gebhart/patrepeval huggingface dataset:
DPGA-coupled microprocessors: commodity ICs for the early 21st Century (2002)

During the past decade, the microprocessor has become a key commodity component for building all kinds of computational systems. During this time frame, large reconfigurable logic arrays have exploited the same advances in IC fabrication technology to emerge as viable system building blocks. Looking at both the technology prospects and application requirements, there is compelling evidence that microprocessors with integrated reconfigurable logic arrays will be a primary building block for future computing systems. In this paper, we look at the role such components can play in building high-performance and economical systems, as well as the ripe technological outlook. We note how the tight integration of reconfigurable logic into the processor can overcome some of the major limitations of contemporary attached reconfigurable computer engines. We specifically consider the use of integrated dynamically programmable gate array (DPGA) structures for the configurable logic, and examine the advantages that rapid reconfiguration provides in this application.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Spectrophotometric determination of oxygen saturation of blood independent of the presence of indocyanine green (1979)

The strong absorbance of indocyanine green in a broad band around lambda = 800 nm invalidates the usual spectrophotometric two-wavelength methods for measuring oxygen saturation operating in the red and near infrared region. By proper wavelength selection, however, the effect of the dye can be eliminated. With the two-wavelength method utilising lambda = 660 and 860 nm oxygen saturation is measured virtually independent of the presence of indocyanine green.
Polyethylene glycol (PEG)-modified granulocyte-macrophage colony-stimulating factor (GM-CSF) with conserved biological activity. (1992)

Polyethylene glycol (PEG) modification improves the pharmacological properties of proteins, usually extending plasma half-life and concomitantly increasing in vivo bioactivity, reducing both antigenicity and immunogenicity, and increasing solubility and resistance to proteolysis. Despite these established benefits, few PEG proteins are in use. Current coupling methods are either traumatic for the protein or involve lengthy and difficult procedures to activate monomethoxyPEG (MPEG). We have applied a new coupling method that allows coupling of MPEG directly to proteins under physiological conditions. Using this method with recombinant human (rh)granulocyte-macrophage colony-stimulating factor (GM-CSF) we were able to construct biologically active PEG-GM-CSF. Fast protein liquid chromatography (FPLC) and phase-partitioning confirmed the presence of PEG modification, and the former was used to fractionate modified and unmodified material. Bioactivity was measured in colony assays of normal human bone marrow cells and by tritiated thymidine uptake (of chronic myeloid leukemia cells and TF-1 cells). With both uptake and colony assays, using unfractionated material, we observed only a modest reduction in biological activity. Assays of FPLC-fractionated material confirmed that much of the bioactivity of the PEG-GM-CSF preparations was due to the modified species and any residual unmodified GM-CSF. Species uncontaminated by tresylmonomethoxyPEG (TMPEG; which was somewhat inhibitory in the thymidine uptake assay and eluted over a broad region of the FPLC profile) had no significant reduction in activity, but we cannot rule out the possibility that PEG-GM-CSF species eluting elsewhere in the profile had modest reduction of activity. Subcutaneous injection into mice confirmed the anticipated improved half-life in vivo and demonstrated a longer uptake from the injection site. This is, as far as we are aware, the first successful construction of PEG-GM-CSF with conserved biological activity.
The Reversion-inducing Cysteine-rich Protein with Kazal Motifs (RECK) Interacts with Membrane Type 1 Matrix Metalloproteinase and CD13/Aminopeptidase N and Modulates Their Endocytic Pathways (2007)

