gebhart/patrepeval huggingface dataset:
The Henry semianalytical solution for saltwater intrusion with reduced dispersion (2012)

The Henry semianalytical solution for salt water intrusion is widely used for benchmarking density dependent flow codes. The method consists of replacing the stream function and the concentration by a double set of Fourier series. These series are truncated at a given order and the remaining coefficients are calculated by solving a highly nonlinear system of algebraic equations. The solution of this system is often subject to substantial numerical difficulties. Previous works succeeded to provide semianalytical solutions only for saltwater intrusion problems with unrealistic large amount of dispersion. In this work, different truncations for the Fourier series are tested and the Levenberg‐Marquardt algorithm, which has a quadratic rate of convergence, is applied to calculate their coefficients. The obtained results provide semianalytical solutions for the Henry problem in the case of reduced dispersion coefficients and for two freshwater recharge values: the initial value suggested by Henry (1964) and the reduced one suggested by Simpson and Clement (2004). The developed semianalytical solutions are compared against numerical results obtained by using the method of lines and advanced spatial discretization schemes. The obtained semianalytical solutions improve considerably the worthiness of the Henry problem and therefore, they are more suitable for testing density dependent flow codes.
Exposure to TiO2 nanoparticles increases Staphylococcus aureus infection of HeLa cells (2016)

Abstract Background Titanium dioxide (TiO2) is one of the most common nanoparticles found in industry ranging from food additives to energy generation. Approximately four million tons of TiO2 particles are produced worldwide each year with approximately 3000 tons being produced in nanoparticulate form, hence exposure to these particles is almost certain. Results Even though TiO2 is also used as an anti-bacterial agent in combination with UV, we have found that, in the absence of UV, exposure of HeLa cells to TiO2 nanoparticles significantly increased their risk of bacterial invasion. HeLa cells cultured with 0.1 mg/ml rutile and anatase TiO2 nanoparticles for 24 h prior to exposure to bacteria had 350 and 250 % respectively more bacteria per cell. The increase was attributed to bacterial polysaccharides absorption on TiO2 NPs, increased extracellular LDH, and changes in the mechanical response of the cell membrane. On the other hand, macrophages exposed to TiO2 particles ingested 40 % fewer bacteria, further increasing the risk of infection. Conclusions In combination, these two factors raise serious concerns regarding the impact of exposure to TiO2 nanoparticles on the ability of organisms to resist bacterial infection.
Enzyme cascade reactions (2015)

A one-pot tandem enzyme reaction using galactose oxidase M3–5 and aldehyde oxidase PaoABC was used to convert hydroxymethylfurfural (HMF) to the pure bioplastics precursor FDCA in 74% isolated yield. A range of alcohols was also converted to carboxylic acids in high yield under mild conditions.
Advanced 60 μm thin 600 V punch-through IGBT concept for extremely low forward voltage and low turn-off loss (2002)

A vertical trench gate 600 V PT (Punch Through) IGBT structure with a new concept of thin substrate wafer with a low dose n-buffer and a transparent p-emitter is proposed to realize an excellent trade-off relation between the device on-state voltage and the switching speed. In this paper, we have fabricated and evaluated 600 V/150 A rated thin wafer PT IGBT in a 60 /spl mu/m thin silicon substrate. It was experimentally confirmed that 60 /spl mu/m PT IGBTs with a transparent p-emitter have an excellent trade-off relation for room temperature and 125/spl deg/C. Especially the fabricated 60 /spl mu/m thin 600 V PT IGBTs have realized an on-state voltage as low as 1.23 V at 150 A/cm/sup 2/ current density with an extremely short fall-time of 60 ns for 25/spl deg/C.
Anderson localization of light in two-dimensional random arrays of semiconductor nanocolumns (2013)

We conducted numerical and experimental studies on Anderson localization of light in two-dimensional random systems of semiconductor columns. We investigated finite size scaling of the localization effect as a function of localization length and system size from the calculation. We therefore obtained a localization parameter map. We also report observations of random lasing in the semiconductor samples. We show that the occurrence of the laser action have a strong relationship to the localization length by comparisons of the map with the experimental results.
Hepatologie (1983)

