gebhart/patrepeval huggingface dataset:
EGFR mutations in men and cigarette smokers with lung adenocarcinoma. (2010)

10538 Background: EGFR mutations underlie the sensitivity of lung cancers to erlotinib and gefitinib and are more commonly found in never smokers and women. Previously, we reported the presence of EGFR mutations in 51% of patients with lung adenocarcinoma who were never smokers (Pham, et al. JCO 2006), with a similar incidence of mutations in men (23%) and women (27%). Here we have examined the frequency of EGFR mutations in former smokers, current smokers, and men. Methods: With IRB approval, we reviewed the medical records of all patients with lung adenocarcinoma and EGFR mutation testing results. We determined the frequency of EGFR mutations and characterized their association with clinical variables, including cigarette smoking status (former, current, never) and gender. Results: EGFR mutation status was determined in 2080 lung adenocarcinomas. Although the frequency of EGFR mutations was significantly higher in never smokers, EGFR mutations in former and current smokers represented 39% of all mutations detected (168/432, 95% CI, 34-44%). EGFR mutations were found in 13% of tumors from former smokers (149/1188, 95% CI, 11-15%), 5% of tumors from current smokers (19/352, 95% CI, 3-8%), and 49% of tumors from never smokers (264/540, 95% CI, 45-53%). EGFR mutations were found in 17% (141/826, 95% CI, 15-20%) of tumors from men and 23% of tumors from women (291/1254, 95% CI, 21-26%), with mutations in men representing 33% (141/432, 95% CI, 28-37%) of all those detected. Conclusions: EGFR mutations occur frequently in patients with a history of cigarette smoking and in men. Testing for activating EGFR mutations (especially exon 19 deletions and exon 21 L858R substitution) should be considered for all patients with adenocarcinoma of the lung at diagnosis, regardless of other clinical characteristics. This strategy can extend the use of tyrosine kinase inhibitors to all individuals with a high likelihood of benefit. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration AstraZeneca, Boehringer Ingelheim, Genentech, Roche
Diameter dependence of polarization resolved reflectance from vertical silicon nanowire arrays: Evidence of tunable absorption (2013)

Vertical silicon nanowire arrays of different diameters ranging from 90 nm to 190 nm with a pitch of 400 nm are fabricated. Nanowires are arranged in a square lattice and have a length of 1 μm. Polarization resolved reflectances from these nanowire arrays are measured and significant differences are observed for the reflectance characteristics of the s- and p-polarized beams. A narrow wavelength band of increased absorption is reported by analyzing the reflectance using the finite difference time domain method. The center wavelength of this band shifts toward higher wavelengths as the diameter of the nanowires increases achieving tunable absorption spectra within the nanowires. The wavelength band shifts at a rate of approximately 3.3 nm with every 1 nm increment in diameter. The increased absorption is achieved due to modal excitation and near-field coupling between the nanowires.
Determination of Antiplasmodial Activity and Binding Affinity of Selected Natural Products towards PfTrxR and PfGR (2013)

In our study, the binding affinities of selected natural products towards PfTrxR, PfGR, human TrxR and human GR were determined using a mass spectrometry based ligand binding assay. The in vitro antimalarial activity and cytotoxicity of these ligands were also determined. Catharanthine, 11-(OH)-coronaridine, hernagine, vobasine and hispolone displayed antiplasmodial activity against PfK1 (IC50 = 0.996-3.63 microg/mL).
Mortality Caused by Kidney Stones in Spinach-Fed Frogs (Rana pipiens) (1965)

Journal Article Mortality caused by kidney stones in spinach-fed frogs (Rana pipiens) Get access M. W. Berns M. W. Berns Department of Biology, Cornell University, Ithaca, N.Y. Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 15, Issue 4, April 1965, Pages 297–298, https://doi.org/10.2307/1293428 Published: 01 April 1965
Time Course of Cerebral Blood Flow Velocity in Central Nervous System Infections (1993)

