gebhart/patrepeval huggingface dataset:
A prokaryotic acyl-CoA reductase performing reduction of fatty acyl-CoA to fatty alcohol (2011)

The reduction of acyl-CoA or acyl-ACP to fatty alcohol occurs via a fatty aldehyde intermediate. In prokaryotes this reaction is thought to be performed by separate enzymes for each reduction step while in eukaryotes these reactions are performed by a single enzyme without the release of the intermediate fatty aldehyde. However, here we report that a purified fatty acyl reductase from Marinobacter aquaeolei VT8, evolutionarily related to the fatty acyl reductases in eukaryotes, catalysed both reduction steps. Thus, there are at least two pathways existing among prokaryotes for the reduction of activated acyl substrates to fatty alcohol. The Marinobacter fatty acyl reductase studied has a wide substrate range in comparison to what can be found among enzymes so far studied in eukaryotes.
Building Footprint Extraction From VHR Remote Sensing Images Combined With Normalized DSMs Using Fused Fully Convolutional Networks (2018)

Automatic building extraction and delineation from high-resolution satellite imagery is an important but very challenging task, due to the extremely large diversity of building appearances. Nowadays, it is possible to use multiple high-resolution remote sensing data sources, which allow the integration of different information in order to improve the extraction accuracy of building outlines. Many algorithms are built on spectral-based or appearance-based criteria, from single or fused data sources, to perform the building footprint extraction. But the features for these algorithms are usually manually extracted, which limits their accuracy. Recently developed fully convolutional networks (FCNs), which are similar to normal convolutional neural networks (CNN), but the last fully connected layer is replaced by another convolution layer with a large “receptive field,” quickly became the state-of-the-art method for image recognition tasks, as they bring the possibility to perform dense pixelwise classification of input images. Based on these advantages, i.e., the automatic extraction of relevant features, and dense classification of images, we propose an end-to-end FCN, which effectively combines the spectral and height information from different data sources and automatically generates a full resolution binary building mask. Our architecture (Fused-FCN4s) consists of three parallel networks merged at a late stage, which helps propagating fine detailed information from earlier layers to higher levels, in order to produce an output with more accurate building outlines. The inputs to the proposed Fused-FCN4s are three-band (RGB) , panchromatic (PAN), and normalized digital surface model (nDSM) images. Experimental results demonstrate that the fusion of several networks is able to achieve excellent results on complex data. Moreover, the developed model was successfully applied to different cities to show its generalization capacity.
Apoptosis in Ischemic and Reperfused Rat Myocardium (1996)

Apoptosis has been observed previously in hearts subjected to either continuous ischemia or ischemia followed by reperfusion. The purpose of this study was to compare the timing and extent of apoptosis in both continuously ischemic and reperfused myocardium. We show that rats subjected to continuous coronary artery occlusion display characteristic signs of apoptosis solely in the ischemic myocardium after only 2.25 hours of ischemia, as illustrated by positive in situ end labeling (ISEL) of apoptotic cardiomyocyte nuclei in tissue sections and/or the presence of DNA "ladders" in agarose gels. In contrast, reperfusion after a 45-minute occlusion accelerated the process, with apoptosis becoming evident solely in the reperfused myocardium after only 1 hour of reperfusion. ISEL and DNA ladder intensity increased with duration of ischemia or reperfusion. The volume of myocardium in which ISEL was observed was smaller in the reperfused hearts, and the ISEL-stained nuclei represented 23% and 33% of the total nuclei in the reperfused and permanently occluded myocardium, respectively. Therefore, the data suggest that reperfusion lowers the extent of apoptosis in ischemic myocardium but, paradoxically, accelerates the residual apoptosis, possibly because of reperfusion injury. A large accumulation of neutrophils was observed in both the permanently occluded and reperfused myocardium, suggesting that the inflammatory response may have contributed to apoptosis in both settings. This study therefore confirms that both ischemic and reperfused rat myocardium can undergo apoptotic cell death. However, the data suggest that although reperfusion lowers the number of myocytes undergoing apoptosis, it accelerates apoptosis in the nonsalvageable cells.
Adaptive input-power processing for mitigation of PAPR in OFDM (2005)

The high peak-to-average-power ratio (PAPR) in orthogonal frequency division multiplexing (OFDM) greatly limits the high power amplifier (HPA) power efficiency. Different from other approaches to PAPR mitigation, the approach in this paper presents a simple new scheme which employs adaptive input power processing to reduce the instantaneous power fluctuation of OFDM signals. Specifically, at the transmitter side, the segments of the OFDM signal with high power are pushed down and the ones with low power are pulled up by adaptive adjustment of input power. As a consequence, the PAPR is greatly mitigated. These results are confirmed by computer simulations.
N-acetyl-seryl-aspartyl-lysyl-proline prevents cardiac remodeling and dysfunction induced by galectin-3, a mammalian adhesion/growth-regulatory lectin (2008)

