gebhart/patrepeval huggingface dataset:
Human Vaccination with Escherichia coli J5 Mutant Induces Cross-Reactive Bactericidal Antibody against Neisseria gonorrhoeae Lipooligosaccharide (1992)

The lipopolysaccharides of enteric gram-negative bacteria and the lipooligosaccharides (LOS) of Neisseria gonorrhoeae may share antigenic determinants that are targets of bactericidal antibody. Natural (disseminated) infection with a serum-resistant gonococcal strain and immunization with Escherichia coli J5 stimulated bactericidal IgG anti-LOS antibodies that recognize different serum-resistant gonococcal LOS epitopes. In bactericidal assays, convalescent serum from disseminated infection killed only the homologous strain while post-J5 vaccination serum killed 6 of 9 additional strains. Both convalescent and post-J5 vaccination sera mediated marker (51Cr) release from liposomes sensitized with serum-resistant gonococcal LOS (homologous strain), linking acquired killing activity to cross-reacting anti-LOS antibody. Post-J5 IgG mediated 51Cr release more effectively than did convalescent IgG. Thus, bactericidal antibody elicited by J5 vaccination is more efficacious and broadly cross-reactive against serum-resistant gonococci than is antibody elicited by natural infection. Moreover, multiple LOS epitopes may serve as bactericidal targets on serum-resistant gonococci.
Foundations of Intelligent Additive Manufacturing (2017)

During the last decade, additive manufacturing has become increasingly popular for rapid prototyping, but has remained relatively marginal beyond the scope of prototyping when it comes to applications with tight tolerance specifications, such as in aerospace. Despite a strong desire to supplant many aerospace structures with printed builds, additive manufacturing has largely remained limited to prototyping, tooling, fixtures, and non-critical components. There are numerous fundamental challenges inherent to additive processing to be addressed before this promise is realized. One ubiquitous challenge across all AM motifs is to develop processing-property relationships through precise, in situ monitoring coupled with formal methods and feedback control. We suggest a significant component of this vision is a set of semantic layers within 3D printing files relevant to the desired material specifications. This semantic layer provides the feedback laws of the control system, which then evaluates the component during processing and intelligently evolves the build parameters within boundaries defined by semantic specifications. This evaluation and correction loop requires on-the-fly coupling of finite element analysis and topology optimization. The required parameters for this analysis are all extracted from the semantic layer and can be modified in situ to satisfy the global specifications. Therefore, the representation of what is printed changes during the printing process to compensate for eventual imprecision or drift arising during the manufacturing process.
Molecular modelling of the multiphosphorylated casein phosphopeptide αS1-casein(59-79) based on NMR constraints (2004)

Casein micelles contain stabilized amorphous calcium phosphate that is bioavailable to the neonate (Holt &amp; Sawyer, 1988). Tryptic phosphopeptides formed from casein digestion associate with amorphous calcium phosphate forming stable nanocomplexes that have been described as calcium phosphate delivery vehicles (Holt et al. 1996; Reynolds et al. 1999, 2003; Farrell et al. 2002).
Differentiation of binding sites on reconstituted hepatic scavenger receptors using oxidized low-density lipoprotein (1992)

Reduced hepatic membrane receptors for acetylated low-density lipoprotein (acetyl-LDL) and maleylated BSA (Mal-BSA) with apparent molecular masses of 35 kDa, 85 kDa and 15 kDa have been extracted from rat liver and separated by affinity chromatography as described by us previously [Ottnad, Via, Sinn, Freidrich, Ziegler &amp; Dresel (1990) Biochem. J. 265, 689-698]. Binding of these three reduced scavenger receptors to oxidatively modified LDL has been now examined. Competition studies with receptor-phosphatidylcholine complexes and 131I-acetyl-LDL and 131I-Mal-BSA as ligands were conducted. Mal-BSA, acetyl-LDL and fully oxidized LDL were used as competitors, and differentiated in the three receptors three types of binding site: a class I binding site for acetyl-LDL, Mal-BSA and fully oxidized LDL; a class II binding site recognizing only 131I-Mal-BSA and class III binding sites recognizing 131I-Mal-BSA and fully oxidized LDL. The results of competition studies with mildly oxidized LDL and polyadenylic acid demonstrated that the binding sites might be even more heterogenous. Thus there is evidence that the reconstituted receptors either have several binding sites for each of the various ligands or are functionally different, despite the fact that they do not differ in their apparent molecular masses.
Dominant negative inhibition of tumorigenesis in vivo by human insulin-like growth factor I receptor mutant. (1994)

