gebhart/patrepeval huggingface dataset:
Biocontrol mechanisms of Trichoderma strains. (2004)

The genus Trichoderma comprises a great number of fungal strains that act as biological control agents, the antagonistic properties of which are based on the activation of multiple mechanisms. Trichoderma strains exert biocontrol against fungal phytopathogens either indirectly, by competing for nutrients and space, modifying the environmental conditions, or promoting plant growth and plant defensive mechanisms and antibiosis, or directly, by mechanisms such as mycoparasitism. These indirect and direct mechanisms may act coordinately and their importance in the biocontrol process depends on the Trichoderma strain, the antagonized fungus, the crop plant, and the environmental conditions, including nutrient availability, pH, temperature, and iron concentration. Activation of each mechanism implies the production of specific compounds and metabolites, such as plant growth factors, hydrolytic enzymes, siderophores, antibiotics, and carbon and nitrogen permeases. These metabolites can be either overproduced or combined with appropriate biocontrol strains in order to obtain new formulations for use in more efficient control of plant diseases and postharvest applications.
Carbohydrate structure of glycopeptides isolated from an hepatic membrane-binding protein specific for asialoglycoproteins. (1976)

Two variant glycopeptide constituents of an hepatic membrane protein responsible for the clearance of circulating asialoglycoproteins have been isolated and characterized. Their relative abundance has been estimated to be 14 and 2 mol, respectively, per mol of intact protein. The larger component, glycopeptide I, is comprised of sialic acid, galactose, mannose, glucosamine, and aspartic acid in a molar ratio of 3:3:2:5:1. The smaller neutral fraction contains only two sugars and the molar relationship of mannose, glucosamine, and aspartic acid is 8:2:1. Based on the results of sequential digestion with specific glycosidases and periodate degradation, a carbohydrate sequence for both glycopeptides is proposed.
Cell Mechanics and Feedback Regulation of Actomyosin Networks (2009)

Actomyosin contractility is the major force-generating machinery that shapes cells and tissues during morphogenesis. New evidence from Drosophila demonstrates that these forces are spatially organized by a combination of biochemical and mechanical signals that provide dynamic feedback in a complex cellular environment.
Gonadotropin alpha-subunit glycoprotein from channel catfish (Ictalurus punctatus) and its expression during hormone-induced ovulation. (1997)

Complementary DNA (cDNA) encoding the channel catfish (Ictalurus punctatus) gonadotropin (GTH) alpha-subunit glycoprotein was cloned by polymerase chain reaction (PCR) from a plasmid library made from pituitary RNA. Complete cDNA cloning was achieved by carrying out two PCR reactions: one with an upstream sense primer plus the universal sequencing primer, located downstream of the poly(A) sequence of the cDNA in the plasmid vector, to amplify the downstream portion of the cDNA; the other with a downstream antisense primer plus the reverse-sequencing primer, located upstream of the very 5' end of the cDNA sense strand in the plasmid vector, to amplify the upstream portion of the cDNA. The two amplified fragments overlapping about 70 bp. Nucleotide sequence analysis revealed that the catfish GTH alpha-subunit was 658 bp encoding 116 amino acids and harboring a 5' nontranslated region (NTR) of 42 bp and a 3' NTR of 265 bp. The deduced amino acid sequence of the catfish GTH alpha-subunit is highly conserved with those from other cloned teleost GTH alpha-subunits. The GTH alpha-subunit was highly expressed even before induction for ovulation in females during spawning season. Administration of carp pituitary extract (a spawning-inducing reagent) induced only 1.4-fold higher expression of the GTH alpha-subunit RNA, but included very rapid egg maturation and ovulation. This unexpected result indicated that the GTH alpha-subunit may not be the limiting factor for ovulation and spawning, which may be regulated by the change of proportional coupling of the GTH alpha-subunit with specific beta-subunit during hormone-induced ovulation.
Use of CO and CO_2 Lasers to Detect Pollutants in the Atmosphere (1971)

