gebhart/patrepeval huggingface dataset:
Nitrite accumulation followed by denitrification using sequencing batch reactor (2004)

Biological ammonia-nitrogen removal utilizes two distinct processes, nitrification and denitrification. In nitrification, ammonia oxidizes to nitrite then to nitrate. In this study, elimination of nitrite oxidation to nitrate step was attempted in order to directly remove nitrite to nitrogen gas by denitrification. For this study the supernatant from an anaerobic digester was used as an ammonia source and a sequencing batch reactor (SBR) was employed. Emphasis was given to the evaluation of the operational factors affecting nitrite accumulation and the elucidation of kinetics for biological nitrification and denitrification. Accumulation of nitrite in the nitrification process was achieved by suppressing the growth of Nitrobacter, a nitrite oxidizer, by loading high concentration ammonia supernatant immediately after all ammonia in the previous loading was oxidized to nitrite. Nitrite oxidation was taking place as the solid retention time (SRT) was increased from 2.5 days to 3.0 days in a continuously aerated SBR mode with daily feeding. However, nitrite accumulation was achieved even at longer SRT of 5 days when the aeration and non-aeration periods were appropriately combined and the non-aeration period can be used for denitrification of the accumulated nitrite with a carbon source supplied.
Distal Recognition Site for Classical Pathway Convertase Located in the C345C/Netrin Module of Complement Component C5 (2000)

Previous studies focused on indels in the complement C345 protein family identified a number of potential protein-protein interaction sites in components C3 and C5. Here, one of these sites in C5, near the alpha-chain C terminus, was examined by alanine-scanning mutagenesis at 16 of the 18 non-alanine residues in the sequence KEALQIKYNFSF RYIYPLD. Alanine substitutions affected activities in the highly variable manner characteristic of binding sites. Substitutions at the lysine or either phenylalanine residue in the central KYNFSF sequence had the greatest effects, yielding mutants with <20% of the normal activity. These three mutants were also resistant to the classical pathway (CP) C5 convertase, with sensitivities roughly proportional to their hemolytic activities, but had normal susceptibilities to the cobra venom factor (CVF)-dependent convertase. Synthetic peptide MGKEALQIKYNFS-NH2 was found similarly to inhibit CP but not CVF convertase activation, and the effects of alanine substitutions in this peptide largely reflected those of the equivalent mutations in C5. These results indicate that residues KYNFSF form a novel, distal binding site for the CP, but not CVF convertase. This site lies approximately 880 residues downstream of the convertase cleavage site within a module that has been independently named C345C and NTR; this module is found in diverse proteins including netrins and tissue inhibitors of metalloproteinases.
Aliasing reduction in staring infrared imagers utilizing subpixel techniques (1995)

We introduce and analyze techniques for the reduction of aliased signal energy in a staring infrared imaging system. A standard staring system uses a fixed two-dimensional detector array that corresponds to a fixed spatial sampling frequency determined by the detector pitch or spacing. Aliasing will occur when sampling a scene containing spatial frequencies exceeding half the sampling frequency. This aliasing can significantly degrade the image quality. The aliasing reduction schemes presented here, referred to as microscanning, exploit subpixel shifts between time frames of an image sequence. These multiple images are used to reconstruct a single frame with reduced aliasing. If the shifts are controlled, using a mirror or beam steerer for example, one can obtain a uniformly sampled microscanned image. The reconstruction in this case can be accomplished by a straightforward interlacing of the time frames. If the shifts are uncontrolled, the effective sampling may be nonuniform and reconstruction becomes more complex. A sampling model is developed and the aliased signal energy is analyzed for the microscanning techniques. Finally, a number of experimental results are presented that illustrate the perlormance of the microscanning methods.
Pharmacodynamic Modelling of Irreversible and Reversible Gastric Proton Pump Inhibitors (2003)

