gebhart/patrepeval huggingface dataset:
Generation of controllable gaseous H2S concentrations using microfluidics (2018)

Hydrogen sulfide (H<sub>2</sub>S) plays an important role as an intercellular and intracellular signaling molecule, yet its targets are not well understood. As a molecule it easily evaporates and it is hard to acquire stable concentration for in vitro studies, constituting a major problem for the field to identify its downstream targets and function. Here we develop a microfluidic system that can provide consistent and controllable H<sub>2</sub>S levels in contrast to the current method of delivering large bolus doses to cells. The system relies on the permeability of H<sub>2</sub>S gas through a polydimethylsiloxane thin membrane. A hydrogen sulfide donor, sodium hydrosulfide, is perfused in the microchannels below the gas permeable membrane and gaseous H<sub>2</sub>S diffuses across the membrane, providing a stable concentration for up to 5 hours. Using electrochemical sensors within 3 ppm range, we found that H<sub>2</sub>S concentration was dependent on two parameters, the concentration of H<sub>2</sub>S donor, sodium hydrosulfide and the flow rate of the solution in the microchannels. Additionally, different H<sub>2</sub>S concentration profiles can be obtained by alternating the flow rate, providing an easy means to control the H<sub>2</sub>S concentration. Our approach constitutes a unique method for H<sub>2</sub>S delivery for in vitro and ex vivo studies and is ideally suited to identify novel biological processes and cellular mechanisms regulated by H<sub>2</sub>S.
Formulation of Analytical Design Derivatives for Nonlinear Unsteady Aeroelasticity (2011)

The engineering community has devoted considerable recent attention to non-traditional aircraft concepts, where nonlinear, unsteady, coupled aeroelastic physics have been found to drive the design process. There is a lack of current research aimed at bringing these physical concepts into a formal optimization environment, which is the focus of the current work. A numerical framework is developed to capture the unsteady aeroelastic interactions between a nonlinear shell and the surrounding flow. An analytical sensitivity analysis of the model is then discussed, computing the derivative of the aerodynamic force production with respect to a large vector of structural design variables. The work concludes with a series of gradient-based aeroelastic optimization studies, demonstrating the efficacy of analytical gradients towards tailoring the complex interaction between fluid and structure for optimal performance. I. Introduction
Differential Gene Expression in Chilling-Acclimated Maize Seedlings and Evidence for the Involvement of Abscisic Acid in Chilling Tolerance (1994)

An acclimation phenomenon was characterized in seedlings of chilling-sensitive maize (Zea mays L.) inbred G50 (Pioneer). Seedlings were germinated at 27[deg]C for 3 d and then exposed to chilling treatments of 4, 5, or 6[deg]C for 2, 4, 7, or 10 d in darkness. Damage symptoms in the more severe treatments included a waterlogged appearance and a discoloration of the tissue. The symptoms were most obvious in the mesocotyl. After a 10-d grow-out period in the greenhouse, moderately damaged seedlings exhibited chlorotic areas, an occasional disruption in leaf expansion, and a constriction of the mesocotyl. Growth and survival were improved by first exposing seedlings to a 14[deg]C acclimation treatment for 3 d before applying the chilling treatment. After chilling at 5[deg]C for 7 d, 79% of the acclimated seedlings survived, whereas only 22% of the nonacclimated seedlings survived. Differences in gene expression between acclimated and control seedlings were investigated using subtraction and differential screening techniques. Transcripts corresponding to three genes, car333, car30, and car757 (chilling acclimation responsive), were present in higher levels in seedlings after acclimation. Sequence analysis identified car333 as cat3, which encodes maize mitochondrial catalase isozyme 3. Characterization of these three clones revealed that all corresponding transcripts were elevated in acclimated seedlings in a manner that depended on the organ, i.e. coleoptile, mesocotyl, or root. Although transcripts were elevated in all three organs in response to acclimation, car30 was most abundant in the coleoptile and root, whereas cat3 and car757 were most abundant in the coleoptile and mesocotyl. Catalase activity followed the same general trend as cat3 transcript levels. Exogenous treatment with abscisic acid (ABA) resulted in an improvement in growth and survival of nonacclimated, chilled seedlings. Inhibition of ABA biosynthesis with fluridone abolished acclimation-induced chilling tolerance, and exogenous application of ABA to fluridone-treated seedlings restored chilling tolerance. Exogenous ABA treatment also resulted in increases in cat3, car30, and car757 transcript levels and catalase activity in the same organ-specific manner as in acclimated seedlings. These results indicate that ABA synthesis is essential for chilling tolerance. However, measurement of ABA levels in mesocotyls during acclimation and chilling revealed only a marginal increase during acclimation and a dramatic increase during chilling, regardless of whether or not seedlings were acclimated. Thus, although ABA may be required for chilling tolerance, we have no conclusive evidence that the acclimation process is mediated by ABA.
Dataset for: Multivascular networks and functional intravascular topologies within biocompatible hydrogels (2019)

