gebhart/patrepeval huggingface dataset:
Studies on production of single cell protein by Aspergillus niger in solid state fermentation of rice bran (2001)

An attempt was made to apply the solid state fermentation (SSF) for the production of single cell protein (SCP) using oil free rice bran waste as substrate. A local isolate of Aspergillus niger, was used as protein source for the studies. Total proteins were extracted to estimate the mycelial biomass from the moldy bran. Carbonate-bicarbonate extraction buffer and a pH 10 was found to be most efficient among the buffers used for the extraction of the proteins from the organism. The effect of supplementation by various sources of nitrogen and mineral solution on the final biomass yield was compared. The influence of C/N ratio on the protein yield was also studied. Sodium nitrate at C/N ratio of 1.387 was found to be an effective nitrogen-supplementing source, as it gave the higher biomass yield.
Chemical Vapor Deposition (CVD) of Manganese Self-Aligned Diffusion Barriers for Cu Interconnections in Microelectronics (2009)

Barriers to prevent diffusion of copper, oxygen and water vapor were formed by CVD using a manganese precursor vapor that reacts with silica surfaces. The manganese metal penetrates only a few nanometers into the silica to make conformal amorphous manganese silicate layers. This MnSixOy was found to be an excellent barrier to the diffusion of Cu, O2 and H2O vapor. The adhesion strength of Cu to the MnSixOy was found to be sufficiently strong to satisfy the semiconductor industry requirements for interconnections in future microelectronic devices. CVD Mn dissolves into copper surfaces and then diffuses to increase adhesion to SiCNO capping layers.
Roles of the Mitotic Inhibitors Wee1 and Mik1 in the G<sub>2</sub> DNA Damage and Replication Checkpoints (2001)

The G(2) DNA damage and DNA replication checkpoints in many organisms act through the inhibitory phosphorylation of Cdc2 on tyrosine-15. This phosphorylation is catalyzed by the Wee1/Mik1 family of kinases. However, the in vivo role of these kinases in checkpoint regulation has been unclear. We show that, in the fission yeast Schizosaccharomyces pombe, Mik1 is a target of both checkpoints and that the regulation of Mik1 is, on its own, sufficient to delay mitosis in response to the checkpoints. Mik1 appears to have two roles in the DNA damage checkpoint; one in the establishment of the checkpoint and another in its maintenance. In contrast, Wee1 does not appear to be involved in the establishment of either checkpoint.
New developments in the InterPro database (2007)

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.
Exhaust and evaporative emissions from gasohol-type fuels (1980)

An experimental study was conducted at the US Department of Energy's Bartlesville (Okla.) Energy Technology Center in cooperation with the Environmental Protection Agency to determine the characteristics of gasohol-type fuels with respect to exhaust and evaporative emissions. Five fuels, 2 gasolines (reference and commercial unleaded) and 3 gasohols (90% gasoline/10% ethanol) were tested in a fleet of 10 late-model automobiles. Six were equipped with oxidation catalysts and 4 were equipped with three-way catalysts. The results obtained from the 1978 Federal test procedure indicate that the addition of ethanol to the base gasoline, whether it is a reference fuel (Indolene) or a commercial fuel, has measurable effects on exhaust and evaporative emissions. However, on the average, the magnitude of these effects was generally within the 1978 emission standards established by the EPA. More specifically, the addition of ethanol, in the case of vehicles with oxidation catalysts, decreased hydrocarbons by an average of 27%, decreased carbon monoxide by 43%, decreased volumetric fuel economy by 3%, and increased oxides of nitrogen by 16%. Evaporative emissions were increased by 40%. In the case of vehicles with three-way catalysts, the addition of ethanol to the base fuel, on the average, decreased carbon monoxide by 7%,more » decreased fuel economy by 5%, increased hydrocarbons by 12%, increased oxides of nitrogen by 7%, and increased evaporative emissions by 49%.« less
A Reactive Oxygen Species–Mediated Loop Maintains Increased Expression of NADPH Oxidases 2 and 4 in Skin Fibroblasts From Patients With Systemic Sclerosis (2015)

Both NOX2 and NOX4 generate ROS in SSc fibroblasts and play a critical role in cell activation and DNA damage. Expression of NOX-2 and NOX-4 in SSc fibroblasts is maintained by a ROS-mediated loop.
Concentration of Transforming Growth Factor Beta in Human Bone Tissue: Relationship to Age, Menopause, Bone Turnover, and Bone Volume (1998)

