gebhart/patrepeval huggingface dataset:
Transcriptome of Pneumocystis carinii during Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite (2007)

Members of the genus Pneumocystis are fungal pathogens that cause pneumonia in a wide variety of mammals with debilitated immune systems. Little is known about their basic biological functions, including life cycle, since no species can be cultured continuously outside the mammalian lung. To better understand the pathological process, about 4500 ESTS derived from sequencing of the poly(A) tail ends of P. carinii mRNAs during fulminate infection were annotated and functionally characterized as unassembled reads, and then clustered and reduced to a unigene set with 1042 members. Because of the presence of sequences from other microbial genomes and the rat host, the analysis and compression to a unigene set was necessarily an iterative process. BLASTx analysis of the unassembled reads (UR) vs. the Uni-Prot and TREMBL databases revealed 56% had similarities to existing polypeptides at E values of<or=10(-6), with the remainder lacking any significant homology. The most abundant transcripts in the UR were associated with stress responses, energy production, transcription and translation. Most (70%) of the UR had similarities to proteins from filamentous fungi (e.g., Aspergillus, Neurospora) and existing P. carinii gene products. In contrast, similarities to proteins of the yeast-like fungi, Schizosaccharomyces pombe and Saccharomyces cerevisiae, predominated in the unigene set. Gene Ontology analysis using BLAST2GO revealed P. carinii dedicated most of its transcripts to cellular and physiological processes ( approximately 80%), molecular binding and catalytic activities (approximately 70%), and were primarily derived from cell and organellar compartments (approximately 80%). KEGG Pathway mapping showed the putative P. carinii genes represented most standard metabolic pathways and cellular processes, including the tricarboxylic acid cycle, glycolysis, amino acid biosynthesis, cell cycle and mitochondrial function. Several gene homologs associated with mating, meiosis, and sterol biosynthesis in fungi were identified. Genes encoding the major surface glycoprotein family (MSG), heat shock (HSP70), and proteases (PROT/KEX) were the most abundantly expressed of known P. carinii genes. The apparent presence of many metabolic pathways in P. carinii, sexual reproduction within the host, and lack of an invasive infection process in the immunologically intact host suggest members of the genus Pneumocystis may be adapted parasites and have a compatible relationship with their mammalian hosts. This study represents the first characterization of the expressed genes of a non-culturable fungal pathogen of mammals during the infective process.
Feasibility Study to Determine the Economic and Operational Benefits of Utilizing Unmanned Aerial Vehicles (UAVs) (2014)

This project explored the feasibility of using Unmanned Aerial Systems (UASs) in Georgia\nDepartment of Transportation (GDOT) operations. The research team conducted 24 interviews with\npersonnel in four GDOT divisions. Interviews focused on (1) the basic goals of the operators in each\ndivision, (2) their major decisions for accomplishing those goals, and (3) the information requirements for\neach decision. Following an interview validation process, a set of UASs design characteristics that fulfill\nuser requirements of each previously identified division was developed. A “House of Quality” viewgraph\nwas chosen to capture the relationships between GDOT tasks and potential UAS aiding those operations.\nAs a result, five reference systems are proposed. The UAS was broken into three components: vehicle,\ncontrol station, and system. This study introduces a variety of UAS applications in traffic management,\ntransportation and construction disciplines related to DOTs, such as the ability to get real time, digital\nphotographs/videos of traffic scenes, providing a "bird’s eye view" that was previously only available with\nthe assistance of a manned aircraft, integrating aerial data into GDOT drawing software programs, and\ndealing with restricted or complicated access issues when terrain, area, or the investigated object make it\ndifficult for GDOT personnel to conduct a task. The results of this study could lead to further research on\ndesign, development, and field-testing of UAVs for applications identified as beneficial to the Department.
Modelling and simulating the selective epitaxial growth of silicon under consideration of anisotropic growth rates (2004)