The reversion-inducing cysteine-rich protein with Kazal motifs (RECK) is anchored to the cell surface via glycosylphosphatidylinositol. This molecule antagonizes the function of membrane type 1 matrix metalloproteinase (MT1-MMP) to promote proMMP-2 maturation. Here, we attempt to clarify the mechanism underlying RECK functions. First, we found that RECK forms a complex with MT1-MMP and inhibits its proteolytic activity. Notably, RECK increases the amount of MT1-MMP that associates with detergent-resistant membranes during sucrose gradient ultracentrifugation. Furthermore, perturbation of membrane cholesterol significantly affected the function of RECK in suppressing MT1-MMP function. These findings indicate that RECK possibly regulates MT1-MMP function by modulating its behavior on the cell surface as well as by enzymatic action; this prompted us to find another molecule whose behavior in detergent-resistant membranes is influenced by RECK. Subsequently, we found that RECK interacts with CD13/aminopeptidase N. Further, we found that RECK inhibits the proteolytic activity of CD13 in a cholesterol perturbation-sensitive manner. Finally, we examined whether RECK influences the behavior of MT1-MMP and CD13 during their internalization from the cell surface. In the absence of RECK, MT1-MMP and CD13 were internalized along with the markers of clathrin- or caveolae-dependent endocytosis. However, interestingly, in the presence of RECK these molecules were internalized preferentially with an endocytic marker that is neither clathrinnor caveolae-dependent, indicating that RECK modulates endocytic pathways of MT1-MMP and CD13. This modulation was correlated with the accelerated internalization and decay of MT1-MMP and CD13. This study unveils the novel function and target molecules of RECK.
Optical coherence tomography of the rat cochlea (2000)

Optical coherence tomography (OCT) was used to image the internal structure of a rat cochlea (ex vivo). Immediately following sacrifice, the temporal bone of a Sprague-Dawley rat was harvested. Axial OCT cross sectional images (over regions of interest, 1x1 mm-2x8 mm) were obtained with a spatial resolution of 10-15 microm. The osseous borders of the lateral membranous labyrinth overlying the cochlea and the scala vestibuli, media, and tympani, which were well demarcated by the modiolus, Reissner's and the basilar membranes, were clearly identified. OCT can be used to image internal structures in the cochlea without violating the osseous labyrinth using simple surgical exposure of the promontory, and may potentially be used to diagnose inner ear pathology in vivo in both animal and human subjects labyrinth.
Biogenic Peptides and Their Potential Use (2003)

This paper reviews bioactive peptides, biogenic peptides, opioid peptides, immunostimulating peptides, mineral soluble peptides, antihypertensive peptides and antimicrobial peptides originating from food materials and enzymatic hydrolysis of proteins. Antihypertensive peptides are extensively reviewed and have been divided into angiotensin I-converting enzyme inhibitory peptides and others. These peptides are produced in the enzymatic hydrolysate of treated food materials such as milk, animal and fish meat, maize, wheat, soybeans and egg, and also from microbe-fermented products. Peptides with strong antihypertensive effects on spontaneously hypertensive rats are discussed and are divided into high and low angiotensin I-converting enzyme inhibitory activities. In addition, new topics from our studies on antihypertensive peptides are introduced. Efficacies of these peptides in clinical studies and differences with medicinal substances are summarized. Recent studies in this area shown the possibility of using biogenic peptides for improvements in treatment or prevention of hypertension.
Complete Genome Sequence of the Facultative Anaerobic Magnetotactic Bacterium Magnetospirillum sp. strain AMB-1 (2005)

Magnetospirillum sp. strain AMB-1 is a Gram-negative alpha-proteobacterium that synthesizes nano-sized magnetites, referred to as magnetosomes, aligned intracellularly in a chain. The potential of this nano-sized material is growing and will be applicable to broad research areas. It has been expected that genome analysis would elucidate the mechanism of magnetosome formation by magnetic bacteria. Here we describe the genome of Magnetospirillum sp. AMB-1 wild type, which consists of a single circular chromosome of 4967148 bp. For identification of genes required for magnetosome formation, transposon mutagenesis and determination of magnetosome membrane proteins were performed. Analysis of a non-magnetic transposon mutant library focused on three unknown genes from 2752 unknown genes and three genes from 205 signal transduction genes. Partial proteome analysis of the magnetosome membrane revealed that the membrane contains numerous oxidation/reduction proteins and a signal response regulator that may function in magnetotaxis. Thus, oxidation/reduction proteins and elaborate multidomain signaling proteins were analyzed. This comprehensive genome analysis will enable resolution of the mechanisms of magnetosome formation and provide a template to determine how magnetic bacteria maintain a species-specific, nano-sized, magnetic single domain and paramagnetic morphology.
A study of fall migration of Nearctic-breeding landbirds in central Costa Rica (1994)

