gebhart/patrepeval huggingface dataset:
Relationship among Shigella spp. and enteroinvasive Escherichia coli (EIEC) and their differentiation (2014)

Shigellosis produces inflammatory reactions and ulceration on the intestinal epithelium followed by bloody or mucoid diarrhea. It is caused by enteroinvasive E. coli (EIEC) as well as any species of the genus Shigella, namely, S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. This current species designation of Shigella does not specify genetic similarity. Shigella spp. could be easily differentiated from E. coli, but difficulties observed for the EIEC-Shigella differentiation as both show similar biochemical traits and can cause dysentery using the same mode of invasion. Sequencing of multiple housekeeping genes indicates that Shigella has derived on several different occasions via acquisition of the transferable forms of ancestral virulence plasmids within commensal E. coli and form a Shigella-EIEC pathovar. EIEC showed lower expression of virulence genes compared to Shigella, hence EIEC produce less severe disease than Shigella spp. Conventional microbiological techniques often lead to confusing results concerning the discrimination between EIEC and Shigella spp. The lactose permease gene (lacY) is present in all E. coli strains but absent in Shigella spp., whereas β-glucuronidase gene (uidA) is present in both E. coli and Shigella spp. Thus uidA gene and lacY gene based duplex real-time PCR assay could be used for easy identification and differentiation of Shigella spp. from E. coli and in particular EIEC.
Протеомный анализ мха Physcomitrella patens (Hedw.) B.S.G (2009)

Для построения референтной протеомной карты мха Physcomitrella patens, основанной на полной нуклео-тидной последовательности генома, проведены двумерные электрофорезы белков, изолированных из протопластов, протонемы и гаметофоров мха. На гелях, обработанных серебром, разрешено в зависимости от фазы развития мха от 500 до 600 белковых пятен. Анализ пептидов, полученных в результате трипсинолиза белков, методом MALDI-TOF-масс-спектрометрии («пептидного отпечатка») позволил идентифицировать 212 индивидуальных белков. В целях расширения спектра изучаемых белков проведен одномерный гель-электрофорез белков экстракта в денатурирующих условиях с последующим анализом триптических пептидов методом LC-ESI-MS/MS. С помощью предложенного метода определено еще 186 белков. Применительно к 398 белкам, идентифицированным двумя методами, проведена классификация в соответствии с системой кластеризации ортологичных генов. Установлено, что 16% белков участвуют в различных клеточных процессах и передаче сигнала, 26% - в процессах метаболизма, 7% - в процессинге и хранении генетической информации. В результате протеомного анализа с использованием флуоресцентных красителей, конъюгированных с белками в тотальных препаратах, обнаружены различия между двумя основными фазами жизненного цикла мха - протонемой и гаметофорами. Выявлены достоверные различия в белковом спектре протопластов, изолированных из протонемы, - они существенно отличаются по составу белков как от протонемы, так и от гаметофоров.
Co-formed accelerometer array for integrated sensor/actuator applications (1996)

This paper describes a fabrication approach for producing high‐sensitivity low‐cost accelerometers. This approach offers the potential for intrinsically combining accelerometers as a dense array within an actuator. Hence sensing and actuation functions can be combined into one co‐formed inexpensive transducer array. Results are presented which show that the combined transducer has predictable properties and is well suited for use in sensing, actuation, and active‐control applications.
Modification of Homologous Recombination Deficiency Score Threshold and Association with Long-Term Survival in Epithelial Ovarian Cancer (2021)