This work presents a new model for the simulation of thin layer deposition and etching processes. Especially suited for the simulation of highly anisotropic processes, the frontier model is introduced in the context of selective epitaxial growth of silicon. The general approach to this new simulation model is described, and the simulation of selective epitaxial growth is validated against experimental results.
Supporting the Requirements Prioritization Process. A Machine Learning approach. (2004)

Requirements prioritization plays a key role in the requirements engineering process, in particular with respect to critical tasks such as requirements negotiation and software release planning. This paper presents a novel framework which is based on a requirements prioritization process that interleaves human and machine activities, enabling for an accurate prioritization of requirements. Similarly to the Analytic Hierarchy Process (AHP) method, our framework adopts an elicitation process based on the acquisition of pairwise preferences. Differently from AHP, where scalability is a big issue, the framework enables a prioritization process even over a large set of requirements, thanks to the exploitation of machine learning techniques that induce requirements ranking approximations at run time, and to the use of a boolean metrics. Moreover the new approach allows to reduce the bias of a dominance hierarchy, a strategy introduced by AHP to deal with the scalability issue. The paper describes also a methodology for the experimental evaluation of the framework and discusses the results of a first set of experiments designed on a real casestudy which shows that an high accuracy in the final ranking can be obtained within a limited elicitation effort. 1.
Narrowband light detection via internal quantum efficiency manipulation of organic photodiodes (2015)

Spectrally selective light detection is vital for full-colour and near-infrared (NIR) imaging and machine vision. This is not possible with traditional broadband-absorbing inorganic semiconductors without input filtering, and is yet to be achieved for narrowband absorbing organic semiconductors. We demonstrate the first sub-100 nm full-width-at-half-maximum visible-blind red and NIR photodetectors with state-of-the-art performance across critical response metrics. These devices are based on organic photodiodes with optically thick junctions. Paradoxically, we use broadband-absorbing organic semiconductors and utilize the electro-optical properties of the junction to create the narrowest NIR-band photoresponses yet demonstrated. In this context, these photodiodes outperform the encumbent technology (input filtered inorganic semiconductor diodes) and emerging technologies such as narrow absorber organic semiconductors or quantum nanocrystals. The design concept allows for response tuning and is generic for other spectral windows. Furthermore, it is material-agnostic and applicable to other disordered and polycrystalline semiconductors.
A single-chip 24 GHz SiGe BiCMOS transceiver for FMCW automotive radars (2009)

The design and measured results of a highly integrated FMCW radar transceiver are presented. The transceiver includes a transmitter with +7dBm output power and −82 dBc/Hz phase noise at 100 kHz, dual I/Q receivers with 10dB NF and 18 dB gain, PLL, 15-bit DAC, instrumentation amplifiers, LDO regulators, and a serial programming interface - all designed to operate from −40 to +125°C at 3.5V, 275 mA. Fabricated using Jazz Semiconductor's 0.18 µm SiGe BiCMOS process and packaged in a 32-pin 5 mm × 5 mm QFN, this RFIC has the highest level of integration at 24 GHz known to the authors.
Automated bone segmentation from large field of view 3D MR images of the hip joint (2013)

Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head-neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone-cartilage interfaces for potential cartilage segmentation.
Constraint projection (1991)

Unification of disjunctive feature descriptions is important for efficient unification-based parsing. This paper presents constraint projection, a new method for unification of disjunctive feature structures represented by logical constraints. Constraint projection is a generalization of constraint unification, and is more efficient because constraint projection has a mechanism for abandoning information irrelevant to a goal specified by a list of variables.
Intranasal vaccination of pigs against pseudorabies: Absence of vaccinal virus latency and failure to prevent latency of virulent virus (1984)