Acid related diseases like GERD, duodenal-and gastric ulcers and H. Pylori-positive peptic ulcer disease are primarily managed by reducing gastric acidity. Irreversible proton pump inhibitors (PPIs) inhibit gastric acid secretion effectively throughout the day by irreversibly inhibiting the gastric proton pump, H+, K+-ATPase, in the parietal cells. Reversible gastric proton pump inhibitors are under development, but have not yet reached clinical use. The pharmacokinetic/pharmacodynamic (PK/PD) relationships of these compounds are nonlinear, with a delay in the effect-time profile compared to the plasma concentration-time course. PK/PD-modelling was used to characterize and quantify the pharmacological effect with regard to onset, intensity and duration of effect. Models based on functional data, that discriminate between drug-and system-specific parameters, were developed. In general, the plasma concentration-time course for each individual was approximated by linear interpolation between time-points and served as input into the pharmacodynamic models. A turnover model of irreversible inhibition of gastric acid secretion by omeprazole in the dog described the data well. The model was challenged and found to be robust under different experimental conditions. This model could predict the effect following different exposure of omeprazole and following different histamine provocation. Different fitting approaches (naïve pooling, standard two-stage and nonlinear mixed effects modelling) were compared and resulted in similar parameter estimates. For the reversible inhibitors, a kinetic binding model was finally selected. With a binding model the delay in the effect-time profile is explained by prolonged binding to the enzyme. Use of these results in drug development can be helpful with regard to selection of drugs for further development and to predict the first clinical dose.
1,5‐Anhydrohexitol Nucleic Acids, a New Promising Antisense Construct (1995)

Abstract For corrigendum see DOI: 10.1002/anie.199521651
Pattern Recognition of Proteins Based on an Array of Functionalized Porphyrins (2006)

A practical protein-detecting array is desirable for its potential application in proteomics, medical diagnostics, and pathogen detection. Here, we report a novel protein-detecting array based on porphyrins containing peripheral amino acids as protein surface receptors. The array of porphyrin receptors showed a unique pattern of fluorescence change upon interaction with certain protein samples. Both metal and nonmetal-containing proteins and mixtures of proteins gave distinct patterns, allowing their unambiguous identification. The composite pattern for each sample was subjected to principal component analysis (PCA) to generate a clustering map for more practical visualization. Increasing the number of porphyrin receptors from eight to sixteen gave improved resolution, suggesting that this array is expandable to give satisfactory resolution for any given sample system by carefully maximizing the chemical diversity of the receptors.
Stereoscopic perception of real depths at large distances (2010)

There has been no direct examination of stereoscopic depth perception at very large observation distances and depths. We measured perceptions of depth magnitude at distances where it is frequently reported without evidence that stereopsis is non-functional. We adapted methods pioneered at distances up to 9 m by R. S. Allison, B. J. Gillam, and E. Vecellio (2009) for use in a 381-m-long railway tunnel. Pairs of Light Emitting Diode (LED) targets were presented either in complete darkness or with the environment lit as far as the nearest LED (the observation distance). We found that binocular, but not monocular, estimates of the depth between pairs of LEDs increased with their physical depths up to the maximum depth separation tested (248 m). Binocular estimates of depth were much larger with a lit foreground than in darkness and increased as the observation distance increased from 20 to 40 m, indicating that binocular disparity can be scaled for much larger distances than previously realized. Since these observation distances were well beyond the range of vertical disparity and oculomotor cues, this scaling must rely on perspective cues. We also ran control experiments at smaller distances, which showed that estimates of depth and distance correlate poorly and that our metric estimation method gives similar results to a comparison method under the same conditions.
Global Program Struggles to Stem the Flood of New Cases (1998)

Geneva—Peter Piot has a seemingly impossible job. As executive director of the United Nations' special program on AIDS (UNAIDS), he is in charge of the international community's global response to the epidemic. With a staff of 130 and a budget of just $60 million a year, Piot is seeking to turn the tide against a disease that has killed more than 11 million people over the past 2 decades and is relentlessly extending its reach. Not only does he have to contend with the labyrinthine political, social, and financial vagaries of the U.N. system, but this balancing act has been made doubly difficult by the fact that his appointment coincided with a major organizational shake-up in the U.N.'s AIDS activities (Science, 25 November 1994, p. 1312). When the dust finally settled, the World Health Organization's Global Programme on AIDS (GPA), which was created in 1986, had been replaced by UNAIDS, a program jointly sponsored by six U.N. agencies, including WHO.
A Total AUTODIN System Architecture (1980)