Dataset for: Multivascular networks and functional intravascular topologies within biocompatible hydrogels Bagrat Grigoryan1,∗, Samantha J. Paulsen1,∗, Daniel C. Corbett2,∗, Daniel W. Sazer1, Chelsea L. Fortin2, Alexander J. Zaita1, Paul T. Greenfield1, Nicholas J. Calafat1, John P. Gounley3, Anderson H. Ta1, Fredrik Johansson2, Amanda Randles3, Jessica E. Rosenkrantz4, Jesse D. Louis-Rosenberg4, Peter A. Galie5, Kelly R. Stevens2,†, Jordan S. Miller1,† 1Department of Bioengineering, Rice University, Houston, TX 77005, USA 2Department of Bioengineering, University of Washington, Seattle, WA 98195, USA 3Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA 4Nervous System, Somerville, MA 02143, USA 5Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA ∗Equal contribution. †Corresponding authors. Email: ksteve@uw.edu (K.R.S.) and jmil@rice.edu (J.S.M.). Solid organs transport fluids through distinct vascular networks that are biophysically and biochemically entangled, creating complex 3D transport regimes that have remained difficult to produce and study. We establish intravascular and multivascular design freedoms with photopolymerizable hydrogels using food dye additives as biocompatible yet potent photoabsorbers for projection stereolithography. We demonstrate monolithic transparent hydrogels produced in minutes comprising efficient intravascular 3D fluid mixers and functional bicuspid valves. We further elaborate entangled vascular networks from space-filling mathematical topologies and explore the oxygenation and flow of human red blood cells during tidal ventilation and distension of a proximate airway. In addition, we deployed structured biodegradable hydrogel carriers in a rodent model of hepatic disease to highlight the potential translational utility of this materials innovation.
Cooperative control of exoskeletal assistive system for paraplegic walk-transferring between sitting posture and standing posture, and going up and down on stairs (2010)

This paper presents a cooperative control algorithm for a paraplegic patient to walk stably as requested. The algorithm generates stable motions of a lower limb for a paraplegic walk, receiving patient's preference related to his/her movement such as stand-to-sit and sit-to-stand transfers, walking and going up and down stairs. An exoskeletal walking support system assists motions of patient's lower limb in accordance with a patient wishes when a patient indicates his/her wishes by using residual functions such as motions of an upper limb. In our project, a pair of gloves with several DOFs was developed to convey wearer's wishes to the walking support system. The gloves measure his/her index fingers' swing that simulates foot motions of his/her walking and measure flexion or deviation of his/her wrist joint. The cooperative control algorithm based on a cart-table model designs trajectories of each joint for stable motions that satisfy the wishes expressed by the wearer's hand and wrist motions and then the designed motions are executed in realtime by the walking support system. As the first trial, a small humanoid robot is used for safety as a control target that corresponds to a combination of the patient body and the walking support system in an actual situation. Through some experiments it is confirmed that our algorithm enables the humanoid robot to start and stop stable walk with variable step length in the desired walking direction from a seated position and that it enables the robot to step aside and to go up and down stairs.
Probabilistic collision state checker for crowded environments (2010)

For path planning algorithms of robots it is important that the robot does not reach a state of inevitable collision. In crowded environments with many humans or robots, the set of possible inevitable collision states (ICS) is often unacceptably high, such that the robot has to stop and wait in too many situations. For this reason, the concept of ICS is extended to probabilistic collision states (PCS), which estimates the collision probability for a given state. This allows to efficiently run planning algorithms through crowded environments when accepting a certain collision probability. A further novelty is that the obstacles possibly react to the robot in order to mitigate the risk of a collision. The results show a significant difference in interaction behavior. Thus, this approach is especially suited for active and non-deterministic moving obstacles in the robot workspace.
Emissions from the laboratory combustion of wildland fuels: Particle morphology and size (2006)

