gebhart/patrepeval huggingface dataset:
Investigation of protein deposition via solution evaporating inside microwells/microchannels (2010)

The solution evaporation leading to solute deposition has been widely studied since long time ago owing to not only the interesting transport phenomena and the deposition behavior of the solutes taking place inside the droplet but also its application to micro/nanofabrication. For example, fabrication of microarray chips [6-8], formation of colloid crystals [9-12] and manufacturing of micropatterns and microstructures [13-17], etc. In general, evaporation process can be divided into two modes: constant contact area or constant contact angle [1]. For evaporation under constant contact area, due to capillary flow induced by the differential evaporation rates across the drop, the liquid evaporating from the edge is replenished by liquid from the interior and nearly all the dispersed material can be carried to the edge to form a “coffee-ring” [2,3]. The situation becomes more complicated when Marangoni effect is involved [5]. This is because the free surface will lose latent heat to cause a temperature gradient and the thermal induced flow is no longer negligible. Besides evaporation of a droplet of solution on a substrate open to the air, it is also found that micro/nanostructures can be formed by solute deposition when evaporation occurs inside microwells and microchannels. Figure 1 shows the deposited bovine serum albumin (BSA) patterns using 1wt% BSA aqueous solution. The polydimethylsiloxane (PDMS) stamps with microchannels or microwells are used and the substrate is cover glass slide. The fluorescein dye was added into BSA solution for visualization. It can be seen that both line and ring structures are clearly observed. Figure 2 shows the deposited structures using BSA solution with different concentrations. The dimension of the microwell array used is 50μm in diameter and 4.5μm in height, and the spacing is 100μm (the stamp with such microwell array is denoted as 50-4.5-100). For 0.1 wt%, the ring structure is not clearly observed and the height is not uniform. As the concentration increases, the ring structure is well formed and the height increases as well as shown in Figure 2(b). However, further increasing the concentration will lead to deposition of BSA in the middle of the ring structure, which forms a crater-like structure as shown in Figure 2(c). When using the microwells with larger depth, i.e. 8μm, the ring structure is relatively smoother as shown in Figure 2(d).
Recombinant actin-depolymerizing factor of the apicomplexan Neospora caninum (NcADF) is susceptible to oxidation (2022)

<i>Neospora caninum</i> is a member of Apicomplexa Phylum and the causative agent of neosporosis, a disease responsible for abortions in cattle. Apicomplexan parasites have a limited set of actin-binding proteins conducting the regulation of the dynamics of nonconventional actin. The parasite actin-based motility is implicated in the parasite invasion process in the host cell. Once no commercial strategy for the neosporosis control is available, the interference in the parasite actin function may result in novel drug targets. Actin-depolymerization factor (ADF) is a member of the ADF/cofilin family, primarily known for its function in actin severing and depolymerization. ADF/cofilins are versatile proteins modulated by different mechanisms, including reduction and oxidation. In apicomplexan parasites, the mechanisms involved in the modulation of ADF function are barely explored and the effects of oxidation in the protein are unknown so far. In this study, we used the oxidants N-chlorotaurine (NCT) and H<sub>2</sub>O<sub>2</sub> to investigate the susceptibility of the recombinant <i>N. caninum</i> ADF (NcADF) to oxidation. After exposing the protein to either NCT or H<sub>2</sub>O<sub>2</sub>, the dimerization status and cysteine residue oxidation were determined. Also, the interference of NcADF oxidation in the interaction with actin was assessed. The treatment of the recombinant protein with oxidants reversibly induced the production of dimers, indicating that disulfide bonds between NcADF cysteine residues were formed. In addition, the exposure of NcADF to NCT resulted in more efficient oxidation of the cysteine residues compared to H<sub>2</sub>O<sub>2</sub>. Finally, the oxidation of NcADF by NCT reduced the ability of actin-binding and altered the function of NcADF in actin polymerization. Altogether, our results clearly show that recombinant NcADF is sensitive to redox conditions, indicating that the function of this protein in cellular processes involving actin dynamics may be modulated by oxidation.
Increased levels of hsp70 transcripts induced when cells are exposed to low frequency electromagnetic fields (1994)

