gebhart/patrepeval huggingface dataset:
Molecular recognition in bone morphogenetic protein (BMP)/receptor interaction (2004)

Bone morphogenetic proteins (BMPs) and other members of the TGF-beta superfamily are secreted signalling proteins determining the development, maintenance and regeneration of tissues and organs. These dimeric proteins bind, via multiple epitopes, two types of signalling receptor chains and numerous extracellular modulator proteins that stringently control their activity. Crystal structures of free ligands and of complexes with type I and type II receptor extracellular domains and with the modulator protein Noggin reveal structural epitopes that determine the affinity and specificity of the interactions. Modelling of a ternary complex BMP/(BMPR-IA(EC))2 / (ActR-II(EC))2 suggests a mechanism of receptor activation that does not rely on direct contacts between extracellular domains of the receptors. Mutational and interaction analyses indicate that the large hydrophobic core of the interface of BMP-2 (wrist epitope) with the type I receptor does not provide a hydrophobic hot spot for binding. Instead, main chain amide and carbonyl groups that are completely buried in the contact region represent major binding determinants. The affinity between ligand and receptor chains is probably strongly increased by two-fold interactions of the dimeric ligand and receptor chains that exist as homodimers in the membrane (avidity effects). BMP muteins with disrupted epitopes for receptor chains or modulator proteins provide clues for drug design and development.
PPG signal reconstruction using a combination of discrete wavelet transform and empirical mode decomposition (2016)

Photoplethysmographic (PPG) signals, which are measured by pulse oximeter embedded in a form of wristband, are typically used for measuring heart rates. Such wearable sensors may be used for early detection of abnormal conditions for preventive actions in monitoring individual health. However, it is challenging to estimate heart rates using PPG signals with high accuracy due to the irregular motion artifacts, thus making the estimation of heart rate unreliable. In this paper, we proposed the use of Empirical Mode Decomposition (EMD) followed by Discrete Wavelet Transform (DWT) for noise reduction of the PPG signals. We calculated the heart beat rate per minute (BPM) from the reconstructed PPG signals and evaluated the performance of the proposed method in terms of Absolute Maximum Error (AME) and Mean Sum Error (MSE) with the provided ground-truth BPM computed from ECG signals. We have shown an improvement in the MSE values from 67% of the datasets used in this study. We also analyzed the relationship between the performances obtained based the level of movement intensity which are measured using the accelerometer.
Risk factors for drug-induced parkinsonism in tardive dyskinesia patients. (1988)

Using multivariate statistical analyses, the authors identified risk factors for development of drug-induced parkinsonism (DIP) in 66 tardive dyskinesia (TD) patients. Older age, recent use of neuroleptics, shorter duration of past neuroleptic exposure, and severity of TD were associated with increased risk of DIP. The clinician should devise treatment strategies in anticipation of the occurrence of DIP regardless of the presence or absence of TD, especially in older patients. New models for the pathophysiology of the two disorders are needed.
EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer (2015)

These data show that EpHA2 is a poor prognostic marker in stage II/III colorectal cancer, which may be due to its ability to promote cell migration and invasion, providing support for the further investigation of EphA2 as a novel prognostic biomarker and therapeutic target.
Tunable singlemode fibre depolariser (1997)

A new fibre tunable depolariser was developed which can be used with conventional laser diodes. Design criteria and principles are discussed. Experimentally, the degree of polarisation was tuned between 99.8 and 1.15%. The authors show how the depolariser can eliminate the effects of polarisation fluctuation in a polarisation-sensitive fibre system.
Sensing With Slow Light in Fiber Bragg Gratings (2011)

On the edge of the bandgap in a fiber Bragg grating (FBG) narrow peaks of high transmission exist at frequencies where light interferes constructively in the forward direction. In the vicinity of these transmission peaks, light reflects back and forth numerous times across the periodic structure and experiences a large group delay. Since the sensitivity of a phase sensor to most external perturbations is proportional to the reciprocal of group velocity, in these slow-light regions the sensitivity of an FBG is expected to be significantly enhanced over traditional FBG sensors operated around the Bragg wavelength. In this paper, we describe means of producing and operating FBGs that support structural slow light with a group index that can be in principle as high as several thousand. We present simulations elucidating how to select the FBG parameters, in particular index modulation, length, and apodization, to generate such low group velocities, and quantify the very large improvement in strain and temperature sensitivities resulting from these new slow-light configurations. As a proof of concept, we report an FBG with a group index of 127, or a group velocity of ~2,360 km/s. This is by far the lowest group velocity reported to date in an FBG. Used as a strain sensor, this slow-light FBG is shown to be able to detect a strain as small as 880 fε/ √Hz , the lowest value reported for a passive FBG sensor.
Effects of AuNPs@PEG-AS1411 nanoparticles on radiosensitization of HeLa cancer cells (2015)

Objective
To study the effects of AuNPs@PEG-AS1411 nanoparticles on radiosensitization of human uterine cervix cancer HeLa cells.


