gebhart/patrepeval huggingface dataset:
Supersampling in PET. A concept for improvement of the resolution of positron emission tomography (2010)

At present, the maximum spatial resolution of state-of-the-art PET scanners is not better than 5 mm, whereas the maximum resolution obtained in the resulting images is approximately 10 mm. At least some of this difference is a result of an inherent, complex noise component that can be eliminated using "supersampling". The aim of the study was to apply the supersampling technique to PET image recordings to lower the noise and to improve the in-plane resolution of the recorded images. A standardized phantom was investigated with the supersampling technique. In addition to the standard CT and PET series, 14 further PET series were recorded with the phantom at exactly the same position, and 4 further series were recorded with the phantom placed in another well defined position. After merging corresponding images, the image noise index and the image resolution are both substantially improved. The suggested PET image recording and processing technique provides a substantial increase in PET image quality without exposing the patient to any additional radiation, and might therefore become a powerful tool for investigative as well as diagnostic purposes.
Effiect of Inhomogeneities on theApparentLocation and Magnitude of a CardiacCurrentDipole Source (1970)

A mathematical modelwasusedtoinvestigate the effects ofelectrical inhomogeneities introduced bytheintracavitary blood massandthelungs ontheapparent location andmagnitude of acurrent dipole source representing local activity inthemyocardium. Radial andtangential current source momentswereconsidered, and lungconductivity wastakenasavariable parameter. Boththeblood massandthelungscauseacurrent source toappear closer tothe heartcenter thanitactually is.Theeffect increases asthesource movesawayfromtheendocardial surface, andmaximumdisplace- mentisestimated tobeoftheorder of1cm.Theneteffect ofthe inhomogeneities istoincrease themagnitude oftheradial com- ponent ofasource dipole while diminishing itstangential component. Theseeffects depend onsource location.
Levels of polyunsaturated fatty acids in tissues from zinc‐deficient rats fed a linseed oil diet (1994)

The effect of zinc deficiency on the levels of n-6 and n-3 polyunsaturated fatty acids (PUFA) in lipids from tissues of rats fed a diet containing linseed oil was investigated. Rats were fed either a control diet (25 mg Zn/kg) or a zinc-deficient diet (0.8 mg Zn/kg) for 10 d. To avoid energy and nutrient deficiency, 11.6 g of diet per day was administered by gastric tube. At the end of the experiment, rats fed the zinc-deficient diet had drastically reduced plasma zinc concentration and alkaline phosphatase activity consistent with severe zinc deficiency in these rats. Zinc-deficient rats had higher levels of n-3 PUFA, in particular eicosapentaenoic acid (EPA), and lower levels of n-6 PUFA, in particular linoleic acid, in liver and plasma phosphatidylcholine (PC) and in erythrocyte membrane total lipids than did control rats. By contrast, the levels of n-3 PUFA in PC from testes and heart, and in phosphatidylethanolamine (PE) from liver, testes and heart, were only slightly different between zinc-deficient and control rats. The study suggests that desaturation of alpha-linolenic acid is not inhibited by zinc deficiency, and that in zinc-deficient rats, n-3 PUFA preferentially incorporated into phospholipids at the expense of n-6 PUFA, especially EPA into PC. The study also shows that the effect of zinc deficiency on PUFA levels is different for PC and PE in rat tissues.
Novel Associations between Common Breast Cancer Susceptibility Variants and Risk-Predicting Mammographic Density Measures (2015)