The morphology of particles emitted by wildland fires contributes to their physical and chemical properties but is rarely determined. As part of a study at the USFS Fire Sciences Laboratory (FSL) investigating properties of particulate matter emitted by fires, we studied the size, morphology, and microstructure of particles emitted from the combustion of eight different wildland fuels (i.e., sagebrush, poplar wood, ponderosa pine wood, ponderosa pine needles, white pine needles, tundra cores, and two grasses) by scanning electron microscopy. Six of these fuels were dry, while two fuels, namely the tundra cores and one of the grasses, had high fuel moisture content. The particle images were analyzed for their density and textural fractal dimensions, their monomer and agglomerate number size distributions, and three different shape descriptors, namely aspect ratio, root form factor, and roundness. The particles were also probed with energy dispersive X‐ray spectroscopy confirming their carbonaceous nature. The density fractal dimension of the agglomerates was determined using two different techniques, one taking into account the three‐dimensional nature of the particles, yielding values between 1.67 and 1.83, the other taking into account only the two‐dimensional orientation, yielding values between 1.68 and 1.74. The textural fractal dimension that describes the roughness of the boundary of the two‐dimensional projection of the particle was between 1.10 and 1.19. The maximum length of agglomerates was proportional to a power a of their diameter and the proportionality constant and the three shape descriptors were parameterized as function of the exponent a .
Automated Registration of 3D Faces using Dense Surface Models (2003)

Dense surface models can be used to register unseen surfaces, using an algorithm which is a hybrid of iterative closest-point (ICP) and active shape model (ASM) fitting. In this paper we give details of this procedure and show how it can be improved by sequentially extending the transform group over which it operates. We also evaluate it for robustness to the position of the target and to shape variation across a set of unseen examples. The fit was successful on all 21 examples in our test set, with an average RMS error of 3.0mm. An initial comparison of 3 people landmarking the same scans suggests that this is within the normal landmark reproducibility range for 3D face scans.
Purification, characterization, and physiological function of Bacillus subtilis ornithine transcarbamylase (1983)

A procedure was developed for purification of ornithine transcarbamylase (OTCase) to near homogeneity from Bacillus subtilis 168. The purified native enzyme existed as a mixture of dimeric, tetrameric, and hexameric forms, but was converted to the dimer in the presence of 2-mercaptoethanol. The molecular weight of the subunit was 44,000. Some general kinetic properties of the enzyme were described. OTCase was repressed by arginine in growing B. subtilis cells, but the enzyme was induced by arginine at the end of exponential growth. Specific antibodies against the purified OTCase were used to show that the same enzyme was produced under all conditions. These results and studies of a mutant lacking OTCase demonstrated that B. subtilis produced only a single OTCase. OTCase was clearly required for arginine biosynthesis, but the physiological function of OTCase induction by arginine was obscure. OTCase was not induced by, or required for, growth on arginine as a carbon and nitrogen source. Absence of OTCase in a mutant did not alter the yield or arginine content of its spores in comparison to a strain containing OTCase.
Geometric confinement is required for recovery and maintenance of chondrocyte phenotype in alginate (2017)

Human articular chondrocytes lose their native phenotype when expanded in traditional monolayer cultures. As a consequence, hydrogel encapsulation has been investigated as a means to maintain the natural phenotype. Alginate has been widely used for cartilage engineering as it has been shown to enable the recovery of a native collagen type II expressing chondrocyte phenotype. This study has evaluated whether the capacity of the materials to maintain/revert the phenotype is due to the composition of the material or the physical entrapment provided by the gel. To achieve this, an alginate "fluid gel" (a shear-thinning structured gel system) was produced of identical chemistry to a traditionally gelled alginate structure. Both were seeded with passaged primary human articular chondrocytes. Chondrocytes in quiescent alginate showed the recovery of the native phenotype and a spherical morphology. Chondrocytes in alginate fluid gel were unable to maintain the recovered phenotype despite having a spherical morphology and were shown to have a lower level of entrapment than those in quiescent alginate. These findings indicate that geometric entrapment is essential for the maintenance of a recovered chondrocyte phenotype in alginate.
In vivo measurement of widespread synaptic loss and associated tau accumulation in early Alzheimer’s disease (2020)

