gebhart/patrepeval huggingface dataset:
Tissue factor pathway inhibitor II as a specific biomarker for pre-operative prediction of clear-cell carcinoma of the ovary. (2020)

e18077 Background: Tissue factor pathway inhibitor 2 (TFPI2) is a novel serum biomarker that discriminates ovarian clear cell carcinomas (CCC) from borderline ovarian tumors (BD) and non-CCC epithelial ovarian cancers (EOC). We examined the prediction performances of TFPI2, including high specificity, for preoperative diagnosis of CCC in multi-center settings. Methods: We collected serum samples obtained preoperatively from patients with ovarian masses who needed surgical treatment to confirm pathological diagnoses in five hospitals in Japan. The diagnostic powers of serum levels of TFPI2 (cutoff value 270 pg/mL) and CA125 (cutoff value 35 U/mL) to discriminate CCC from BD, non-CCC-EOC, and benign lesions were compared. Results: A total of 351 patients (77 ovarian benign lesions, 65 BD and 209 EOC including 69 CCC) were analyzed. Serum TFPI2 levels were significantly higher in CCC patients (mean±SD, 508.2±812.0 pg/mL) than in patients with benign lesions (154.7±46.5), BD (181±95.5) and non-CCC EOC (265.4±289.1). TFPI2 had a high diagnostic specificity to CCC (sensitivity and specificity: 43.5% and 79.5%, respectively). The sensitivity of TFPI2 was improved to 71.1% when combined with CA125, and it was increased in Stage II–IV CCC (66.7%) compared with Stage I CCC (33.3%). In patients with benign endometriotic cysts (BEM), no patient was positive for TFPI2 but 71.4% (15/21) were CA125 positive. TFPI2 showed good performance in discriminating Stage II–IV CCC from BD and non-CCC EOC patients (AUC 0.815 for TFPI2 versus 0.505 for CA125) or from BEM (AUC 0.957 for TFPI2 versus 0.748 for CA125). Conclusions: High specificity of TFPI2 for the preoperative detection of CCC was re-verified with the defined cutoff level of TFPI2 in practice. TFPI2 and CA125 may have a substantial contribution to the precise prediction of intractable CCC. [Table: see text]
1-cycle code decompression circuitry for performance increase of Xtensa-1040-based embedded systems (2003)

Code compression is known to be an effective technique to reduce the instruction memory size of an embedded system. However code compression can also be very effective in increasing the processor-to-memory bandwidth and hence provide increased system performance. In this paper we describe our design of the world's first running prototype of a 1-cycle code decompression circuitry that decompresses Xtensa 1040 instructions on-the-fly. The circuitry is a standalone unit that does not require any modifications on the Xtensa 1040 processor core. We observed an average code size reduction of about 35% of programs running on the system and an average of 45% of performance increase due to the increased bandwidth and memory hierarchy effects.
PMD compensation in multilevel coded-modulation schemes with coherent detection using BLAST algorithm and iterative polarization cancellation (2008)

We present two PMD compensation schemes suitable for use in multilevel (M>or=2) block-coded modulation schemes with coherent detection. The first scheme is based on a BLAST-type polarization-interference cancellation scheme, and the second scheme is based on iterative polarization cancellation. Both schemes use the LDPC codes as channel codes. The proposed PMD compensations schemes are evaluated by employing coded-OFDM and coherent detection. When used in combination with girth-10 LDPC codes those schemes outperform polarization-time coding based OFDM by 1 dB at BER of 10(-9), and provide two times higher spectral efficiency. The proposed schemes perform comparable and are able to compensate even 1200 ps of differential group delay with negligible penalty.
Abstract 4213: Stool-derived eukaryotic RNA (seRNA) assay for noninvasive detection of colorectal cancer and high-risk adenomas (2019)

