gebhart/patrepeval huggingface dataset:
Agrobacterium Ti plasmid indoleacetic acid gene is required for crown gall oncogenesis (1982)

A gene (iaaP) necessary for virulence and indoleacetic acid (IAA) production has been located on a nopaline Ti plasmid of Agrobacterium tumefaciens C58. iaaP function was established by using transformation to insert nopaline or octopine Ti plasmids into an avirulent, Ti plasmid-free mutant 1D1293-3 that was defective in IAA synthesis (iaaC(-)). The resulting transformants produced increased levels of IAA and virulence was restored. When these transformants were cured of their Ti plasmid, virulence and high IAA production levels were concomitantly lost. A Tn5 mutagenized TiC58 plasmid, deficient in the ability to direct increased synthesis of IAA, was inserted by transformation into mutant 1D1293-3. The resulting transformants 1D1293-3 (TiC58::Tn5) remained avirulent and iaaP(-). Restriction analysis of the TiC58::Tn5 plasmid DNA identified the iaaP gene at 20.9 kilobases to the left of the T-DNA. A major aromatic-amino-acid aminotransferase is coded by the iaaC gene, but not by the iaaP gene. The possible reasons for the iaaP locus to be situated outside the T-DNA region are discussed.
A Mutation that Creates a Pseudoexon in SOD1 Causes Familial ALS (2009)

Summary Amyotrophic lateral sclerosis (ALS) is an adult onset neurodegenerative disease which targets motor neurons of the cortex, brainstem and spinal cord. About 5–10% of all amyotrophic lateral sclerosis cases are familial (FALS), and 15–20% of FALS cases are caused by mutations in the zinc‐copper superoxide dismutase gene ( SOD1 ). We identified a large family from France with ten members affected with ALS. Linkage was established to the SOD1 locus on chromosome 21 and genomic and cDNA sequencing was performed for the SOD1 gene. This revealed an activated pseudoexon between exons 4 and 5 that was present in two tested members of the family. Translation of this 43 base pair exon results in the introduction of seven amino acids before a stop codon is present, leading to a prematurely truncated SOD1 protein product of 125 amino acids. Sequencing intron 4 in a patient revealed a heterozygous change 304 bp before exon 5 (c.358 – 304C &gt; G), but only 5 bp after the cryptic exon, thus causing this alternative splice product. This mutation segregated in all affected individuals of the family. This adds an additional genetic mechanism for developing SOD1 ‐linked ALS and is one which can be more readily targeted by gene therapy.
Cloning and Characterization of the Human Megakaryocyte Growth and Development Factor (MGDF) Gene (1995)

The megakaryocyte growth and development factor (MGDF) is a cytokine that regulates megakaryocyte development and is a ligand for the MPL receptor. In this study, we describe the genomic structure of the human MGDF gene. The MGDF gene was found to consist of seven exons and six introns spanning 8 kilobases. The protein is encoded by exons 3 through 7. The human MGDF gene has been mapped to chromosome 3q26.3. In addition to the previously described full-length cDNA, two cDNA variants were isolated from human fetal liver. Comparison of these two cDNA sequences with the genomic sequence indicates that they arise by differential splicing.
A Home Diary to Assess Functional Status in Patients with Parkinson's Disease with Motor Fluctuations and Dyskinesia (2000)

In clinical trials for patients with Parkinson's disease (PD) with motor fluctuations, efficacy is generally ascribed to an intervention if motor function is significantly improved or if "off" time is significantly reduced. However, we have argued that patients might not be improved if off time is reduced only to the extent that unwanted dyskinesia is increased. Therefore, a home diary should include an assessment of dyskinesia to provide an accurate reflection of clinical status over a period of time. We undertook two studies to develop a home diary to assess functional status in patients with PD with motor fluctuations and dyskinesia. In both studies, patients concurrently completed a test and a reference diary. In Study I, we evaluated the impact of different severities of dyskinesia on patient-defined functional status. There were 1,149 evaluable half-hour time periods from 24 patients; 94.3% of off time was considered "bad" time and 90.2% of "on" time without dyskinesia, 72.6% of on time with mild dyskinesia, 43.0% of on time with moderate dyskinesia, and 15.2% of on time with severe dyskinesia was considered "good" time. In Study II, we evaluated a new home diary designed to separate dyskinesia that had a negative impact on patient-defined functional status from dyskinesia that did not. There were 816 evaluable time periods from 17 patients; 84.9% of off time and 89.9% of on time with troublesome dyskinesia was considered bad time while 85.5% of on time without dyskinesia and 93.8% of on time with nontroublesome dyskinesia was considered good time. With this diary (Diary II), the effect of an intervention can be expressed as the change in off time and the change in on time with troublesome dyskinesia (bad time). The sum can be used as an outcome variable and compared to baseline or across groups. In evaluating the efficacy of an intervention, assessment of change in off time and change in on time with troublesome dyskinesia provides a more accurate reflection of clinical response than change in off time alone.
Induction of carcinogenesis by concurrent inactivation of p53 and Rb1 in the mouse ovarian surface epithelium. (2003)