Abstract Background Using [ 11 C]UCB‐J–PET we have shown significant reductions in hippocampal SV2A specific binding as a marker of synaptic density in participants with early Alzheimer’s disease (AD). However, postmortem studies have suggested more widespread neocortical reductions in synaptic density that are associated with fibrillary tau accumulation. Methods We measured SV2A binding with [ 11 C]UCB‐J‐PET in 34 participants with early AD (MMSE=23.1±4.1, CDR=0.5‐1.0) and 19 cognitively normal (CN) participants (MMSE=29.3±1.1, CDR=0). Amyloid status was confirmed by [ 11 C]PiB‐PET. For [ 11 C]UCB‐J‐PET, we calculated the distribution volume ratio ( DVR ) using a cerebellum reference. In a subset of 10 CN and 10 AD participants, we measured tau accumulation using [ 18 F]flortaucipir‐PET. [ 18 F]Flortaucipir standardized uptake value ratios ( SUVR s) were calculated using an inferior cerebellum reference. Results Our primary analysis of group differences in SV2A binding demonstrated a significant effect of group (F(1,51)=33.4, P &lt;0.00001) and group*region (F(10,510)=2.4, P =0.01) as predictors of SV2A binding ( DVR ). Post‐hoc comparisons revealed significant group differences in all medial temporal regions and more broadly in neocortical regions (Figure 1). SV2A reductions in AD were most pronounced in the hippocampus ( DVR –17.3%, P&lt;0.00001; BP ND –19.8%) and entorhinal cortex ( DVR –15.7%, P&lt;0.00001; BP ND –17.6%), but also present in parahippocampal, amygdala, lateral temporal, prefrontal, posterior cingulate/precuneus, lateral parietal, and pericentral regions. These reductions were largely maintained after correction for volume loss and were more extensive than decreases in gray matter volume. In a smaller sample of participants with tau PET, AD participants demonstrated significantly higher entorhinal cortical (ERC) [ 18 F]flortaucipir binding compared to CN participants (CN SUVR =1.11±0.12, AD SUVR =1.68±0.16, p&lt;0.00001). ERC‐tau was inversely associated with hippocampal synaptic density (r=‐0.63, P =0.005). Synaptic density and tau were inversely associated in regions of early and later Braak stages (r=‐0.45 to ‐0.59, P &lt;0.05). Conclusion We observed widespread reductions of synaptic density with [ 11 C]UCB‐J‐PET in medial temporal and neocortical regions in early AD. ERC tau accumulation was associated with lower hippocampal synaptic density. This inverse association may reflect synaptic failure due to tau pathology in ERC neurons projecting to the hippocampus. Further longitudinal studies are needed to elucidate the chronology and topography of tau accumulation and synaptic loss in AD and their relationship.
Lagotoside: A New Phenylpropanoid Glycoside from Lagotis stolonifera (1991)

Abstract From the aerial parts of Lagotis stolonifera (Scrophulariaccae), a new phenylpropanoid glycoside, lagotoside ( 8 ), and the three known glycosides ehrenoside ( 5 ), verbascoside (= acteoside; 6 ), and plantamajoside ( 7 ) were isolated, together with the four known iridoid glucosides aucubin ( 1 ), catalpol( 2 ), globularin ( 4 ), and lythantosalin ( 3 ). The structure of the new compound 8 was elucidated on the basis of chemical and spectral data as 2‐(3‐hy‐droxy‐4‐methoxyphenyl)ethyl O ‐[α‐ L ‐arabinopyranosyl‐(1 → 2)]‐ O ‐[α‐ L ‐rhamnopyranosyl‐(1 → 3)]‐4‐ O ‐feruloyl‐β‐ D ‐glucopyranoside.
Surface Analysis with FT-IR Emission Spectroscopy (1992)