Galectin-3 (Gal-3) is secreted by activated macrophages. In hypertension, Gal-3 is a marker for hypertrophic hearts prone to develop heart failure. Gal-3 infused in pericardial sac leads to cardiac inflammation, remodeling, and dysfunction. N-acetyl-seryl-aspartyl-lysyl-proline (Ac-SDKP), a naturally occurring tetrapeptide, prevents and reverses inflammation and collagen deposition in the heart in hypertension and heart failure postmyocardial infarction. In the present study, we hypothesize that Ac-SDKP prevents Gal-3-induced cardiac inflammation, remodeling, and dysfunction, and these effects are mediated by the transforming growth factor (TGF)-beta/Smad3 signaling pathway. Adult male rats were divided into four groups and received the following intrapericardial infusion for 4 wk: 1) vehicle (saline, n = 8); 2) Ac-SDKP (800 microg x kg(-1) x day(-1), n = 8); 3) Gal-3 (12 microg/day, n = 7); and 4) Ac-SDKP + Gal-3 (n = 7). Left ventricular ejection fraction, cardiac output, and transmitral velocity were measured by echocardiography; inflammatory cell infiltration, cardiomyocyte hypertrophy, and collagen deposition in the heart by histological and immunohistochemical staining; and TGF-beta expression and Smad3 phosphorylation by Western blot. We found that, in the left ventricle, Gal-3 1) enhanced macrophage and mast cell infiltration, increased cardiac interstitial and perivascular fibrosis, and causes cardiac hypertrophy; 2) increased TGF-beta expression and Smad3 phosphorylation; and 3) decreased negative change in pressure over time response to isoproterenol challenge, ratio of early left ventricular filling phase to atrial contraction phase, and left ventricular ejection fraction. Ac-SDKP partially or completely prevented these effects. We conclude that Ac-SDKP prevents Gal-3-induced cardiac inflammation, fibrosis, hypertrophy, and dysfunction, possibly via inhibition of the TGF-beta/Smad3 signaling pathway.
THE KAOLIN MINERALS 1 (1930)

ABSTRACT A report of an investigation of the clay minerals, nacrite, diekite, and kaolinite is presented in which the methods of study are explained. The optical and physical properties, chemical composition, and X‐ray studies of these kaolin minerals are discussed and the results of the study are outlined.
Phylogenetic basis for a taxonomic dissection of the genusClostridium (1999)

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.
Measuring Method of Three Thermophysical Parameters of Solids by a Thermal Probe with Instantaneous Point Contact. (Discussion about Applicability and Measuring Conditions). (1999)

点接触式温度ブローブによる固体熱3定数測定法は手軽な装置で現場測定が容易であることから、いわゆる熱物性テスターとも言える簡便法である。前報ではその測定原理を示したが、続報として、ここでは本計測法が適用できる被測定物の形状や大きさについて調べ、その場合に必要な測定条件を検討する。また、温度ブローブと被測定物との接触面積による非定常温度応答への影響を明らかにすることによって、本測定法において熱3定数の算定が接触面積によって左右されないことを示す。
Synthesis, Biological Evaluation, and Live Cell Imaging of Novel Fluorescent Duocarmycin Analogs (2012)

For a better understanding of the mode of action of duocarmycin and its analogs, the novel fluorescent duocarmycin derivatives 13-15 and 17b-19b were synthesized, and their bioactivity as well as their cellular uptake investigated using confocal laser scanning microscopy (CLSM) in live-cell imaging experiments.
Prevention of vasospasm by anti-CD11/CD18 monoclonal antibody therapy following subarachnoid hemorrhage in rabbits (2004)

This study supports the concept that leukocyte-endothelial cell interactions play an important role in the pathophysiology of chronic vasospasm after SAH. Systemic therapy with an anti-CD11/CD18 mAb prevents vasospasm after SAH by inhibiting adhesion of neutrophils and macrophages and their migration into the periadventitial space.
Derivatives of indole‐3‐oxyacetic acid (1979)

Abstract The synthesis of 1‐benzyl‐2‐methyl‐5‐methoxyindole‐3‐oxyacetic acid ( 11 ) and of 1‐benzyl‐2‐methylindole‐3‐oxyacetic acid ( 17 ) was undertaken in the course of a study aimed at the preparation of potential anti‐inflammatory agents.
New aspects of glycoside bond formation (1999)