Several spectral coincidences between CO laser emission lines and infrared absorption lines of oxides of nitrogen have recently been observed. Using existing infrared spectroscopy data, we predict additional spectral coincidences; the Q-switched CO laser emits certain lines which overlap SO(2) absorption lines, and certain frequency-doubled CO(2) laser lines overlap NO and CO absorption lines. Other spectral overlaps involving the CO(2) laser have been reported elsewhere. Based on such coincidences remote sensing of these atmospheric constituents can be accomplished by observing resonant absorption, thermal emission, or fluorescence. We discuss sensitivities for each of these methods, using data on line strengths and pressure-broadened line widths. Wide band heterodyne receivers offer high sensitivity when they can be used; our discussion includes the use of this type of receiver system.
SMPLIFIED INDEPENDENCE PROOFS BOOLEAN VALUED MODELS OF SET THEORY (1971)

By J. Barkley Rosser: pp. xv, 217; $10.00 (Academic Press Inc., New York, 1969).
Quantitative Models for Privacy Protection (2003)

We assume a database consists of records of individuals with private or sensitive fields. Queries on the distribution of a sensitive field within a selected population in the database can be submitted to the data center. The answers to the queries leak private information of individuals though no identification information is provided. Inspired by decision theory, we present two quantitative models for the privacy protection problem in such a database query or linkage environment in this paper. One is for modeling the value of information from the viewpoint of the querier and the other is for the damage and compensation of privacy leakage. In both models, we define the information state by a class of probability distributions on the set of possible confidential values. These states can be modified and refined by the user’s knowledge acquisition actions. In the first model, the value of information is defined as the expected gain of the privacy receiver and the privacy is protected by imposing costs on the answers of the queries for balancing the gain. In the second one, the safety is guaranteed by enforcing that anyone misusing the private information must pay more compensation than the possible gain.
13-(S)-Hydroxyoctadecadienoic acid (13-HODE) incorporation and conversion to novel products by endothelial cells (1999)

13(S)-Hydroxy-[12,13-3H]octadecadienoic acid (13-HODE), a linoleic acid oxidation product that has vasoactive properties, was rapidly taken up by bovine aortic endothelial cells. Most of the 13-HODE was incorporated into phosphatidylcholine, and 80% was present in the sn -2 position. The amount of 13-HODE retained in the cells gradually decreased, and radiolabeled metabolites with shorter reverse-phase high-performance liquid chromatography retention times (RT) than 13-HODE accumulated in the extracellular fluid. The three major metabolites were identified by gas chromatography combined with mass spectrometry as 11-hydroxyhexadecadienoic acid (11-OH-16:2), 9-hydroxytetradecadienoic acid (9-OH-14:2), and 7-hydroxydodecadienoic acid (7-OH-12:2). Most of the radioactivity contained in the cell lipids remained as 13-HODE. However, some 11-OH-16:2 and several unidentified products with longer RT than 13-HODE were detected in the cell lipids. Normal human skin fibroblasts also converted 13-HODE to the three major chain-shortened metabolites, but Zellweger syndrome fibroblasts produced only a very small amount of 11-OH-16:2. Therefore, the chain-shortened products probably are formed primarily by peroxisomal beta-oxidation. These findings suggest that peroxisomal beta-oxidation may constitute a mechanism for the inactivation and removal of 13-HODE from the vascular wall. Because this is a gradual process, some 13-HODE that is initially incorporated remains in endothelial phospholipids, especially phosphatidylcholine. This may be the cause of some of the functional perturbations produced by 13-HODE in the vascular wall.
Automated Segmentation for Hyperdense Middle Cerebral Artery Sign of Acute Ischemic Stroke on Non-Contrast CT Images (2019)

The hyperdense middle cerebral artery (MCA) dot sign has been reported as an important factor in the diagnosis of acute ischemic stroke due to large vessel occlusion. Interpreting the initial CT brain scan in these patients requires high level of expertise, and has high inter-observer variability. An automated computerized interpretation of the urgent CT brain image, with an emphasis to pick up early signs of ischemic stroke will facilitate early patient diagnosis, triage, and shorten the door-to-revascularization time for these group of patients. In this paper, we present an automated detection method of segmenting the MCA dot sign on non-contrast CT brain image scans based on powerful deep learning technique.
A neural network for optimum Neyman-Pearson classification (1990)

