gebhart/patrepeval huggingface dataset:
Biochemical characterization of the HydE and HydG iron‐only hydrogenase maturation enzymes from Thermatoga maritima (2005)

Fe-only hydrogenases contain a di-iron active site complex, in which the two Fe atoms have carbon monoxide and cyanide ligands and are linked together by a putative di(thiomethyl)amine molecule. We have cloned, purified and characterized the HydE and HydG proteins, thought to be involved in the biosynthesis of this peculiar metal site, from the thermophilic organism Thermotoga maritima. The HydE protein anaerobically reconstituted with iron and sulfide binds two [4Fe-4S] clusters, as characterized by UV and EPR spectroscopy. The HydG protein binds one [4Fe-4S] cluster, and probably an additional one. Both enzymes are able to reductively cleave S-adenosylmethionine (SAM) when reduced by dithionite, confirming that they are Radical-SAM enzymes.
P204 Immune Responses To Single And Repeated Administration Of Pgm169/gl67a: The Uk Cf Gene Therapy Consortium Clinical Trials (2014)

<h3></h3> Although most CF patients express CFTR protein (albeit mutant) and should therefore not recognise the wild-type CFTR protein as foreign, there is an inherent risk of activation of T-cells against the recombinant wild-type protein after gene therapy. In addition, we have previously shown that approximately 10% of CF and non-CF subjects carry self-reactive CFTR-specific T-cells (<i>Calcedo <i>et al</i>, Hum Gene Ther Clin Dev 2013</i>). The reason for this is unknown and it is also unclear whether being positive for self-reactive T-cells affects disease severity or increases the risk of further T-cell activation after gene therapy. As part of the UKCFGTC Phase I/IIa Pilot study [in which patients received a single dose (5, 10 or 20 mls) of the non-viral formulation pGM169/GL67A] peripheral blood mononuclear cells (PBMC) were collected prior to dosing and approximately 4 weeks after nebulisation of 5 ml (n = 2), 10 ml (n = 6) or 20 ml (n = 17) of pGM169/GL67A. IFN-g ELISPOT to detect CFTR-specific T-cells in PBMC was performed. CFTR-specific T-cells were detectable in one patient pre- and post-dosing. In the remaining 18 patients we did not detect CFTR-specific T-cells. In addition we quantified anti-DNA antibodies (anti-nuclear and anti-cytoplasmic) in blood samples taken pre- and approximately 4 weeks post-dosing (n = 7 (5 ml), n = 10 (10 ml) and n = 17 (20 ml). We did not observe any evidence for induction of anti-DNA antibodies after a single dose of pGM169/GL67A. The UKCFGTC has now completed a Phase IIb multi-dose clinical trial in May 2014 (ClinicalTrials.gov identification number – NCT01621867). CF patients received 12 monthly doses of pGM169/GL67A (115 completed nine or more doses), or placebo by aerosol. PBMC were collected on two occasions prior to dose 1 to establish baseline levels for CFTR-specific T-cells, approximately 4 weeks after Dose 4 or 5, and 2 to 4 weeks after Dose 12 and the ELISPOT was performed. In addition anti-DNA antibodies were quantified. The Phase IIb trial will be unblinded in Summer 2014 to allow data analysis and all data will be presented at the conference. Funded by the NIHR/EME Programme and the Cystic Fibrosis Trust.
Stress mode of gate oxide charging during the MERIE and the ICP processing and its effect on the gate oxide reliability (2002)

The gate oxide charging (stressing) mode during plasma processing was investigated from the experimental data of two TDDB measurements, Q/sub bd/ and t/sub bd/ testings and the gate current behaviour in t/sub bd/ testing after the plasma treatment and the post-process current injection (electrical stress). It was confirmed that in some cases the t/sub bd/, which determines the oxide lifetime under operating conditions, increases after the plasma treatments in both MERIE (magnetically enhanced RIE) and ICP processing.
Computer vision to locate fruit on a tree (1985)