Mammographic density measures adjusted for age and body mass index (BMI) are heritable predictors of breast cancer risk, but few mammographic density-associated genetic variants have been identified. Using data for 10,727 women from two international consortia, we estimated associations between 77 common breast cancer susceptibility variants and absolute dense area, percent dense area and absolute nondense area adjusted for study, age, and BMI using mixed linear modeling. We found strong support for established associations between rs10995190 (in the region of ZNF365), rs2046210 (ESR1), and rs3817198 (LSP1) and adjusted absolute and percent dense areas (all P < 10(-5)). Of 41 recently discovered breast cancer susceptibility variants, associations were found between rs1432679 (EBF1), rs17817449 (MIR1972-2: FTO), rs12710696 (2p24.1), and rs3757318 (ESR1) and adjusted absolute and percent dense areas, respectively. There were associations between rs6001930 (MKL1) and both adjusted absolute dense and nondense areas, and between rs17356907 (NTN4) and adjusted absolute nondense area. Trends in all but two associations were consistent with those for breast cancer risk. Results suggested that 18% of breast cancer susceptibility variants were associated with at least one mammographic density measure. Genetic variants at multiple loci were associated with both breast cancer risk and the mammographic density measures. Further understanding of the underlying mechanisms at these loci could help identify etiologic pathways implicated in how mammographic density predicts breast cancer risk.
An update on pathobiologic roles of anti-glycan antibodies in Guillain-Barré syndrome (2010)

Anti-glycan antibodies directed against gangliosides are now considered the major immune effectors that induce damage to intact nerve fibers in some variants of the monophasic neuropathic disorders that comprise Guillain-Barré syndrome. Recent experimental studies elucidating the complexity of anti-glycan antibody-mediated pathobiologic effects on intact and injured nerves undergoing repair are discussed.
A Comparative Study of Therapeutic Response of Patients With Clinical Chancroid to Ciprofloxacin, Erythromycin, and Cotrimoxazole (1998)

Ciprofloxacin and erythromycin are equally effective in chancroid. Ciprofloxacin is better in terms of dosage schedule, duration of treatment, and low cost. Cotrimoxazole should be discontinued as drug of choice because of high failure rates.
Hydrostatic Pressure Increases Apoptosis in Cartilage-Constructs Produced From Human Osteoarthritic Chondrocytes (2006)

Tissue-engineering is considered a promising avenue for developing human articular cartilage implants that can be employed for resurfacing damaged cartilage in the early stages of osteoarthritis. In the present study, human cartilage-constructs were produced from human osteoarthritic chondrocytes maintained on a scaffold of HYAFFR-11 in perfusion mini-bioreactors or after implantation and recovery from nude or SCID mice after 3 weeks. The human cartilage-construct extracellular matrix reacted positively with anti-Type II collagen monoclonal antibody, but not with anti-Type I or anti-Type X collagen monoclonal antibodies. A significant portion of the cartilage-construct extracellular matrix stained metachromatic with Toluidine blue-O indicative of sulfated-proteoglycan deposition. Cyclic hydrostatic pressure applied for 4 hrs at 5 MPa using a 1 Hertz sinusoidal frequency significantly increased (p < 0.02) the proportion of apoptotic cells in the cartilage-constructs (41% +/- 4.2%; mean +/- SD) compared to control cartilage-constructs (28.5 +/- 8.4%).
Automated Whole Sentence Grammar Correction Using a Noisy Channel Model (2011)

Automated grammar correction techniques have seen improvement over the years, but there is still much room for increased performance. Current correction techniques mainly focus on identifying and correcting a specific type of error, such as verb form misuse or preposition misuse, which restricts the corrections to a limited scope. We introduce a novel technique, based on a noisy channel model, which can utilize the whole sentence context to determine proper corrections. We show how to use the EM algorithm to learn the parameters of the noise model, using only a data set of erroneous sentences, given the proper language model. This frees us from the burden of acquiring a large corpora of corrected sentences. We also present a cheap and efficient way to provide automated evaluation results for grammar corrections by using BLEU and METEOR, in contrast to the commonly used manual evaluations. 1
Creation of a Knowledge Management System for QT Analyses (2010)