Colorectal cancer (CRC) is the second leading cause of cancer related deaths in the United States. The high mortality rate for CRC is largely attributable to the frequency of late-stage diagnoses, caused by low patient compliance with screening guidelines. A novel nucleic acid extraction method that isolates stool-derived eukaryotic RNA (seRNA) has permitted development of a colorectal cancer stool diagnostic test (CRC-SDT) that uses a fecal immunochemical test (FIT) and 11 seRNA transcripts to serve as a reliable and noninvasive screening alternative to lower mortality associated with CRC. Stool samples were obtained from 190 individuals prior to undergoing a screening colonoscopy. Patients were diagnosed as either having colorectal cancer, having high-risk adenomas (high-grade dysplasia, villous growth pattern, or >1.0cm in size), or healthy (low-risk adenomas, benign polyps, and/or no findings on a colonoscopy). FITs were obtained for each sample. Samples that had a positive FIT were considered positive for the CRC-SDT. Samples that had a negative FIT underwent seRNA isolation, library preparation (Illumina TruSeq Targeted RNA) and subsequent sequencing (Illumina NextSeq 550). A random forest model was built using 11 transcripts that were differentially expressed (log2 fold-change > 1; ANOVA p < 0.05) between diseased patients (CRC and high-risk adenomas) relative to the healthy cohort. Internal 10-fold cross-validation was performed for the training set and a receiver operating characteristic (ROC) area under the curve (AUC) determined model accuracy for cancer and high-risk adenomas relative to the healthy cohort. Model predictions for an independent hold-out test set were used to determine model accuracy for colorectal cancer and high-risk adenomas. Internal cross-validation for 154 samples attained a ROC AUC of 0.82. The trained model was employed on the independent hold-out test set of 36 samples and model predictions were compared to colonoscopy results. The model attained a 100% sensitivity for CRC (n = 7), a 60% sensitivity for high-risk adenomas (n = 5), and an 88% combined specificity for the healthy cohort (n = 24). CRC-SDT uses 12 biomarkers (FIT and expression from 11 seRNA transcripts) to accurately detect CRC and high-risk adenomas. Use of seRNA biomarkers dramatically improves detection of high-risk adenomas relative to existing noninvasive screening methods for CRC.Citation Format: Erica K. Barnell, Yiming Kang, Katie M. Campbell, Kimberly R. Kruse, Andrew R. Barnell, Elizabeth M. Wurtzler. Stool-derived eukaryotic RNA (seRNA) assay for noninvasive detection of colorectal cancer and high-risk adenomas [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 4213.
Plasma etching of aluminum (1976)

Experimental plasma etching apparatus and methods utilizing BCl <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> etch gas have been developed for the accurate patterning of thin Al and Al-Si alloy metallization as used in integrated circuit fabrication. A two micron linewidth capability has been achieved for the patterning of 0.5 micron thick metallization on three inch diameter wafers with positive and negative photoresist etch masks as thin as 2500Å. Etchrates of 500 to 1000 Å/min. are typical, and there is negligible etching of both the photoresist and the underlying SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> layers. The process is CMOS compatibles, yielding threshold voltage shift and temperature-bias stability specifications of less than ±0.050 volts that are comparable to those for wet chemically etched devices.
Endothelial progenitor cell: ongoing controversy for defining these cells and their role in neoangiogenesis in the murine system (2009)

To fully appreciate the orchestrated cellular events participating in new vessel formation in the tumor microenvironment, better methods of cell identification and functional validation will be necessary to specify which cells in which tumors are facilitating and forming new vessels in which tissues at which stage of the disease.
A NEURO-FUZZY APPROACH FOR THE SENSOR-BASED DRIVING SITUATION IDENTIFICATION (1998)

In this paper, the authors present a neuro-fuzzy system that identifies a driving situation using vehicular sensor information. Based on monitored data, features are computed via a sensor fusion step and evaluated with a fuzzy classifier. The model is optimized using a bi-directional neuro-fuzzy transformation and a dedicated neural network topology.
Quantitation of anti–factor VIII antibodies in human plasma (2009)