Summary In the course of a 13-year study of fall migration of Nearctic-breeding landbirds through a site in the Valle Central of Costa Rica, 5,549 migrant birds of 63 species, and 782 local residents of 28 species, were banded. Arrival dates of migrant species were fairly constant from year to year with passage migrants tending to arrive earlier than winter resident species. Differences in numbers and timing of first-year vs. older birds were noted in some species. Passage migrants showed higher fat deposits than did winter resident species and were virtually never recaptured in succeeding years, indicating a lack of fidelity to specific stopover sites. Winter resident species were recaptured in years following banding at frequencies approaching those for many resident species. Among winter resident species, individuals arriving early had higher fat deposits and were recaptured less frequently than those arriving later; apparently the latter were most likely to remain for the winter in or near the study area. This arrangement probably reduces intraspecific competition between transient and resident individuals of these species. Both at regional and local levels, migrant and local resident species differed in size distributions and to some extent in diet; these differences may reduce competition between these groups. Resident species had generally ceased to nest by the time the migrants arrivedin large numbers, but usually were feeding fledglings and/or moulting, suggesting that the presence of the migrants does not result in a scarcity of resources. The long-term but low-intensity, low-budget nature of this study may make it feasible to duplicate in many areas of the Neotropics, where information is needed regarding effects of land-use changes on resident and migrant avifaunas.
Phase I clinical and pharmacokinetic study of leucovorin and infusional hepatic arterial fluorouracil. (1995)

A regimen that combines 5-FU and FA has been identified for regional chemotherapy in patients with hepatic metastases from colorectal cancer. The systemic levels of 5-FU achieved are similar to the conventional IV de Gramont regimen using an identical schedule of 5-FU and FA, which implies that this chemotherapy has the best of both worlds, ie, a regional advantage in delivering high drug concentrations to the target organ with adequate systemic cover for extrahepatic micrometastases.
Abstract 2677: MSIClass–Identification and classification of microsatellite unstable using cell-free DNA from ultra-low-pass sequencing (2019)

Abstract The acquisition of mismatch repair deficiency is common in many tumor types. A unique subtype of mismatch repair deficient tumors, called tumors with microsatellite instability (MSI), has been recently approved for treatment with PD-1\PD-L1 blockade immunotherapy. Therefore, developing a quick, inexpensive, and easy-to-implement technique for classifying tumors as MSI is of utmost importance. Here, we describe such a method using next-generation sequencing data, and show that it can detect MSI from cell-free DNA (cfDNA), even when there is low fraction of tumor DNA in the cfDNA. We first analyzed the unique mutational features of MSI vs. microsatellite stable (MSS) tumors. Using our SignatureAnalyzer tool, we analyzed the signatures of the different insertions and deletions within microsatellite loci (MS-indels), and found that MSI tumors harbor elevated MS-indels of certain types, which we further validated using whole genome sequencing data from The Cancer Genome Atlas. We next used this information to develop a method (MSIClass) that analyzes the WGS data of a given sample by capturing the features unique to MSI tumors. This method assigns each sample a score based on aggregating information from all MS loci simultaneously; since MSIClass is a sample-based tool, it can call the MSI status of tumor samples that have no patient-matched normal sample. We further demonstrate that MSIClass requires minimal genomic information; indeed, sequencing coverage as low as 0.05x (current sequencing cost of ~$2/sample) is sufficient for accurate classification by MSIClass. Using in silico and in vitro DNA mixing we show that MSIClass can accurately identify MSI cases in very low purity cases, at 0.1% tumor DNA (using 0.5x sequencing coverage). We show that MSIClass, applied on cfDNA, could accurately classify 29 colon cases – 22 MSS and 7 MSI cases, 3 of which are early stage disease and with low tumor content. These results demonstrate that MSIClass is an inexpensive MSI test that can be applied in various cases: bulk sequencing where a matched normal is not available, cases of very low purity tumors, and even using cfDNA from blood in cases a biopsy is not available or possible. Finally, this methodology can be the basis for monitoring minimal residual disease, and potential be used for early detection of MSI tumors. Citation Format: Yosef E. Maruvka, Ruslana Frazer, Jonna Grimsby, Carrie Cibulskis, Viktor Adalsteinsson, Ryan Corcoran, Gad Getz. MSIClass–Identification and classification of microsatellite unstable using cell-free DNA from ultra-low-pass sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2677.
β-Alanine suppresses heat inactivation of lactate dehydrogenase (2005)