Die chronisch aktive Hepatitis (CAH) ist ein ätiologisch heterogenes Krankheitsbild. Autoantikörper gegen ein mikrosomales Antigen aus Leber und Niere (LKM) scheinen eine Subgruppe der CAH zu charakterisieren (Rizetto et al. 1973, 1974) [1, 2]. In der bisher angewendeten Immunfluoreszenztechnik (IF) an Nierenschnitten können diese Antikörper nur sehr schwer von antimitochondrialen (AMA) und anderen zytoplasmatischen Antikörpern unterschieden werden. Es ist bisher nicht geklärt, ob bei der primär biliären Zirrhose (PBC) zusätzlich zu AMA LKM-Antikörper vorkommen. Mit der Immunfluoreszenz kann ein zusätzliches Auftreten von LKM-Antikörpern nicht differenziert werden. Außerdem stand bisher ein spezifisches serologisches Testsystem nicht zur Verfügung.
Electromechanically Tunable Diamond Color Centers Coupled to Nanophotonic Waveguides (2018)

We present a platform for the generation and high-efficiency collection of indistinguishable photons from spatially separated silicon-vacancy (SiV) color centers by use of waveguide-coupled nanoelectromechanical systems (NEMS).
Excitation Transfer Engineering in Ce‐Doped Oxide Crystalline Scintillators by Codoping with Alkali‐Earth Ions (2018)

Time‐resolved spectroscopic study of the photoluminescence response to femtosecond pulse excitation and free carrier absorption at different wavelengths, thermally stimulated luminescence measurements and investigation of differential absorption are applied to amend the available data on excitation transfer in GAGG:Ce scintillators, and an electronic energy‐level diagram in this single crystal is suggested to explain the influence of codoping with divalent Mg on luminescence kinetics and light yield. The conclusions are generalized by comparison of the influence of aliovalent doping in garnets (GAGG:Ce) and oxyorthosilicates (LSO:Ce and YSO:Ce). In both cases, the codoping facilitates the energy transfer to radiative Ce 3+ centers, while the light yield is increased in the LYSO:Ce system but reduced in GAGG:Ce.
ABSL-4 Aerobiology Biosafety and Technology at the NIH/NIAID Integrated Research Facility at Fort Detrick (2014)

The overall threat of a viral pathogen to human populations is largely determined by the modus operandi and velocity of the pathogen that is transmitted among humans. Microorganisms that can spread by aerosol are considered a more challenging enemy than those that require direct body-to-body contact for transmission, due to the potential for infection of numerous people rather than a single individual. Additionally, disease containment is much more difficult to achieve for aerosolized viral pathogens than for pathogens that spread solely via direct person-to-person contact. Thus, aerobiology has become an increasingly necessary component for studying viral pathogens that are naturally or intentionally transmitted by aerosol. The goal of studying aerosol viral pathogens is to improve public health preparedness and medical countermeasure development. Here, we provide a brief overview of the animal biosafety level 4 Aerobiology Core at the NIH/NIAID Integrated Research Facility at Fort Detrick, Maryland, USA.
Efficient export of secretory proteins through a vacuolized golgi complex (1987)

The transport of the secretory proteins fibronectin (FN) and procollagen (PC) was studied in cells infected with the temperature-sensitive mutant ts 12 of Uukuniemi virus. Using pulse-labeling followed by immunoprecipitation and SDS-PAGE (FN), or by determination of radioactivity incorporated into hydroxyproline (PC) at different time points we could show that the secretion rates for these proteins were normal although the Golgi complex had become vacuolized as a result of infection with the virus. We conclude that such a morphologically altered Golgi can still carry out effective transport of secretory proteins.
Preparation of a Delivery System for Smart Coatings by Electrostatic Deposition (2010)