Alterations in p53 and Rb pathways are observed frequently in epithelial ovarian cancer (EOC).However, their roles in EOC initiation remain uncertain. Using a single intrabursal administration of recombinant adenovirus expressing Cre, we demonstrate that concurrent inactivation of p53 and Rb1 is sufficient for reproducible induction of ovarian epithelial carcinogenesis in mice homozygous for conditional gene alleles. Similarly to progression of disease in women, ovarian neoplasms spread i.p., forming ascites, and metastasize to the contralateral ovary, the lung, and the liver. These results establish critical interactions between p53 and Rb1 pathways in EOC pathogenesis, and provide a genetically defined immunocompetent mouse model of sporadic EOC.
<title>Theory and experiments of resonant waveguide gratings under Brewster incidence</title> (1999)

Guided-mode resonance refers to a sharp resonance effect in waveguide gratings where efficient energy exchange between reflected and transmitted waves occurs in a small parameter (wavelength, angle, or refractive index) range. High- efficiency optical reflection filters are obtainable using zero-order waveguide gratings based on this effect. In this paper, a new type of high-contrast (high efficiency and low- sideband) guided-mode resonance reflection filter is studied theoretically and experimentally. Low-reflection sidebands and symmetrical resonance lineshapes are achieved by incorporating thin-film Brewster effects for a TM-polarized incident wave. Experimental results verifying the feasibility of this concept are presented.
Glycogen synthase kinase-3β mediates convergence of protection signaling to inhibit the mitochondrial permeability transition pore (2004)

Environmental stresses converge on the mitochondria that can trigger or inhibit cell death. Excitable, postmitotic cells, in response to sublethal noxious stress, engage mechanisms that afford protection from subsequent insults. We show that reoxygenation after prolonged hypoxia reduces the reactive oxygen species (ROS) threshold for the mitochondrial permeability transition (MPT) in cardiomyocytes and that cell survival is steeply negatively correlated with the fraction of depolarized mitochondria. Cell protection that exhibits a memory (preconditioning) results from triggered mitochondrial swelling that causes enhanced substrate oxidation and ROS production, leading to redox activation of PKC, which inhibits glycogen synthase kinase-3beta (GSK-3beta). Alternatively, receptor tyrosine kinase or certain G protein-coupled receptor activation elicits cell protection (without mitochondrial swelling or durable memory) by inhibiting GSK-3beta, via protein kinase B/Akt and mTOR/p70(s6k) pathways, PKC pathways, or protein kinase A pathways. The convergence of these pathways via inhibition of GSK-3beta on the end effector, the permeability transition pore complex, to limit MPT induction is the general mechanism of cardiomyocyte protection.
Manipulating Electromagnetic Wave Polarizations by Anisotropic Metamaterials (2007)

We show that the polarization states of electromagnetic waves can be manipulated through reflections by an anisotropic metamaterial plate, and all possible polarizations (circular, elliptic, and linear) are realizable via adjusting material parameters. In particular, a linearly polarized light converts its polarization completely to the cross direction after reflection under certain conditions. Microwave experiments were performed to successfully realize these ideas and results are in excellent agreement with numerical simulations.
High Resolution Dune Complex Mapping for the Monitoring of Coastal Landform Change, First Landing State Park, Virginia (2007)