The technique of infrared emission spectroscopy (IRES) is reviewed and further examined in this study as a surface analysis tool. A system has been designed which allows simultaneous kinetic and in situ infrared emission analysis of catalyst surfaces. IRES spectra of several gas mixture/solid systems are obtained in order to examine sample preparation and spectra processing issues; these systems include Pt/Al 2 O 3 exposed to CO and CO-NO mixtures, an oxidized copper plate, and a zeolite exposed to inert atmospheres. For the temperature range of importance to catalysis (300–600 K), IRES is limited to frequencies less than 2500 cm −1 . However, IRES is especially well suited for studying solid-state vibrational modes (&lt;1000 cm −1 ). Moreover, IRES allows catalyst samples to be studied without dilution or extensive sample preparation. The thin samples required for IRES make it possible to study both surface adsorbate and the solid-state lattice vibrations simultaneously. This information can provide useful insight into the interpretation of kinetic data of reactions on metal oxide catalysts. However, samples which are too thick or are supported on a high-emissivity surface will not yield satisfactory spectra. Two correction techniques are examined which reduce background and sample-reflectance effects in the emission spectra. Some of the IRES data are compared to the corresponding spectra obtained by transmission and diffuse-reflectance spectroscopy. IRES is shown to be competitive with these more popular techniques for IR surface analysis.
Enantioselective Organocatalytic Michael Addition of Malonate Esters to Nitro Olefins Using Bifunctional Cinchonine Derivatives. (2006)

Abstract For Abstract see ChemInform Abstract in Full Text.
Combined use of tamoxifen, cyclosporin A, and verapamil for modulating multidrug resistance in human hepatocellular carcinoma cell lines (1993)

The intensive use of chemotherapeutic agents for the treatment of cancer has resulted in the cure or improved survival of many patients. But unfortunately, many cancers including human hepatocellular carcinoma (HCC) don't respond to chemotherapy. One of the major mechanisms for the drug resistance in the HCC is an elevated MDR1 RNA expression which makes cells become multidrug resistant. To overcome the multidrug resistance (MDR) phenotype, a high dose of verapamil is required both clinically and experimentally. Accordingly we have examined the MDR modulating effects with combinations of tamoxifen, cyclosporin A, and verapamil in vitro with the physiologically achievable concentrations of each agent, i.e., 2.0 microM/L for tamoxifen, 1.6 microM/L for cyclosporin A, and 2.5 microM/L for verapamil respectively in HCC lines. As expected, verapamil alone with the physiologically achievable concentration at which we tested didn't enhance the doxorubicin cytotoxicity in the HCC lines. Furthermore, any verapamil combination with cyclosporin A or tamoxifen was not effective in overcoming the doxorubicin resistance in the high MDR1 expressor (Hep-G2) line. However tamoxifen reduced the IC50 of doxorubicin by a factor of 1.9 in the low MDR1 expressor (SK-Hep1) and 1.1 in the high MDR1 expressor line (p < 10(-5) respectively). Of interest, combinations of tamoxifen and cyclosporin A showed a significant reduction in the IC50 of doxorubicin in both HCC lines. The IC50 of doxorubicin was reduced by a factor of 3.9 and 1.3, i.e., from 0.023943 micrograms/ml to 0.006157 micrograms/ml (p < 10(-5)) in the SK-Hep1 cell line, and 0.068819 micrograms/ml to 0.052442 micrograms/ml (p < 10(-5)) in Hep-G2 respectively when tamoxifen and cyclosporin A were administered together. Both the estrogen and progesterone receptors in the SK-Hep1 and Hep-G2 lines were less than 0.01 fmol/mg of cytosol protein, respectively. It is therefore suggested that the reversal of doxorubicin resistance is unrelated to their anti-estrogenic activity in the HCC lines. Three modulator combinations of tamoxifen, cyclosporin A, and verapamil were not more effective than the combination of tamoxifen and cyclosporin A on the sensitivity to doxorubicin. MDR modulators of tamoxifen, cyclosporin A, and verapamil didn't reduce the IC50 of cisplatin to the clinically achievable concentration range in HCC lines. In summary, the combination of tamoxifen and cyclosporin A at the concentrations normally seen after clinical administration of these modulators showed significant synergism on the sensitivity to doxorubicin in both low and high MDR1 expressor HCC lines. These data indicate the need for in vivo trials.