jimnoneill/paper-to-field-training huggingface dataset:
Effects of external driving on the coherence time of a Josephson junction qubit in a bath of two-level fluctuators

Field: Physics and Astronomy (Physical Sciences)

We study the effect of external driving on the two level systems (TLSs)\nassumed to be a major obstacle in increasing the coherence time of solid state\nJosephson-junction qubits. We find, by use of a Bloch-Redfield approach, that\nexternal driving has two major effects on the TLS. The first is increased\nfluctuations between the two states of the TLS, the significance of this effect\ncompared to thermal fluctuations depend on the energy splitting of the TLS\ncompared to temperature. The second effect is a reduction in the intensity of\nthe noise spectrum at low frequencies, and at the same time an increase in\nintensity around the renormalized Rabi frequency of the TLS, the driving\nfrequency and at beatings between these two frequencies. Finally we study the\nensemble averaged noise spectrum for a typical distribution of TLSs known to\ngive origin to $\\propto 1/f$ noise. We find that strong driving leads to\nreduced noise at low frequencies, and therefore to an increased dephasing time\n$T_2^Q$ of the qubit. However this effect is exponentially suppressed when the\ndriving frequency is large compared to temperature, as we typically find for\nJosephson qubits. We suggest that external driving at frequencies much lower\nthan the qubit frequency might be used in order to enhance the the qubit\ncoherence time.\n
Ca2+ accumulation in the hydrogenosomes of Neocallimastix frontalis L2: a mitochondrial-like physiological role

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

AbstractThe anaerobic fungus Neocallimastix frontalis L2 does not carry out oxidative phosphorylation but instead obtains energy from a fermentative metabolism. It does not have mitochondria, but does contain specialised redox organelles, the hydrogenosomes. With the aid of confocal laser scanning microscopy, we were able to follow the compartmentalisation of the ΔpH probe BCECF-AM (bis-(3-propyl-5-oxoisoxazol-4-yl)pentamethine(oxonolVi),2′,7′-bis-(2-carboxyethyl)-5-carboxyfluorescein acetomethyl ester) into hydrogenosomes in situ. Association of the Ca2+-specific dye Fluo-3AM (1-[2-amino-5-(2,7-dichloro 6-hydroxy-3-oxy-9-xanthenyl)-phenoxyl]-2-[2-amino-5-methylphenoxy]ethane-N,N,N′,N′-tetraacetic acid acetomethyl ester) within the lumen of the hydrogenosomes was also observed. In addition, transmission electron microscopy revealed that the hydrogenosomes contained electron-dense inclusions. X-ray microanalysis of these granules indicated the presence of calcium and phosphate. Our results indicate that hydrogenosomes from N. frontalis L2 maintain an internal alkaline pH and are involved in the calcium regulation of the cell. These physiological features resemble those of mitochondria from aerobic fungi.
Role of feeder cells in spreading and cytoskeleton organization of newborn rat keratinocytes.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Abstract We studied the effect of feeder cells (fibroblasts) and a mixture of the extracellular matrix components, Matrigel, on spreading and cytoskeleton organization of newborn rat keratinocytes (REK). REK formed lamellipodia on being plated together with feeder cells and on the Matrigel as a substrate whereas the same REK plated alone on a plastic surface formed filopodia. REK lamellipodia formation in co‐cultures depended on the fibroblast addition time. Although conditioned medium from fibroblast cultures was not enough to induce lamellipodia, the extracellular matrix left after fibroblast removal was as effective as Matrigel. Our results indicate that lamellipodia formation seems to depend on the factor(s) secreted by fibroblasts and associated with the extracellular matrix.
Numerical modelling of multiphase immiscible flow in double‐porosity featured groundwater systems

Field: Environmental Science (Physical Sciences)