Transforming growth factor beta (TGF-beta) is thought to play an important role in bone metabolism, but its relationship to human bone turnover and bone mass has not been examined yet. In this study, we measured the concentration of TGF-beta in 811 samples of male and female bone from four representative sites of the human skeleton and in the supernatants of 72 short-term human bone marrow cultures from the iliac crest. The concentrations of TGF-beta1 and TGF-beta2 in the bone matrix were positively correlated with histomorphometric indices of bone resorption and bone formation and with serum levels of osteocalcin and bone-specific alkaline phosphatase. We also observed a positive association between the release of TGF-beta in the bone marrow cultures and serum osteocalcin. Changes in the rate of cancellous or cortical bone remodeling with age or menopause were accompanied by corresponding changes in skeletal TGF-beta. In contrast, there was no significant relationship between the concentration of TGF-beta and bone volume at any skeletal site. In conclusion, our study supports the hypothesis that TGF-beta plays an important role in human bone remodeling, but fails to demonstrate an association between the skeletal concentration of TGF-beta and human bone mass.
The Urgency of Preaching in Challenging Times (2020)

In light of these challenging days of pandemic and prejudice, the Editorial Board urged that the September 2020 edition of The Journal of the Evangelical Homiletics Society focus on the theme of preaching on race, racism, prejudice, ethnocentrism, xenophobia, etc. Together we agreed that a themed on this topic issue was indeed necessary.
The society is well equipped to address this topic as demonstrated in the articles in this edition. Preachers are to preach the good news—the gospel—the life, death, burial, resurrection, ascension, and promised return of Jesus Christ. This gospel is to extend into every aspect of life. It is an urgent message for congregations, classrooms, our country—our world. Without the gospel, all effort for change is limp.
New 224 nm Hollow Cathode Laser-UV Raman Spectrometer (2001)

We have developed an optimized high-throughput UV Raman spectrometer that utilizes a simple, inexpensive new 224.3 nm hollow cathode laser. This quasi-continuous wave (CW) 224.3 nm laser can be used to detect sub-ppm concentrations of aromatic and polycyclic aromatic hydrocarbons in aqueous solutions. This excitation is also useful for studying aromatic amino acids in proteins. We demonstrate the utility of this spectrometer to study the environments of tyr and trp in horse heart myoglobin.
PBTree - A new progressive and hierarchical representation for network-based navigation in urban environments (2003)

This paper describes a novel progressive and hierarchical representation for densely built urban areas. It aims at navigating through huge urban environments with network-based client-sever systems. Thanks to this method, navigation is no longer limited to walkthrough, but allows to fly over the city. This can be achieved through a set of dedicated algorithms allowing the decomposition of city into a multi-resolution representation. The method efficiently exploits the fact that automated modeling technologies of urban scene are generally based on the processing of 2D data (video, photographs, cadastral map, ...), to model 2D 1 data (building footprint, height, altitude, ...) which turns out to be more compact. From this pre-computed representation of buildings, a server can progressively send the perceptible details to the client for all the regions visible from a given viewpoint.
THE INFLUENCE OF THE LIGANDS ON THE LUMINESCENCE OF METAL IONS* (1990)

Abstract— The nature of the ligands determines the luminescence properties of the central metal ion. This is illustrated on the following examples: (i) nonradiative transitions in the strong coupling model; (ii) nonradiative transitions in the weak coupling model; (iii) energy transfer from ligand to central ion. Several applications are dealt with. The cryptand ligands appear to play a special role.
Use of pattern recognition for unaliasing simultaneously acquired slices in simultaneous multislice MR fingerprinting (2016)

T<sub>1</sub> and T<sub>2</sub> values can be quantified at a multiband acceleration factor of two using our proposed acquisition even in a single-channel receive coil. Further acceleration could be achieved by combining this method with parallel imaging or iterative reconstruction. Magn Reson Med 78:1870-1876, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Theta phase precession in hippocampal neuronal populations and the compression of temporal sequences (1996)

