2S,4S)-4-fluoroproline residues were synthesized, and their trans/cis ratios were shown to be invariant in a particular solvent. Thus, the substitution of a proline residue on C-4 affects the trans/cis ratio by altering the pucker of its pyrrolidine ring. This finding has implications for the conformation of collagen, which has an abundance of 2S-proline and (2S,4R)-4-hydroxyproline residues, and can be stabilized by (2S,4R)-4-fluoroproline and (2S,4S)-4-fluoroproline residues.
Spectral reflectance estimation of organic tissue for improved color correction of video-assisted surgery (2018)

With video-assisted surgery devices becoming more common in all fields of diagnostics and therapy, the question of how well such systems are able to reproduce surface colors of organic tissue arises, especially in cases where a proper distinction of different kinds of tissue-not only through their texture but also through their color-might be crucial for the success of a surgery. Since modern devices are usually made of a highly efficient, multispectral LED light source in combination with some light-guiding structures and a digital camera system, an approach of optimizing these systems' color reproduction properties based on the estimation of in-situ spectral reflectances is proposed. Following the International Organization for Standardization (ISO) standard procedure of colorimetric characterization, an initial color correction matrix was determined first by solving a linear least-mean-squares optimization problem for a small set of artificial color samples mapping the corresponding camera responses onto the samples' tristimulus values. This initial matrix was then used as a starting point for a second, nonlinear optimization, which makes use of the estimated reflectance spectra in order to minimize the average squared color difference between the color corrected and the actually perceived tristimulus values of the individual organic tissue samples. Compared to the ISO standard, which only knows simple color patches to be used for the nonlinear optimization, a significant enhancement in the color reproduction of organic tissue could be confirmed with the newly proposed method being applied instead.
Development of a Partial Discharge Inception Calculation Model of a Nonuniform Air Gap Considering the Effect of Humidity (2013)

SUMMARY Insulation design employing discharge simulation based on physics phenomena is used in designing electrical instruments to facilitate their miniaturization and obtain high insulation reliability. We developed a partial discharge inception calculation model for a nonuniform air gap based on the theories of electron avalanche and streamer phenomena. The calculated and experimental PDIVs (Partial Discharge Inception Voltages) were compared under conditions of constant humidity, and we confirmed that these agreed well with each other to within about 10%. Furthermore, we incorporated a relationship between negative ions and humidity into the model and confirmed that the calculated and experimental PDIVs agreed to within about 15%. Therefore, this model was judged to be an effective method for predicting changes in the PDIV when the humidity changes. © 2013 Wiley Periodicals, Inc. Electr Eng Jpn, 186(3): 1–9, 2014; Published online in Wiley Online Library ( wileyonlinelibrary.com ). DOI 10.1002/eej.22351
Serum bicarbonate, anion gap and insulin resistance in the National Health and Nutrition Examination Survey (2008)

Lower bicarbonate and higher anion gap are independently associated with insulin resistance. Further research is needed to elucidate the relations between organic acid production, insulin resistance, and the pathogenesis of Type 2 diabetes.
MIPA4k: A 64&#x00D7;64 cell mixed-mode image processor array (2009)

This paper presents the MIPA4k, a 64times64 cell mixed-mode image processor array chip. The processor cell includes an image sensor, A/D/A conversion, embedded digital and analog memories and hardware-optimized grayscale and binary processing cores. This paper presents the architecture of the processor cell and the different functional hardware. The processor has been manufactured in a 0.13 micron CMOS technology and the chip size is 5.1times4.5 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with a cell area of 72times61 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Silicone implant to extra-ocular muscles. (1966)