Although insulin-like growth factor I (IGF-I) is a mitogenic growth factor, its role in tumorigenesis is unclear. We therefore transfected wild-type and truncated beta-subunit mutant (952STOP) human IGF-I receptor cDNAs into Rat-1 fibroblasts. Rat-1 transfectants expressed 2.5- to 7-fold increased IGF-I receptor mass, while the Kd for IGF-I binding was unchanged. The Rat-1 cells transfected with wild-type receptor cDNA responded to in vitro IGF-I treatment by increased proliferation and DNA synthesis. Cells overexpressing wild-type receptors were also transformed as evidenced by ligand-dependent colony proliferation in soft agar. After injection into athymic nude mice, all wild-type transfectants formed solid sarcomas within 3 weeks, and ex vivo tumor cell assays confirmed continued overexpression of human IGF-I receptors. In contrast, both DNA synthesis and proliferation of 952STOP-transfected cells were attenuated below that of untransfected cells. 952STOP cells were nonresponsive to IGF-I in vitro and were unable to sustain anchorage-independent growth. No tumors were induced for up to 8 weeks after injection of 952STOP transfectants into athymic mice, despite the presence of demonstrable endogenous IGF-I receptors on the 952STOP-transfected cells. Therefore, 952STOP behaves as a dominant negative inhibitor of endogenous IGF-I receptor function, probably by assembling nonfunctional hybrid rat/mutant human receptor tetramers.
Glue protein genes in Drosophila virilis: their organization, developmental control of transcription and specific mRNA degradation (1990)

The gene Lgp-1, which is localized in the intermoult puff 16A of D. virilis polytene chromosomes, encodes the major larval glue protein Igp-1. The gene consists of two exons interrupted by a short intron. In the 5' flanking region of Lgp-1, we find putative ecdysone receptor binding sites and two proximal conserved sequence motifs which are possibly involved in gene regulation. The amino acid sequence deduced from the DNA sequence reveals a relationship to the 68C glue protein family of D. melanogaster. The size of the Lgp-1 transcripts decreases in late third instar larvae concomitantly with their disappearance. This is caused by deadenylation followed by distinct nucleolytic attacks in the 3' untranslated region. Preliminary data suggest the presence of another glue protein gene in the 16A puff region which is related to the Lgp-1 gene.
Integrating mouse anatomy and pathology ontologies into a phenotyping database: Tools for data capture and training (2008)

The Mouse Disease Information System (MoDIS) is a data capture system for pathology data from laboratory mice designed to support phenotyping studies. The system integrates the mouse anatomy (MA) and mouse pathology (MPATH) ontologies into a Microsoft Access database facilitating the coding of organ, tissue, and disease process to recognized semantic standards. Grading of disease severity provides scores for all lesions that can then be used for quantitative trait locus (QTL) analyses and haplotype association gene mapping. Direct linkage to the Pathbase online database provides reference definitions for disease terms and access to photomicrographic images of similar diagnoses in other mutant mice. MoDIS is an open source and freely available program (http://research.jax.org/faculty/sundberg/index.html). This provides a valuable tool for setting up a mouse pathology phenotyping program.
Non-contact and Unrestrained Respiration Monitoring System for Sleeping Person Using Near-infrared Bright Spots Matrix Irradiation (2004)