The avirulent Bartha's K strain of pseudorabies virus (PRV) was used to vaccinate 8 pigs at 10 weeks of age by the intransal route (experiment 1). On postvaccination days (PVD) 63 and 91, pigs were treated with corticosteroids. Viral shedding could not be detected. Explant cultures of trigeminal ganglia and tonsils did not produce virus. Four pigs with maternal antibody were vaccinated intranasally with Bartha's (attenuated) K strain of PRV at 10 weeks of age and were challenge exposed with a virulent strain of PRV on PVD 63 (experiment 2). Corticosteroid treatment, starting on postchallenge exposure day 70 (PVD 133) resulted in viral shedding in 1 of 4 pigs. In another pig of these 4, a 2nd corticosteroid treatment was required to trigger reactivation. In both pigs, sufficient reactivated virus was excreted to infect susceptible sentinel pigs. Restriction endonuclease analysis indicated that viruses isolated from the 2 pigs after challenge exposure and corticosteroid treatment were indistinguishable from the virulent virus. Evidence was not obtained for simultaneous excretion of vaccinal and virulent virus. Of 4 pigs without maternal antibody vaccinated twice with 1 of 2 inactivated PRV vaccines, challenge exposed on PVD 84, and treated with corticosteroids on postchallenge exposure day 63 (PVD 147), 1 was latently infected, as evidenced by the shedding of PRV (experiment 3). However, its sentinel pig remained noninfected.(ABSTRACT TRUNCATED AT 250 WORDS)
Digestion of complex carbohydrates and large bowel fermentation in rats fed on raw and cooked peas (Pisum sativum) (1992)

Rats were fed on four semi-purified diets in which raw or cooked peas (Pisum sativum var. Sentinel) provided 250 or 500 g/kg diet. Pressure-cooking of peas followed by rapid freezing and freeze-drying increased the proportion of starch resistant to alpha-amylase (EC 3.2.1.1) without previous treatment with dimethyl sulphoxide. There were only minor effects of cooking on the digestibilities of non-starch polysaccharides and their constituent sugars. With the higher dietary pea concentration there were marked increases in the flow of organic matter to, and fermentation in, the large bowel. These increases were associated with significant increases in colonic tissue and contents weights, and in colonic transit time. Both cooking and dietary pea inclusion rate altered the pattern of volatile fatty acids in caecal contents and in portal blood.
Role of Endothelin and Inflammatory Cytokines in Pre-eclampsia - A Pilot North Indian Study (2010)

We conclude that pre-eclampsia is associated with increased levels of both endothelin-1 and circulating inflammatory cytokines, which points toward the role of endothelial and inflammatory components.
HowPAH gene mutations cause hyper-phenylalaninemia and why mechanism matters: Insights from in vitro expression (2003)

Mutations in the human PAH gene, which encodes phenylalanine hydroxylase are associated with varying degrees of hyperphenylalaninemia (HPA). The more severe of these manifest as a classic metabolic disease--phenylketonuria (PKU). In vitro expression analysis of PAH mutations has three major applications: 1) to confirm that a disease-associated mutation is genuinely pathogenic, 2) to assess the severity of a mutation's impact, and 3) to examine how a mutation exerts its deleterious effects on the PAH enzyme, that is, to elucidate the molecular mechanisms involved. Data on expression analysis of 81 PAH mutations in multiple in vitro systems is summarized in tabular form online at www.pahdb.mcgill.ca. A review of these findings points in particular to a prevalent general mechanism that appears to play a major role in the pathogenicity of many PAH mutations. Amino acid substitutions promote misfolding of the PAH protein monomer and/or oppose the correct assembly of monomers into the native tetrameric enzyme. The resulting structural aberrations trigger cellular defenses, provoking accelerated degradation of the abnormal protein. The intracellular steady-state levels of the mutant PAH enzyme are therefore reduced, leading to an overall decrease in phenylalanine hydroxylation within cells and thus to hyperphenylalaninemia. There is considerable scope for modulation of the enzymic and metabolic phenotypes by modification of the cellular handling--folding, assembly, and degradation--of the mutant PAH protein. This has major implications, both for our understanding of genotype-phenotype correlations and for the development of novel therapeutic approaches.
High-finesse interferometers (1995)