An increasing number of thorough QT (TQT) reports are being submitted to the US Food and Drug Administration's interdisciplinary review team for QT (IRT-QT), requiring time-intensive quantitative analyses by a multidisciplinary review team within 45 days. This calls for systematic learning to guide future trials and policies by standardizing and automating the QT analyses to improve review efficiency, provide consistent advice, and enable pooled data analyses to answer key regulatory questions. The QT interval represents the time from initiation of ventricular depolarization to completion of ventricular repolarization recorded by electrocardiograph (ECG) and is used in the proarrhythmic risk assessment. The developed QT knowledge management system is implemented in the R package "QT." Data from 11 crossover TQT studies including time-matched ECGs and pharmacokinetic measurements following single doses of 400 to 1200 mg moxifloxacin were used for the QT analysis example. The automated workflow was divided into 3 components (data management, analysis, and archival). The generated data sets, scripts, tables, and graphs are automatically stored in a queryable repository and summarized in an analysis report. More than 100 TQT studies have been analyzed using the system since 2007. This has dramatically reduced the time needed to review TQT studies and has made the IRT-QT reviews consistent across reviewers. Furthermore, the system enables leveraging prior knowledge through pooled data analyses to answer policy-related questions and to understand the various effects that influence study results.
Estimation of Hydrocarbon Viscosity with Multiple TE Dual Wait-Time MRIL Logs (1998)

Abstract In this paper, we report a successful example of using multiple TE dual wait-time (TW) log acquisitions for quantitative characterization of San Jorge Basin reservoir oil viscosity. Previously, dual TW logs have been used to separate gas and oil, while dual TE logs have been used as a qualitative light oil indicator. Although theoretically simple, quantitative determination of viscosity from dual TE logs is complicated by several factors, including poor signal-to-noise ratio, difficulties in separating oil from water, and the uncertainty of internal gradient strength. We used multiple TE acquisitions of dual TW logs to isolate the oil from the water signal. The values of viscosity of the reservoir fluids can be estimated from three NMR properties: intrinsic T2, apparent T2, and T1. All three approaches have advantages and disadvantages. Since T1estimates are not affected by diffusion, the uncertainty in the internal field gradient has no effect on T1-based viscosity. However, T1 is difficult to estimate because it relies on small differences in the dual TW echo data. In estimation of the apparent T2, we used a model that does not explicitly require knowledge of the internal gradient, thereby minimizing the effects arising from the uncertainty of the internal and tool gradient strengths. Since T1 and intrinsic T2 are estimated independently, the degree of agreement between the two values provides an indication of the reliability of the two estimates. The method has been used successfully in San Jorge Basin, Argentina. Three values of TE, 1.2, 2.4, and 3.6 ms were used and a dual TW log was acquired for each TE. The data were analyzed without need for other geological information or log data from other logging tools. To complicate the matter, previous NMR core analysis of the core plugs cut from another well in San Jorge Basin showed great porosity and permeability variations. Furthermore, no reliable reservoir fluid measurements were available. Thus, interpretation was based only on the NMR log data. The four zones selected for this study were thought to contain heavy, viscous oil. However, our analysis indicated that the viscosity values of the oil are less than 5 cP. Our predictions have been substantiated by production of light hydrocarbons from the three zones that have been perforated. Further, viscosity measurements on the reservoir fluid from one of the three zones is 2.6 cP, which is in good agreement with the NMR-derived estimate of 3.3 cP.
Anencephalic Infants as Organ Donors and the Brain Death Standard (1989)

The authors comment on essays by R.C. Cefalo and H.T. Engelhardt,\nF.K. Beller and J. Reeve, R.M. Zaner, and H.-M. Sass in this issue of the
Machine Perfusion of Porcine Livers with Oxygen-Carrying Solution Results in Reprogramming of Dynamic Inflammation Networks (2016)