In a 3-year period, 110 patients with central nervous system infections of various causes were examined serially by means of transcranial Doppler sonography. In viral-induced infections, no changes of flow velocity in basal cerebral arteries were seen, whereas in bacterial meningitis, a significant increase of blood flow velocity in the middle cerebral artery was recorded. Its extent was mainly associated with the type of the infectious agent, most frequently observed in pneumococcal meningitis (77%). The increase was up to 100% of the baseline values and was reversible in all cases. All patients were offered full-scale neurointensive care, and all subjects with bacterial meningitis were fully heparinized.
Metabolic carotenemia and carotenoderma in a child. (1995)

We describe a 3-year-old girl with long-standing yellow discoloration of her skin and a 3-fold increase in the plasma carotenoid concentration compared to normal, but no history of excessive carotene intake or familial carotenemia. When put on a carotene-deficient diet for 8 months she still had some remaining yellow discoloration in the nasolabial folds and on the palms and soles. The results of an oral loading with beta-carotene (1 mg/kg) provide indirect evidence that the girl's carotenemia is due to a probably genetic defect in the metabolism of carotenoids.
In-process height control during laser metal deposition based on structured light 3D scanning (2018)

Laser metal deposition is an additive manufacturing process capable of layer by layer construction of solid parts. An incorrect deposition distance between nozzle and substrate can result in height deviations from the ideal building path. The error can be propagated along layers, leading to an irreversible defect. Maintaining an optimal distance between the nozzle and the substrate is therefore a critical aspect. This paper introduces an off-line geometric control system for in-process measurement and build path correction. A structured light based 3D scanner measures the build height from an external, fixed position, providing more precise results than moving measuring systems. The deposition is stopped in certain stages of the process and the piece is scanned generating a three-dimensional point cloud. Processing of the collected data allows the build height determination. A control algorithm was developed to take corrective actions in accordance with the measured error. The system enables an accurate control of the generated geometry and permits the comparison with the original computer design. This approach reduces the required human supervision during the process and the occurrence of non-valid parts. The effectiveness of the method was proved through the contrast of parts built with and without control, showing a more accurate reproduction of the generated solid parts when corrections are applied.
Root-music based direction-of-arrival estimation methods for arbitrary non-uniform arrays (2008)

Two computationally efficient high-resolution methods are proposed for direction-of-arrival (DOA) estimation in arbitrary nonuniform sensor arrays. Our first algorithm is based on the fact that the spectral MUSIC function is periodic in angle. Expanding this function using Fourier series, we reformulate the DOA estimation problem as an equivalent polynomial rooting problem. Our second approach applies the inverse Fourier transform to the so-obtained root-MUSIC polynomial to compute the null-spectrum without any polynomial rooting, using a simple line search. The proposed techniques are shown to offer substantially improved performance-to- complexity tradeoffs as compared to the existing root-MUSIC-type methods applicable to non-uniform arrays.
Ho-doped fiber for high energy laser applications (2014)

Ho-doped fiber lasers are of interest for high energy laser applications because they operate in the eye safer wavelength range and in a window of high atmospheric transmission. Because they can be resonantly pumped for low quantum defect operation, thermal management issues are anticipated to be tractable. A key issue that must be addressed in order to achieve high efficiency and minimize thermal issues is parasitic absorption in the fiber itself. Hydroxyl contamination arising from the process for making the Ho-doped fiber core is the principal offender due to a combination band of Si-O and O-H vibrations that absorbs at 2.2 &mu;m in the Ho<sup>3+</sup> emission wavelength region. We report significant progress in lowering the OH content to 0.16 ppm, which we believe is a record level. Fiber experiments using a 1.94 &mu;m thulium fiber laser to resonantly clad pump a triple clad Ho-doped core fiber have shown a slope efficiency of 62%, which we also believe is a record for a cladding-pumped laser. Although pump-power limited, the results of these studies demonstrate the feasibility of power scaling Ho-doped fiber lasers well above the currently-reported 400-W level.<sup>1</sup>
Performance of a Continuously Sampling Hand-Held Digitizer for Residual-Limb Shape Measurement (1997)

Published quarterly by the AAOP, JPO: Journal of Prosthetics and Orthotics provides information on new devices, fitting and fabrication techniques, and patient management experiences. The focus is on prosthetics and orthotics, with timely reports from related fields such as orthopaedic research, occupational therapy, physical therapy, orthopaedic surgery, amputation surgery, physical medicine, biomedical engineering, psychology, ethics, and gait analysis. Each issue contains research-based articles reviewed and approved by a highly qualified editorial board, and two Academy self-study quizzes offering a total of two CEUs.
Topology Optimization of the Interior Structure of Blades with an Outer Surface Determined Through Aerodynamic Design (2018)