A PROCEDURE which would allow the lengthening of an extra-ocular muscle beyond that which is usually obtained from the conventional surgical techniques would be of definite advantage in large-angle strabismus and strabismus fixus. Since silicone rubber is well tolerated by ocular and non-ocular tissues, the implantation of a small, thin sheet of this material to lengthen an extra-ocular muscle is a logical approach in this situation. The purpose of this paper is to report an experimental study, using rabbit eyes, and clinical observations in two patients with strabismus, in which this surgical procedure was applied. A long-term follow-up of these two patients and a report of several other clinical cases will be published at a later date.
Perfluoropropylation of Furans, Thiophenes, and Pyridines with Bis(heptafluorobutyryl) Peroxide (1986)

Abstract Bis(heptafluorobutyryl) peroxide (1) smoothly reacted with furans and thiophenes under mild conditions to regioselectively give 2-perfluoropropylfurans and thiophenes in high yields. Mechanistically, reactions with furans or thiophenes are considered to be initiated by one-electron transfers from substrates to 1. On the other hand, the perfluoropropylation of pyridine was proceeded by the usual free-radical substitution to a pyridinium salt by a heptafluoropropyl radical produced by the homolytic decomposition of 1.
Injectable anti-malarials revisited: discovery and development of new agents to protect against malaria (2018)

Over the last 15 years, the majority of malaria drug discovery and development efforts have focused on new molecules and regimens to treat patients with uncomplicated or severe disease. In addition, a number of new molecular scaffolds have been discovered which block the replication of the parasite in the liver, offering the possibility of new tools for oral prophylaxis or chemoprotection, potentially with once-weekly dosing. However, an intervention which requires less frequent administration than this would be a key tool for the control and elimination of malaria. Recent progress in HIV drug discovery has shown that small molecules can be formulated for injections as native molecules or pro-drugs which provide protection for at least 2 months. Advances in antibody engineering offer an alternative approach whereby a single injection could potentially provide protection for several months. Building on earlier profiles for uncomplicated and severe malaria, a target product profile is proposed here for an injectable medicine providing long-term protection from this disease. As with all of such profiles, factors such as efficacy, cost, safety and tolerability are key, but with the changing disease landscape in Africa, new clinical and regulatory approaches are required to develop prophylactic/chemoprotective medicines. An overall framework for these approaches is suggested here.
An examination of the steric effects of 5-tert-butylproline on the conformation of polyproline and the cooperative nature of type II to type I helical interconversion (2000)

The influence of steric effects on the helical geometry and the interconversion of type II to type I polyproline in water was examined by the synthesis and analysis of proline dimers and hexamers containing up to three (2S,5R)-5-tert-butylproline residues. In the dimers, the bulky 5-tert-butyl substituent was found to exert a significant influence on the local prolyl amide geometry such that the predominant trans-isomer in N-(acetyl)prolyl-prolinamide (1) was converted to 63% cis isomer in N-(acetyl)prolyl-5-tert-butylprolinamide (2) as measured by (1)H-nmr spectroscopy. Similarly, the presence of a 5-tert-butyl group on the C-terminal residue in the polyproline hexamer Ac-Pro(5)-t-BuPro-NH(2) (4) produced a local 5-tert-butylprolyl amide population containing 61% cis isomer in water. In spite of the presence of a local prolyl cis amide geometry, the downstream prolyl amides in 4 remained in the trans isomer as determined by NOESY spectroscopy. Conformational analysis by (13)C-nmr and CD spectroscopy indicated that Ac-Pro(6)-NH(2) (3) adopted the all-trans amide polyproline type II helix in water. As the amount of 5-tert-butylproline increased from one to three residues in hexamers 4-6, a gradual destabilization of the polyproline type II helical geometry was observed by CD spectroscopy in water; however, no spectrum was obtained, indicative of a complete conversion to a polyproline type I helix. The implications of these results are discussed with respect to the previously proposed theoretical mechanisms for the helical interconversion of polyproline, which has been suggested to occur by either a cooperative C- to N-terminal isomerization of the prolyl amide bonds or via a conformational intermediate composed of dispersed sequences of prolyl amide cis and trans isomers.
Unemployment, Labor Costs, and Recessions: Implications for the Inflation Outlook (2011)