ABSTRACT RESEARCH on the application of computer vision as a sensing system for robotic harvesting of fruit was performed. A vision system was developed to collect images. Testing was conducted during the day and at night on peach and apple trees. A computer algorithm was developed to enhance and extract information from images. This extracted information was used to classify objects within these images as either **multiple fruit, ^'single fruit, or '*noise. The algorithm correctly handled approximately 92% of the objects and identified approximately 89% of the fruit found in images obtained at night. Computer vision was determined to be a viable technique for detecting and identifying fruit on trees..
Modelling and Enforcing Privacy for Medical Data Disclosure across Europe (2009)

The harmonization of data protection legislation in Europe has been theoretically achieved by means of the EU directive on data protection. In practice the harmonization is not absolute and conflicts and inconsistencies continue to exist in the way Member States are implementing the directive. The integration of different European medical systems by means of grid technologies will continue to be challenging if technology does not intervene to enhance interoperability between national regulatory frameworks on data protection. In this paper we present an approach to automate privacy requirements for the sharing of patient data across Europe on a healthgrid domain and ensure its enforcement internally and within external domains where the data might travel. This approach is based on the semantic modelling of privacy obligations that are of legal, ethical or cultural nature. These requirements are for the sharing of personal data between different European Member States. Our model reflects both similarities and conflicts, if any, between the different Member States. This allows us to reason on the safeguards a data controller should ask from an organization belonging to another Member State before disclosing medical data to them. The system will also generate the relevant set of policies to be enforced at the process level of the grid to ensure privacy compliance before allowing access to the data.
Spinal Cord Toll-Like Receptor 4 Mediates Inflammatory and Neuropathic Hypersensitivity in Male But Not Female Mice (2011)

The innate immune system is increasingly appreciated to play an important role in the mediation of chronic pain, and one molecule implicated in this process is the Toll-like receptor 4 (TLR4). Here, using pharmacological and genetic manipulations, we found that activating TLR4 in the spinal cord, with the agonist lipopolysaccharide (LPS), causes robust mechanical allodynia but only in male mice. Spinal LPS had no pain-producing effect in female mice. TLR4 also has a sex-specific role in inflammatory (complete Freund's adjuvant) and neuropathic (spared nerve injury) pain: pain behaviors were TLR4 dependent in males but TLR4 independent in females. The sex differences appear to be specific to the spinal cord, as LPS administered to the brain or the hindpaw produces equivalent allodynia in both sexes, and specific to pain, as intrathecal LPS produces equivalent hypothermia in both sexes. The involvement of TLR4 in pain behaviors in male mice is dependent on testosterone, as shown by gonadectomy and hormone replacement. We found no sex differences in spinal Tlr4 gene expression at baseline or after LPS, suggesting the existence of parallel spinal pain-processing circuitry in female mice not involving TLR4.
A Numerical Investigation of Transonic Axial Compressor Rotor Flow Using a Low Reynolds Number k-ε Turbulence Model (1997)

We have developed a computer simulation code for three-dimensional viscous flow in turbomachinery based on the time-averaged compressible Navier-Stokes equations and a low Reynolds number k-ε turbulence model. It is described in detail in this paper. The code is used to compute the flow fields for two types of rotor (a transonic fan NASA Rotor 67 and a transonic axial compressor NASA rotor 37), and numerical results are compared to experimental data based on aerodynamic probe and laser anemometer measurements. In the case of Rotor 67, calculated and experimental results are compared under the design speed to validate the code. The calculated results show good agreement with the experimental data, such as the rotor performance map and the spanwise distribution of total pressure, total temperature, and flow angle downstream of the rotor. In the case of Rotor 37, detailed comparisons between the numerical results and the experimental data are made under the design speed condition to assess the overall quality of the numerical solution. Furthermore, comparisons under the part speed condition are used to investigate a flow field without passage shock. The results are well predicted qualitatively. However, considerable quantitative discrepancies remain in predicting the flow near the tip. In order to assess the predictive capabilities of the developed code, computed flow structures are presented with the experimental data for each rotor and the cause of the discrepancies is discussed.
Three-dimensional model for acoustic field created by a piezoelectric plate in a resonator (2017)