A three-layer feedforward neural network (NN) that implements the optimum Neyman-Pearson (N-P) classifier is described. This NN is useful whenever it is appropriate to characterize (1) input classes as multivariate random variables, and (2) input data vectors as realizations of one of the multivariate random variables. The purpose of the NN is thus simply to compute the conditional likelihoods necessary for the N-P classifier. Because the N-P classifier is optimal, the classification performance of the NN is optimal too. Therefore, three-layer feedforward NN classifiers can equal but not exceed the performance of the N-P classifier. The optimal N-P classifier requires multivariate probability density functions (PDFs) characterizing the input classes. Class PDFs are approximated (arbitrarily closely) by mixtures of multivariate Gaussian PDFs. Supervised training of the class PDFs from input data vectors is, thus, equivalent to training the NN. Maximum likelihood training of the PDFs is performed by the EM algorithm (or by any other suitable optimization method)
Stem cell therapy for muscular dystrophy (2004)

Muscular dystrophy is a heterogeneous group of neuromuscular disorders that manifests as progressive muscle weakness, muscle wasting and, in many cases, death. Although there has been enormous progress in the molecular understanding of muscular dystrophy, there is still no cure. There are, however, several different therapeutic options under investigation, including adult-derived stem cell transplantation. Encouraging and pioneering experiments in mouse models for Duchenne’s muscular dystrophy (DMD) demonstrated that myoblasts could be transplanted into dystrophic muscle; these myoblasts repaired a small proportion of damaged myofibres. Subsequent work has been devoted to optimisation of this technique. In doing so, a number of adult-derived stem cells have been isolated, characterised and used in promising animal transplantation experiments. Further research is ongoing, and is clearly necessary to make this therapy a viable treatment option for patients with muscular dystrophy.
Developing a design system to help reduce design cycle time (2013)

In this paper, we introduce the RDS system that is used by Skyworks' design community to perform design tasks. Integration of EDA tools, design kits, and environment infrastructure is introduced. A centralized computing pool to leverage computing power with effective cost structure is discussed. We elaborate on multi-site and project data management to ensure data integrity. We also describe the PDK concept and optimized hybrid design flows used by Skyworks' design teams.
High-performance dual-layer channel indium gallium zinc oxide thin-film transistors fabricated in different oxygen contents at low temperature (2014)

In this work, fully transparent dual-layer channel amorphous indium gallium zinc oxide thin-film transistors (a-IGZO TFTs) are fabricated on glass substrates at low temperature. Dual-layer channel a-IGZO TFTs are studied by changing the partial pressure of oxygen while sputtering IGZO layers for comparison with single-layer channel TFTs which are fabricated with a constant oxygen content. All four types of dual-layer channel TFT sample demonstrate better performance, on-to-off ratios of ∼10 8 and low subthreshold swing (SS) of less than 200 mV/decade, than the single-layer ones. TFTs with two layers, a low-oxygen layer and a high-oxygen layer formed using oxygen partial pressures of 0.01 and 0.05 Pa, respectively demonstrate relatively better performance with a mobility of more than 60 cm 2 V −1 s −1 . Among them, the TFTs with a channel layer thickness ratio of 3 : 1 show the best transfer characteristics with a high on-to-off current ratio ( I on/off ) of 1.8 × 10 8 and a low SS of 135 mV/decade.
Unique DNA Methylation Loci Distinguish Anatomic Site and HPV Status in Head and Neck Squamous Cell Carcinoma (2013)

Novel epigenetic biomarkers derived from clinical HNSCC specimens can be used as molecular classifiers of this disease, revealing many new avenues of investigation for this disease.
Expression of CD44 is repressed in neuroblastoma cells. (1991)