A detailed plan for the construction and use of a nonconfocal cavity used as a high-finesse interferometer is presented. The interferometer has a free spectral range of l5 GHz, with a finesse of over 30,000.
Ligand Inhibition of the Platelet Glycoprotein IIb-IIIa Complex Function as a Calcium Channel in Liposomes (1989)

Platelet glycoproteins IIb and IIIa function as a fibrinogen receptor on the activated platelet. We have shown that these glycoproteins can be incorporated onto the surface of phosphatidylcholine vesicles with retention of fibrinogen and antibody binding properties and can permit Ca2+ transit across the phospholipid bilayer. In the current study we demonstrate that this apparent Ca2+ channel function is specifically inhibited by the synthetic analogue of the fibrinogen gamma COOH-terminal peptide, His-His-Leu-Gly-Gly-Ala-Lys-Gln-Ala-Gly-Asp-Val (His-12-Val), but not by the adhesive protein sequence Arg-Gly-Asp-Ser (RGDS). Prior incubation of IIb-IIIa liposomes with RGDS prevented Ca2+ transit inhibition by 25 microM His-12-Val, analogous to RGDS inhibition of His-12-Val binding to platelets. His-12-Val inhibited a minor component of transmembrane Ca2+ influx into ADP and thrombin-activated human platelets but had no effect on steady-state platelet 45Ca flux. These data indicate that ligand binding may exert a regulatory influence on transmembrane Ca2+ influx into activated platelets. The difference in inhibitory potency of the peptides studied may be related to differences in conformational changes in the glycoprotein IIb-IIIa complex induced by His-12-Val and RGDS, steric considerations, or differences in interactions with glycoprotein IIb Ca2+ binding domains.
New IRCMOS architecture applied to uncooled microbolometers developed at LETI (2007)

Thermal imaging market is today more and more attracted by systems with "instant-on" and low power consumption. Therefore the "TECless" operation of uncooled microbolometer detectors, that is where no Peltier module is needed, is the major step to fulfill the market requirement. In order to fulfill this trend, LETI/SLIR is working on a new IRCMOS architecture. This new design is based on a differential reading implemented with current mirrors that simultaneously reduces focal plane temperature sensitivity and simplifies the detector driving. An IRCMOS prototype (320 x 240 with a pitch of 25 &mgr;m) has been designed, processed, and characterized. This paper presents an overall view of this new design and the preliminary characterization results got from this focal plane array.
Automatic Extraction of Formant Frequencies from Continuous Speech (1956)

Two electronic devices for automatically extracting the first three formant frequencies from continuous speech are described. Both devices are designed to yield three continuous dc output voltages whose magnitudes, as functions of time, represent the formant frequencies of the input speech. The principles of operation and the design features of both devices are discussed, and typical examples of the operation of each are presented.
Lipolysis—Not inflammation, cell death, or lipogenesis—Is involved in adipose tissue loss in cancer cachexia (2008)

The current findings indicated that subcutaneous WAT does not contribute to the systemic inflammatory reaction and does not induce adipocyte insulin resistance in cancer cachexia. Moreover, increased fat cell lipolysis, not reduced lipogenesis or adipocyte cell death, appeared to be the primary cause of fat loss in this condition.
Calibration model of a dual gain flat panel detector for 2D and 3D x‐ray imaging (2007)