Multilayer composites that utilize polymer and metal oxide thin films are the enabling technology for many flexible electronic devices. However, crack formation within the brittle inorganic layers that arise from defects as well as the flexing of these multilayer composite materials allow the influx of atmospheric water, a major source of device degradation. Thus, a composite material that can initiate self-healing upon the influx of environmental water through defects or stress induced cracks would find potential applications in permeation barriers. In the present study, reactive metal oxide precursors such as titanium(IV) chloride (TiCl4) or trimethylaluminum (AlMe3) were encapsulated within the pores of a degradable polymer such as polylactic acid (PLA). The PLA polymer containing metal oxide healing agent were prepared as spheres or fibers. The PLA spheres or fibers were reactive under controlled humidity resulting in hydrolysis of the degradable polymer shell and subsequent release of the reactive metal oxide precursor. Hydrolysis of the metal oxide precursors results in formation of solid titanium oxides or aluminum oxides at the surface of the delivery vehicle. The efficacy of this self-healing delivery system was further demonstrated by the integration of these reactive fibers or spheres in a polymer planarization layer (PMMA) of a multilayer barrier film. The introduction of nanocracks in the barrier film led to the release of the metal oxide precursor and the formation of titanium oxide or aluminium oxide nanoparticles in the cracks. In this study we have established the first site-specific, smart, self-healing system for multilayer barrier films through the delivery of metal oxide nanoparticles by reactive composite fibers or spheres.
Gestational administration of glucocorticoid alters baroreceptor and chemoreceptor reflexes in rat (2008)

In the rat, administration of high levels of glucocorticoid during pregnancy produces late onset hypertension in the offspring. The causes of hypertension are not known, but may involve alterations in cardiovascular autonomic control. We examined baro‐ and chemoreflex changes in heart rate (HR) and sympathetic nerve activity (SNA) in the rat following gestational dexamethasone administration (DEX), using the in situ working heart brainstem preparation. Pregnant dams were administered DEX (200 μg/kg s.c.) at E15–16. At 3–5 weeks, perfusion pressure, HR, and activity of the phrenic nerve and thoracic sympathetic chain were measured in the in situ preparation of DEX offspring and naive controls. HR and SNA responses to baroreceptor (increase in pressure of 20–30 mmHg) and chemoreceptor (injection of 20–100 μL 0.03% NaCN) stimulation were measured. Baroreflex changes in HR gain (control, 1.3+0.2 v 0.8+0.2 bpm/mmHg) and SNA (16+4 v 6+1 %baseline/mmHg) were lower in the DEX rat than control (P&lt;0.05, n=4), whereas the chemoreflex responses were augmented (bradycardia of 161+30 v 217+15 bpm and sympathoexcitation of 60+14 v 106+13 %baseline, P&lt;0.05, n=4). The results indicate that cardiovascular autonomic reflexes are altered in the DEX hypertension in such a way as to facilitate an increase in sympathetic drive. This may contribute to the ontogeny of hypertension in this model. Support: British Heart Foundation
Pathogenic effect of interleukin-17A in induction of Sjogren's syndrome-like disease using adenovirus-mediated gene transfer (2010)

(Funding) Publication of this article was funded in part by the University of Florida Open-Access publishing Fund.
Plasmon-molecule remote coupling via column-structured silica layer for enhancing biophotonic analysis (2022)

We demonstrated remote plasmonic enhancement (RPE) by a dense random array of Ag nanoislands (AgNIs) that were partially gold-alloyed and attached with column-structured silica (CSS) overlayer of more than 100 nm in thickness. The physical and chemical protection of the CSS layer could lead to reducing the mutual impact between analyte molecules and metal nanostructures. RPE plate was realized just by sputtering and chemical immersion processes, resulting in high productivity. We found a significant enhancement on the order of 10$^7$-fold for Raman scattering and 10$^2$-fold for fluorescence by RPE even without the proximity of metal nanostructures and analyte molecules. We confirmed the feasibility of RPE for biophotonic analysis. RPE worked for dye molecules in cells cultured on the CSS layer, enabling the enhanced fluorescence biosensing of intracellular signaling dynamics in HeLa cells. RPE also worked for biological tissues, enhancing Raman histological imaging of esophagus tissues with esophageal adventitia of a Wistar rat attached atop the CSS layer. We also investigated the wavelength dependency of RPE on the on- or off-resonant with the dye molecular transition dipoles with various molecular concentrations. The results suggested that the RPE occurred by remote resonant coupling between the localized surface plasmon of AgNIs and the molecular transition dipole of the analyte via the CSS structure. The RPE plate affords practical advantages for potential biophotonic analyses such as high productivity and biocompatibility. We thus anticipate that RPE will advance to versatile analytical tools in chemistry, biology, and medicine.
Extending and manipulating long DNA molecules for high resolution analysis-development of a novel nanobiotechnological tool for atomic force microscopy (2002)