The presence of antibodies (Abs) in hemophilia A patients can potentially influence the therapeutic qualities of factor VIII (fVIII) administration. Much work has been focused on the presence of inhibitory antibodies, whereas the quantitation of noninhibitory anti-fVIII antibodies has been largely undetermined. Our objective was to develop a sensitive and specific fluorescence-based immunoassay (FLI) for the quantitation of anti-fVIIIAbs in human plasma. Affinity-purified human anti-fVIIIAb, isolated from a hemophilia A subject, was used as a calibrator with a detectability limit of 40 (+/-1.5) pM. The calibrator and the human plasma anti-fVIIIAb were captured on recombinant fVIII (rfVIII)- coupled microspheres and probed with mouse anti-human Ig-R-phycoerythrin. Plasma samples from 150 healthy donors and 39 inhibitor-negative hemophilia A subjects were compared with 4 inhibitor-positive hemophilia A plasma samples with inhibitor titers of 1 BU/mL (94.6 +/- 0.8 nM), 11 BU/mL (214.3 +/- 7.1 nM), 106 BU/mL (2209.4 +/- 84.9 nM), 140 BU/mL (2417.7 +/- 3.8 nM) as measured by the Nijmegen method. We also describe the validation of a mouse anti-human fVIIIAb as a surrogate calibrator. Four healthy individuals (3%) showed detectable anti-fVIIIAb in the range of 0.6 to 6.2 nM, whereas 13 (33%) of the 39 inhibitor-free hemophilia A subjects were positive for anti-fVIIIAb in the range of 0.5 to 20 nM. The method may be useful for therapeutic management of hemophilia A patients.
Novel liquid crystal resins for stereolithography – processing parameters and mechanical analysis (2000)

The build characteristics of two liquid crystal (LC) reactive monomers were studied using a table‐top stereolithography apparatus (TTSLA). LC materials contain stiff, rod‐like mesogenic segments in their molecules, which can be aligned causing an anisotropy in properties. When cured in the aligned state the anisotropic structure is “locked in” resulting in materials with anisotropic physical and mechanical properties. By varying the alignment of layers, properties such as thermal expansion coefficient can be optimized. High heat distortion (or glass transition) temperatures are possible depending on the monomer chemical structure. Working curves for the LC resins were developed under various conditions. A permanent magnet placed outside the TTSLA vat was used to uniformly align the monomer in the nematic state. Photo‐initiator type and content; alignment of the nematic phase; and operating conditions affected the working curve parameters. Glass transition temperatures of post‐cured parts ranged from 75 to 1488C depending on the resin and processing conditions. Mechanical analysis data revealed a factor of two difference between glassy moduli measured in the molecular alignment versus the transverse alignment directions. Based on these initial studies, more advanced resins with higher glass transitions are being developed at the University of Dayton.
Immunochemical properties of the aminopropeptide of procollagen type III (1983)

The precursor-specific aminopropeptide of bovine type III procollagen is a strong immunogen in rabbits, guinea pigs and mice and induces antibodies which do not cross-react with type I procollagen. The antibody response is regulated by immune response genes associated with the major histocompatibility complex. Major antigenic determinants were found in the compact, non-collagenous domain (fragment Col 1) located at the N terminus of the aminopropeptide and were destroyed by reduction of disulfide bonds. Minor antigenic determinants independent of disulfide bonds also exist in fragment Col 1 and could be localized on a distinct tryptic peptide. Fragment Col 1 showed a lower affinity for antibody when compared with the intact aminopropeptide which causes a non-parallel shift in radioimmuno-inhibition profiles. Monovalent antibody fragments showed an average tenfold reduction in affinity constant and failed to distinguish between aminopropeptide and fragment Col 1. This indicates that the stronger binding of bivalent antibody by the triple-stranded aminopropeptide is due to multiple interactions with both antibody binding sites which are lost for a single-stranded antigen (Col 1) or with monovalent antibody fragments.
Vanadium-pumped titanium x-ray laser (1990)

A new laboratory x-ray laser is described that is resonantly photopumped by two 3d ? 2p emission lines in fluorinelike vanadium (Z = 23) and lases on several 3p ? 3s transitions in neonlike titanium (Z = 22). Calculations show that five of the laser lines have gains greater than 5 cm(-1) for reasonable values of the pump lines, with the shortest wavelength of the five being at 32.65 nm.
Model-based Sensor Fault Detection and Isolation for X-By-Wire Vehicles Using a Fuzzy Logic System with Fixed Membership Functions (2007)