New therapies, such as poly-ADP ribose polymerase inhibitors (PARPi), and immunotherapy treatments have generated great interest in enhancing individualized molecular profiling of epithelial ovarian cancer (EOC) to improve management of the disease. In EOC patients, putative biomarkers for homologous recombination deficiency (HRD), microsatellite instability (MSI), and tumor mutational burden (TMB) were characterized and correlated with survival outcomes. A series of 300 consecutive EOC patients were enrolled. Patients underwent neoadjuvant chemotherapy (<i>n</i> = 172) or primary cytoreductive surgery (<i>n</i> = 128). Molecular profiling and survival analyses were restricted to the primary cytoreductive surgery cohort due to tissue availability. All patients underwent germline testing for HRD- and MSI-related gene mutations. When sufficient tissue was available, screening for somatic BRCA1/2 mutations, BRCA1 promoter methylation, HRD score (a measure of genomic instability), MSI, and TMB testing were performed. HRD score ≥33 was associated with improved overall survival on multivariable analysis. In the era of biomarker-driven clinical care, HRD score ≥33 may be a useful adjunctive prognostic tool and should be evaluated in future studies to predict PARPi benefits.
Effect of impurities on the quantized conductance of narrow channels (1989)

The conductance G of narrow channels has been observed recently to be quantized in integer multiples of 2${e}^{2}$/h. We have calculated G for the case that an impurity is present in the channel. The channel is modeled as an electron waveguide, and the impurity is assumed to be an isotropic (s-like) scatterer. An analytic expression for G is obtained. We find that G is reduced below the unperturbed plateau values, and that for very strong scatterers the plateaus disappear. However, G exhibits two interesting features: First, G is pinned such that whenever the Fermi level is at the band bottom of the (n+1)th transverse subband G=n(2${e}^{2}$/h). Second, for attractive impurity potentials that have phase shift ${\ensuremath{\delta}}_{0}$\ensuremath{\lesssim}30\ifmmode^\circ\else\textdegree\fi{}, the conductance is found to have a deep downward dip between adjacent conductance plateaus. We attribute these features to multiple scattering between the impurity and the waveguide walls.
Dynamic Maneuvers in Local Staging of Head and Neck Malignancies with Current Imaging Techniques: Principles and Clinical Applications (2003)

Imaging has been widely demonstrated to be important in local staging of head and neck malignancies as a complement to clinical examination, including endoscopy. Recent developments in multidetector row computed tomography (CT) provide better anatomic resolution within a shorter acquisition time and wider anatomic coverage. However, in many cases lesions still remain undefined. In such cases, performance of dynamic maneuvers could provide useful information about the local extent of a tumor. The usefulness of dynamic maneuvers has increased with the improvement in temporal and spatial resolution that resulted from the most recent techniques of multidetector row CT. The puffed cheek technique and the modified Valsalva maneuver allow evaluation of a lesion that was poorly demonstrated owing to apposition of mucosal surfaces. In some cases, phonation improves demonstration of small lesions of the vocal cords and allows more precise anatomic localization. The open mouth technique allows demonstration of a lesion that was previously overlooked due to dental amalgam artifacts.
Ruthenium(II) Biscarboxylate‐Catalyzed Borylations of C(sp2)−H and C(sp3)−H Bonds (2016)

Versatile borylations of C(sp<sup>2</sup> )-H and C(sp<sup>3</sup> )-H were achieved with ruthenium(II) biscarboxylate complexes. The robust nature of the ruthenium(II) catalyst enabled C(sp<sup>3</sup> )-H borylation on pyrrolidines, piperidines, and azepanes with ample scope and excellent positional selectivity control.
Pseudoelastic intramedullary nailing for tibio–talo–calcaneal arthrodesis (2011)

Tibio-talo-calcaneal (TTC) arthrodesis is a procedure to treat severe ankle arthropathy by providing a pain-free and stable fusion. Intramedullary (IM) nails offer a method of internal fixation for TTC arthrodesis by providing compressive stability, as well as shear and torsional rigidity. IM nails have been developed to apply compression to the TTC complex during installation; however, current designs are highly susceptible to a loss of compression when exposed to small amounts of bone resorption and cyclic loading. Nickel titanium (NiTi) is a shape-memory alloy capable of recovering large amounts of deformation via shape-memory or pseudoelasticity. Currently, the next generation of IM nails is being developed to utilize the adaptive, pseudoelastic properties of NiTi and provide a fusion nail that is resistant to loss of compression or loosening. Specifically, the pseudoelastic IM nail contains an internal NiTi compression element that applies sustained compression during the course of fusion, analogous to external fixators.
Investigation of Low-flow Phenomenon in Case of Droughts (1989)