Methods
AuNPs were synthesized by citrate reduction method and then functioned with PEG and PEG-AS1411, respectively. CCK-8 assay and colon forming assay were used to detect the acute and chronic toxicity effects of AuNPs on HeLa cells, respectively. At the same time, clonogenic survival assay was applied to measure the cell survival rate of HeLa cells after exposure to AuNPs@PEG and AuNPs@PEG-AS1411 combined with X-ray radiation. The intracellular uptake of AuNPs@PEG and AuNPs@PEG-AS1411 in HeLa cells were detected by ICP-MS.


Results
The CCK-8 assay showed that AuNPs@PEG and AuNPs@PEG-AS1411 were not toxical on HeLa cells(P>0.05). But the clonogenic survival assay showed that AuNPs@PEG and AuNPs@PEG-AS1411 had toxicity on HeLa cells significantly after 10 d(t=4.38-11.60, P<0.05). AuNPs functioned with AS1411 could increase the cellular uptake of AuNPs. AuNPs@PEG and AuNPs@PEG-AS1411 both had significant radiosensitive effect on HeLa cells (F=7.90, 48.23, P<0.05). The values of SERDo for AuNPs@PEG and AuNPs@PEG-AS1411 were 1.12 and 1.20, respectively, when the concentration of Au was 10 mg/L.


Conclusions
AuNPs@PEG and AuNPs@PEG-AS1411 could cause chronic toxicity on HeLa cells instead of acute effect. PEGylated AuNPs functioned with AS1411 could enhance the radiosensitivity of HeLa cells in vitro.


Key words: 
AS1411; Au nanoparticles; Radiosensitization
Role of pH in production of hydrogen from carbohydrates by colonic bacterial flora. Studies in vivo and in vitro. (1981)

Hydrogen produced by colonic bacteria and excreted in breath is a useful index of carbohydrate malabsorption. Since colonic contents are often acidic in individuals with carbohydrate malabsorption and in normal newborns, we determined the effect of colonic acidification on H2 production. Acidification of colonic contents by dietary means significantly reduced excess breath H2 excretion from 55.4 +/- 11.1 (SEM) to 12.2 +/- 3.1 ml/4 h (P less than 0.05) after administration of 0.3 g/kg of the nonabsorbable sugar lactulose to five normal adult subjects. Similarly, the breath H2 response to lactose was reduced or eliminated in two proven lactose malabsorbers after acidification. The correlation between pH and H2 production from carbohydrate was further investigated in adults and neonates, using an in vitro fecal incubation system. Glucose disappearance and H2 production were pH dependent and highly correlated (r = 0.94) in the pH range 5.5-7.6. Maximal production of H2 from glucose by fecal incubates occurred at pH 7.0-7.45. Inhibition of H2 production from carbohydrate occurred at acid pH. H2 per hour from glucose at pH 6.2 and 5.5 averaged 60.2% and 24.2%, respectively, of that produced at neutral pH. Rapid reversal of pH-induced inhibition by neutralization indicated a metabolic, rather than a bactericidal process. The observations indicate that the breath H2 response to malabsorbed carbohydrate is affected by colonic pH. It appears that the efficiency of bacterial carbohydrate metabolism in the colon is pH dependent.
TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects (1995)