The continuing research and further development in flat panel detector technology have led to its integration into more and more medical x-ray systems for two-dimensional (2D) and three-dimensional (3D) imaging, such as fixed or mobile C arms. Besides the obvious advantages of flat panel detectors, like the slim design and the resulting optimum accessibility to the patient, their success is primarily a product of the image quality that can be achieved. The benefits in the physical and performance-related features as opposed to conventional image intensifier systems, (e.g., distortion-free reproduction of imaging information or almost linear signal response over a large dynamic range) can be fully exploited, however, only if the raw detector images are correctly calibrated and postprocessed. Previous procedures for processing raw data contain idealizations that, in the real world, lead to artifacts or losses in image quality. Thus, for example, temperature dependencies or changes in beam geometry, as can occur with mobile C arm systems, have not been taken into account up to this time. Additionally, adverse characteristics such as image lag or aging effects have to be compensated to attain the best possible image quality. In this article a procedure is presented that takes into account the important dependencies of the individual pixel sensitivity of flat panel detectors used in 2D or 3D imaging and simultaneously minimizes the work required for an extensive recalibration. It is suitable for conventional detectors with only one gain mode as well as for the detectors specially developed for 3D imaging with dual gain read-out technology.
Induction of zebrafish (<i>Brachydanio rerio</i>) P450<i>in vivo</i>and in cell culture (1994)

1. Induction of zebrafish P450 by 2,3,7,8-tetrachloro-dibenzo-p-dioxin (TCDD) was studied in liver tissue, primary liver cell culture and multipassage cell culture derived from zebrafish haploid and diploid embryos and liver. 2. TCDD induced two hepatic proteins (54 and 50 kDa) in vivo which were recognized by anti-trout P4501A1 IgG. The 54-kDa protein was induced by TCDD in primary and multipassage hepatocyte cultures and in haploid and diploid embryo-derived cells. The proteins in liver homogenates were not induced by aqueous exposure of zebrafish to beta-naphthoflavone (BNF). 3. Homogenates of zebrafish liver, cultured hepatocytes and embryo-derived cells also exhibited increased ethoxyresorufin O-deethylase (EROD) and 7-12-dimethyl-benz[a]anthracene (DMBA) hydroxylase activity following TCDD exposure.
Reactively steered adaptive array using microstrip patch elements at 4 gigahertz (1983)

A reactively steered adaptive array (RESAA) has one element connected by a transmission line to a receiver and a number of closely spaced parasitic elements, each of which is terminated by an adjustable reactive load. The pattern is formed by adaptive control of the reactive loads. A five-element linear RESAA fabricated from microstrip patch antennas was evaluated at 4.0 GHz. Manual adaptive control was used to form a pattern with a minimum in the direction of an interference signal. A minimum could always be formed in the direction of the interference that had a depth (relative to the pattern maximum) of 30 dB and a width of 25 degrees. The theory of the array was developed using an N-port network formalism, and simulations with this theory reproduced the essential features of the experimental measurements. The potential advantages of a RESAA, as compared with a conventional adaptive array, include the elimination of the mixers and other hardware needed to perform the complex weighting of the output of each element at an intermediate frequency, greater dynamic range, and smaller overall size. (Author)
Expression of cytokeratins in normal and diseased livers and in primary liver carcinomas. (1989)

Hepatocytes and bile duct epithelium express several types of cytokeratins, the characteristic intermediate-filament proteins of epithelial cells. The cytokeratin antigen expression was studied in normal and diseased livers, intrahepatic cholangiocarcinomas, and hepatocellular carcinomas by immunohistochemical methods using a panel of polyclonal and monoclonal antibodies to cytokeratins. Ten percent formaldehyde solution-fixed, paraffin-embedded sections obtained from ten patients without liver disease, 18 patients without liver disease, 18 patients with different stages of primary biliary cirrhosis, 14 patients with alcoholic hepatitis, ten patients with fatty liver hepatitis secondary to diabetes mellitus or morbid obesity, five patients with hepatocellular carcinomas, and five patients with cholangiocarcinomas were examined. The results suggested that hepatocytes and bile duct epithelium retain their distinct cytokeratin profiles in liver disease, including malignant transformation. Therefore, demonstration of cytokeratins in the liver is useful in establishing the cellular origin of neoplasms and understanding the pathogenesis of liver diseases.