SUMMARY A numerical model describing the flow of multiphase, immiscible fluids in a deformable, double‐porosity featured soil has been developed. The model is focused on the modelling of the secondary porosity features in soil, which is more relevant to groundwater contamination problems. The non‐linear saturation and relative permeabilities were expressed as functions of the capillary pressures. The governing partial differential equations in terms of soil displacement and fluid pressures were solved numerically. Galerkin's weighted‐residual finite element method was employed to obtain the spatial discretization whereas temporal discretization was achieved using a fully implicit scheme. The model was verified against established, peer‐reviewed works, and the assumption that the immiscible fluids (non‐aqueous phase liquids) will flow preferentially through the secondary porosity features in soil was validated. Copyright © 2011 John Wiley & Sons, Ltd.
The GRDP Per Capita Gap between Provinces in Indonesia and Modeling with Spatial Regression

Field: Economics, Econometrics and Finance (Social Sciences)

Gross Regional Domestic Product (GRDP) is one of the key indicators to determine the economic conditions in an area within a certain period, both based on current prices and constant prices. The GRDP per capita shows the value of GRDP divided by the mid-year population. According to data from Statistic Indonesia (BPS), the distribution of GRDP is concentrated in Java. About 59 percent of Indonesia's economy in 2021 was contributed by Java. The contribution of other islands is not more than 10 percent, except for Sumatra at 21 percent. One of the government's policies to equalize the economy announced in 2019 was the relocation of the nation's capital city from DKI Jakarta to East Kalimantan. This policy has generated polemics in various circles of society regarding priorities, urgency, procedures, and risks. The economic inequality between regions in Indonesia involves various regions or provinces with different characteristics. Spatial regression is a model that accommodates spatial effects because the observation unit is a location. The aim of this study is to determine the level of economic disparities between provinces in Indonesia, resulting in the decision to relocate the nation's capital city. In addition, the aim is to determine the significance of several factors that affect GRDP per capita as a measure of regional prosperity, namely population density, number of workers, and the Human Development Index.
Overuse of Antimicrobial Prophylaxis in Community Practice Urology

Field: Medicine (Health Sciences)

We documented considerable variation in antimicrobial prophylaxis for urological surgery. Compliance with AUA Best Practices increased with time but overall rates remain less than 60%. Efforts are needed to better understand the reasons for variation from recommended antimicrobial prophylaxis for common inpatient urological procedures to help decrease resultant complications and improve outcomes.
Genotype‐environment associations support a mosaic hybrid zone between two tidal marsh birds

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh‐level characteristics in shaping a hybrid zone between two recently diverged avian taxa – Saltmarsh ( Ammodramus caudacutus ) and Nelson's ( A. nelsoni ) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co‐occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid sparrows and assessed the degree of overlap in the ecological niche of each taxon. To do this, we sampled and genotyped 305 sparrows from 34 marshes across the hybrid zone and from adjacent regions. We used linear regression to test for associations between marsh characteristics and the distribution of pure and admixed sparrows. We found a positive correlation between genotype and environmental variables with a patchy distribution of genotypes and habitats across the hybrid zone. Ecological niche models suggest that the hybrid niche was more similar to that of A. nelsoni and habitat suitability was influenced strongly by distance from coastline. Our results support a mosaic model of hybrid zone maintenance, suggesting a role for local environmental features in shaping the distribution and frequency of pure species and hybrids across space.
Limitations in Impedance Reshaping of Grid Forming Converters for Instability Prevention

Field: Engineering (Physical Sciences)

Under a weak grid scenario, Grid Forming (GFM) converters have superior impedance-based small-signal stability compared to Grid Following (GFL) converters. The underlying assumption in defining a weak grid has traditionally been consideration of the inductive behaviour of the power grid load. In this paper, it is shown that, in presence of a non-inductive grid load, impedance-based small-signal instability is unavoidable in specific condition for Virtual Synchronous Machine (VSM)-based GFM. To prevent such instability, the classical way is to reshape the impedance through controller re-tuning in the frequency range of concern. For this purpose, the impedance reshaping capability of GFM is analysed and sensitivity analysis is performed with different control parameters. The simulation results are presented to verify the risk of unavoidable impedance-based small-signal instability due to very limited impedance reshaping capability of the GFM controller.
Development of an Irregularity in the Laminar-Turbulent Transition of the Spot