First Landing State Park is located on the southern shore of the mouth of the Chesapeake Bay. The park contains a prograding shoreline and dune complex that has been steadily growing northward. Accurate three dimensional mapping of the resident coastal dune features is challenging due to the dynamic nature of the dunescape. Precise mapping within First Landing was accomplished through careful planning, employ of advanced Global Positioning System (GPS) technology, and intensive data analysis. Mapping ensued during a period of optimal satellite signal availability and strength. Data points were collected at manual intervals with a Leica GS50+ GPS receiver, utilizing real-time kinematic (RTK) corrections from ground control stations. Vertical data accuracies of less than 5cm were achieved. Horizontal accuracies were near 1cm. The resultant data was interpolated to create realistic contour maps, triangulated irregular networks (TINS), and raster elevation models of the study area. The methods employed may be replicated at standard time intervals for the purpose of establishing a database to maintain an inventory of dune features within First Landing. Temporal changes in this inventory may be monitored to illustrate rates of change and illuminate conditions that may require management intervention.
Experimental characterization of sectorized antennas in dense 802.11 wireless mesh networks (2009)

Sectorized antennas can increase wireless network capacity through greater spatial reuse. Despite their increasing popularity, their real-world performance characteristics in dense wireless mesh networks are not well understood. This paper conducts a systematic experimental study on a mesh network testbed using commodity 802.11 hardware and multi-sector antennas.
Acidification of the cytosol inhibits endocytosis from coated pits. (1987)

Acidification of the cytosol of a number of different cell lines strongly reduced the endocytic uptake of transferrin and epidermal growth factor. The number of transferrin binding sites at the cell surface was increased in acidified cells. Electron microscopic studies showed that the number of coated pits at the cell surface was not reduced in cells with acidified cytosol. Experiments with transferrin-horseradish peroxidase conjugates and a monoclonal anti-transferrin receptor antibody demonstrated that transferrin receptors were present in approximately 75% of the coated pits both in control cells and in cells with acidified cytosol. The data therefore indicate that the reason for the reduced endocytic uptake of transferrin at internal pH less than 6.5 is an inhibition of the pinching off of coated vesicles. In contrast, acidification of the cytosol had only little effect on the uptake of ricin and the fluid phase marker lucifer yellow. Ricin endocytosed by cells with acidified cytosol exhibited full toxic effect on the cells. Although the pathway of this uptake in acidified cells remains uncertain, some coated pits may still be involved. However, the data are also consistent with the possibility that an alternative endocytic pathway involving smooth (uncoated) pits exists.
Fluctuations in blood flow to acral skin in humans: connection with heart rate and blood pressure variability. (1993)

1. Spontaneous fluctuations in blood flow in arteries supplying acral skin were investigated with Doppler ultrasound in human subjects. Finger blood pressure, heart rate (HR) and cardiac output were measured simultaneously and noninvasively. 2. Synchronous fluctuations in flow were found in arteries supplying the hands and feet. The fluctuations were larger and more rapid than the flow variations which have been demonstrated with other methods. The magnitude of the total flow fluctuations in the hands and feet was estimated to be 5-10% of cardiac output in resting subjects. This range of flow fluctuations is made possible by spontaneous opening and closing of skin arteriovenous anastomoses (AVAs). 3. The fluctuations in skin blood flow were accompanied by inverse fluctuations in mean blood pressure (MAP). The power spectra of skin vascular conductance and MAP both contained maximum intensity at low frequencies, below 0.15 Hz, with high coherence. 4. The central circulatory events connected with the skin blood flow fluctuations were calculated from the experimental data with the use of transfer function analysis. There was a rise in HR, cardiac output and MAP starting 1-4 s before a cutaneous vasoconstriction. This indicates that the HR and MAP responses are not only passive effects of changes in peripheral resistance, but are the result of a simultaneous activation of the peripheral vascular and cardiac efferent branches of the autonomic nervous system. The HR and MAP responses are then modified, probably by baroreceptor activation.
Three dynamic problems in robot force control (1992)

Three dynamic characteristics of robot systems are discussed: rigid-body bandwidth, dynamically noncolocated flexible modes, and dynamically colocated flexible modes. All of these combine to limit the closed-loop bandwidth achievable in the individual joint control loops of the robot. They play a particularly important role in establishing performance limits for robots under force control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rapid and effective DNA amplification by polymerase chain reaction directly from paraffin-embedded tissue (2004)