We have used cDNA subtractive cloning to identify a group of human genes that are expressed in diverse differentiated derivatives of neural crest origin but not in neuroblastoma cell lines. One of these genes was identified as CD44, which encodes an integral membrane glycoprotein that serves as the principal receptor for hyaluronate and participates in specific cell-cell and cell-extracellular matrix interactions. The repression of CD44 expression in neuroblastoma cell lines might be relevant to their high metastatic potential. We have cloned full-length cDNAs corresponding to CD44 trancscripts and identified a novel splice variant of CD44 lacking 31 amino acids of the extracellular domain. As a first step toward analysis of CD44 downregulation in neuroblastoma cells, we have mapped the CD44 RNA initiation site and analyzed the structure of the upstream regulatory region. We constructed a series of plasmids containing different amounts of CD44 upstream regulatory region linked to the bacterial chloramphenicol acetyltransferase gene and then analyzed their ability to promote transcription in neuroblastoma and melanoma cells. We found that a DNA segment including about 150 bp of the CD44 upstream region and the 5' end of the gene itself was sufficient to induce substantial transcription of the chloramphenicol acetyltransferase gene in both neuroblastoma and melanoma cells. Several upstream cis-acting elements contribute to the downregulation of CD44 in neuroblastoma cells, the most prominent being a 120-bp DNA fragment located 450 bp upstream to the RNA initiation site. Our data suggest that multiple factors might be involved in downregulation of CD44 in neuroblastoma cells.
Magnetically responsive diclofenac sodium-loaded erythrocytes: Preparation and in vitro characterization (1994)

Diclofenac sodium-bearing magnetic erythrocytes were prepared using a preswell technique. The optimum loading of drug and magnetite achieved were 63-73 and 12-18 per cent, respectively. Drug-loaded erythrocytes and drug-loaded magnetic erythrocytes were characterized for in vitro drug and haemoglobin release, magnetic responsiveness, osmotic fragility, turbulence shock, morphology and percentage cell recovery. The drug-loaded magnetic erythrocytes were found less resistant to osmotic and turbulence shock when compared with the normal and drug-loaded erythrocytes. However, in optimum concentration erythrocytes tolerated drug and coated magnetite appreciably. The drug-loaded magnetic erythrocytes responded effectively for an external magnetic field of 8.0 kOe. The study suggested the potentiality of diclofenac sodium-loaded magnetic erythrocytes, for active delivery of drug to painful inflamed joints.
An Experimental Study of Nonlinear Effects on 43 Gb/s Electronic Pre-equalized Transmission (2013)

We have studied the impact of nonlinear effects on 43 Gb/s electronically pre-equalized DQPSK signals. A nonlinear power threshold around 1 dB higher than for conventional DQPSK signals with optical dispersion compensation was confirmed.
The Serving CSCF Assignment Algorithm in Wireless IP Multimedia Networks (2006)

It is necessary that the serving-call session control function (S-CSCF) be assigned by the operator of IP multimedia networks for user-based call session control. If the assignment of the S-CSCF to the user is not adaptive, the user may not be provided with IP multimedia services and network resources are wasted because of the overload of the specific S-CSCF. But 3GPP standardization organization has taken over the issue of S-CSCF selection by I-CSCF to the operator's implementation role and has not explicitly described it. Therefore to resolve this problem, in this paper, we design the data structure for S-CSCF selection and a three-step S-CSCF selection algorithm which assigns the adaptive S-CSCF by the I-CSCF and effectively uses the network resources on IP multimedia subsystems.
<scp>US</scp> Guidelines for immune tolerance induction in patients with haemophilia a and inhibitors (2015)

Evidence-based recommendations to guide treatment decisions may increase the likelihood of successful inhibitor eradication and the induction of FVIII tolerance in patients with hemophilia A who develop inhibitory antibodies.
Authenticated Denial of Existence in the DNS (2014)

Authenticated denial of existence allows a resolver to validate that a certain domain name does not exist.It is also used to signal that a domain name exists but does not have the specific resource record (RR) type you were asking for.When returning a negative DNS Security Extensions (DNSSEC) response, a name server usually includes up to two NSEC records.With NSEC version 3 (NSEC3), this amount is three.This document provides additional background commentary and some context for the NSEC and NSEC3 mechanisms used by DNSSEC to provide authenticated denial-of-existence responses.
Encoding Data by Frequency Modulation of a High-Low Siren Emitted by an Emergency Vehicle (2014)