A new approach to assembling large, random shotgun sequencing projects has been developed. The TIGR Assembler overcomes several major obstacles to assembling such projects: the large number of pairwise comparisons required, the presence of repeat regions, chimeras introduced in the cloning process, and sequencing errors. A fast initial comparison of fragments based on oligonucleotide content is used to eliminate the need for a more sensitive comparison between most fragment pairs, thus greatly reducing computer search time. Potential repeat regions are recognized by determining which fragments have more potential overlaps than expected given a random distribution of fragments. Repeat regions are dealt with by increasing the match criteria stringency and by assembling these regions last so that maximum information from nonrepeat regions can be used. The algorithm also incorporates a number of constraints, such as clone length and the placement of sequences from the opposite ends of a clone. TIGR Assembler has been used to assemble the complete 1.8 Mbp Haemophilus influenzae (Fleischmann et al., 1995) and 0.58 Mbp Mycoplasma genitalium (Fraser et al., 1995) genomes.
CXXIII.—The intermolecular condensation of acetyl-methylanthranilic acid by means of phosphorus pentachloride and the formation of a complex isocyanine dye (1928)

I. M. Heilbron, S. L. Holt and F. N. Kitchen, J. Chem. Soc., 1928, 934 DOI: 10.1039/JR9280000934
Molecular Cloning and Expression of Two Types of Rabbit β-Galactoside α1,2-Fucosyltransferase (1995)

Two DNA clones encoding rabbit beta-galactoside alpha 1,2-fucosyltransferase (RFT-I and RFT-II) have been isolated from a rabbit genomic DNA library. The DNA sequences revealed open reading frames coding for 373 (RFT-I) and 354 (RFT-II) amino acids, respectively. The deduced amino acid sequences of RFT-I and RFT-II showed 56% identity with each other, and that of RFT-I showed 80% identity with that of human H blood type alpha 1,2-fucosyltransferase. Northern blot analysis of embryo and adult rabbit tissues revealed that the RFT-I gene was expressed in adult brain, and that the RFT-II gene was expressed in salivary and lactating mammary glands. The identities of these enzymes were confirmed by constructing recombinant fucosyltransferases in which the N-terminal part including the cytoplasmic tail and signal anchor domain was replaced with the immunoglobulin signal peptide sequence. RFT-I expressed in COS-7 cells exhibited similar transferase activity to that of human H blood type alpha 1,2-fucosyltransferase. RFT-II expressed in COS-7 cells showed higher affinity for type 1 (Gal beta 1,3GlcNAc) and type 3 (Gal beta 1,3GalNAc) acceptors than type 2 (Gal beta 1,4GlcNAc) ones, which suggested that RFT-II was a putative secretor-type alpha 1,2-fucosyltransferase.
Review of AVLIS technology for production-scale LIS systems and construction (1983)

The use of lasers for uranium and/or plutonium isotope separation is expected to be the first application of lasers utilizing specific atomic processes for large-scale materials processing. Specific accomplishments toward the development of production-scale technology for LIS systems will be presented, along with the status of major construction projects. 24 figures.
Improved Lossy Image Compression with Priming and Spatially Adaptive Bit Rates for Recurrent Networks (2018)

We propose a method for lossy image compression based on recurrent, convolutional neural networks that outperforms BPG (4:2:0), WebP, JPEG2000, and JPEG as measured by MS-SSIM. We introduce three improvements over previous research that lead to this state-of-the-art result using a single model. First, we modify the recurrent architecture to improve spatial diffusion, which allows the network to more effectively capture and propagate image information through the network's hidden state. Second, in addition to lossless entropy coding, we use a spatially adaptive bit allocation algorithm to more efficiently use the limited number of bits to encode visually complex image regions. Finally, we show that training with a pixel-wise loss weighted by SSIM increases reconstruction quality according to multiple metrics. We evaluate our method on the Kodak and Tecnick image sets and compare against standard codecs as well as recently published methods based on deep neural networks.
Tumor Necrosis Factor (TNF) and Phorbol Ester Induce TNF-related Apoptosis-inducing Ligand (TRAIL) under Critical Involvement of NF-κB Essential Modulator (NEMO)/IKKγ (2001)

We show that tumor necrosis factor (TNF) and phorbol 12-myristate 13-acetate (PMA) induce TNF-related apoptosis-inducing ligand (TRAIL) in T cells. In cells deficient for NF-kappaB essential modulator (NEMO)/IKKgamma, an essential component of the NF-kappaB-inducing I-kappaB kinase (IKK) complex, induction of TRAIL expression was completely abrogated but was recovered in cells restored for IKKgamma expression. In cells deficient for receptor-interacting protein expression TNF, but not PMA-induced TRAIL expression was blocked. Inhibition of protein synthesis with cycloheximide blocked PMA, but not TNF-induced up-regulation of TRAIL. As both TNF and PMA rapidly induce NF-kappaB activation this suggests that NEMO/IKKgamma-dependent activation of the NF-kappaB pathway is necessary but not sufficient for up-regulation of TRAIL in T cells. The capability of the NF-kappaB pathway to induce the potent death ligand TRAIL may explain the reported proapoptotic features of this typically antiapoptotic pathway.
Characterization and Cloning of a Receptor for BMP-2 and BMP-4 from NIH 3T3 Cells (1994)