<b>Background:</b><i>Ex vivo</i> machine perfusion (MP) can better preserve organs for transplantation. We have recently reported on the first application of an MP protocol in which liver allografts were fully oxygenated, under dual pressures and subnormothermic conditions, with a new hemoglobin-based oxygen carrier (HBOC) solution specifically developed for <i>ex vivo</i> utilization. In those studies, MP improved organ function post-operatively and reduced inflammation in porcine livers. Herein, we sought to refine our knowledge regarding the impact of MP by defining dynamic networks of inflammation in both tissue and perfusate. <b>Methods:</b> Porcine liver allografts were preserved either with MP (<i>n</i> = 6) or with cold static preservation (CSP; <i>n</i> = 6), then transplanted orthotopically after 9 h of preservation. Fourteen inflammatory mediators were measured in both tissue and perfusate during liver preservation at multiple time points, and analyzed using Dynamic Bayesian Network (DyBN) inference to define feedback interactions, as well as Dynamic Network Analysis (DyNA) to define the time-dependent development of inflammation networks. <b>Results:</b> Network analyses of tissue and perfusate suggested an NLRP3 inflammasome-regulated response in both treatment groups, driven by the pro-inflammatory cytokine interleukin (IL)-18 and the anti-inflammatory mediator IL-1 receptor antagonist (IL-1RA). Both DyBN and DyNA suggested a reduced role of IL-18 and increased role of IL-1RA with MP, along with increased liver damage with CSP. DyNA also suggested divergent progression of responses over the 9 h preservation time, with CSP leading to a stable pattern of IL-18-induced liver damage and MP leading to a resolution of the pro-inflammatory response. These results were consistent with prior clinical, biochemical, and histological findings after liver transplantation. <b>Conclusion:</b> Our results suggest that analysis of dynamic inflammation networks in the setting of liver preservation may identify novel diagnostic and therapeutic modalities.
Genomics for Biodefense (2005)

Francisella tularensis is the aetiological agent of tularemia, a plague-like disease of rodents capable of being transmitted to man. Tularemia is a zoonosis, found in a wide range of animals such as rabbits, hares, rodents, and beavers (). Transmission occurs usually through the bite of an insect, such as a tick, biting fly, or mosquito (2–5) but can also be through ingestion of infected foodstuffs (3) and drinking water (6), or through inhalation of the bacterium (7). In humans, the most common presentation is ulceroglandular tularemia, a disease typified by flu-like symptoms, normally with a low mortality rate (8). An ulcer forms at the site of infection, which can persist for several months. Other forms of tularemia, such as typhoidal, gastrointestinal, and pneumonic tularemia, are more serious diseases and may have mortality rates up to 60%, depending on the type of strain causing infection (7). F. tularensis subspecies tularensisis one of the most infectious pathogens known, with an infectious dose of less than 10 colony-forming units (CFU) in humans (9,10).
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation (2008)

Since its beginning as a data collection more than 20 years ago, the TRANSFAC project underwent an evolution to become the basis for a complex platform for the description and analysis of gene regulatory events and networks. In the following, I describe what the original concepts were, what their present status is and how they may be expected to contribute to future system biology approaches.
An autonomous excavator with vision-based track-slippage control (2004)

This paper describes a vision-based control system for a tracked mobile robot (an excavator). The system includes several controllers that collaborate to move the mobile vehicle from a starting position to a goal position. First, the path planner designs an optimum path using a predefined elevation map of the work space. Second, a fuzzy logic path-tracking controller estimates the rotational and translational velocities for the vehicle to move along the predesigned path. Third, a cross coupling controller corrects the possible orientation error that may occur when moving along the path. A motor controller then converts the track velocities to the corresponding rotational wheel velocities. Fourth, a vision-based motion tracking system is implemented to find the three-dimensional (3-D) motion of the vehicle as it moves in the work space. Finally, a specially-designed slippage controller detects slippage by comparing the motion through reading of flowmeters and the vision system. If slippage has occurred, the remaining path is corrected within the path tracking controller to stop at the goal position. Experiments are conducted to test and verify the presented control system. An analysis of the results shows that improvement is achieved in both path-tracking accuracy and slippage control problems.
Modeling of ice flow and internal layers along a flowline through Swiss Camp, West Greenland (2002)