This paper concerns data communications in the U.S Department of Defense. It includes a historical perspective on DoD common-user data systems: AUTODIN I, ARPANET, and AUTODIN II. It treats data communications on an end-to-end basis, including automation of communications center functions by the user. The Integrated AUTODIN System Architecture (IASA) project was defined by DoD to provide a total data communications system design on an end-to-end basis. The main results of this paper are based on IASA work and include the use of AUTODIN II as the IAS backbone, the integration of AUTODIN I and AUTODIN II, the definition of a new DoD program called the Inter-Service/Agency Automated Message Processing Exchange (I-S/A AMPE), the development of DoD standard protocols, formats and procedures, a brief description of the IAS security architecture, and a plan for internetting different networks via gateways and internet protocols. A plan for the future disposition of the ARPANET is included. The paper concludes with some speculative material on the long-range future of United States military data communications.
Cyclic AMP-Responsive DNA-Binding Protein: Structure Based on a Cloned Placental cDNA (1988)

Cyclic AMP (cAMP) is an intracellular second messenger that activates transcription of many cellular genes. A palindromic consensus DNA sequence, TGACGTCA, functions as a cAMP-responsive transcriptional enhancer (CRE). The CRE binds a cellular protein of 38 kD in placental JEG-3 cells. A placental lambda gt11 library was screened for expression of specific CRE-binding proteins with the CRE sequence as a radioactive probe. A cDNA encoding a protein of 326 amino acids with the binding properties of a specific CRE-binding protein (CREB) was isolated. The protein contains a COOH-terminal basic region adjacent to a sequence similar to the "leucine zipper" sequence believed to be involved in DNA binding and in protein-protein contacts in several other DNA-associated transcriptional proteins including the products of the c-myc, c-fos, and c-jun oncogenes and GCN4. The CREB protein also contains an NH2-terminal acidic region proposed to be a potential transcriptional activation domain. The putative DNA-binding domain of CREB is structurally similar to the corresponding domains in the phorbol ester-responsive c-jun protein and the yeast transcription factor GCN4.
Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region (2006)

The mechanisms that regulate variable (V) gene selection during the development of the mouse IgH repertoire are not fully understood, due in part to the absence of the complete locus sequence. To better understand these processes, we have assembled the entire 2.5-Mb mouse IgH (Igh) V region sequence of the C57BL/6 strain from public sequences and present the first complete annotated map of the region, including V genes, pseudogenes, repeats, and nonrepetitive intergenic sequences. In so doing, we have discovered a new V gene family, VH16. We have identified clusters of conserved region-specific intergenic sequences and have verified our assembly by genic and intergenic Southern blotting. We have observed that V pseudogenes are not evenly spread throughout the V region, but rather cluster together. The largest J558 family, which spans more than half of the locus, has two strikingly different domains, which suggest points of evolutionary divergence or duplication. The 5' end contains widely spaced J558 genes interspersed with 3609 genes and is pseudogene poor. The 3' end contains closely spaced J558 genes, no 3609 genes, and is pseudogene rich. Each occupies a different branch of the phylogenetic tree. Detailed analysis of 500-bp upstream of all functional genes has revealed several conserved binding sites, general and B cell-specific, as well as key differences between families. This complete and definitive assembly of the mouse Igh V region will facilitate detailed study of promoter function and large-scale mechanisms associated with V(D)J recombination including locus contraction and antisense intergenic transcription.
Molecular Cloning and Nucleotide Sequence Analysis of Complementary Deoxyribonucleic Acid for the β-Subunit of Rat Follicle Stimulating Hormone (1987)

To provide a hybridization probe for analysis of the regulation of rat gonadotropin subunit mRNA levels, an effort was made to isolate a cloned cDNA for the beta-subunit of rat FSH (FSH beta). Using a cloned bovine FSH beta cDNA as a hybridization probe, a rat pituitary lambda gt10 cDNA library was screened and a single, strongly hybridizing clone identified. The 874 base pair cDNA insert from this clone contains the complete sequence of rat FSH beta including an amino-terminal precursor segment. Hybridization of this cloned cDNA to rat pituitary RNA demonstrated the presence of an approximately 2.0 kilobase RNA species containing FSH beta sequences. Cloned rat cDNA was also used to demonstrate that estrogen treatment of ovariectomized female rats results in decreases in mRNA concentrations for FSH beta and the beta-subunit of LH with somewhat smaller decreases in alpha-subunit mRNA concentrations. Little or no change was detected in the mRNA for the beta-subunit of TSH.
Robust polymer microfluidic device fabrication via contact liquid photolithographic polymerization (CLiPP) (2004)