The bone morphogenetic proteins (BMPs) are a group of transforming growth factor beta (TGF-beta)-related factors whose only receptor identified to date is the product of the daf-4 gene from Caenorhabditis elegans. Mouse embryonic NIH 3T3 fibroblasts display high-affinity 125I-BMP-4 binding sites. Binding assays are not possible with the isoform 125I-BMP-2 unless the positively charged N-terminal sequence is removed to create a modified BMP-2, 125I-DR-BMP-2. Cross-competition experiments reveal that BMP-2 and BMP-4 interact with the same binding sites. Affinity cross-linking assays show that both BMPs interact with cell surface proteins corresponding in size to the type I (57- to 62-kDa) and type II (75- to 82-kDa) receptor components for TGF-beta and activin. Using a PCR approach, we have cloned a cDNA from NIH 3T3 cells which encodes a novel member of the transmembrane serine/threonine kinase family most closely resembling the cloned type I receptors for TGF-beta and activin. Transient expression of this receptor in COS-7 cells leads to an increase in specific 125I-BMP-4 binding and the appearance of a major affinity-labeled product of approximately 64 kDa that can be labeled by either tracer. This receptor has been named BRK-1 in recognition of its ability to bind BMP-2 and BMP-4 and its receptor kinase structure. Although BRK-1 does not require cotransfection of a type II receptor in order to bind ligand in COS cells, complex formation between BRK-1 and the BMP type II receptor DAF-4 can be demonstrated when the two receptors are coexpressed, affinity labeled, and immunoprecipitated with antibodies to either receptor subunit. We conclude that BRK-1 is a putative BMP type I receptor capable of interacting with a known type II receptor for BMPs.
Light Emission by Nonequilibrium Bodies: Local Kirchhoff Law (2018)

The goal of this paper is to introduce a local form of Kirchhoff law to model light emission by nonequilibrium bodies. While absorption by a finite-size body is usually described using the absorption cross section, we introduce a local absorption rate per unit volume and also a local thermal emission rate per unit volume. Their equality is a local form of Kirchhoff law. We revisit the derivation of this equality and extend it to situations with subsystems in local thermodynamic equilibrium but not in equilibrium between them, such as hot electrons in a metal or electrons with different Fermi levels in the conduction band and in the valence band of a semiconductor. This form of Kirchhoff law can be used to model (i) thermal emission by nonisothermal finite-size bodies, (ii) thermal emission by bodies with carriers at different temperatures, and (iii) spontaneous emission by semiconductors under optical (photoluminescence) or electrical pumping (electroluminescence). Finally, we show that the reciprocity relation connecting light-emitting diodes and photovoltaic cells derived by Rau is a particular case of the local Kirchhoff law.
Genetic Evaluation of Somatic Cell Scores for United States Dairy Cattle (1994)

Increases in milk yield from genetic selection may be accompanied by correlated increases in genetic susceptibility to clinical mastitis and somatic cells. Unlike clinical mastitis, somatic cell scores can be easily determined and recorded and are related to milk loss from subclinical mastitis. Selection against high somatic cell scores should decrease incidence of clinical mastitis and provide direct economic benefits through higher milk quality premiums. Genetic evaluation for lactation means of linear somatic cell scores has been implemented by USDA and parallels that for yield traits. Because additive genetics accounts for only about 10% of differences in somatic cell scores among cows, more information is needed for the same degree of confidence in genetic estimates as for yield. Only 80% of DHIA cows currently have somatic cell records. Thus, reliabilities of somatic cell evaluations are smaller than those for yield traits. Most progress in selection for lower somatic cell scores will come through sires of cows considered as bull dams. Somatic cell evaluations may best be reported through an economic index with a small amount of emphasis on somatic cell score relative to yield traits. Greater emphasis on somatic cell scores would decrease genetic gain in yield traits, which are economically more important.
Semi-nested, multiplex polymerase chain reaction for detection of human malaria parasites and evidence of Plasmodium vivax infection in Equatorial Guinea. (1999)