Field: Engineering (Physical Sciences)

A spot, generated by an artificial disturbance introduced into a laminar boundary layer, had a highly reproducibility in its velocity perturbations during the initial stage of its downstream development. Thus, we called it a ``laminar spot'' and investigated its downstream development in detail. The purpose of this study was to investigate the generation and the development of an irregularity observed in the velocity waves during the laminar-turbulent transition of the spot. The results obtained show that those irregularities appeared locally in the low-speed region away from the wall and spread wide close to the wall. In the beginning, lateral distortion of velocity profile due to the vortex-interaction caused the irregularity of the velocity-wave amplitude in the boundary between the low- and high-speed regions in the spot. In addition, the crossover of legs of the longitudinal vortices occurred incidentally in the spot and generated a local ejection of low-momentum fluid. Afterwards, some crossovers of legs were produced in a chain reaction. Consequently, the reproducibility in the velocity waves disappeared almost in the downstream and turbulent regions increased rapidly everywhere in the spot.
Pathological Observations Concerning the Regression of Experimental Atherosclerosis

Field: Medicine (Health Sciences)

In the present study we attempted to quantify the sequential changes occurring in cholesterolinduced aortic and coronary lesions in normotensive and renovascular hypertensive rabbits, which were placed on a 0.5% cholesterol diet for 16 weeks and observed up to 104 weeks after being withdrawn from the diet. After measuring the degree of surface involvement, a representative section covering the whole length of the aorta was obtained, and a histometric quantitative analysis was performed using an image-processing system. Furthermore, ten continuous step sections of the left coronary artery bed were prepared from each animal, and the degree of luminal stenosis was estimated in all the arterial segments contained. The results indicated a significant reduction of aortic lesions and a reversal of the luminal narrowing of the coronary artery in normotensive, as well as hypertensive, animals. It seems likely that, even in hypertensive animals, substantial regression of both aortic and coronary atherosclerosis can be expected after normalization of hypercholesterolemia.
Combination of nonspecific PDE inhibitors with inhaled prostacyclin in experimental pulmonary hypertension

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Inhalation of aerosolized prostacyclin (PGI 2 ) exerts selective pulmonary vasodilation, but its effect is rapidly lost after termination of nebulization. Amplification of the vasodilatory response to inhaled PGI 2 might be achieved by phosphodiesterase (PDE) inhibitors to stabilize its second messenger, cAMP. We established stable pulmonary hypertension in perfused rabbit lungs by continuous infusion of U-46619. Short-term (10-min) aerosolization maneuvers of PGI 2 effected a rapid, moderate decrease in pulmonary arterial pressure, with post-PGI 2 vasorelaxation being lost within 10–15 min, accompanied by a marginal reduction in shunt flow. Preceding administration of subthreshold doses of the PDE inhibitors theophylline, dipyridamole, and pentoxifylline via the intravascular or inhalational route, which per se did not influence pulmonary hemodynamics, caused more than doubling of the immediate pulmonary arterial pressure drop in response to PGI 2 and marked prolongation of the post-PGI 2 vasorelaxation to >60 min (all PDE inhibitors via both routes of application). This was accompanied by a reduction in shunt flow in the case of aerosolized theophylline (27.5%), pentoxifylline (30.5%), and dipyridamole (33.4%). Coaerosolization of PGI 2 and PDE inhibitors may be considered as a therapeutic strategy in pulmonary hypertension.
Identification of a lung adenocarcinoma cell line with CCDC6‐RET fusion gene and the effect of RET inhibitors in vitro and in vivo

Field: Medicine (Health Sciences)