A three-dimensional model is developed to describe an acoustic field excited by a piezoelectric plate of finite size in a fluid filled resonator. First, the eigenfunctions (modes) of a bare plate are derived using general piezoelectric equations considering the elastic and electric properties of the plate. Then, the piezoelectric plate is placed into a fluid media such that only one plate side is in fluid and an acoustic field generated by the plate in the fluid is estimated. Finally, a reflector is placed to be parallel to the piezoelectric plate and acoustic field in a resonator is evaluated. The solution for a piezoelectric plate of finite size is obtained using Singular Value Decomposition (SVD) method. Equations for acoustic and electric variables are presented. Radiation force on spherical particles in the standing wave field is derived and discussed. Numerical results are presented to show the three-dimensional modal displacement and electrical characteristics of the plate at various frequencies and aspect ratio. Finally, the analytical results are compared with two-dimensional and three-dimensional finite element results using COMSOL Multiphysics commercial software.
Development of a Method for the Synthesis of 4-Aryl-Functionalized 2-Azabicyclo[3.2.1]octanes (2017)

A method for the synthesis of 4-substituted azabicyclo[3.2.1]octanes from N-tosyl-2-azabicyclo[3.2.1]octa-3,6-diene, a versatile bicyclic heterocycle not commonly used in medicinal chemistry research, is presented. The method uses bromination, followed by Suzuki­ coupling, and subsequent reduction and deprotection. The desired 4-substituted azabicyclo[3.2.1]octanes were obtained in moderate to high yields.
RADT-47. A MULTICENTER OBSERVATIONAL STUDY OF SURGICALLY TARGETED RADIATION THERAPY (START) USING IMPLANTED CS-131 SEEDS IN A COLLAGEN-BASED CARRIER TILE IN INTRACRANIAL BRAIN NEOPLASMS - PROTOCOL IN PROGRESS (2020)

Abstract INTRODUCTION Post-resection radiotherapy (RT) is the most effective adjuvant treatment for brain tumors. However, there is no current consensus as to the “best” type of post-resection RT, either at diagnosis or recurrence. The use of internally placed radiation (brachytherapy) allows immediate initiation of RT when residual tumor burden is minimal, which theoretically should lessen the risk of recurrence. Brachytherapy placement intraoperatively allows more precise identification of the tumor margins than by postoperative imaging. Traditional brachytherapy methods have several drawbacks, including uneven dose distribution, long operating room times, a need for expensive equipment, and/or frequent adverse events (AE). To address these issues, a device with Cs-131 radiation seeds in a resorbable collagen-based carrier tile (GammaTile, GT Medical Technologies, Tempe AZ) was developed and is described as Surgically Targeted Radiation Therapy or STaRT. The device has demonstrated excellent safety and local control in early commercial use. OBJECTIVE The objectives of this registry study are to evaluate real-world clinical outcomes and patient reported outcomes that measure the effectiveness and safety of STaRT. METHOD Patients (N=600) with surgically resected (R) brain tumors of any pathology who have undergone STaRT are eligible. Accrual to start at 20+ sites in Q3 2020. Data collected includes local control, overall survival, QOL, neurocognition, functional decline, and surgical and radiation associated AE’s. Data will be collected at 1, 3, 6, 9, and 12 months, then every 6 months through 5 years. RESULT Data will be used to benchmark clinical outcomes of STaRT therapy and allow for comparisons to existing standard-of-care treatments. CONCLUSION This will be the first observational registry study of R+STaRT, delivered by Cs-131 sources in permanently implanted resorbable collagen tile carriers. The outcome measures captured will allow for evaluation of the potential risks and benefits of this treatment approach for patients in a real-world setting.
14C‐Markierung von D 16 427, einer neuen positiv inotropen Wirksubstanz (1986)

Abstract D 16 427 (D,L‐1(3‐Hydroxy‐4‐methyl‐phenyl)‐1‐hydroxy‐2‐(3‐phenyl‐propylamino)‐propan‐hydrochlorid), ein neues positives Inotropikum mit β‐adrenergem Wirkmechanismus, wird in einer 8‐Stufen‐Synthese 14 C‐markiert.
Adaptation of multiple access parameters in time hopping UWB cluster based wireless sensor networks (2005)