A semi-nested, multiplex polymerase chain reaction (PCR) based on the amplification of the sequences of the 18S small subunit ribosomal RNA (ssrRNA) gene was tested in a field trial in Equatorial Guinea (a hyperendemic focus of malaria in west central Africa). The method uses a primary PCR amplification reaction with a universal reverse primer and two forward primers specific for the genus Plasmodium and to mammals (the mammalian-specific primer was included as a positive control to distinguish uninfected cases from inhibition of the PCR). The second amplification is carried out with the same Plasmodium genus-specific forward primer and four specific reverse primers for each human Plasmodium species. The PCR amplified products are differentiated by fragment size after electrophoresis on a 2% agarose gel. Four villages from three regions of the island of Bioko (Equatorial Guinea) and two suspected Plasmodium vivax-P. ovale infections from the hospital of Malabo were tested by microscopy and PCR. The PCR method showed greater sensitivity and specificity than microscopic examination and confirmed the existence of a focus of P. vivax infections in Equatorial Guinea suspected by microscopic examination. It also provided evidence of several mixed infections, mainly P. falciparum and P. malariae, the two predominant species causing malaria in Equatorial Guinea.
High‐yield enzymatic glycerolysis of fats and oils (1991)

Several triglyceride fats and oils were reacted with glycerol using lipase as catalyst. A batch system with magnetic stirring was used without the addition of any solvents or emulsifiers. In all cases a mixture of mono‐, di‐ and triglycerides was obtained. However, the yield of monglyceride (MG) depended strongly on the reaction temperature: at higher temperatures approximately 30% MG was produced at equilibrium while at lower temperatures a yield of 65%–90% MG was obtained for most of the fats examined. The upper temperature limit below which a high MG yield could be attained was designated the critical temperature (T c ). The value of T c depended on the fat type and was found to vary between 30°C and 46°C for naturally occurring hard fats. A high MG yield could not be obtained for fully hydrogenated tallow and lard under the conditions described here. Of the three liquid oils examined, rapeseed oil and olive oil had a T c of 5°C and 10°C respectively whereas a high yield of MG could not be obtained with corn oil at 5°C or greater. The maximum yield of MG below T c also depended on the fat type: the highest yields being obtained for olive oil (90%), palm stearin and milk fat (80%) and the lowest yield for palm oil (67%). In all cases a high yield of MG was accompanied by solidification of the reaction mixture. The effect of enzyme type on MG production was examined for palm oil and palm stearin and the effect of water concentration was examined for palm oil.
De novo synthesis and photophysical characterization of annulated bacteriochlorins. Mimicking and extending the properties of bacteriochlorophylls (2011)

Bacteriochlorophylls contain the bacteriochlorin chromophore and a fifth, five-membered oxopentano ring that encompasses positions 13–15 known as the “isocyclic” ring E. Such bacterio-131-oxophorbines have heretofore only been available in the naturally occurring compounds, and analogues bearing six-membered rings have only been available by derivatization of bacteriochlorophylls. A de novo route to synthetic bacteriochlorins, which bear a geminal dimethyl group in each pyrroline ring, has been extended to gain access to a bacterio-131-oxophorbine and bacteriochlorin-13,15-dicarboximides. The route relies on acid-catalyzed condensation of a dihydrodipyrrin-acetal to form the bacteriochlorin, which then is subjected to regioselective 15-bromination. Pd-mediated cyclization of the 15-bromobacteriochlorin bearing a 13-acetyl group (intramolecular α-arylation) or 13-ethoxycarbonyl group (carbamoylation and intramolecular imidation) gives the bacterio-131-oxophorbine or bacteriochlorin-13,15-dicarboximide, respectively. The resulting macrocycles exhibit absorption in the near-infrared spectral region (733–818 nm), which extends the spectral coverage beyond that obtained previously with synthetic bacteriochlorins that lack a fifth ring. The macrocycles also exhibit excited singlet-state lifetimes (1.9–4.6 ns) comparable to or longer than those of natural photosynthetic pigments. Density functional theory calculations predict that the bathochromically shifted absorption is primarily due to lowering of the energy of the lowest unoccupied molecular orbital. The new route complements existing semisynthetic routes and should enable fundamental spectroscopic studies and diverse photochemical applications.