Measurement of biological information appears to be an effective method to obtain an understanding of health conditions measures to maintain and improve the health of elderly people. However, every conventional bioinstrumentation technique imposes a sense of restraint that results in aversion against measurements that would last over consecutive days. To solve this problem, we propose a system for monitoring the respiration of sleepers, and it uses a fiber grating vision sensor, which is a type of optical range finder, to achieve non-contact and unrestrained monitoring. The signals obtained by the system include the respiration rate, shifts of the ventilation, and the body movement interval of the sleeper. The information enables to investigate the stability of the sleeper throughout the night.We examined the measuring accuracy, validity, and effectiveness of our proposed system. And all-night monitoring performed at elderly care facility revealed that respiratory disturbances during sleep occurred in many of the residents and that sleep apnea is a common syndrome, especially among residents who have senile dementia or have had a stroke. We were able to carry out the all-night monitoring with this system for a total of about 370 times, according to our schedule, without experiencing any failure, accident, or interruption. Our proposed system is highly effective for monitoring elderly dementia patients who are likely to become uncooperative during measurement with existing monitoring methods that use certain amounts of restraint.
Comparison of Isochrysis galbana and Chlorella sp. microalgae on growth and survival rate of European flat oyster (Ostrea edulis, Linnaeus 1758) larvae (2011)

Influence of microalgal feeding with Isochrysis galbana and Chlorella sp. on the growth and survival rate of larvae of European flat oyster, Ostrea edulis, was investigated. Larvae were reared with four food regimes: I. galbana, Chlorella sp., mixture of both and unfed for 16 days. After 16 days, it was observed that the larvae reached the umbo stage with a mean size in length 220±4.12 μm and 219±5.76 μm (initial length, 159 μm) (P > 0.05). Larvae were fed on I. galbana and mixture diet. At this stage, survival rate was 30% and 24%, respectively (P > 0.05). Growth and survival rates for the feeding regimes were significantly higher than the Chlorella sp. and unfed groups (P < 0.05).
Spherosomes of Castor Bean Endosperm (1980)

The membrane components of the castor bean spherosomes were characterized. The storage triacylglycerols of isolated spherosomes were extracted with diethyl ether, and the membrane was isolated by sucrose gradient centrifugation. It had an apparent equilibrium density of 1.12 grams per cubic centimeter, and possessed an antimycin A-insensitive NADH cytochrome c reductase and an acid lipase. Phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol in roughly equal amounts were the major phospholipids. The membrane proteins were resolved into several major and minor protein bands of molecular weights ranging from 10,000 to 70,000 by acrylamide gel electrophoresis, and the protein pattern in the gel was different from those of the endoplasmic reticulum, mitochondrial, and glyoxysomal membranes.The varying amounts of spherosomal components in the seed were followed throughout seed maturation and germination. A striking similarity existed in the developmental pattern of each of the spherosomal components. This finding suggests that the spherosome is synthesized and degraded as one individual unit. The spherosomes isolated from maturing seeds exhibited rapid hydrolysis of the storage lipid in vitro, thus raising the problem of cellular control in preventing in vivo autolysis of the spherosomes during seed maturation.
Platelet-Derived Growth Factor D Induces Cardiac Fibrosis and Proliferation of Vascular Smooth Muscle Cells in Heart-Specific Transgenic Mice (2005)

Platelet-derived growth factor (PDGF)-D is a member of the PDGF/vascular endothelial growth factor family that activates PDGF receptor beta (PDGFR-beta). We show that PDGF-D is highly expressed in the myocardium throughout development and adulthood, as well as by arterial vascular smooth muscle cells (vSMCs). To obtain further knowledge regarding the in vivo response to PDGF-D, we generated transgenic mice overexpressing the active core domain of PDGF-D in the heart. Transgenic PDGF-D stimulates proliferation of cardiac interstitial fibroblasts and arterial vSMCs. This results in cardiac fibrosis followed by dilated cardiomyopathy and subsequent cardiac failure. Transgenic mice also display vascular remodeling, including dilation of vessels, increased density of SMC-coated vessels, and proliferation of vSMCs, leading to a thickening of tunica media. The thickening of arterial walls is a unique feature of PDGF-D, because this is not seen when PDGF-C is overexpressed in the heart. These results show that PDGF-D, via PDGFR-beta signaling, is a potent modulator of both vascular and connective tissue growth and may provide both paracrine and autocrine stimulation of PDGFR-beta. Our data raise the possibility that this growth factor may be involved in cardiac fibrosis and atherosclerosis.
Doped amorphous semiconductors (1977)