By the use of streamflow and truncation levels, hydrologic droughts are defined. Flows of different truncation level are obtained from each selected subbasin. Flow ratio is calculated by dividing subbasin flow of a certain truncation level by its corresponding outlet flow. Eighteen streamflow gage stations in the Scioto River Basin, Ohio were used for this investigation. It was found that the flow ratios in the basin decrease significantly with increasing truncation levels and mean-flow ratios are approximately equal to their corresponding area ratios. This implies that the use of drainage area ratio for flow estimation is impractical in case of droughts.
The Role of Understaffing in Central Venous Catheter-Associated Bloodstream Infection (1996)

Abstract Objective: To determine risk factors for central venous catheter-associated bloodstream infections (CVC-BSI) during a protracted outbreak. Design: Case-control and cohort studies of surgical intensive care unit (SICU) patients. Setting: A university-affiliated Veterans Affairs medical center. Patients: Case-control study: all patients who developed a CVC-BSI during the outbreak period (January 1992 through September 1993) and randomly selected controls. Cohort study: all SICU patients during the study period (January 1991 through September 1993). Measurements: CVC-BSI or site infection rates, SICU patient clinical data, and average monthly SICU patient-to-nurse ratio. Results: When analyzed by hospital location and site, only CVC-BSI in the SICU had increased significantly in the outbreak period compared to the previous year (January 1991 through December 1991: pre-outbreak period). In SICU patients, CVC-BSI were associated with receipt of total parenteral nutrition [TPN]; odds ratio, 16; 95% confidence inter val, 4 to 73). When we controlled for TPN use, CVC-BSI were associated with increasing severity of illness and days on assisted ventilation. SICU patients in the out-break period had shorter SICU and hospital stays, were younger, and had similar mortality rates, but received more TPN compared with patients in the pre-outbreak period. Furthermore, the patient-to-nurse ratio significantly increased in the outbreak compared with the pre-outbreak period. When we controlled for TPN use, assisted ventilation, and the period of hospitalization, the patient-to-nurse ratio was an independent risk factor for CVC-BSI in SICU patients. Conclusions: Nursing staff reductions below a critical level, during a period of increased TPN use, may have contributed to the increase in CVC-BSI in the SICU by making adequate catheter care difficult. During healthcare reforms and hospital downsizing, the effect of staffing reductions on patient outcome (ie, nosocomial infection) needs to be critically assessed.
Establishing use of asphalt binder cracking tests for prevention of pavement cracking (2014)

AbstractPremature loss of serviceability due to cracking remains one of the most prominent distress modes afflicting asphalt pavements today. Although there has been significant progress in developing binder fracture tests, concerns exist about a number of the assumptions used in current analysis methods. In particular are three related main issues: (1) sorting the total failure energy into time-dependent flow and fracture energy; (2) defining the role of binder fracture in pavement cracking; and (3) selecting relevant loading rates such as to correspond to binder thermal strain during pavement cooling. This study aims to investigate and address all three of the aforementioned issues to establish the use of binder crack resistance tests as an effective tool for preventing pavement cracking. Pseudo-strain analysis showed that separation of viscous dissipation and time-independent fracture energy is unnecessary to relate binder failure energy to mixture fracture. Finite element analysis showed that even in the presence of aggregates, crack initiation in fine-aggregate mixtures is directly related to the experimentally derived binder fracture properties. Finally, multi-scale analysis was used to derive the binder strain rates in the pavement during cooling, and successfully used to develop a practical method for selection of binder fracture test loading rates that are comparable to field cooling rates and conditions.Keywords: fracture mechanicsfinite elementenergy dissipationsingle-edged notched bendingglass transitionmulti-scale modelling AcknowledgementsThe authors like to acknowledge the insightful input and contributions of Mr Amir Arshadi of UW-Madison and Dr Raul Velasquez (formerly of UW-Madison). The results and opinions presented are those of the authors and do not necessarily reflect those of the sponsoring agencies.FundingThis research was in part sponsored by the Western Research Institute "Asphalt Research Consortium" as well as the Transportation Pooled Fund Study on Low Temperature Cracking. This support is gratefully acknowledged.Notes†This material is published by permission of the Modified Asphalt Research Center operated by University of Wisconsin Madison for the US Department of Transportation under Contract No. [DTFH61-07-H-00009]. The US Government retains for itself and others acting on its behalf a paid-up non-exclusive and irrevocable worldwide license in said article to reproduce prepare derivative works distribute copies to the public and perform publicly display publicly by or on behalf of the Government.
Prediction and Measurement of Thermal Transport Across Interfaces Between Isotropic Solids and Graphitic Materials (2011)