Rearrangements of the proto‐oncogene RET are newly identified potential driver mutations in lung adenocarcinoma ( LAD ). However, the absence of cell lines harboring RET fusion genes has hampered the investigation of the biological relevance of RET and the development of RET ‐targeted therapy. Thus, we aimed to identify a RET fusion positive LAD cell line. Eleven LAD cell lines were screened for RET fusion transcripts by reverse transcription‐polymerase chain reaction. The biological relevance of the CCDC6‐RET gene products was assessed by cell growth, survival and phosphorylation of ERK 1/2 and AKT with or without the suppression of RET expression using RNA interference. The efficacy of RET inhibitors was evaluated in vitro using a culture system and in an in vivo xenograft model. Expression of the CCDC6‐RET fusion gene in LC ‐2/ad cells was demonstrated by the mRNA and protein levels, and the genomic break‐point was confirmed by genomic DNA sequencing. Mutations in KRAS and EGFR were not observed in the LC ‐2/ad cells. CCDC 6‐ RET was constitutively active, and the introduction of a siRNA targeting the RET 3 ' region decreased cell proliferation by downregulating RET and ERK 1/2 phosphorylation. Moreover, treatment with RET ‐inhibitors, including vandetanib, reduced cell viability, which was accompanied by the downregulation of the AKT and ERK 1/2 signaling pathways. Vandetanib exhibited anti‐tumor effects in the xenograft model. Endogenously expressing CCDC 6‐ RET contributed to cell growth. The inhibition of kinase activity could be an effective treatment strategy for LAD . LC ‐2/ad is a useful model for developing fusion RET ‐targeted therapy.
Neoplastic progression evidenced in the L929 cell system. I. Selection of tumorigenic and metastasizing cell variants.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Starting with a L929 cell strain of low tumorigenicity, and through in vivo and combined in vivo--in vitro manipulation, we have isolated a number of related culture cell lines with different tumorigenicity and metastasis ability in C3HA/H mice. Within our system, tumorigenicity can be greatly enhanced without the simultaneous development of metastasis ability, the latter arising only after long-term in vivo serial transplantation. Metastatic variants express better the ability to undergo to cascade of metastasis than the primary tumor. The selection of metastatic variants from a tumor, using its subcutaneous inoculation, renders cell lines with different behavior. Finally, viable cells are recovered from lungs of animals inoculated with metastatic variants that would not be expected to show true metastatic foci; the results are commented in relation to the phenomenon of metastasis dormancy. Our experiments are discussed under the scope of the hypothesis of neoplastic progression as a multistep process.
Coupling Stokes-Darcy flow with transport on irregular geometries

Field: Mathematics (Physical Sciences)

This thesis studies a mathematical model, in which Stokes-Darcy flow system is coupled with a transport equation. The objective is to develop stable and convergent numerical schemes that could be used in environmental applications. Special attention is given to discretization methods which can handle irregular geometry. \n \nFirst, we will use a multiscale mortar finite element method to discretize coupled Stokes-Darcy flows on irregular domains. Especially, we will utilize a special discretization method called multi-point flux mixed finite element method to handle Darcy flow. This method is accurate for rough grids and rough full tensor coefficients, and reduces to a cell-centered pressure scheme. On quadrilaterals and hexahedra the method can be formulated either on the physical space or on the reference space, leading to a non-symmetric or symmetric scheme, respectively. While Stokes region is discretized by standard inf-sup stable elements. The mortar space can be coarser and it is used to approximate the normal stress on the interface and to impose weakly continuity of normal flux. The interfaces can be curved and matching conditions are imposed via appropriate mappings from physical grids to reference grids with flat interfaces. \n \nAnother approach that we use to deal with the flow equations is based on non-overlapping domain decomposition. Domain decomposition enables us to solve the coupled Stokes-Darcy flow problem in parallel by partitioning the computational domain into subdomains, upon which families of coupled local problems of lower complexity are formulated. The coupling of the subdomain problems is removed through an iterative procedure. We investigate the properties of this method and derive estimates for the condition number of the associated algebraic system. \n \nTo discretize the transport equation we develop a local discontinuous Galerkin mortar method. In the method, the subdomain grids need not match and the mortar grid may be much coarser, giving a two-scale method. We weakly impose the boundary condition on the inflow part of the interface and the Dirichlet boundary condition on the elliptic part of the interface via Lagrange multipliers. We develop stability for the concentration and the diffusive flux in the transport equation.
DEVELOPING AN IOT SYSTEM TO ALERT HEAT-STRESS FOR LIVESTOCK