Previous experiments have shown that the steady state levels of some RNA transcripts are increased when cells are exposed to extremely low frequency electric or magnetic fields. Experiments have exposed a variety of cell types, including dipteran salivary gland cells, yeast and human HL-60 cells. The range of responsive transcripts includes oncogenes such as c-myc, as well as transcripts associated with growth and development. One hypothesized mechanism of how cells respond to electromagnetic (EM) fields assumes that the response represents or mimics a generalized physiological stress response. RNA from exposed HL-60 cells, previously shown to have increased transcript levels for c-myc, was analyzed for hsp70 transcripts levels. The hsp70 transcripts were found to be elevated in all cases, even though the cells were exposed to various fields at normal growth temperatures. The conditions of maximum induction for hsp70 were coordinate with those of c-myc. In yeast cells, the SSA1 gene (homologous to hsp70) was found to be elevated in cells exposed to EM fields at 0.8−80 μT. In the case of yeast, conditions for maximum induction of SSA1 were coordinate with those for URA3, the gene for uracil metabolism. Thus the model of cell interaction with electric and/or magnetic fields appears to be related to the stress response model for heat shock.
Volumetric quantification ofin vitrosonothrombolysis with microbubbles using high-resolution optical coherence tomography (2012)

Several in vitro and in vivo studies have established accelerated thrombolysis using ultrasound (US) induced microbubble (MB) cavitation. However, the mechanisms underlying MB mediated sonothrombolysis are still not completely elucidated. We performed three-dimensional (3-D) volumetric optical coherence tomography (OCT) imaging before and after the application of contrast US to thrombus. The most dramatic reduction in clot volume was observed with US + MB + recombinant tissue plasminogen activator (rt-PA). Thrombus surface erosion in this group on the side of the thrombus exposed to MB and ultrasound was evident on the OCT images. This technique may assist in clarifying the mechanisms underlying sonothrombolysis, especially regarding the importance of US transducer orientation on lytic efficacy and the effects of MB cavitation on thrombus structure.
A preliminary comparison of flow cytometry and tube agglutination assays in detecting red blood cell‐associated C3d (2003)

This study compared flow cytometric analysis with tube agglutination assays for the detection of red blood cell (RBC)-associated complement and immunoglobulins (Igs). RBCs from 20 patients with reactive tube direct antiglobulin tests (DATs) were evaluated by flow cytometry with anti-C3d, anti-IgG, anti-IgM and anti-IgA. Serial samples were also tested from a patient at risk of passenger lymphocyte haemolysis. Results of flow cytometry and tube assays for anti-IgG were as follows: 12 of 20 samples reactive in both; six of 20 nonreactive in both; two of 20 discordant with a reactive tube and a nonreactive flow cytometry assay. Anti-C3d results showed nine of 20 reactive in both and 11 of 20 discordant with a nonreactive tube and a reactive flow cytometry assay. In the IgM flow cytometry assay, three samples were reactive with anti-IgM. Samples from a group A woman who was transplanted with stem cells from a group B donor showed that on days 3 through 6 post-transplant, the flow cytometry assays for anti-IgG and/or anti-C3d were reactive, whilst the tube assays were nonreactive. In conclusion, flow cytometric analysis is more sensitive than the tube assay for the detection of RBC-associated C3d. Further studies are needed to determine the correlation of C3d levels with clinical sequelae.
Aerosol Synthesis of Self-Organized Nanostructured Hollow and Porous Carbon Particles Using a Dual Polymer System (2014)

A facile method for designing and synthesizing nanostructured carbon particles via ultrasonic spray pyrolysis of a self-organized dual polymer system comprising phenolic resin and charged polystyrene latex is reported. The method produces either hollow carbon particles, whose CO2 adsorption capacity is 3.0 mmol g(-1), or porous carbon particles whose CO2 adsorption capacity is 4.8 mmol g(-1), although the two particle types had similar diameters of about 360 nm. We investigate how the zeta potential of the polystyrene latex particles, and the resulting electrostatic interaction with the negatively charged phenolic resin, influences the particle morphology, pore structure, and CO2 adsorption capacity.
Statistical modeling of F0 dynamics in singing voices based on Gaussian processes with multiple oscillation bases (2010)