Economists have been arguing about the connection between unemployment and inflation for decades. Critics claim that the connection is unreliable and leads policymakers astray, while others argue that the relationship is useful for forecasting. We examine the more direct connections between elevated unemployment levels and the rate of increase in wage and labor costs, more generally. We find that wage and labor cost growth has declined markedly following recent recessions. It has again declined sharply in the most recent recession. We also find that compensation typically remains subdued during the initial phases of recent recoveries. This is again the case in the current recovery, making labor costs a significant restraining force on inflation going forward.
Aggrecan core protein is expressed in membranous bone of the chick embryo. Molecular and biomechanical studies of normal and nanomelia embryos. (1992)

The recessive mutation nanomelia blocks the synthesis of a large aggregating proteoglycan (aggrecan) by avian embryo chondrocytes. Lack of aggrecan is associated with short stature, multiple morphological defects in cartilage, and embryo lethality. Bony defects have also been described, but were assumed to be a secondary consequence of the cartilage defect. However, two lines of evidence presented in this paper indicate that the aggrecan deficiency directly affects intramembranous bone. First, the morphology (i.e. projected area and shape) of certain membranous bones of nanomelia embryos was abnormal. Second, membranous bone from nanomelia embryos proved to be significantly stiffer in biomechanical tests that measured functional properties of the extracellular matrix. These findings were unexpected because intramembranous bones normally develop from mesenchyme and not from a cartilage intermediate, and they prompted a search for evidence of aggrecan expression in the bone of normal chick embryos. We report that: 1) aggrecan mRNA was identified by PCR analysis of total RNA isolated from day-13 chick embryo calvarium, 2) the PCR method successfully amplified aggrecan mRNA from primary chick embryo osteoblasts in culture, 3) in situ hybridization of membranous bone tissue sections demonstrated aggrecan expression by chick embryo osteoblasts in vivo, and 4) the aggrecan message was identified in Northern blots of calvarial mRNA probed at high stringency. The results of the molecular and biomechanical studies provide evidence that aggrecan is indeed expressed in membranous bone as well as cartilage. Altogether, these results suggest that aggrecan may contribute to the functional properties and the normal growth and development of avian membranous bone.
Characterization of the Sortase Repertoire in Bacillus anthracis (2011)

LPXTG proteins, present in most if not all Gram-positive bacteria, are known to be anchored by sortases to the bacterial peptidoglycan. More than one sortase gene is often encoded in a bacterial species, and each sortase is supposed to specifically anchor given LPXTG proteins, depending of the sequence of the C-terminal cell wall sorting signal (cwss), bearing an LPXTG motif or another recognition sequence. B. anthracis possesses three sortase genes. B. anthracis sortase deleted mutant strains are not affected in their virulence. To determine the sortase repertoires, we developed a genetic screen using the property of the gamma phage to lyse bacteria only when its receptor, GamR, an LPXTG protein, is exposed at the surface. We identified 10 proteins that contain a cell wall sorting signal and are covalently anchored to the peptidoglycan. Some chimeric proteins yielded phage lysis in all sortase mutant strains, suggesting that cwss proteins remained surface accessible in absence of their anchoring sortase, probably as a consequence of membrane localization of yet uncleaved precursor proteins. For definite assignment of the sortase repertoires, we consequently relied on a complementary test, using a biochemical approach, namely immunoblot experiments. The sortase anchoring nine of these proteins has thus been determined. The absence of virulence defect of the sortase mutants could be a consequence of the membrane localization of the cwss proteins.
Конкурентная динамика и бистабильность в двухкомпонентнойсинтетической генной сети (2014)

We suggest a scheme of a two-component synthetic gene network with competitive dynamics and study its model. The whole network comprises two parts which are separated between cell populations and mutually suppress each other''s activity. Bistability is shown to exist for a lumped model describing local dynamics. For a distributed model, which describes spatio-temporal dynamics of a mixture of both populations, we have shown the existence of either static fronts in the case of symmetry between the competiting parts or propagating fronts in the case of asymmetry.