Ultrawideband (UWB) is an attractive physical layer technology for wireless sensor networks due to its unique characteristics. Flexibility in adjusting the processing gain of UWB systems makes it possible to tune the data rate and transmission range to fulfill the requirements of specific applications. Conventional systems assign identical multiple access parameters to all users regardless of the signal-to-interference plus noise ratio of the received signal. An adaptive assignment scheme for multiple access parameters in cluster based wireless sensor networks is investigated. First, an orthogonal time hopping sequence construction is proposed for synchronous communications (downlink), where the number of pulses per symbol are adjusted to meet the bit error rate requirement of an application. Then, adaptation of multiple access parameters in asynchronous scenarios (uplink) is evaluated using a Gaussian approximation method to model the multiple access interference in two cases: one with fixed frame duration, where the goal is to increase the average throughput, and the other with fixed symbol duration, where the goal is to increase the network lifetime. Finally, a mathematical framework is developed for approximating the interference when the number of pulses per symbol and the frame duration vary.
<title>Photoacoustic tissue scanning (PATS)</title> (1999)

We developed Photoacoustic Tissue Scanning to tomografically image optically absorbing structures in tissue. With 532 nm light depths down to 6-9 mm were reached. As the samples we used capillaries with blood, human hairs or a variable dilution of Evans blue, embedded in real tissue (chicken breast) or a 10 % solution of Intralipid-10%. Small PVdF piezoelectric hydrophones were used for detection, in scanning mode for imaging purposes. The depth resolution is about 10 ?m, and the lateral resolution is limited by the diameter of the detector (200 ?m in our case).
Development of the integrated environmental control model: Performance and cost models for fabric filters. Quarterly progress report, January--March 1994 (1994)

The present report summarizes recent progress on the Phase I effort during the period January 1, 1994 through March 30, 1994. This report summarizes progress to date in refining the existing analytical models implemented in the IECM. In this report, the authors described the development of analytical models for the performance and costs of high-performance particulate control technologies, focusing on fabric filters. They pay special attention to developing models which can be used to estimate costs for systems whose performance is up to a factor of three below the present NSPS standards of 0.03 lb/MMBtu. Typically, the cost models relate the capital costs and the operating and maintenance (O&M) costs to process parameters and the costs of labor and materials. The capital cost models are anchored to a base capital cost for a specific size unit and adjusted according to the actual or design parameters. The performance models are constructed to estimate the process parameters for a desired level of emission control. The primary motivation for these models is to estimate the costs of complying with environmental standards on a basis which reflects recent advances in control technology. Finally, the authors incorporate the uncertainties in various process parameters and inputs costs so as to allow a more rational and robust basis for comparing different technologies. In the following sections the authors discuss the initial development of the performance and cost models for fabric filters followed by a numerical example which illustrates the use of these new models. The next quarterly report will provide a similar update of the IECM electrostatic precipitator models, plus a brief discussion of the comparative advantages of different particulate control.
Emerging Prominence of Sessile Serrated Polyps in a Large Colonoscopy Practice: Distribution Trends by Year, Anatomic Site, Age, and Sex (2013)

Purpose: Sessile serrated polyps (SSPs) are now recognized as critical colorectal cancer precursors. Their reported prevalence ranges widely, and longitudinal observations are lacking. In this study, we sought to examine changes in the frequency of SSPs by year, site, age, and sex. Methods: Trends in the proportional distribution of SSPs, hyperplastic polyps (HPs), and adenomas (ADs) from 2002 to 2012 were assessed from electronic medical records at Mayo Clinic in Rochester, MN. SSP site and dysplasia data were derived from 2011-2012 to reflect current practice. Patients with inflammatory bowel disease or high-risk conditions for cancer were excluded. Results: From >120,000 colonoscopies, 56,605 polyps were identified during 2002-2012 (4,508-6,003 polyps/year). Since first noted in 2007, the frequency of SSPs increased annually to 17% of all polyps with a parallel proportional decrease in HPs (Figure). The proximal proportion of all polyps increased progressively with age from 29.6% in those <40 (years) to 59.5% in those ≥90 (p<0.0001) and of SSPs from 57.2% to 83.3%, respectively (p<0.0001). SSPs accounted for 19.5% of polyps in women vs 13.3% of men (p<0.0001); SSPs were proximal in 68.4% vs 62.0%, respectively (p=0.006). Dysplasia occurred in 15.4% of SSPs, was more common proximally (p=0.02), and increased from 5.7% in those age <40 to 19.7% in those ≥70 (p<0.0001). Dysplasia was high grade in 0.8% and seen only in those age ≥60.FigureConclusion: SSP diagnoses have increased dramatically since 2007. The concordant proportional decrease in HPs suggests that re-classification explains some of the SSP increase. SSPs are more likely in the proximal colon and in women, and risk of dysplasia rises with age and proximal site.
Risk assessment of catastrophic leak of R452B from packaged unit into a residential space. (2018)