We present a novel statistical model for dynamics of various singing behaviors, such as vibrato and overshoot, in a fundamental frequency (F0) contour. These dynamics are the important cues for perceiving individuality of a singer, and can be a useful measure for various applications, such as singing skill evaluation and singing voice synthesis. While most previous studies have modeled the dynamics using a second-order linear system, the automatic and accurate estimation of model parameters has yet to be accomplished. In this paper, we first develop a complete stochastic representation of the second-order system with Gaussian processes from parametric discretization, and propose a complete, efficient scheme for parameter estimation using the Expectation-Maximization (EM) algorithm. Experimental results show that the proposed method can decompose an F0 contour into a musical component and a dynamics component. Finally, we discuss estimating singing styles from the model parameters for each singer. Index Terms: Singing voices, Fundamental frequency (F0), Gaussian Processes, EM algorithm, Singing voice synthesis
Design and performance of a modular jack type Mini-MT connector for high-density optical duplex connection (1999)

We have developed a modular jack type Mini-MT that employs a compact two-fiber ferrule in a housing. The connector mechanism is similar to that of a conventional electric modular jack type connector. The connector also has a locking mechanism to prevent accidental disconnection and a high packaging density of 2 fibers/cm/sup 2/. Fabricated connectors for single-mode two-fiber ribbons exhibit a low insertion loss of 0.17 dB and a high return loss of more than 40 dB.
Rhizosphere engineering: Innovative improvement of root environment (2017)

Abstract The ability of roots to extract water and nutrients from soil depends on the biophysical properties of the rhizosphere, which are strongly influenced by mucilage secretion. The aim of this study was to introduce the concept of rhizoligands to engineer the biophysical properties of the rhizosphere. A rhizoligand is defined as an additive that increases the wettability of the rhizosphere and links the mucilage network to main intimate contact with the root surface. We hypothesize that rhizoligands: i) facilitate the rewetting of the rhizosphere during repeated drying and wetting cycles; ii) enhance rhizosheath formation; iii) increase enzyme activities in the rhizosphere; and iv) increase plant biomass. A commercial surfactant was selected as the prototype rhizoligand to test the effect on the rhizosphere biophysical properties of white lupin grown in quartz sand and subjected to six drying-rewetting cycles. Half of the plants were irrigated with water and the other half with the rhizoligand solution. When plants were 50 days old, we measured: i) soil water content; ii) rhizosheath mass; iii) activity of selected enzymes; iv) carbon content in the rhizosphere; and v) plant biomass. Rhizoligand increased rewetting rate of the rhizosphere after drying and subsequent rewetting, resulting in a greater soil water content. Rhizosheath formation was improved in plants irrigated with rhizoligand and sand particles attached to the roots increased by 1.64 times compared to plants irrigated with water. Activity of the enzymes chitinase, sulfatase, and β-glucosidase were 4, 7.9, and 1.5 times greater in the rhizosphere of plants irrigated with rhizoligand than in the rhizosphere of plants irrigated with water. Plant biomass was 1.2 fold greater in samples irrigated with rhizoligand solution than in samples irrigated with water. We conclude that application of rhizoligand improves plant performance by influencing the water dynamics in the rhizosphere and the plant, increasing the mechanical stability of the rhizosheaths and increasing the enzyme activities in the rhizosphere. Such effects are probably triggered by the interaction between mucilage and the applied rhizoligand, which reduces mucilage swelling (possibly by cross-linking mucilage polymers) and thus by increasing its viscosity keeps the mucilage close to the root surface. We propose the rhizoligand concept as a strategy to engineer the rhizosphere properties and to improve plant tolerance to water shortage.
Immunohistochemical Study of the Expression of MUC6 Mucin and Co-expression of Other Secreted Mucins (MUC5AC and MUC2) in Human Gastric Carcinomas (2000)