Field: Engineering (Physical Sciences)

Recently, climate change has posed a significant challenge to humanity, with temperature increment being a conspicuous phenomenon. The rise in global temperature has impacts not only humans but also animals leading to health issues, particularly heat stress in livestock. With the advancement of science and technology, numerous intelligent systems have been developed to support the livestock industry. In this study, we present the development of an Internet of Things system designed to monitor and alert heat stress conditions in livestock. As a result, the designed IoT system could track the temperature both inside and outside the livestock house. By depending on Temperature Humidity Index, the system also makes alters if the temperature is at risk of causing heat shock to livestock. In the future, the system could be developed to be applied in livestock farming and help mitigate heat stress in livestock.
On the cluster structures in Collatz level sets

Field: Mathematics (Physical Sciences)

The cluster structures that can be observed in the first few level sets of the Collatz tree are maintained through all its levels, provided that the orbit steadiness \[ \prod_{\substack{k \in R(n)\\ k \equiv 4\ (\mathrm{mod}\ 6)}} \frac{k-1}k \] of the elements $n$ of the Collatz tree is suitably bounded from below, where $R(n)$ denotes the Collatz orbit of $n$.
Trawl rationalization trailing actions: chafing gear : environmental assessment

Field: Environmental Science (Physical Sciences)

"The action modifies chafing gear regulations that apply to all midwater trawl gear used in the Pacific Coast groundfish fishery. Chafing gear is webbing or other material attached to the codend to minimize damage from rubbing against the stern ramp and from contact with the ocean floor. The proposed action is neither expected to compromise the sustainability of any target or non-target species, nor is it expected to result in significant social or economic impacts interrelated with significant natural or physical environmental effects. Increased chafing gear coverage may result in fewer small fish escaping from the codend by reducing the effective mesh size or creating the effect of a double-walled codend. Small fish include juvenile Pacific whiting and non-groundfish species such as coastal pelagic species, eulachon, and small forage fish. Eulachon is listed as threatened under the Endangered Species Act. Because vessels targeting Pacific whiting have less market opportunity for small fish, they are expected to take measures to reduce the catch of small unmarketable Pacific whiting. The catch of small non-target species, including eulachon is not expected to increase substantially. Eulachon will continue to be monitored and managed to stay within thresholds identified in the current Endangered Species Act Section 7 biological opinion for the groundfish fishery. Increased chafing gear coverage may result in midwater trawl gear being used to fish in a manner that results in more contact with ocean floor than is currently occurring. Historical data indicate that the midwater trawl gear used to target Pacific whiting does occasionally make contact with the ocean floor (approximately 8 percent of the hauls). The vulnerability of the net to damage from bottom contact means that increases in chafing gear are not likely to result in substantial increases in bottom contact. The expected impact to EFH and bottom habitat is minor"--Cover letter summary.
Multiplex Assay for Detection of Strain-Specific Antibodies against the Two Variable Regions of the G Protein of Respiratory Syncytial Virus

Field: Immunology and Microbiology (Life Sciences)

ABSTRACT The role of strain differences in respiratory syncytial virus (RSV) disease has not been clearly defined. To investigate the possibility that strain differences contribute to susceptibility to repeat infections, we developed assays to detect antibodies to the two variable regions of the RSV G protein by cloning and expressing the internal variable region at amino acids (aa) 60 to 172 (g1) and the carboxy-terminal variable region at aa 193 to the carboxy terminus (g2) from different genotypes of RSV. The purified proteins were covalently linked to beads with different proportions of red and orange fluorescent dyes and reacted against serum specimens. Antibody reacting against the differently colored beads, and thus against different G polypeptides, was detected by use of flow cytometry and the Luminex system. This assay system detected group- and, to some extent, genotype-specific responses to RSV infection and can be used to investigate the role of strain differences in RSV disease.