In this paper, a supervisory sensor diagnostics system for x-by-wire vehicles is described. The x-by-wire vehicle has brake-by-wire as well as front and rear steer-by- wire subsystems. A detailed discussion of a model-based diagnostics approach that is used for detecting, as well as determining the location and type of sensor faults is given. The sensors under study are vehicle front and rear road wheel angles, lateral acceleration, yaw rate and four wheel speeds. A multi-model-based methodology is utilized for estimation of yaw rate, lateral acceleration and road wheel angle signals. Three estimates of the vehicle system behavior are generated and compared to the actual measurements. The differences between the measurements and the estimates are used to generate four residuals. Fuzzy membership functions for each of the residuals are defined and the degree-of-membership of the residuals is continuously evaluated. Fuzzy rules are developed and used to detect, isolate and determine the fault type. Specific patterns are used to detect and identify the location and type of sensors faults. The fuzzy rules implement the fault-symptoms relationships. The output of the fuzzy reasoning system is a crisp number, according to Sugeno fuzzy system, that can be interpreted as the probability of the occurrence of a specific fault.
Purification and Characterization of a High-Molecular-Weight Insecticidal Protein Complex Produced by the Entomopathogenic Bacterium <i>Photorhabdus luminescens</i> (1998)

Photorhabdus luminescens is a gram-negative enteric bacterium that is found in association with entomopathogenic nematodes of the family Heterorhabditidae. The nematodes infect a variety of soil-dwelling insects. Upon entering an insect host, the nematode releases P. luminescens cells from its intestinal tract, and the bacteria quickly establish a lethal septicemia. When grown in peptone broth, in the absence of the nematodes, the bacteria produce a protein toxin complex that is lethal when fed to, or injected into the hemolymph of, Manduca sexta larvae and several other insect species. The toxin purified as a protein complex which has an estimated molecular weight of 1,000,000 and contains no protease, phospholipase, or hemolytic activity and only a trace of lipase activity. The purified toxin possesses insecticidal activity whether injected or given orally. Analyses of the denatured complex by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed it to be composed of several protein subunits ranging in size from 30 to 200 kDa. The complex was further separated by native gel electrophoresis into three components, two of which retained insecticidal activity. The purified native toxin complex was found to be active in nanogram concentrations against insects representing four orders of the class Insecta.
Local Binary Pattern Networks (2020)

Emerging edge devices such as sensor nodes are increasingly being tasked with non-trivial tasks related to sensor data processing and even application-level inferences from this sensor data. These devices are, however, extraordinarily resource-constrained in terms of CPU power (often Cortex M0-3 class CPUs), available memory (in few KB to MBytes), and energy. Under these constraints, we explore a novel approach to character recognition using local binary pattern networks, or LBPNet, that can learn and perform bit-wise operations in an end-to-end fashion. LBPNet has its advantage for characters whose features are composed of structured strokes and distinctive outlines. LBPNet uses local binary comparisons and random projections in place of conventional convolution (or approximation of convolution) operations, providing an important means to improve memory efficiency as well as inference speed. We evaluate LBPNet on a number of character recognition benchmark datasets as well as several object classification datasets and demonstrate its effectiveness and efficiency.
Hydrogel particles sequester and preserve low molecular weight, low abundance cancer biomarkers in blood (2008)

2434 There is an urgent need to discover novel biomarkers that provide sensitive and specific cancer detection. One of the major problems associated with biomarker discovery has been degradation of biomarkers. Degradation can occur immediately following the collection of blood or body fluid as a result of endogenous or exogenous proteinases and can greatly bias subsequent analysis. The goal of this study was to incorporate a bait in “smart” nano-particles in order to sequester and concentrate selected classes of proteins and peptides from complex mixtures of biomolecules such as serum, and protect them from degradation during subsequent sample handling.  N-isopropylacrylamide/acrylic acid (NIPAm/AAc) particles were synthesized by precipitation polymerization and characterized by means of light scattering and atomic force microscopy. The AAc component acted as bait for cationic proteins. Two different technologies were used to detect the particles’ ability to isolate low molecular weight, low abundance polypeptides, namely SDS PAGE and flow cytometry. Bait particles incubated with a solution containing platelet derived growth factor (PDGF, 14,000 Da) and bovine serum albumin (BSA, 66,000 Da) completely sequestered PDGF and totally excluded BSA, with PDGF being a representative model for low abundance low molecular weight protein biomarker in blood. By using a solution of protein molecular weight markers, the molecular weight cut off (MWCO) of the proteins sequestered by the particles was found to be around 20,000 Da, which is significant since the vast majority of possible biomarkers are thought to reside in the MW range from 0 to 20,000 Da.  Flow cytometry studies demonstrated that particles captured low molecular weight protein (i.e. FITC labeled insulin) spiked in human serum. Uptake was very rapid since it occurred in less than five minutes, as was quantified by reverse phase protein arrays.  Particles were incubated with human serum, and the captured proteins were electroeluted from particles. Analysis of the electroeluted proteins with mass spectrometry indicated that the particles had sequestered rare and small-sized serum proteins and peptide fragments with total exclusion of albumin and other large and high abundant proteins.  By means of two different proteases (trypsin and chymotrypsin) with different incubation times (1 hour, 3 hours and overnight) it was demonstrate that NIPAm/AAc particle completely blocked protease degradation of captured proteins even at 37 oC.  Taken together, these results provide evidence that such particles are a very promising tool that could help the discovery of novel biomarkers for early stage diseases such as cancer.
Elongase Gene And Production Of Delta9-polyunsaturated Fatty Acids (Patent US 7601889 B2) (2009)