O'Keefe and Recce [1993] Hippocampus 3:317-330 described an interaction between the hippocampal theta rhythm and the spatial firing of pyramidal cells in the CA1 region of the rat hippocampus: they found that a cell's spike activity advances to earlier phases of the theta cycle as the rat passes through the cell's place field. The present study makes use of large-scale parallel recordings to clarify and extend this finding in several ways: 1) Most CA1 pyramidal cells show maximal activity at the same phase of the theta cycle. Although individual units exhibit deeper modulation, the depth of modulation of CA1 population activity is about 50%. The peak firing of inhibitory interneurons in CA1 occurs about 60 degrees in advance of the peak firing of pyramidal cells, but different interneurons vary widely in their peak phases. 2) The first spikes, as the rat enters a pyramidal cell's place field, come 90 degrees-120 degrees after the phase of maximal pyramidal cell population activity, near the phase where inhibition is least. 3) The phase advance is typically an accelerating, rather than linear, function of position within the place field. 4) These phenomena occur both on linear tracks and in two-dimensional environments where locomotion is not constrained to specific paths. 5) In two-dimensional environments, place-related firing is more spatially specific during the early part of the theta cycle than during the late part. This is also true, to a lesser extent, on a linear track. Thus, spatial selectivity waxes and wanes over the theta cycle. 6) Granule cells of the fascia dentata are also modulated by theta. The depth of modulation for the granule cell population approaches 100%, and the peak activity of the granule cell population comes about 90 degrees earlier in the theta cycle than the peak firing of CA1 pyramidal cells. 7) Granule cells, like pyramidal cells, show robust phase precession. 8) Cross-correlation analysis shows that portions of the temporal sequence of CA1 pyramidal cell place fields are replicated repeatedly within individual theta cycles, in highly compressed form. The compression ratio can be as much as 10:1. These findings indicate that phase precession is a very robust effect, distributed across the entire hippocampal population, and that it is likely to be inherited from the fascia dentata or an earlier stage in the hippocampal circuit, rather than generated intrinsically within CA1. It is hypothesized that the compression of temporal sequences of place fields within individual theta cycles permits the use of long-term potentiation for learning of sequential structure, thereby giving a temporal dimension to hippocampal memory traces.
Isolation and expression of rat liver sepiapterin reductase cDNA. (1990)

Sepiapterin reductase (7,8-dihydrobiopterin: NADP+ oxidoreductase, EC 1.1.1.153) catalyzes the terminal step in the biosynthetic pathway for tetrahydrobiopterin, the cofactor necessary for aromatic amino acid hydroxylation. We report here the isolation of a cDNA clone for rat liver sepiapterin reductase. The cDNA has been excised from a lambda vector and the DNA sequence was determined. The insert contains the coding sequence for at least 95% of the rat enzyme and is fused to the Escherichia coli beta-galactosidase N-terminal segment and the lac promoter. The N-terminal region of the clone contains an extraordinarily high G + C content. The amino acid sequence deduced from the clone is in agreement with the size and composition of the enzyme and was matched to several tryptic peptide sequences. The enzyme encoded by the cDNA insert was shown to have sepiapterin reductase activity after expression in E. coli. Structural similarities were identified between this protein and several enzymes that should contain similar nucleotide and pteridine binding sites.
Structure of genipin in solution: a combined experimental and theoretical study (2013)

A combined experimental and theoretical study is here presented on the structure of genipin, a widely used molecule, whose applications range from natural cross-linker for proteins to regulating agent for drug delivery to precursor of natural dye. In particular the tridimensional structure of the genipin in solution has been studied by NMR spectroscopy and the experimental outcomes have been then supported by Density Functional Theory (DFT) calculations on the electronic structure and spectroscopic parameters. The equilibrium between open and closed-ring tautomers of genipin in solution has been also theoretically investigated. The mechanism of ring opening has been elucidated and the catalytic role of water has been clearly shown. Beyond the excellent agreement between experiments and theoretical calculations (in particular concerning 1H-NMR data), our results unravel the nature of the most stable isomer of genipin and related reactive species in solution.
Occurrence of autoantibodies in chronic graft vs. host disease after allogeneic stem cell transplantation (2005)

Chronic graft vs. host disease (GVHD) remains a major cause of morbidity and mortality after allogeneic stem cell transplantation (SCT). Chronic GVHD (cGVHD) has many similarities to de novo autoimmune disorders. While the presence and association of autoantibodies is well reported in these disorders, their role and clinical use remains a less studied area after SCT. We report the presence of autoantibodies in SCT recipients and a possible association with presence of cGVHD. During routine follow-up visits peripheral blood samples were tested for: rheumatoid factor (RF), antinuclear antibody (ANA), double stranded DNA (dsDNA), antimitochondrial antibody, antismooth muscle antibody (Anti Sm), antiendomysial, antireticulin antibodies, antithyroid peroxidase antibodies and an extractable nuclear antigen screen, in 13 SCT recipients. Six of 13 (46%) patients had one or more autoantibodies. All the patients with antibodies had cGVHD where as none of the patients without cGVHD had any autoantibodies (P = 0.025). Three (23%) patients had only one autoantibody and three (23%) of them had more than one autoantibody. ANA was positive in three (23.3%) patients, double stranded DNA in four (30.7%) patients, RF in one (7.6%) and Anti Sm muscle in two (15.3%) patients. In the present study, autoantibodies were detected predominantly in patients with presence of cGVHD. They also appeared to be more frequent in an unmanipulated graft and so less in patients with a T-cell depleted allograft. In two of 13 patients only there appeared to be an association between the antibody titre and flare up in skin symptoms. In conclusion, this small series raises interesting questions about the presence and role of autoantibodies after SCT and their association with cGVHD.
PubChem in 2021: new data content and improved web interfaces (2020)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Composting process design criteria (1986)