Many methods were developed to image DNA by AFM both in ambient conditions and under physiological ones. The main difficulty in physically mapping DNA molecules is that they exist as random coils. Such conformation makes it difficult or impossible to obtain quantitative structural information especially when a DNA fragment longer than several thousands bases is used. Using a very low concentration of silane to introduce limited number of amino groups to the surface was a key point in fine tuning the crosslinking reaction without strongly adsorbing DNA to the surface. Such treatment allowed stretching the tethered molecules in one direction.
Speech Graphs Provide a Quantitative Measure of Thought Disorder in Psychosis (2012)

The results demonstrate that alterations of the thought process manifested in the speech of psychotic patients can be objectively measured using graph-theoretical tools, developed to capture specific features of the normal and dysfunctional flow of thought, such as divergence and recurrence. The quantitative analysis of speech graphs is not redundant with standard psychometric scales but rather complementary, as it yields a very accurate sorting of schizophrenics and manics. Overall, the results point to automated psychiatric diagnosis based not on what is said, but on how it is said.
Thermodynamic and exergetic assessment of a biomass derived syngas fueled gas turbine powered trigeneration system (2022)

Processing of waste materials for the generation of renewable fuels, and the development of trigeneration systems are known as the sustainable procedure for satisfying the diverse energy demands. In this regard, this study aims at developing and analyzing a trigeneration system which consists of a gasifier, combined power cycle, and a vapor absorption refrigeration (VAR) system. A model based on equilibrium thermodynamics was developed which has considered the tar formation and char conversion, and accordingly, composition of biomass derived syngas was predicted by employing the MATLAB software. The gasifier operating performance is assessed for the effect of change in gasification equivalence ratio (GER), steam-to-biomass ratio (SBR), and type of biomass feed. Increase in GER from 0.3 to 0.6 for saw dust gasification reduces the energy and exergy efficiencies of gasifier from 44% to 27.5%, and from 51% to 34%, respectively. Finally, a computational method for the energetic and exergetic assessment of the trigeneration was developed using the EES software and a parametric analysis was conducted. CCHP system efficiencies are found considerably influenced by change in SBR and type of biomass feed. Having 40% second law efficiency gasifier has been determined as the most exergy destructive component in the system proposed.
A quantization method based on threshold optimization for microarray short time series (2005)

The quantization method, evaluated in comparison with two standard methods, 5% threshold based on experimental error and rank sorting, improves the ability of Reveal and Dynamic Bayesian Networks to identify relations among genes.
Understanding the DNA binding of novel non-symmetrical guanidinium/2-aminoimidazolinium derivatives (2010)

Biophysical studies have been carried out on a family of asymmetric guanidinium-based diaromatic derivatives to assess their potential as DNA minor groove binding agents. To experimentally assess the binding of these compounds to DNA, solution phase biophysical studies have been performed. Thus, surface plasmon resonance, UV-visible spectroscopy and circular and linear dichroism have been utilized to evaluate binding constants, stoichiometry and mode of binding. In addition, the thermodynamics of the binding process have been determined by using isothermal titration calorimetry. These results show significant DNA binding affinity that correlates with the expected 1 : 1 binding ratio usually observed for minor groove binders. Moreover, a simple computational approach has been devised to assess the potential as DNA binders of this family of compounds.
Comparing Implementations of Near-Data Computing with In-Memory MapReduce Workloads (2014)

The emergence of 3D stacking and the imminent release of Micron's Hybrid Memory Cube (HMC) device have made it more practical to move computation near memory. This work presents a detailed analysis of in-memory MapReduce in the context of near-data computing (NDC). MapReduce is a good fit for NDC because it is embarrassingly parallel and has highly localized memory accesses. This article considers two NDC architectures: one that exploits HMC devices and one that does not. It thus provides insight on the benefits of different NDC approaches and quantifies the potential for improvement for an important emerging big-data workload.
Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells (2016)