Due to the high intrinsic thermal conductivity of carbon allotropes, there have been many attempts to incorporate such structures into existing thermal abatement technologies. In particular, carbon nanotubes (CNTs) and graphitic materials (i.e., graphite and graphene flakes or stacks) have garnered much interest due to the combination of both their thermal and mechanical properties. However, the introduction of these carbon-based nanostructures into thermal abatement technologies greatly increases the number of interfaces per unit length within the resulting composite systems. Consequently, thermal transport in these systems is governed as much by the interfaces between the constituent materials as it is by the materials themselves. This paper reports the behavior of phononic thermal transport across interfaces between isotropic thin films and graphite substrates. Elastic and inelastic diffusive transport models are formulated to aid in the prediction of conductance at a metal-graphite interface. The temperature dependence of the thermal conductance at Au-graphite interfaces is measured via transient thermoreflectance from 78 to 400 K. It is found that different substrate surface preparations prior to thin film deposition have a significant effect on the conductance of the interface between film and substrate.
Laplace's Law: What It Is About, Where It Comes from, and How It Is Often Applied in Physiology [Retrospectroscope] (2011)

Have you ever seen a birthday party balloon shaped as a bunny rabbit or a teddy bear or Mickey Mouse? Sure, you have. Did you know that Laplace's law governs the mechanical behavior at every single point over their respective surfaces? Ha-ha-ha... a healthy laugh comes out, `cause it sounds like Alice's little fancy joke! Imagine... His Honor, Le Marquis de Laplace, playing with puppets!
Trichomonas vaginalis infection and prostate‐specific antigen concentration: Insights into prostate involvement and prostate disease risk (2019)

Overall, our findings do not provide strong support for prostate involvement during T. vaginalis infection, although our suggestive positive findings for higher PSA concentrations do not rule out this possibility entirely. These suggestive findings may be relevant for prostate condition development because higher early- to mid-life PSA concentrations have been found to predict greater prostate cancer risk later in life.
High-purity nano silica powder from rice husk using a simple chemical method (2012)

A highly pure, small particle-sized and high surface area nano silica powder was prepared from rice husk using alkali extraction, followed by an acid precipitation method. The composition, phase, morphology, size and surface area of the as-synthesised nano silica powder was investigated by energy-dispersive spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, particle size analyser and BET surface area analyser. High-purity nano silica powder was obtained by sodium hydroxide (NaOH) purification treatment (0.5, 1, 1.5, 2 and 2.5 N). The high purity of silica (∼99.9%) was obtained at 2.5 N NaOH treatment. The pure nano silica powder that is obtained shows an average particle size of ∼25 nm with a high-specific surface area (SSA) of 274 m2 g−1, with an average pore diameter of 1.46 nm.
Using NMR to Validate First-Principles Granular Flow Equations (2005)