This work performs a topology optimization of the interior structure of engine blades in compressors with any given geometry of the desired outer-surface shape that may be determined by CFD and aerodynamic design software for the desired performance for thermal and fluid flows. A lofted compressor airfoil surface from the aerodynamic design was used to create a three-dimensional (3D) solid in SolidWorks. This was converted to an .IGS file that would be imported into HyperMesh® for the meshing and submitted to OptiStruct® for optimization. An optimization process is designed to produce an optimal interior structure, considering both pressure on the outer surface and centrifugal forces produced by rotational movements. The optimized blade becomes hollow in an optimal pattern with minimum materials needed for the pressure loading on outer skin and the distributed centrifugal forces. The final design was compared to the initial design using finite element method (FEM) to confirm that the mass, stress, strain, and displacement were reduced. The mass was reduced by 59.8% and the stresses reduced by a factor of 3.66! These results were validated by conducting a mesh independence study. 3D printers were used to produce the optimized blades in both plastic and metal.
Characterization of Escherichia coli Isolates from Hospital Inpatients or Outpatients with Urinary Tract Infection (2013)

Uropathogenic Escherichia coli (UPEC) is the most common cause of community- and hospital-acquired urinary tract infections (UTIs). Isolates from uncomplicated community-acquired UTIs express a variety of virulence traits that promote the efficient colonization of the urinary tract. In contrast, nosocomial UTIs can be caused by E. coli strains that differ in their virulence traits from the community-acquired UTI isolates. UPEC virulence markers are used to distinguish these facultative extraintestinal pathogens, which belong to the intestinal flora of many healthy individuals, from intestinal pathogenic E. coli (IPEC). IPEC is a diarrheagenic pathogen with a characteristic virulence gene set that is absent in UPEC. Here, we characterized 265 isolates from patients with UTIs during inpatient or outpatient treatment at a hospital regarding their phylogenies and IPEC or UPEC virulence traits. Interestingly, 28 of these isolates (10.6%) carried typical IPEC virulence genes that are characteristic of enteroaggregative E. coli (EAEC), Shiga toxin-producing E. coli (STEC), and atypical enteropathogenic E. coli (aEPEC), although IPEC is not considered a uropathogen. Twenty-three isolates harbored the astA gene coding for the EAEC heat-stable enterotoxin 1 (EAST1), and most of them carried virulence genes that are characteristic of UPEC and/or EAEC. Our results indicate that UPEC isolates from hospital patients differ from archetypal community-acquired isolates from uncomplicated UTIs by their spectrum of virulence traits. They represent a diverse group, including EAEC, as well as other IPEC pathotypes, which in addition contain typical UPEC virulence genes. The combination of typical extraintestinal pathogenic E. coli (ExPEC) and IPEC virulence determinants in some isolates demonstrates the marked genome plasticity of E. coli and calls for a reevaluation of the strict pathotype classification of EAEC.
Comparative activity of ampicillin, amoxycillin, amoxycillin/clavulanate and cefotaxime against 189 penicillin-susceptible and -resistant pneumococci (1995)

Agar dilution and E-test MICs of penicillin G, ampicillin, amoxycillin, amoxycillin/clavulanate and cefotaxime were determined against 189 pneumococci. Addition of clavulanate did not influence amoxycillin MICs, MIC50/MIC90 (mg/L) for penicillin G, ampicillin, amoxycillin and cefotaxime were: Penicillin susceptible strains (62): 0.03/0.03; 0.03/0.06; 0.015/0.03; 0.015/0.06. Penicillin intermediate strains (69): 0.25/1.0; 0.25/4.0; 0.125/1.0; 0.125/1.0. Penicillin resistant strains (58): 2.0/4.0; 4.0/4.0; 1.0/2.0; 1.0/2.0. E-test MICs correlated well with those obtained by agar dilution.
Toward Bioelectronic Medicine—Neuromodulation of Small Peripheral Nerves Using Flexible Neural Clip (2017)