Glycoside bond formation generally requires activation of the sugar at the anomeric center. To this end, anomeric oxygen exchange reactions, resulting in the Koenigs-Knorr method and variations or, alternatively, activation through retention of the anomeric oxygen, resulting in the trichloroacetimidate method and in the phosphite method, have been proposed. The successful application of the trichloroacetimidate method to the total synthesis of GPI anchors is particularly worth mentioning. a(2-3)-Sialylation can be based on sialyl phosphites as glycosyl donors and on the nitrile effect for anomeric stereocontrol. This is exhibited for a preparative synthesis of ganglioside GM2 which is required for tumor vaccine studies. For the generation of a(2-8)-linkage between neuraminic acid residues anchimeric assistance by a 3-thiocarbonyloxy group is introduced. The required sialyl donor can be efficiently prepared and a-linkage to 8-O-unprotected neuraminic acid derivatives is almost quantitative. The limitations of chemical glycopeptide synthesis encourage to employ the protein biosynthesis machinery in combination with an expanded genetic code. This is exhibited for the synthesis of glycosylated hARF-1 protein.
Glutamine and the regulation of intestinal permeability (2016)

Glutamine is a major nutrient to maintain intestinal barrier function in animals and humans. Depletion of glutamine results in villus atrophy, decreased expression of tight junction proteins and increased intestinal permeability. Moreover, glutamine supplementation can improve gut barrier function in several experimental conditions of injury and in some clinical situations. Furthermore, preventive effects of glutamine in experimental models of intestinal injuries have been recently reported. Despite promising data in experimental models, further studies are needed to evaluate glutamine supplementation in clinical practice.
Isolation, incubation, and parallel functional testing and identification by FISH of rare microbial single-copy cells from multi-species mixtures using the combination of chemistrode and stochastic confinement (2009)

This paper illustrates a plug-based microfluidic approach combining the technique of the chemistrode and the principle of stochastic confinement, which can be used to i) starting from a mixture of cells, stochastically isolate single cells into plugs, ii) incubate the plugs to grow clones of the individual cells without competition among different clones, iii) split the plugs into arrays of identical daughter plugs, where each plug contained clones of the original cell, and iv) analyze each array by an independent technique, including cellulase assays, cultivation, cryo-preservation, Gram staining, and Fluorescence In Situ Hybridization (FISH). Functionally, this approach is equivalent to simultaneously assaying the clonal daughter cells by multiple killing and non-killing methods. A new protocol for single-cell FISH, a killing method, was developed to identify isolated cells of Paenibacillus curdlanolyticus in one array of daughter plugs using a 16S rRNA probe, Pc196. At the same time, live copies of P. curdlanolyticus in another array were obtained for cultivation. Among technical advances, this paper reports a chemistrode that enables sampling of nanoliter volumes directly from environmental specimens, such as soil slurries. In addition, a method for analyzing plugs is described: an array of droplets is deposited on the surface, and individual plugs are injected into the droplets of the surface array to induce a reaction and enable microscopy without distortions associated with curvature of plugs. The overall approach is attractive for identifying rare, slow growing microorganisms and would complement current methods to cultivate unculturable microbes from environmental samples.
Transcriptome Analysis of K-877 (a Novel Selective PPARα Modulator (SPPARMα))-Regulated Genes in Primary Human Hepatocytes and the Mouse Liver (2015)

These results indicate that changes in the gene expression induced by K-877 treatment are mainly mediated through PPARα activation. K-877 regulates the hepatic gene expression as a SPPARMα and thus may improve dyslipidemia as well as metabolic disorders, such as metabolic syndrome and type 2 diabetes, without untoward side effects.
High-speed Internet access via HVAC ducts: a new approach (2002)

We report a novel technique for inexpensive high-speed Internet access in buildings. Our work shows that, one can use heating, ventilation, and air conditioning (HVAC) ducts for indoor wireless transmission systems and networks. Measurements and system calculations show that coverage distances in excess of 100 meters from the base station and data rates of up to 100 Mbps should be possible, when HVAC system is used in conjunction with OFDM technology.
Multiple mutagenesis of non-universal serine codons of the Candida rugosa LIP2 gene and biochemical characterization of purified recombinant LIP2 lipase overexpressed in Pichia pastoris (2002)