With the effort to find alternative refrigerants with lower global warming potential (GWP), challenges have arisen due to the flammability risk for many of the alternatives. One of the new alternatives is R452B, which is recommended as a replacement for R410A. R452B is classified as a mildly flammable refrigerant (A2L) by ASHRAE 34. This paper summarizes a CFD simulation study of a leak incident of R452B from a 3-ton packaged unit which serves a 167 m2 residence. The R452B leak is assumed to be downstream of the evaporator coil. The simulated residence has four rooms and a hall way. The packaged unit distributes the conditioned air through a supply duct system delivering the air through registers. The dispersion of R452B is characterized for two scenarios: one with underfloor supply air ducts and another with ceiling supply air ducts. The mass flow rate of R452B exiting the duct outlets is quantified and the refrigerant volume fraction is monitored inside the residential space.
How computational rock-physics tools can be used to simulate geologic processes, understand pore-scale heterogeneity, and refine theoretical models (2014)

Abstract Rock physics allows us to link geologic processes with geophysical observables through a multiscale integration of data. This integrated analysis is typically done using empirical or theoretical rock-physics models, which are often calibrated with laboratory or field data. With the advent of computational rock physics, a new set of tools can be used to simulate geologic processes and interpret their signatures in the geophysical cross-property domain by computing macroscopic properties on a common or shared rock model. Furthermore, these computational tools allow us to probe, in ways that are nearly impossible with macroscopic physical samples, microscopic (pore-scale) distributions of structural and mechanical heterogeneities, which can have significant effect on macroscopic properties. This in turn can aid in refining conventional theoretical models by accounting for more complex, realistic, and heterogeneous features of porous media, thus taking the theoretical models beyond their limiting, simplifying assumptions and making them more practically applicable. The three key advantages of a computational rock-physics-based modeling approach are (1) use of a common rock model, (2) use of methods based on geologic processes, and (3) use of pore-scale understanding to refine simple yet widely applicable theoretical models. The effects of geologic processes such as compaction, sorting, and diagenesis on elastic and transport property trends not only can be modeled using this computational approach, but pore-scale insights further allow us to critically review simplistic assumptions of commonly used contact-based effective-medium models for these processes.
Full resolution of subacute acetabular osteomyelitis in an 11-year-old patient following nonsurgical management (2017)

Subacute acetabular osteomyelitis is uncommon and often misdiagnosed due to ill-defined symptomology and indolent disease course. An afebrile 11-year-old boy re-presented with 4 weeks atraumatic limp and increasingly severe right hip pain previously believed to be transient synovitis. Examination revealed hip tenderness and reduced mobility. X-rays showed loss of bone density in the proximal femur and a visible joint effusion. T2-weighted magnetic resonance imaging demonstrated the regions of high signal superior to the triradiate cartilage, widening of the cartilage space and a sympathetic effusion, consistent with acetabular osteomyelitis. Six weeks following antibiotic therapy, pain subsided and normal hip mobility was achieved. Review magnetic resonance scan confirmed clinical findings with reduced bone marrow edema, surrounding swelling, and hip effusion. Clinical resolution was confirmed 8 weeks postpresentation. Subacute acetabular osteomyelitis is rare and largely misdiagnosed at first presentation. It should be considered in all cases of atraumatic limp and low-grade hip pain.