Neural modulation technology and the capability to affect organ function have spawned the new field of bioelectronic medicine. Therapeutic interventions depend on wireless bioelectronic neural interfaces that can conformally and easily attach to small (few hundred micrometers) nerves located deep in the body without neural damage. Besides size, factors like flexibility and compliance to attach and adapt to visceral nerves associated moving organs are of paramount importance and have not been previously addressed. This study proposes a novel flexible neural clip (FNC) that can be used to interface with a variety of different peripheral nerves. To illustrate the flexibility of the design, this study stimulates the pelvic nerve, the vagus nerve, and branches of the sciatic nerve and evaluates the feasibility of the design in modulating the function of each of these nerves. It is found that this FNC allows fine-tuning of physiological processes such as micturition, heart rate, and muscle contractions. Furthermore, this study also tests the ability of wirelessly powered FNC to enable remote modulation of visceral pelvic nerves located deep in the body. These results show that the FNC can be used with a range of different nerves, providing one of the critical pieces in the field of bioelectronics medicines.
2. African swine fever virus: cellular and molecular aspects (2021)

The introduction of genotype II African swine fever (ASF) virus (ASFV) into the Caucasus in 2007 resulted in unprecedented disease propagation via slow geographical expansion through wild boar populations, short- and long-distance human-mediated translocations, and incursions into naïve wild boar and domestic pig populations. The disease is now widespread in eastern and central Europe as well as in Asia, including China. The global dimension of the current epidemic shows that all countries need to be prepared for an introduction. In its natural habitat in Africa, ASFV is maintained within an ancient cycle between soft argasid ticks and the common warthog. Once introduced to the domestic pig population, direct and indirect virus transmission occurs with or without involvement of the tick vector in the pig-tick and domestic pig epidemiological cycles respectively. In the domestic pig cycle, human activities involving pigs or pig derived products are the dominating driver of virus transmission. ASF epidemiology in the presence of wild boar and northern European climates has proved to have specific characteristics, described in the wild boar-habitat epidemiological cycle. In this cycle wild boar carcasses and the resulting contamination of the environment play key roles in virus persistence. In both the wild boar-habitat and the domestic pig epidemiological cycle, fully implemented biosecurity is the key for stopping virus transmission and controlling the disease. Positive examples from the Czech Republic and Belgium show that control and eradication of ASF from the wild boar-habitat cycle can be achieved. Both these cases, as well as the example of Sardinia, where ASFV genotype I now seem very close to eradication after more than 40 years presence, further underline the importance of involving, engaging and understanding all stakeholders in the value chains from farm and forest to fork in order to accomplish ASF control and eradication.
Funktion von extrazellulären Vesikeln und Bedeutung für die labormedizinische Diagnostik (2017)

Zusammenfassung: Gesunde und pathologisch veränderte Zellen des Körpers setzen extrazelluläre Vesikel (EV) frei, welche eine Vielzahl an Botenstoffen wie Proteine, Nukleinsäuren und Lipiden beinhalten. Diese beeinflussen nicht nur das umgebende Gewebe, in dem sie freigesetzt werden, sondern haben auch systemische Funktionen. Zahlreiche Studien belegen, dass EV im gesunden wie im pathologischen Kontext als Mediatoren in der interzellulären Kommunikation von großer Bedeutung sind. Ihre Funktion ist durch ihre spezifische Zusammensetzung bestimmt, die nicht allein Zelltyp-, sondern auch Kontext-abhängig ist und von Zellstress und Mutationen beeinflusst wird. EV pathologisch veränderter Zellen unterscheiden sich damit von EV gesunder Zellen. Aufgrund dieser Eigenschaft sind extrazelluläre Vesikel prinzipiell auch als Biomarker in der klinischen Diagnostik interessant. In diesem Übersichtsartikel fassen wir das aktuelle Verständnis der physiologischen Funktion von EV zusammen und erörtern den möglichen Einsatz von EV als prognostische und diagnostische Biomarker.
Diode-pumped mode-locked Nd:glass lasers with an antiresonant Fabry–Perot saturable absorber (1995)