The 17 non-universal serine codons (CTG) in the Candida rugosa LIP2 gene have been converted into universal serine codons (TCT) by overlap extension PCR-based multiple site-directed mutagenesis. An active recombinant LIP2 lipase was overexpressed in Pichia pastoris and secreted into the culture medium. The recombinant LIP2 showed distinguishing catalytic activities when compared with recombinant LIP4 and commercial C. rugosa lipase. The purified enzyme showed optimum activity at pH 7 and a broad temperature optimum in the range 30-50 degrees C. The enzyme retained 80% of residual activity after being heated at 70 degrees C for 10 min. Recombinant LIP2 demonstrated high esterase activity towards long-chain (C12-C16) p-nitrophenyl esters. Tributyrin was the preferred substrate among all triacylglycerols tested for lipolysis. Among cholesteryl esters, LIP2 showed highest lipolytic activity towards cholesteryl laurate. The esterification of myristic acid with alcohols of various chain lengths showed that the long-chain n-octadecanol (C18) was the preferred substrate. In contrast, the esterification of n-propanol with fatty acids of various chain lengths showed that the short-chain butyric acid was the best substrate. From comparative modelling analysis, it appears that several amino acid substitutions resulting in greater hydrophobicity in the substrate-binding site might play an important role in the substrate specificity of LIP2.
Complex biosynthesis of the muscle-enriched iron regulator RGMc (2006)

The recently discovered repulsive guidance molecule c (RGMc or hemojuvelin) gene encodes a putative glycosylphosphatidylinositol (GPI)-anchored protein that is expressed in striated muscle and in liver. Mutations in this gene have been linked to the severe iron storage disease, juvenile hemochromatosis, although the mechanisms of action of RGMc in iron metabolism are unknown. As a first step toward understanding the molecular physiology of this protein, we studied its biosynthesis, processing and maturation. Production of RGMc occurs as an early and sustained event during skeletal muscle differentiation in culture and is secondary to RGMc gene activation. As assessed by pulse-chase studies and cell-surface labeling experiments, two classes of GPI-anchored and glycosylated RGMc molecules are targeted to the membrane and undergo distinct fates. Full-length RGMc is released from the cell surface and accumulates in extracellular fluid, where its half-life exceeds 24 hours. By contrast, the predominant membrane-associated isoform, a disulfide-linked heterodimer composed of N- and C-terminal fragments, is not found in the extracellular fluid, and is short-lived, as it disappears from the cell surface with a half-life of <3 hours after interruption of protein synthesis. A natural disease-associated RGMc mutant, with valine substituted for glycine at residue 320 (313 in mouse RGMc), does not undergo processing to generate the heterodimeric membrane-linked isoform of RGMc, and is found on the cell surface only as larger protein species. Our results define a series of biosynthetic steps leading to the normal production of different RGMc isoforms in cells, and provide a framework for understanding the biochemical basis of defects in the maturation of RGMc in juvenile hemochromatosis.
Profile-directed restructuring of operating system code (1998)

In this paper we describe how a profiling system can be successfully used to restructure the components of an operating system for improved overall performance. We discuss our choice of a profiling system and how it was applied to the AS/400® (Application System/400®) operating system for the purpose of reordering code. Previous work in the industry has been mainly useful only for application programs. Our work demonstrates how such techniques can be applied to operating system code, while preserving maintainability of the operating system in the customer's environment.
Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. (1990)

The Klenow fragment structure, together with many biochemical experiments, has suggested a region of the protein that may contain the polymerase active site. We have changed 7 amino acid residues within this region by site-directed mutagenesis, yielding 12 mutant proteins which have been purified and analyzed in vitro. The results of steady-state kinetic determinations of Km(dNTP) and kcat for the polymerase reaction, together with measurements of DNA binding affinity, suggest strongly that this study has succeeded in targeting important active site residues. Moreover, the in vitro data allow dissection of the proposed active site region into two clusters of residues that are spatially, as well as functionally, fairly distinct. Mutations in Tyr766, Arg841, and Asn845 cause an increase in Km(dNTP), suggesting that contacts with the incoming dNTP are made in this region. Mutations in the second cluster of residues, Gln849, Arg668, and Asp882, cause a large decrease in kcat, suggesting a role for these residues in catalysis of the polymerase reaction. The DNA-binding properties of mutations at positions 849 and 668 may indicate that the catalytic role of these side chains is associated with their interaction with the DNA substrate. Screening of the mutations in vivo for the classical polA-defective phenotype (sensitivity to DNA damage) demonstrated that a genetic screen of this type may be a reasonable predictor or kcat or of DNA binding affinity in future mutational studies.
Translating the Histone Code (2001)

Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a "histone code" that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.