Abstract The article reviews the advances that have been made during the past two years in the new field of substitutionally doped a-semiconductors, particularly a-Si. After introducing some of the basic concepts used in the treatment of a-materials, the preparation and doping of a-semiconductors from the gas phase and the role of hydrogen are discussed in some detail. Recent results on doping by ion implantation have also been included. The following sections are concerned with the effect of n and p-type impurities on the electronic transport properties of a-Si and a-Ge. The discussion is based on results from conductivity, drift mobility, Hall effect and thermoelectric power measurements and leads to the main conclusion that the donors introduce a new hopping path through the system which begins to dominate over tail-state hopping when their density exceeds about 1018 cm-3. Recent photo-conductivity and luminescence results on doped a-Si are then discussed; they give information on recombination and also demonstrate the pronounced effect of doping on these properties. In the final section amorphous p-n junctions are considered as well as their possible applications in photovoltaic solar energy conversion.
Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells (1988)

Examination of collections of 16S rRNA sequences revealed sequence domains that were unique to (and invariant within) the three primary lines of cellular descent: the archaebacteria, the eubacteria, and the eucaryotes. Oligodeoxynucleotides complementary to these conserved sequence domains were synthesized and used as hybridization probes. Each of the radiolabeled probes specifically hybridized to nylon membrane-bound 16S rRNA from the targeted kingdom. A probe complementary to a universally conserved sequence in 16S rRNAs was used as a positive control, while its complement provided a negative control for nonspecific binding. The abilities of the probes to bind specifically to whole, fixed cells representing a broad array of phylogenetic diversity were tested in whole-cell dot blot assays. Again, all of the probes specifically bound the targeted groups. By microautoradiography, the method was extended to permit phylogenetic identification of single cells microscopically.
Learning, tracking and recognition of 3D objects (2002)

In this contribution we describe steps towards the implementation of an active robot vision system. In a sequence of images taken by a camera mounted on the hand of a robot, we detect, track, and estimate the position and orientation (pose) of a three-dimensional moving object. The extraction of the region of interest is done automatically by a motion tracking step. For learning 3-D objects using two-dimensional views and estimating the object's pose, a uniform statistical method is presented which is based on the expectation-maximization-algorithm (EM-algorithm). An explicit matching between features of several views is not necessary. The acquisition of the training sequence required for the statistical learning process needs the correlation between the image of an object and its pose; this is performed automatically by the robot. The robot's camera parameters are determined by a hand/eye-calibration and a subsequent computation of the camera position using the robot position. During the motion estimation stage the moving object is computed using active, elastic contours (snakes). We introduce a new approach for online initializing the snake on the first images of the given sequence, and show that the method of snakes is suited for real time motion tracking.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutation Detection and Mutation Databases (1998)

Detection of mutations in genes is vital throughout biology, however, this activity is time-consuming, expensive and requires a high degree of skill. This is unsatisfactory in a field which is increasing importance. Around 10-12 methods are commonly used with some predominating. All have their advantages and disadvantages and none is perfect. Sequencing is said to be the gold standard for detecting new mutations (and must be used to define it), but six or so methods have been described to make the search quicker to avoid sequencing the whole gene. These are called scanning methods. Other methods are used to detect known mutations and referred to as diagnostic methods. These methods will be briefly reviewed. Once mutations are described, they are usually published. The mutation lists are collected for convenience, analysis or research. In recent years, it has been realised that these lists are vital for research, patient care and commercial activities. These activities will be reviewed and the co-ordinating role of the HUGO Mutation Database Initiative will be outlined.
Expression of monocyte chemoattractant protein-1 in delayed type hypersensitivity reactions in the skin. (1994)