A large number of archival paraffin-embedded tissue banks have been established during diagnostic surgical pathology, forming a precious resource of tissues for retrospective molecular studies of cancer and a variety of other diseases. Extraction of DNA from formalin-fixed paraffin-embedded tissue samples was previously accomplished. However, this procedure is labor intensive, time-consuming and expensive. This study demonstrated the successful use and optimization of a rapid, reliable and effective protocol for DNA amplification directly from paraffin-embedded tissue eliminating the deparaffinization and DNA isolation steps. In the course of this study effectiveness of a commercially available, ready-to-use PCR master mix kit was also tested. Once the presented protocol for DNA amplification is applied correctly, large quantities of paraffin-embedded material stored in our pathology departments will be available for molecular diagnostics and research.
Localization and Translocation of MMP-2 during Aggregation of Human Platelets (1998)

We have previously shown that human platelets express matrix metalloproteinase-2 (MMP-2) and that the release of this enzyme during platelet activation mediates the ADP- and thromboxane-independent part of aggregation. We have now used immunogold electron microscopy, flow cytometry. Western blot analysis and zymography methods to study the ultrastructural localization of MMP-2 in human washed platelets. Platelet aggregation was stimulated by collagen and the MMP-2 immunoreactivity of platelets was followed during various stages of aggregation. In resting platelets, MMP-2 was randomly distributed in the platelet cytosol without detectable association with platelet granules. Platelet aggregation caused the translocation of MMP-2 from the cytosol to the extracellular space. During the early stages of aggregation, MMP-2 remained in close association with the platelet plasma membrane. We conclude that the interactions of MMP-2 with platelet surface membranes mediate the aggregatory response induced by this enzyme.
Elastin point mutations cause an obstructive vascular disease, supravalvular aortic stenosis (1997)

Supravalvular aortic stenosis (SVAS) is an inherited obstructive vascular disease that affects the aorta, carotid, coronary and pulmonary arteries. Previous molecular genetic data have led to the hypothesis that SVAS results from mutations in the elastin gene, ELN. In these studies, the disease phenotype was linked to gross DNA rearrangements (35 and 85 kb deletions and a translocation) in three SVAS families. However, gross rearrangements of ELN have not been identified in most cases of autosomal dominant SVAS. To define the spectrum of ELN mutations responsible for this disorder, we refined the genomic structure of human ELN and used this information in mutational analyses. ELN point mutations co-segregate with the disease in four familial cases and are associated with SVAS in three sporadic cases. Two of the mutations are nonsense, one is a single base pair deletion and four are splice site mutations. In one sporadic case, the mutation arose de novo. These data demonstrate that point mutations of ELN cause autosomal dominant SVAS.
Peripheral Blood T Cell Dynamics Predict Relapse in Multiple Sclerosis Patients on Fingolimod (2015)

The CD4+TCM percentages at 2 weeks to 12 months during fingolimod therapy are related to relapse.
Detection of Mycoplasma genitalium by PCR Amplification of the 16S rRNA Gene (2003)

In order to develop a species-specific PCR for the detection of Mycoplasma genitalium, the sequence of 1,490 bases of the 16S rRNA gene was determined for M. genitalium G37 (type strain) and four Danish isolates of M. genitalium. The sequences of the four Danish strains, mutually different with respect to their MgPa gene, were 100% homologous, although they carried a single common base substitution compared to the type strain. Among members of the Mycoplasma pneumoniae phylogenetic cluster, M. genitalium showed the most-prominent homology to the 16S rRNA sequence of M. pneumoniae (98% homology). From regions showing the least homology to the M. pneumoniae 16S rRNA gene sequence, primers were chosen to amplify DNA from M. genitalium only. Two sets of primers were selected for their ability to detect <10 to 50 M. genitalium genome copies without cross-reactions with M. pneumoniae. The performance of these primers was compared to the performance of two pairs of primers amplifying parts of the MgPa adhesin gene; 1,030 randomly selected specimens submitted for Chlamydia trachomatis culture were screened with one of the 16S rRNA gene primer sets. A total of 41 specimens were found to be positive for this gene; 40 of these could be confirmed by one of the MgPa primer sets, whereas the other MgPa primer set detected only 21 positive specimens out of 40. These results indicate that estimates of the prevalence of M. genitalium in various populations using MgPa PCR primers could be incorrectly low if the PCR primers are located in variable regions of the MgPa gene.
Untersuchung der Einwirkung ionisierender Strahlung auf die Gas‐ und Wasserdampf‐Durchlässigkeit von Verpackungs‐Folien (1961)