Self-renewing tissue-resident macrophages are thought to be exclusively derived from embryonic progenitors. However, whether circulating monocytes can also give rise to such macrophages has not been formally investigated. Here we use a new model of diphtheria toxin-mediated depletion of liver-resident Kupffer cells to generate niche availability and show that circulating monocytes engraft in the liver, gradually adopt the transcriptional profile of their depleted counterparts and become long-lived self-renewing cells. Underlining the physiological relevance of our findings, circulating monocytes also contribute to the expanding pool of macrophages in the liver shortly after birth, when macrophage niches become available during normal organ growth. Thus, like embryonic precursors, monocytes can and do give rise to self-renewing tissue-resident macrophages if the niche is available to them.
ChemInform Abstract: Highly Modular P‐OP Ligands in Asymmetric Allylic Substitution. (2011)

Abstract A library of P‐OP ligands is prepared and used in Pd‐catalyzed allylic substitutions with C‐ and N‐nucleophiles.
Shortest path segmentation: a method for training a neural network to recognize character strings (2003)

The authors describe a method which combines dynamic programming and a neural network recognizer for segmenting and recognizing character strings. The method selects the optimal consistent combination of cuts from a set of candidate cuts generated using heuristics. The optimal segmentation is found by representing the image, the candidate segments, and their scores as a graph in which the shortest path corresponds to the optimal interpretation. The scores are given by neural net outputs for each segment. A significant advantage of the method is that the labor required to segment images manually is eliminated. The system was trained on approximately 7000 unsegmented handwritten zip codes provided by the United States Postal Service. The system has achieved a per-zip-code raw recognition rate of 81% on a 2368 handwritten zip-code test set.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Halogen Bonding Based Recognition Processes:  A World Parallel to Hydrogen Bonding (2005)

Halogen bonding is the noncovalent interaction between halogen atoms (Lewis acids) and neutral or anionic Lewis bases. The main features of the interaction are given, and the close similarity with the hydrogen bonding will become apparent. Some heuristic principles are presented to develop a rational crystal engineering based on halogen bonding. The focus is on halogen-bonded supramolecular architectures given by halocarbons. The potential of the interaction is shown by useful applications in the field of synthetic chemistry, material science, and bioorganic chemistry.
Prediphant: Short Term Heavy User Prediction (2022)

Traffic prediction is of paramount importance for the correct management of network infrastructures. Most research efforts try to forecast the aggregated traffic over the network and over large time windows. In this work, we tackle the problem the other way around. That is, we predict the behaviour of individual users over short time windows. First, we investigate the contribution of the most data eager users to the global network traffic. We do it by analyzing network traces coming from several thousand real users. Then, we design a technique, based on a combination of Natural Language Processing (NLP) and Long Short-Term Memory (LSTM) machine learning models, that leverages past navigation patterns to predict sudden changes in the amount of resources consumed by each user. Finally, we evaluate our method using real data finding it is able to predict about 80% of the users that will rump up their network needs in most realistic scenarios.
Chemical resistance of carbon fiber‐reinforced poly(ether ether ketone) and poly(phenylene sulfide) composites (1992)

Abstract Studies have been conducted to investigate the aircraft fluid and chemical solvent resistance of the carbon fiber‐reinforced poly(phenylene sulfide) (PPS) and poly(ether ether ketone) (PEEK) composites. The solvents and aircraft fluids utilized in this work include hydraulic fluid, paint stripper, JP‐4 jet fuel, methyl ethyl ketone, and methylene chloride. The weight gain of the composites as a function of time is measured. Tensile and flexural strength, thermal behavior, and dynamic mechanical properties of the composites are examined. The alteration of crystallinity change of the composites is investigated by X‐ray diffraction. It is found that paint stripper degraded the mechanical properties of the composites significantly. Furthermore, crystallization enhancement of the low crystallinity composites in the presence of solvents and aircraft fluids is also observed.