Beta-Alanine exhibits neurotransmitter activity and is a component of the anti-glycation agent carnosine. We propose that beta-alanine may have additional properties which may be of physiological significance. Interestingly, stress modulates the level of beta-alanine, which regulates excitotoxicity responses and prevents neuronal cell death. We hypothesize that beta-alanine's protective role may involve preservation of enzyme structure and function, suggesting that beta-alanine may act as a chemical chaperone. We used light scattering, enzyme activity and intrinsic fluorescence to monitor heat-induced changes in lactate dehydrogenase (LDH) in the presence and absence of beta-alanine. We observed that beta-alanine suppressed heat-induced LDH inactivation, prevented LDH aggregation, ameliorated the decrease in intrinsic fluorescence and reactivated thermally denatured LDH. These observations support the hypothesis that beta-alanine has chaperone-like activity and may play a cellular role in the preservation of enzyme function.
Comparison of inhaled mannitol, daily rhDNase and a combination of both in children with cystic fibrosis: a randomised trial (2009)

Inhaled mannitol was at least as effective as rhDNase after 3 months treatment. There was a marked individual variation in tolerance to mannitol and in response to treatment however. Children who do not respond to rhDNase many benefit from a trial of inhaled mannitol. The combination of mannitol and rhDNase was not useful.
Identification of antimicrobial peptides by using combinatorial libraries made up of unnatural amino acids (1994)

The use of water-soluble synthetic peptide combinatorial libraries permits the systematic examination of tens to hundreds of millions of peptides in existing microdilution assays. In the present study, we prepared and determined the antistaphylococcal activities of two new synthetic peptide combinatorial libraries (one N-acetylated, the other not) composed of tetrapeptides having one position defined and the remaining three positions made up of mixtures of L-, D-, and unnatural amino acids (a total of 58 different amino acids). These libraries, when used in conjunction with an iterative selection process, allowed for the development of a series of individually defined tetrapeptides with high levels of activity against Staphylococcus aureus. The activities of the final individual peptides against two additional strains of gram-positive bacteria (methicillin-resistant S. aureus and Streptococcus sanguis), a gram-negative bacterium (Escherichia coli), as well as the yeast Candida albicans were also determined. Cell viability assays showed that the identified peptides are bacteriostatic against both S. aureus and E. coli.
Lysis of Escherichia coli by.-Lactam Antibiotics: Deletion Analysis of the Role of Penicillin-binding Proteins 1A and 1B (1985)

Deletions of the ponA and ponB genes of Escherichia coli have been constructed in vitro and recombined into the chromosome to produce strains that completely lack penicillin-binding protein 1A or penicillin-binding protein 1B. In each case a DNA fragment internal to the gene was replaced by a fragment encoding an antibiotic resistance. The ponA and ponB deletions can therefore be readily introduced into other E. coli strains by P1 transduction of the antibiotic resistance. Although the complete absence of penicillin-binding protein 1A or penicillin-binding protein 1B was tolerated, the absence of both of these proteins was shown to result in bacterial lysis.
Nucleotide sequence analysis of the non-structural NS1 (1C) and NS2 (1B) protein genes of bovine respiratory syncytial virus (1995)