Nuclear magnetic resonance (NMR) experiments are described for two granular-flow systems, the vibrofluidized bed and the gas-fluidized bed. Using pulsed field gradient, magnetic resonance imaging, and hyperpolarized gas NMR, detailed information is obtained for the density and motions of both grains and interstitial gas. For the vibrofluidized bed, the granular temperature profile is measured and compared with a first-principles formulation of granular hydrodynamics. For the gas-fluidized bed, dynamic correlations in the grain density are used to measure the bubble velocity and hyperpolarized xenon gas NMR is used to measure the bubble-emulsion exchange rate. A goal of these measurements is to verify in earth gravity first-principles theories of granular flows, which then can be used to make concrete predictions for granular flows in reduced gravity.
Probing Local Potentials inside Metallic Nanopores with SERS and Bipolar Electrochemistry (2017)

It is essential to understand the local potential distribution of solid‐state nanopores in nanofluidic systems. However, applying gate voltage or adding external electrical probes tends to disturb the electric field and/or flow patterns. To solve this problem, an approach is described to monitor the local potential using electrochemical surface enhanced Raman spectroscopy (EC‐SERS) in two types of nanocavity pores: doubled‐sided gold nanopores (MM nanopores) and single‐sided gold nanopores with a dielectric passivation layer on the backside (MD nanopores). Numerical simulations predict an electrical polarization reversal in the two nanopore geometries. Consequently, the redox SERS changes of Nile Blue A on the two gold nanopores are found to be reversed, which is consistent with the variation of polarizations. The driving voltage of metallic nanopore devices is about an order of magnitude lower than that of microfluidic bipolar devices. Our method will not only prove valuable for the design of metallic nanopores, but also will find applications in the measurement of contactless metallized nanofluidic devices.
Optical and Magnetic Microstructures in YIG Ferrite Fabricated by Femtosecond Laser (2015)

Optical and magnetic microstructures are directly fabricated inside a film of cerium-substituted yttrium iron garnet (Ce:YIG) by using a direct femtosecond laser writing. The laser irradiation induces local changes in both optical and magnetic properties of Ce:YIG. A quantitative phase imaging technique proves that the refractive index is increased by 0.015 0.001, which is about 0.7% of Ce:YIG refrative index 2.2 at 632.8 nm. The magneto-optical polar Kerr effect measurement shows that the magnetization property is changed from hard to soft, decreasing the coercivity. Our proposed technique paves the way toward the development of novel three-dimensional magneto-optical devices for optical communication and photonic applications.
SU‐E‐T‐384: Dosimetry Studies for Radioactive Gold Nanoparticles (2011)

Purpose: This investigation was initiated to determine the absorbed dose and radioactivity distribution of radioactive gold nanoparticles.Methods: Polymer gel dosimeter was prepared using about 12% gelatin (Sigma Aldrich, 300 bloom type A), 9% methacrylic acid(Sigma Aldrich), 10mM THPC (Sigma Aldrich), 18mM hydroquinone (Sigma Aldrich) in deionized water. These dosimeters are used for calibration purpose and meant to estimate the absorbed dose in the medium from the radiation emitted by the radioactive gold nanoparticles. The high energy gamma dose, activity distribution were measured using SPECT imaging and the phantom used was the ball of play‐doh made by Hasbro Toys. A previously constructed acrylic cast of beagle dogˈs head was used in this study to place the phantom. The radioactive gold nanoparticles were synthesized at the University owned nuclear reactor with the high neutron flux of ∼10e14 neutrons/cm2/sec.Results: Carbohydrate suspended radioactive nanoparticles with approximately 200 microCuries were injected in a play doh ball, depicting the prostate gland of beagle dog, approximately 1 inch diameter (8–10ml) in size. The phantom was placed on the SPECT imaging table near the isocenter of the imaging plane. The Gamma camera was peaked for the 411keV photon and equipped with a high energy (Iodine collimator). The phantom was then imaged using SPECT imaging protocol. The activity imaged at various planes and count rates was evenly distributed as predicted Conclusions: The activity distribution as seen in the SPECT imaging indicated active hot and cold spots of radioactive gold nanoparticles. The use of play‐doh determines the activity distribution but uneven diffusion. To compensate for that polymer gel dosimeters, equivalent to the tissue densities may be considered, besides there is also an advantage of estimating the absorbed doses.