We demonstrate passively mode-locked diode-pumped Nd:glass lasers with different media such as silicate, phosphate, and fluorophosphate that are homogeneously or inhomogeneously broadened. An antiresonant Fabry-Perot saturable absorber starts and stabilizes the soliton mode-locked Nd:glass lasers, producing pulses as short as 130 fs at an average output power of 100 mW. With a cw Ti:sapphire pump laser we obtain pulses as short as 90 fs.
FPGA developments for the SPARTA project (2005)

The European Southern Observatory (ESO) and Durham University's Centre for Advanced Instrumentation (CfAI) are currently designing a standard next generation Adaptive Optics (AO) Real-Time Control System. This platform, labelled SPARTA 'Standard Platform for Adaptive optics Real-Time Applications' will initially control the AO systems for ESO's 2<sup>nd</sup> generation VLT instruments, and will scale to implement the initial AO systems for ESO's future 100m telescope OWL. Durham's main task is to develop the Wavefront Sensor (WFS) front end and Statistical Machinery for the SPARTA platform using Field Programmable Gate Arrays (FPGA). SPARTA takes advantage of a FPGA device to alleviate the highly parallel computationally intensive tasks from the system processors, increasing the obtainable control loop frequency and reducing the computational latency in the control system. The WFS pixel stream enters a PMC hosted FPGA card contained within the SPARTA platform via optical fibres carrying the VITA 17.18/10 standard 2.5Gbps<sup>-1</sup> serial Front Panel Data Port (sFPDP) protocol. Each FPGA board can receive a maximum of 10Gbs<sup>-1</sup> of data via on-board optical transceivers. The FPGA device reduces WFS frames to gradient vectors before passing the data to the system processors. The FPGA allows the processors to deal with other tasks such as wavefront reconstruction, telemetry and real-time data recording, allowing for more complex adaptive control algorithms to be executed. This paper overviews the SPARTA requirements and current platform architecture, Durham's Wavefront Processor FPGA design and it concludes with a future plan of work.
Power frequency magnetic field from a 275 KV GIS substation in Malaysia (2004)

Gas insulated substations (GIS) have received much consideration from utilities and are preferred for service in urban areas due to its compactness. Consequently, for concerned utilities it is important to address the issue of environmental conditions in and around their GIS. One of which is the issue of magnetic field exposures, which have drawn a great deal of attention recently due to its possible health hazards. This paper presents the results of measurements of the power frequency magnetic fields or a 275 kV GIS substation in Malaysia. The measurements carried out covers the magnetic field from substation equipment, the in-coming and out-going power lines aid cables to and from the substation. Substations loading at the time of measurement were recorded. Results obtained were presented in various formats such as linear, contour aid three-dimensional plots. Statistical representation of the measured data showing the minimum, maximum, mean, standard deviation and median magnetic field for all measured areas were presented. Based on the results, the main sources of magnetic fields within the substation were identified. Results from the measurements will be used as raw data for future simulations and case studies on the substation.
Targeted redox inhibition of protein phosphatase 1 by Nox4 regulates eIF 2α‐mediated stress signaling (2016)

Phosphorylation of translation initiation factor 2α (eIF2α) attenuates global protein synthesis but enhances translation of activating transcription factor 4 (ATF4) and is a crucial evolutionarily conserved adaptive pathway during cellular stresses. The serine-threonine protein phosphatase 1 (PP1) deactivates this pathway whereas prolonging eIF2α phosphorylation enhances cell survival. Here, we show that the reactive oxygen species-generating NADPH oxidase-4 (Nox4) is induced downstream of ATF4, binds to a PP1-targeting subunit GADD34 at the endoplasmic reticulum, and inhibits PP1 activity to increase eIF2α phosphorylation and ATF4 levels. Other PP1 targets distant from the endoplasmic reticulum are unaffected, indicating a spatially confined inhibition of the phosphatase. PP1 inhibition involves metal center oxidation rather than the thiol oxidation that underlies redox inhibition of protein tyrosine phosphatases. We show that this Nox4-regulated pathway robustly enhances cell survival and has a physiologic role in heart ischemia-reperfusion and acute kidney injury. This work uncovers a novel redox signaling pathway, involving Nox4-GADD34 interaction and a targeted oxidative inactivation of the PP1 metal center, that sustains eIF2α phosphorylation to protect tissues under stress.