To investigate the expression of MUC6 mucin in gastric carcinomas, we generated a novel monoclonal antibody (MAb CLH5) using an MUC6 synthetic peptide. MAb CLH5 reacted exclusively with the MUC6 peptide and with native and deglycosylated mucin extracts from gastric tissues. MAb CLH5 immunoreactivity was observed in normal gastric mucosa restricted to pyloric glands of the antrum and mucopeptic cells of the neck zone of the body region. In a series of 104 gastric carcinomas, 31 (29.8%) were immunoreactive for MUC6. The expression of MUC6 was not associated with histomorphological type or with clinicopathological features of the carcinomas. Analysis of the co-expression of MUC6 with other secreted mucins (MUC5AC and MUC2) in 20 gastric carcinomas revealed that different mucin core proteins are co-expressed in 55% of the cases. MUC6 was co-expressed and co-localized with MUC5AC in 45% and with MUC2 in 5% of the cases. Expression of MUC2 alone was observed in 25% of the cases. All carcinomas expressing MUC2 mucin in more than 50% of the cells were of the mucinous type according to the WHO classification. The co-expression of mucins was independent of the histomorphological type and stage of the tumors. In conclusion, we observed, using a novel well-characterized MAb, that MUC6 is a good marker of mucopeptic cell differentiation and is expressed in 30% of gastric carcinomas, independent of the clinicopathological features of the cases. Furthermore, we found that co-expression and co-localization of mucins in gastric carcinomas is independent of histomorphology and staging. Finally, we observed that intestinal mucin MUC2 is expressed as the most prominent mucin of the mucins tested in mucinous-type gastric carcinomas.
Convergence rates for distributed stochastic optimization over random\n networks (2018)

We establish the O($\\frac{1}{k}$) convergence rate for distributed stochastic\ngradient methods that operate over strongly convex costs and random networks.\nThe considered class of methods is standard each node performs a weighted\naverage of its own and its neighbors solution estimates (consensus), and takes\na negative step with respect to a noisy version of its local functions gradient\n(innovation). The underlying communication network is modeled through a\nsequence of temporally independent identically distributed (i.i.d.) Laplacian\nmatrices connected on average, while the local gradient noises are also i.i.d.\nin time, have finite second moment, and possibly unbounded support. We show\nthat, after a careful setting of the consensus and innovations potentials\n(weights), the distributed stochastic gradient method achieves a\n(order-optimal) O($\\frac{1}{k}$) convergence rate in the mean square distance\nfrom the solution. This is the first order-optimal convergence rate result on\ndistributed strongly convex stochastic optimization when the network is random\nand/or the gradient noises have unbounded support. Simulation examples confirm\nthe theoretical findings.\n
Digital Twin for HVAC Load and Energy Storage based on a Hybrid ML Model with CTA-2045 Controls Capability (2022)

Building modeling, specifically heating, ventilation, and air conditioning (HVAC) load and equivalent energy storage calculations, represent a key focus for decarbonization of buildings and smart grid controls. Widely used white box models, due to their complexity, are too computationally intensive to be employed in high resolution distributed energy resources (DER) platforms without simulation time delays. In this paper, an ultra-fast one-minute resolution Hybrid Machine Learning Model (HMLM) is proposed as part of a novel procedure to replicate white box models as an alternative to wide spread experimental big data collection. Synthetic output data from experimentally calibrated EnergyPlus models for three existing smart homes managed by the Tennessee Valley Authority is used. The HMLM employs combined k-means clustering and multiple linear regression (MLR) models to predict minutely HVAC power with satisfactory nRMSE error of less than 10% across an entire year test set. An approach is provided to characterize HVAC systems through the newly proposed hybrid model as a generalized storage (GES) device suitable for DER control and event types in accordance with the Communication Technology Association (CTA) 2045 standard and Energy Star metrics such as “energy take”, currently developed by industry, to unify household appliance controls.
Programming of Rate Responsive Pacemakers (1989)