Microfluidic devices are commonly fabricated in silicon or glass using micromachining technology or elastomers using soft lithography methods; however, invariable bulk material properties, limited surface modification methods and difficulty in fabricating high aspect ratio devices prevent these materials from being utilized in numerous applications and/or lead to high fabrication costs. Contact Liquid Photolithographic Polymerization (CLiPP) was developed as an alternative microfabrication approach that uniquely exploits living radical photopolymerization chemistry to facilitate surface modification of device components, fabrication of high aspect ratio structures from many different materials with numerous covalently-adhered layers and facile construction of three-dimensional devices. This contribution describes CLiPP and demonstrates unique advantages of this new technology for microfabrication of polymeric microdevices. Specifically, the procedure for fabricating devices with CLiPP is presented, the living radical photopolymerization chemistry which enables this technology is described, and examples of devices made using CLiPP are shown.
Serum Levels of Squamous Cell Carcinoma Antigen and Ovarian Carcinoma Antigen (CA 125) in Patients with Benign and Malignant Diseases of the Uterine Cervix (1994)

In the present study we evaluated the clinical usefulness of the tumor antigens, squamous cell carcinoma antigen (SCC) and ovarian carcinoma antigen (CA 125), in populations of patients with benign and malignant cervical disease. SCC and CA 125 levels were determined in the serum of 59 patients with invasive carcinoma of the uterine cervix and in 21 patients with benign cervical diseases. Before treatment of cervical cancer, SCC levels were elevated in 63% of the patients with squamous cell cancer while all 5 patients with adenocarcinoma had normal levels. CA 125 levels were elevated in 21% of the patients with cervical squamous cell cancer and in 3 of the 5 cases of adenocarcinoma of the cervix. In patients with benign cervical diseases, only 1 had a positive SCC level and none were positive for CA 125. No correlation was found between SCC levels and histological differentiation or clinical stage. In positive patients, serial SCC determinations correlated with the clinical course in 72.2%. Increasing levels were always associated with progression and increased on average 3 months before there was clinical evidence for disease progression. It is concluded from these studies that SCC levels are a useful marker for cervical cancer progression and recurrence. Levels of CA 125 were more likely to be elevated in patients with adenocarcinoma than squamous cell carcinoma, but when elevated in these latter patients, it also tended to predict tumor recurrence.
Progression of Diabetic Macular Edema: Correlation with Blood–Retinal Barrier Permeability, Retinal Thickness, and Retinal Vessel Diameter (2007)

Progression to photocoagulation treatment for CSME was associated with higher retinal vascular leakage at baseline, whereas baseline retinal vessel diameters and retinal thickness were comparable in progressing and nonprogressing eyes. Baseline leakage was the strongest predictor of progression from non-CSME to photocoagulation for CSME.
A Random shRNA-Encoding Library for Phenotypic Selection and Hit-Optimization (2008)

RNA interference (RNAi) is a mechanism for inhibiting gene expression through the action of small, non-coding RNAs. Most existing RNAi libraries target single genes through canonical pathways. Endogenous microRNAs (miRNAs), however, often target multiple genes and can act through non-canonical pathways, including pathways that activate gene expression. To interrogate all possible functions, we designed, synthesized, and validated the first shRNA-encoding library that is completely random at the nucleotide level. Screening in an IL3-dependent cell line, FL5.12, yielded shRNA-encoding sequences that double cell survival upon IL3 withdrawal. Using random mutagenesis and re-screening under more stringent IL3-starvation conditions, we hit-optimized one of the sequences; a specific nucleotide change and the creation of a mismatch between the two halves of the stem both contributed to the improved potency. Our library allows unbiased selection and optimization of shRNA-encoding sequences that confer phenotypes of interest, and could be used for the development of therapeutics and tools in many fields of biology.
Human Blue-Opsin Promoter Preferentially Targets Reporter Gene Expression to Rat S-Cone Photoreceptors (2006)