Abstract An anisotropic-ice flowline model is applied to a flowline through Swiss Camp (69.57° N, 49.28° W), West Greenland, to estimate the dates of internal layers detected by radio-echo sounding measurements. The effect of an anisotropic-ice fabric on ice flow is incorporated into the steady-state flowline model. The stress–strain-rate relationship for anisotropic ice is characterized by an enhancement factor based on the laboratory observations of ice deformation under combined compression and shear stresses. By using present-day data of accumulation rate, surface temperature, surface elevation and ice thickness along the flowline as model inputs, a very close agreement is found between the isochrones generated from the model and the observed internal layers with confirmed dates. The results indicate that this part of the Greenland ice sheet is primarily in steady state.
Brittle fracture: Its study and application (1971)

Abstract Brittle fracture is a challenging problem both from theoretical and experimental viewpoints. Once a crack starts to propagate in a brittle solid its velocity may quickly reach several thousands of metres/sec. Various high resolution techniques including high-speed photography, ultrasonics and electrical methods have been developed for fracture propagation studies. For many brittle solids a maximum crack velocity exists. Crack branching can occur either when a crack reaches a high velocity or when a stress wave passes over it. Brittle fracture is frequently an undesirable event, but there are situations where it has great practical importance. Examples of the beneficial application of fracture are discussed including gem stone cleaving, the interruption of electric current and rock fragmentation.
Synthesis of some hydroxamic acid derivatives of benzimidazole and their antibacterial and antifungal activities. (1992)

A number of 1H-benzimidazole-2-propanoic acid derivatives have been synthesized by Phillips method, and their antibacterial and antifungal activities have been tested. The chemical structures of the synthesized compounds were elucidated by spectroscopic (IR, NMR, mass) and elementary analysis. Investigation of antimicrobial activity of the compounds was done by agar dilution technique using bacteria (Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Mycobacterium smegmatis ATCC 607) and yeast-like fungi (Candida albicans, Candida tropicalis, Candida pseudotropicalis, Candida kruzei, Candida globrata). Among the compounds tested N-hydroxy-3-(1H-benzimidazol-2-yl)-propionamide (Compound 6) showed considerable activity against both Candida albicans and Candida tropicalis.
Back focal plane imaging of Tamm plasmons and their coupled emission (2014)

The unique optical properties of TPs - such as flexible wavevector matching conditions including in-plane wavevector within the light line, existing both S- and P-polarized TPs and ability of populating with KR and RK illuminations - facilitate them for direct optical excitation. The Tamm plasmon Coupled emission (TPCE) from a combined photonic-plasmonic structure sustaining both surface plasmons (SPs) and Tamm plasmons (TPs) is described. The sensitivity of TPCE to the emission wavelength and polarization is examined with back focal plane imaging and verified with the numerical calculations. The results reveal that the excited probe can couple with both TPs and SPs, resulting in SPCE and TPCE, respectively. The TPCE angle is strongly dependent on the wavelength allowing for spectral resolution using different observation angles. These Tamm structures provide a new tool to control the optical emission from dye molecules and have many potential applications in fluorescence based-sensing and imaging.
Hematopoietic stem cells: cancer involvement and myeloid leukemia. (2015)

Hematopoietic stem cells (HSCs) are rare multipotent cells that possess ability to self-renew and differentiate to progenitor cells, which give rise to all blood cell lineages. The process involves specific regulation of gene transcription and its deregulation resulting in imbalance between self-renew and differentiation, can lead to cellular transformation and cancers. Substantial evidence indicates that accumulated mutations in HSCs contribute to the initiation and pathogenesis of at least some hematopoietic cancers. In particular, myeloid leukemias have been extensively characterized with regard to HSC and progenitor involvement. Thus, as a focal point for scientific and therapeutic endeavours, formation of cancer cells from HSCs represents a critical area of investigation. Consequently, understanding how HSCs function and how they undergo to transformation, is of fundamental importance to get insight in their contribution to the hematopoietic cancer development.