Rate adaptive pacing adds a new dimension to pacemaker therapy. The possibility of near physiological pacing utilizing the piezoelectric sensor is now offered to a broad range of patients with varied clinical problems. Improved cardiac output during exercise increases exercise capabilities and patient satisfaction. Single‐chamber rate adaptive pacing has been demonstrated to improve cardiac performance. The expansion of this technology into a dual‐chamber pacing unit achieves the combined benefit of AV synchrony with synthesized chronotropic competence. The challenge in clinical practice is to construct an appropriate rate responsive regimen and then to confirm the adequacy and safety of the programmed parameters. Considerable experience with single‐ and dual‐chamber rate adaptive pacemakers led us to develop a protocol for initial pacemaker selection, subsequent programming of these units, and confirmation of optimal function. A practical method for evaluation of rate adaptive pacemaker patients is outlined with programming guidelines.
Estimation of Air Mass into Cylinder with Extended Kalman Filter for the Control of Injected SI Engine (1997)

The problem of controlling the Air-Fuel Ratio can be reduced to the problem of estimating air mass absorbed into cylinder. In current commercial engines, air mass taken into cylinder is estimated by table look-up. This method is incapable of coping with secular change of the engine. Also, to make tables for every kind of engine requires enormous amount of manpower. To circumvent these difficulties, we propose a model-based method using extended Kalman filter. The effectiveness of our method is demonstrated by simulation in comparison with experimental data.
High performance near-IR to longwave-IR broadband omnidirectional antireflection coating by differential evolution (2022)

Broadband and omnidirectional antireflection coatings in the 3-5 &mu;m and 3-12 &mu;m infrared ranges are of crucial importance in maximizing quantum efficiency in MWIR and LWIR photodetectors, as well as in improving the efficiency of LWIR thermophotovoltaic devices. Conventional approaches to AR coatings on semiconductors, such as quarter-wavelength optical thickness layers, fail to provide consistently high transmission over mid-IR bandwidths and acute angles of incidence. Unconventional approaches such as metasurface and nanostructure AR coatings are difficult and expensive to fabricate on a large scale. We discuss ultra-broadband antireflection coating designed through an inverse design procedure driven by a differential evolution optimization algorithm. Our approach iteratively simulates the transmission characteristics of a multilayer structure using the Transfer-Matrix Method and optimizes layer parameters to maximize the average transmission within a given wavelength band and range of angles of incidence. We present AR coatings which exhibit 98% and 96% average transmission over the 3 &mu;m - 5 &mu;m and 3 &mu;m - 12 &mu;m ranges respectively, over angles of incidence between 0&deg; and 70&deg;. Compared to quarter optical wavelength antireflection coatings over the same ranges, our structures exhibit significantly higher broadband transmission – quarter-wavelength structures saturate near 80% transmission over the 3-5 &mu;m or 3-12 &mu;m ranges, with transmission significantly lowered at large angles. As such, our results rival the transmission performance of state-of-the-art nanostructure AR coatings even at large angles of incidence but are significantly easier to fabricate using standard e-beam evaporation and/or sputtering.
Reduction and Elimination of Humic Acid Fouling in Air Sparged Membrane Distillation Using Nanocarbon Immobilized Membrane (2022)

In this paper, we present the treatment of humic acid solution via carbon nanotube immobilized membrane (CNIM) distillation assisted by air sparging (AS). Carbon nanotubes offer excellent hydrophobicity to the modified membrane surface and actively transport water vapor molecules through the membrane to generate higher vapor flux and better rejection of humic acid. The introduction of air sparging in the membrane distillation (MD) system has changed the humic substance fouling by changing the colloidal behavior of the deposits. This modified MD system can sustain a higher run time of separation and has enhanced the evaporation efficiency by 20% more than the regular membrane distillation. The air sparging has reduced the deposition by 30% in weight and offered lesser fouling of membrane surface even after a longer operating cycle. The water vapor flux increased with temperature and decreased as the volumetric concentrating factor (VCF) increased. The mass transfer coefficient was found to be the highest for the air sparged-carbon nanotube immobilized membrane (AS-CNIM) integrated membrane distillation. While the highest change in mass transfer coefficient (MTC) was found for polytetrafluoroethylene (PTFE) membrane with air sparging at 70 °C.