We observed an enhanced expression of MCP-1 in inflammatory skin conditions. The expression of MCP-1 provides a mechanistic explanation for the increased recruitment of monocytes/macrophages in cell-mediated immune response such as delayed type hypersensitivity reactions in the skin.
Ribosome-inactivating proteins from the seeds of Saponaria officinalis L. (soapwort), of Agrostemma githago L. (corn cockle) and of Asparagus officinalis L. (asparagus), and from the latex of Hura crepitans L. (sandbox tree) (1983)

Ribosome-inactivating proteins, similar to those already known [Barbieri & Stirpe (1982) Cancer Surveys 1, 489-520] were purified from the seeds of Saponaria officinalis (two proteins), of Agrostemma githago (three proteins), and of Asparagus officinalis (three proteins), and from the latex of Hura crepitans (one protein). The yield ranged from 8 to 400 mg/100 g of starting material. All proteins have an Mr of approx. 30000 and an alkaline isoelectric point. Their sugar content varies from 0 (proteins from S. officinalis) to 40% (protein from H. crepitans). The ribosome-inactivating proteins inhibit protein synthesis by rabbit reticulocyte lysate, the ID50 (concentration giving 50% inhibition) ranging from 1 ng/ml (a protein from S. officinalis) to 18 ng/ml (a protein from A. githago). Those which were tested (the proteins from S. officinalis and from A. githago) also inhibit polymerization of phenylalanine by isolated ribosomes, acting in an apparently catalytic manner. The protein from H. crepitans inhibited protein synthesis by HeLa cells, with an ID50 of 4 micrograms/ml, whereas the proteins from S. officinalis and from A. githago had an ID50 of more than 50-100 micrograms/ml. The ribosome-inactivating proteins from S. officinalis and from A. githago reduced the number of local lesions by tobacco-mosaic virus in the leaves of Nicotiana glutinosa.
A comparative analysis of methodologies for database schema integration (1986)

One of the fundamental principles of the database approach is that a database allows a nonredundant, unified representation of all data managed in an organization. This is achieved only when methodologies are available to support integration across organizational and application boundaries. Methodologies for database design usually perform the design activity by separately producing several schemas, representing parts of the application, which are subsequently merged. Database schema integration is the activity of integrating the schemas of existing or proposed databases into a global, unified schema. The aim of the paper is to provide first a unifying framework for the problem of schema integration, then a comparative review of the work done thus far in this area. Such a framework, with the associated analysis of the existing approaches, provides a basis for identifying strengths and weaknesses of individual methodologies, as well as general guidelines for future improvements and extensions.
Role of the Nrf2-Mediated Signaling Pathway as a Negative Regulator of Inflammation: Implications for the Impact of Particulate Pollutants on Asthma (2006)

Particulate matter (PM) is an environmental factor that may contribute to the exacerbation and possibly the development of asthma. PM contain redox-active chemicals and transition metals which generate reactive oxygen species (ROS). Excessive ROS can induce oxidative stress, which proceeds in hierarchical fashion to generate cellular responses. The most sensitive cellular response to mild oxidative stress is the activation of antioxidant and phase II enzymes (tier 1). If this protection fails, further increase of oxidative stress can induce inflammation (tier 2) and cell death (tier 3). Tier 1 antioxidant defenses are critical for protecting against airway inflammation and asthma. The expression of these antioxidant enzymes is regulated by the transcription factor, Nrf2. In response to oxidative stress, Nrf2 escapes from Keap1-mediated proteasomal degradation resulting in prolonged protein half-life and its nuclear accumulation. Nrf2 interacts with the antioxidant response element (ARE) in the promoters of phase II enzyme genes, leading to their transcriptional activation. Several phase II expression polymorphisms are associated with an increased risk of asthma. The indispensable role of Nrf2 in tier-1 oxidative stress response suggests that polymorphisms of Nrf2-regulated genes may be useful susceptibility markers for asthma. Moreover, chemopreventive Nrf2 inducers may be used for treating PM-exacerbated asthma.