Process criteria developed in parts 1, 2 and 3 of this series of papers were applied to design of a sludge composting facility for the Cities of Oxnard and Ventura. The facility is designed to achieve the goals established for the Project and to take advantage of climatic and other environmental conditions unique to the site. A reactor (in-vessel) process was selected for the first-stage of composting to reduce odor potential, assure pathogen destruction, and improve process control. The circular, agitated bed reactor was selected as best meeting the site specific goals and conditions of this design. Reactor HRT is 12 days under worst case loading conditions. A covered, windrow process was selected for the second-stage of composting to enhance air drying, reduce amendment requirements, and provide curing. Three windrow sizing criteria are used (1) a minimum HRT of 20 days, (2) sufficient HRT to give an Nh of 0.167, and (3) and SRT sufficient to achieve the minimum system SRT. Minimum system SRT is 60 days. Air drying of wet sludge cake will be used during arid months to reduce amendment requirements and equalize peak loadings. Reducing amendment use is a project goal which will be achieved by maximizingmore » dewatered cake solids, air drying of dewatered cake, air drying during windrow curing, and use of locally available waste materials. Procedures discussed in these papers provide an integrated approach to process design of the first and second-stages of composting which is scientifically sound and yet practical and usable. 3 references.« less
Prediction of Running Injuries from Training Load: a Machine Learning Approach. (2017)

The prediction of the running injuries based on selfreported training data on load is difficult. At present, coaches and researchers have no validated system to predict if a runner has an increased risk of injuries. We aim to develop an algorithm to predict the increase of the risk of a runner to sustain an injury. As a first step Self-reported data on training parameters and injuries from high-level runners (duration=37 weeks, n=23, male=16, female=7) were used to identify the most predictive variables for injuries, and train a machine learning tree algorithm to predict an injury. The model was validated by splitting the data in training and a test set. The 10 most important variables were identified from 85 possible variables using the Random Forest algorithm. To predict at an earliest stage, so the runner or the coach is able to intervene, the variables were classified by time to build tree algorithms up to 7 weeks before the occurrence of an injury. By building machine learning algorithms using existing self-reported training data can enable prospective identification of high-level runners who are likely to develop an injury. Only the established prediction model needs to be verified as correct
Extracting the Combinatorial Test Parameters and Values from UML Sequence Diagrams (2014)

In the current practice, the Combinatorial Test Design Model (CTDM) is designed by the test designers manually leveraging their experience in testing. Their involvement, perception, domain knowledge and testing proficiency are needed to analyze the requirements document and design the test model. Till date we know of no automated method that has eased the process of deriving the Combinatorial Test Design Model. Requirements document and analysis artifacts like UML activity diagrams and sequence diagrams hold information on parameters, values and constraints of the underlying CTDM. Our research focus is to develop a tool that assists test designers in coming up with the CTDM. This paper presents an approach to extract CTDM related information such as parameters and values from sequence diagrams. Our key contribution in this paper includes proposing a rule-based method for identifying the model elements from the sequence diagrams with the supporting rules and extraction algorithms. The rules have been applied onto individual sequence diagrams and results qualitatively discussed based on the general understanding of the requirements.
An efficient method for introducing block mutations into specific regions of a gene. (1990)

The introduction by Kunkel of a method which uses uracil-containing single-stranded DNA as a template for site-directed mutagenesis has greatly simplified the procedure for introducing point mutations into DNA in a phagemid vector. We have extended the use of this method to introduce block mutations into specific regions of DNA, using oligonucleotide primers containing multiple nucleotide mismatches which contain new restriction sites. The oligonucleotides, with up to 15 mismatches, can specifically and stably bind to the predicted target sequence. Because of the high mutation rate and convenient selection by restriction enzyme digestion, this method of introducing site-specific block mutations into DNA is very easy and efficient. We have constructed a series of block mutations in the promoter of the gene for the cytosolic form of P-enolpyruvate carboxykinase (GTP) (EC4.1.1.32) (PEPCK) by this method showing that a block mutation in the cAMP responsive element (CRE-1) completely disrupts protein binding to CRE-1 in vitro and causes a dramatic decrease in the basal transcription from the PEPCK promoter in vivo.