It is important for people in surrounding vehicles to detect and respond appropriately to emergency vehicle sirens. This is a problem for everyone, but for the hearing impaired it can be particularly difficult. In addition, it would be useful if the siren could convey other information, such as the location of a shelter in the event of a disaster. The present study proposes data embedding into a high-low siren by frequency modulation. This information, including the location of the emergency vehicle, for example, can be extracted and utilized by a smartphone or car navigation system. The proposed method is more robust to Doppler shifts of siren frequencies, additive long-path echoes, and background noise than a previously proposed method. The current implementation can embed payload at a bit-rate of 12.3 bps. However, this rate can be more than doubled by using harmonics of the siren tone, which would provide a higher payload bit-rate than the previous method.
Accurate segmentation and contrast measurement of microcalcifications in mammograms: A phantom study (1998)

The authors are developing a computer-aided diagnostic method to assist radiologists in differentiating between malignant and benign clustered microcalcifications in mammograms. In earlier studies we investigated shape and contrast features of microcalcifications for classification. It was found that segmentation strongly influences classification results. For this reason a phantom study has been carried out. The CDMAM phantom, consisting of a pattern of dots with known size and object contrast is used for evaluation of contrast measurement and segmentation. Dots in the range of 0.2-0.8 mm are taken as a model for microcalcifications. In this article performances of different methods for segmentation of microcalcifications are compared. An iterative method based on a Markov random field and a signal dependent criterion give satisfying results. The segmentation performances of both methods are comparable. Also the influence of the modulation transfer function on contrast estimates is determined and effect of exposure level on segmentation is analyzed.
Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice (2016)

Dysbiosis potentially contributes to the pathogenesis of IBD by augmenting host proinflammatory immune responses. Transcript profiling: GSE73882.
Photocatalytic degradation of dyes and organic contaminants in water using nanocrystalline anatase and rutile TiO<sub>2</sub> (2007)

Nanocrystalline TiO2 was synthesized by controlled hydrolysis of titanium tetraisopropoxide. The anatase phase was converted to rutile phase by thermal treatment at 1023 K for 11 h. The catalysts were characterized by X-ray diffraction (XRD), diffuse reflectance spectroscopy (DRS), Fourier-transform infrared absorption spectrophotometry (FT-IR) and N2 adsorption (BET) at 77 K. This study compare the photocatalytic activity of the anatase and rutile phases of nanocrystalline TiO2 for the degradation of acetophenone, nitrobenzene, methylene blue and malachite green present in aqueous solutions. The initial rate of degradation was calculated to compare the photocatalytic activity of anatase and rutile nanocrystalline TiO2 for the degradation of different substances under ultraviolet light irradiation. The higher photocatalytic activity was obtained in anatase phase TiO2 for the degradation of all substances as compared with rutile phase. It is concluded that the higher photocatalytic activity in anatase TiO2 is due to parameters like band-gap, number of hydroxyl groups, surface area and porosity of the catalyst.
The offset cube: a three-dimensional multicomputer network topology using through-wafer optics (1998)

Three-dimensional packaging technologies are critical for enabling ultra-compact, massively parallel processors (MPPs) for embedded applications. Through-water optical interconnect has been proposed as a useful technology for building ultra-compact MPPs since it provides a simplified mechanism for interconnecting stacked multichip substrates. This paper presents the offset cube, a new network topology designed to exploit the packaging benefits of through-wafer optical interconnect in ultra-compact MPP systems. We validate the offset cube's topological efficiency by developing deadlock-free adaptive routing protocols with modest virtual channel requirements (only two virtual channels per link needed for full adaptivity). A preliminary analysis of router complexity suggests these protocols can be efficiently implemented in hardware. We also present a 3D mesh embedding for the offset cube. Network simulations show the offset cube performs comparably to a bidirectional 3D mesh of equal size under uniform, hot-spot, and trace-driven traffic loads. While the offset cube is not proposed as a general replacement for the mesh topology it leverages the benefits of through-wafer optical interconnect more effectively than a mesh by completely eliminating chip-to-chip wires for data signals. Hence, the offset cube is an effective topology for interconnecting ultra-compact MCM-level MPP systems.