AAV5.HB.GFP vector injected into the subretinal space of Sprague-Dawley rats targeted gene expression to photoreceptor cells with an efficiency approximately 20-fold higher than that for AAV2.HB.GFP. Transgene expression regulated by the human blue cone-promoter persisted at least for 20 months. Cones coexpressing S-opsin and the GFP transgene appeared to prevail, confirming that in addition to having properties of the AAV serotype, the promoter choice is key to fine-tuning transgene delivery and expression in specific retinal cells. The system described here may be effective in a therapeutic setting in which strong S-cone transgene expression is required.
Calcitonin gene-related peptide levels are elevated in patients with sepsis. (1990)

Calcitonin gene-related peptide (CGRP), an endogenous vasoactive peptide encoded by the calcitonin gene in nerve cells, is distributed throughout the cardiovascular system and is a potent vasodilator. Plasma levels of CGRP have been elevated in animal models with sepsis. This study was designed to determine whether plasma CGRP levels are elevated in patients with sepsis and perhaps contribute to the hyperdynamic cardiovascular state in sepsis. Plasma CGRP levels were obtained from normal healthy volunteers and from patients with sepsis. Volunteers were afebrile and had normal pulse and blood pressure. Patients with sepsis were selected according to the following criteria: (1) temperature higher than 38.5 degrees C, (2) white blood count greater than 14,000/ml, (3) positive blood culture of bacterial organisms, (4) hemodynamic parameters consistent with hyperdynamic sepsis, and (5) negative history of thyroid or other endocrine abnormalities. CGRP was extracted and assayed by radioimmunoassay for iodine 125-labeled human CGRP. In patients with sepsis, the cardiac index was 5.4 +/- 0.5 L/min/m2 (normal, 3.0); systemic vascular resistance was 7.1 +/- 0.5 mm Hg/L/min (normal, 16); oxygen delivery was 1496 +/- 137 ml/min (normal, 1000). Plasma CGRP levels were significantly elevated in the patients with sepsis, 14.9 +/- 3.2 pg/ml, compared to plasma CGRP levels in control volunteers, 2.0 +/- 0.3 pg/ml (p less than 0.0005). These elevated levels of CGRP may contribute to the decreased vascular resistance and increased cardiac output in the hyperdynamic septic state.
Purification, Characterization, and Cloning of Enamel Matrix Serine Proteinase 1 (1998)

The maturation of dental enamel succeeds the degradation of organic matrix. Inhibition studies have shown that this degradation is accomplished by a serine-type proteinase. To isolate and characterize cDNA clones encoding this proteinase, we used two degenerate primer approaches to amplify part of the coding region using polymerase chain-reaction (PCR). First, we purified the proteinase from porcine transition-stage enamel matrix and characterized it by partial protein sequencing. The enzyme was isolated from the neutral soluble enamel extract by successive ammonium sulfate precipitations, hydroxyapatite HPLC, reverse-phase HPLC, DEAE ion exchange, and affinity chromatography with a Benzamidine Sepharose 6B column. The intact protein and lysylendopeptidase-generated cleavage products were characterized by amino acid sequence analyses. Degenerate oligonucleotide primers encoding two of the polypeptide sequences were synthesized. In a complementary strategy, degenerate oligonucleotide primers were designed against highly conserved active-site regions of chymotrypsin-like proteinases. Both approaches yielded PCR amplification products that served as probes for screening a porcine enamel organ epithelia-specific cDNA library. The longest full-length clone is 1133 nucleotides and encodes a preproprotein of 254 amino acids. We designate this protein enamel matrix serine proteinase 1 or EMSP1. The active protein has 224 amino acids, an isotope-averaged molecular mass of 24.1 kDa, and an isoelectric point of 6.0. Multiple-tissue Northern analysis indicates that EMSP1 is a tooth-specific protein. Gelatin enzymography shows a dramatic increase in EMSP1 activity in the transition-stage enamel matrix. EMSP1 is most homologous to kallikriens and trypsins.