Abstract Bei der Bestimmung der Wasserdampf‐Durchlässigkeit von Verpackungs‐Folien werden die Folien verschiedener Zusammensetzung und unterschiedlicher Eigenschaften Röntgenstrahlungen von 60 und 150 keV Energie und monoenergetischer Elektronenstrahlung von 1 MeV ausgesetzt. Bei der Bestrahlung von Folienmaterial und von verpackten Modellsubstanzen, die anstelle von Lebensmitteln verwendet werden, kann praktisch keine Änderung der Durchlässigkeit der Folien festgestellt werden.
PrediSi: prediction of signal peptides and their cleavage positions (2004)

We have developed PrediSi (Prediction of Signal peptides), a new tool for predicting signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences. In contrast to previous prediction tools, our new software is especially useful for the analysis of large datasets in real time with high accuracy. PrediSi allows the evaluation of whole proteome datasets, which are currently accumulating as a result of numerous genome projects and proteomics experiments. The method employed is based on a position weight matrix approach improved by a frequency correction which takes in to consideration the amino acid bias present in proteins. The software was trained using sequences extracted from the most recent version of the SwissProt database. PrediSi is accessible via a web interface. An extra Java package was designed for the integration of PrediSi into other software projects. The tool is freely available on the World Wide Web at http://www.predisi.de.
Synthesis and Properties of PNA/DNA Chimeras (1996)

Unambiguous binding to complementary DNA and RNA, stability toward 3′-exonucleases, and a similar uptake by cells as DNA oligomers characterize the PNA/DNA chimeras of type 1 described here. These chimeric oligomers are accessible in an automated synthesis sequence.
A new sensitive sandwich enzyme-linked immunosorbent assay to detect galactofuran in patients with invasive aspergillosis (1995)

A double-direct sandwich enzyme-linked immunosorbent assay that uses a rat anti-galactomannan monoclonal antibody as the acceptor and detector antibody was designed. This immunoassay, which detects less than 1 ng of galactomannan per ml, was assessed in a retrospective study with samples from patients with invasive aspergillosis. Serum is more appropriate than urine for use in the search for circulating galactomannan. Antigenemia does not have a transient character. Galactomannan can be detected at least 39 days before the death of the patients.
Effects of Acetate on Facultative Autotrophy inChlamydomonas reinhardtii Assessed by Photosynthetic Measurements and Stable Isotope Analyses (2000)

The green alga Chlamydomonas reinhardtii can grow photoautotrophically utilizing CO(2), heterotrophically utilizing acetate, and mixotrophically utilizing both carbon sources. Growth of cells in increasing concentrations of acetate plus 5% CO(2) in liquid culture progressively reduced photosynthetic CO(2) fixation and net O(2) evolution without effects on respiration, photosystem II efficiency (as measured by chlorophyll fluorescence), or growth. Using the technique of on-line oxygen isotope ratio mass spectrometry, we found that mixotrophic growth in acetate is not associated with activation of the cyanide-insensitive alternative oxidase pathway. The fraction of carbon biomass resulting from photosynthesis, determined by stable carbon isotope ratio mass spectrometry, declined dramatically (about 50%) in cells grown in acetate with saturating light and CO(2). Under these conditions, photosynthetic CO(2) fixation and O(2) evolution were also reduced by about 50%. Some growth conditions (e.g. limiting light, high acetate, solid medium in air) virtually abolished photosynthetic carbon gain. These effects of acetate were exacerbated in mutants with slowed electron transfer through the D1 reaction center protein of photosystem II or impaired chloroplast protein synthesis. Therefore, in mixotrophically grown cells of C. reinhardtii, interpretations of the effects of environmental or genetic manipulations of photosynthesis are likely to be confounded by acetate in the medium.