This invention relates to a new elongase gene having the sequence SEQ ID NO: 1 or its derivatives, to a gene construct comprising this sequence or its derivatives and to its use. The inventive nucleic acid sequence encodes a polypeptide which elongates alpha-linolenic acid (C18:3 d9, 12, 15) by at least two carbon atoms whereas gamma-linolenic acid (C18:3 d6, 9, 12) is not elongated. The invention additionally relates to vectors or organisms comprising an elongase gene having the sequence SEQ ID NO: 1 or its derivatives. The invention further relates to a process for the production of polyunsaturated fatty acids (=PUFAs) with an organism which comprises the elongase gene and which organism produces high amounts of oils and especially oils with a high content of unsaturated fatty acids. Additionally the invention relates to an oil and/or fatty acid composition with a higher content of polyunsaturated C20 or C22 fatty acids with at least two double bonds and/or to a triacylglycerol composition with a higher content of said polyunsaturated fatty acids.\n\n
Solid freeform fabrication of soybean oil‐based composites reinforced with clay and fibers (2004)

Abstract Soybean oil/epoxy‐based composites were prepared by an extrusion freeform fabrication method. These composites were reinforced with a combination of organically modified clay and fibers. The intercalated behavior of the epoxy resin in the presence of organo‐modified clay was investigated by X‐ray diffraction and transmission electron microscopy. The mixture of epoxidized soybean oil and EPON ® 828 resin was modified with a gelling agent to solidify the materials until curing occurred. The flexural modulus reached 4.86 GPa with glass fiber reinforcement at 50.6 wt% loading. It was shown that the fiber orientation followed the direction of motion of the writing head that deposited the resins and had an influence on the properties of the composite. The composites cured by curing agent jeffamine EDR‐148 were found to have lower mechanical properties than those cured with triethylenetetramine, diethylenetriamine, and polyethylenimine. In addition, the effects of clay loading and fiber loading on mechanical properties of the composites were studied and reported.
Model driven security accreditation (MDSA)for agile, interconnected it landscapes (2009)

Assurance accreditation of agile, interconnected IT landscapes is a great challenge, and is currently often cited as one of the show-stoppers for the adoption of modern IT architectures (e.g. agile, model-driven, process-led SOA and Cloud) in mission critical domains. This paper presents Model Driven Security Accreditation (MDSA), a novel approach for automating large parts of the compliance and assurance accreditation management processes (e.g. Common Criteria) to achieve reduced cost / effort, and increased reliability / traceability. MDSA is related to Model Driven Security (MDS), an approach that automatically generates fine-grained technical security rules from intuitive, generalized security policy models. MDSA automatically analyzes and documents two main compliance aspects: 1) Does the actual security match with the stated requirements? MDSA is a system and method for managing and analyzing security and information assurance requirements in reusable models, and for (mostly) automating the verification of the traceable correspondence between functional models, security models, and requirements models. 2) Do any changes impact the current accreditation? MDSA automatically identifies changes to any aspect of the "system of systems", and evaluates whether changes impact the current accreditation and whether manual corrections and re-accreditation are required.