The nucleotide and deduced amino acid sequences of the non-structural (NS) protein genes of bovine respiratory syncytial virus (BRSV) strain A51908 were determined. The NS1 and NS2 genes were 524 and 489 nucleotides long with single open reading frames, encoding polypeptides of 136 and 124 amino acids, respectively. Comparison of the NS1 gene of BRSV with the corresponding sequences of ovine respiratory syncytial virus (ORSV) and human respiratory syncytial virus (HRSV) subgroups A and B revealed 82, 67 and 65% identity at the nucleotide level, and 89, 69 and 68% identity at the amino acid level, respectively. The nucleotide identity of the NS2 gene of BRSV to those of ORSV and HRSV subgroups A and B was 80, 69 and 67% and the predicted amino acid identity was 87, 84 and 83%, respectively. The intergenic sequences of the NS1-NS2 and NS2-N gene junctions of BRSV were determined and found to be 13 nucleotides shorter and 29 nucleotides longer, respectively, than the corresponding regions of HRSV.
Effects of Genomic Position on the Expression of Transduced Copies of the white Gene of Drosophila (1985)

The white gene of Drosophila is expressed normally when introduced at many different sites in the genome by P-element-mediated DNA transformation, but is expressed abnormally when inserted at two particular genomic positions. It is now demonstrated that the mutant expression in these two cases is caused by the surrounding chromosomal region into which the white gene has been inserted. The white gene could be moved from these two positions, where it confers a mutant phenotype, to other positions in the genome where it confers a wild-type phenotype. However, flies in which white has been moved to one new location have an unusual mosaic phenotype.
Preeclampsia (1994)

Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee Women's Hospital, University of Pittsburgh, Pittsburgh, Pennsylvania
Serum p53 antibodies: predictors of survival in small-cell lung cancer? (2000)

Serum p53 antibodies have been shown to be a poor prognostic marker in resected non-small-cell lung cancer (NSCLC), but studies in small-cell lung cancer (SCLC) have been contradictory. We have studied the incidence of p53 antibodies in a large SCLC cohort treated at one oncology centre and correlated the results with survival. 231 patients (63% male, median age 65), diagnosed and treated for SCLC between 1987 and 1994 at The Royal Marsden Hospital NHS Trust, had sera stored pretreatment. All samples were tested for p53 antibodies (p53-Ab) using a standardized ELISA technique with a selection of strongly ELISA positive, weakly ELISA positive and negative samples being confirmed with immunoprecipitation. 54 patients were positive for p53-Ab (23%). The presence of a high titre of p53-Ab (titre ratio >5) appears to be associated with a survival advantage with a relative risk of death of 1.71 (95% CI: 1.14-2.58) in those without the antibody (P = 0.02). This study, the largest homogeneous group so far looking at p53-Ab in SCLC, suggests that p53 antibody detection may have a role in predicting outcome in this type of cancer.
Cosine-modulated analysis-synthesis filterbank with critical sampling and perfect reconstruction (1991)

The authors present a simple derivation of a parallel filterbank based on cosine-modulated versions of a model low-pass filter. With a nonuniform channel separation an efficient implementation consisting of a DFT (discrete Fourier transform) related transform and subfilters is possible. Using critical sampling of each channel and FIR (finite impulse response) filters, the conditions for perfect reconstruction are given. The computational complexity of the derived FIR filterbank is much lower than for a tree-structured FIR filterbank but cannot compete with the most efficient IIR filterbanks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Atomic-resolution structure of the cellulose synthase regulator cyclic diguanylic acid. (1990)

Cyclic diguanylic acid acts as a regulator for cellulose synthase activity in the bacterium Acetobacter xylinum. We report the x-ray crystal structure of the regulator at atomic resolution. The structure contains two independent molecules that adopt almost identical conformations. The two molecules form self-intercalated units that are stacked on each other. Two different G.G base-pairing modes occur between the stacks. The more stable one has two or possibly three hydrogen bonds between two guanines and is related to the type of hydrogen bonding that is believed to exist between G-rich strands at the ends of chromosomes.
Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments (2006)

Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens.