gebhart/patrepeval huggingface dataset:
The sex determination process in maize (1994)

Maize partitions the sexes into different flowers on the plant, a condition called monoecy, which facilitates outcrossing. Sex determination in maize is a complex process involving an interplay between genetic determinants, the environment, and hormones. Unisexuality of flowers is achieved by the process of selective arrest and abortion of the inappropriate organ primordia within a bisexual floral meristem. Floral organ abortion is associated with the degeneration of cells within an immature primordia. Masculinizing genes are required for gynoecial abortion, feminizing genes arrest stamen development, and both types also control secondary sexual traits involving morphological characteristics of floral tissues. Gibberellins, steroid-like plant hormones, appear to play a pivotal role in the stamen abortion process and the feminization of floral tissues.
<title>Automatic and accurate measurement of a cross-sectional area of vessels in 3D x-ray angiography images</title> (2000)

Variation in the diameter of vessels is a key information for treatment of stenosis. This information is usually obtained from standard 2-D projective acquisitions. We propose an automatic method for the quantification of vessels cross- sections in 3D vascular reconstructions from x-ray images. First, a closed continuous surface is extracted. This surface represents the vessels contours selected with a given centerline. Then, the area of the cross-sections along the central axis is obtained by intersection of the contour and the plane of each cross-section. A model of the vessels allows to correct the first estimation. Tests on phantom images give a precision of the vessels radius below 0.5 voxel. Results are also presented on real vessels containing stenosis.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Opposing roles of Akt and STAT3 in the protection of the maternal heart from peripartum stress (2014)

Postpartum Akt activation is detrimental for the peripartum heart as it lowers anti-oxidative defence and in combination with low STAT3 conditions, accelerate cardiac inflammation and fibrosis. PRL and its cleaved 16 kDa form are central for Akt-induced PPCM as indicated by the protection from the disease by PRL blockade.
MALDI imaging mass spectrometry revealed atropine distribution in the ocular tissues and its transit from anterior to posterior regions in the whole-eye of rabbit after topical administration (2019)

It is essential to elucidate drug distribution in the ocular tissues and drug transit in the eye for ophthalmic pharmaceutical manufacturers. Atropine is a reversible muscarinic receptor used to treat various diseases. However, its distribution in ocular tissues is still incompletely understood. Matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS) evaluates drug distribution in biological samples. However, there have been few investigations of drug distribution in ocular tissues, including whole-eye segments. In the present study, we explored the spatial distribution of atropine in the whole-eye segment by MALDI-IMS, and then evaluated the changes in atropine level along the anterior-posterior and superior-inferior axes. A 1% atropine solution was administered to a rabbit and after 30 min, its eye was enucleated, sectioned, and analyzed by MALDI-IMS. Atropine accumulated primarily in the tear menisci but was found at substantially lower concentrations in the tissue surrounding the conjunctival sacs. Relative differences in atropine levels between the anterior and posterior regions provided insights into the post-instillation behavior of atropine. Atropine signal intensities differed among corneal layers and between the superior and inferior eyeball regions. Differences in signal intensity among tissues indicated that the drug migrated to the posterior regions via a periocular-scleral route. Line scan analysis elucidated atropine transit from the anterior to the posterior region. This information is useful for atropine delivery in the ocular tissues and indicates that MALDI-IMS is effective for revealing drug distribution in whole-eye sections.
Predicting Cognitive Load and Operational Performance in a Simulated Marksmanship Task (2020)

Modern operational environments can place significant demands on a service member's cognitive resources, increasing the risk of errors or mishaps due to overburden. The ability to monitor cognitive burden and associated performance within operational environments is critical to improving mission readiness. As a key step toward a field-ready system, we developed a simulated marksmanship scenario with an embedded working memory task in an immersive virtual reality environment. As participants performed the marksmanship task, they were instructed to remember numbered targets and recall the sequence of those targets at the end of the trial. Low and high cognitive load conditions were defined as the recall of three- and six-digit strings, respectively. Physiological and behavioral signals recorded included speech, heart rate, breathing rate, and body movement. These features were input into a random forest classifier that significantly discriminated between the low- and high-cognitive load conditions (AUC = 0.94). Behavioral features of gait were the most informative, followed by features of speech. We also showed the capability to predict performance on the digit recall (AUC = 0.71) and marksmanship (AUC = 0.58) tasks. The experimental framework can be leveraged in future studies to quantify the interaction of other types of stressors and their impact on operational cognitive and physical performance.
Adaptive Step Sizes in Variance Reduction via Regularization (2019)

The main goal of this work is equipping convex and nonconvex problems with Barzilai-Borwein (BB) step size. With the adaptivity of BB step sizes granted, they can fail when the objective function is not strongly convex. To overcome this challenge, the key idea here is to bridge (non)convex problems and strongly convex ones via regularization. The proposed regularization schemes are \textit{simple} yet effective. Wedding the BB step size with a variance reduction method, known as SARAH, offers a free lunch compared with vanilla SARAH in convex problems. The convergence of BB step sizes in nonconvex problems is also established and its complexity is no worse than other adaptive step sizes such as AdaGrad. As a byproduct, our regularized SARAH methods for convex functions ensure that the complexity to find $\mathbb{E}[\| \nabla f(\mathbf{x}) \|^2]\leq ε$ is ${\cal O}\big( (n+\frac{1}{\sqrtε})\ln{\frac{1}ε}\big)$, improving $ε$ dependence over existing results. Numerical tests further validate the merits of proposed approaches.
Methylprednisolone Delivery to the Back of the Eye using Hydrogel Iontophoresis (2008)

A short, low-current noninvasive iontophoretic treatment, using methylprednisolone-loaded hydrogels, has potential clinical value in treating ocular inflammatory diseases.
Agglomeration at the Micrometer Length Scale of Cobalt Nanoparticles in Alumina‐Supported Fischer–Tropsch Catalysts in a Slurry Reactor (2013)

Detached from it all: Cobalt sintering leading to the formation of large, individually detached microscopic metal agglomerates is detected in alumina-supported cobalt catalysts after Fischer–Tropsch synthesis in a slurry reactor. The macroscopic sintering depends on the H2/CO ratio, the partial pressure of water, and the conversion of carbon monoxide, all of which lead to dramatic catalyst deactivation.
Serum Phosphate and Retinal Microvascular Changes: The Multi-Ethnic Study of Atherosclerosis and the Beaver Dam Eye Study (2017)

Among community-living individuals with low prevalence of CKD, higher serum phosphate was associated with prevalent retinopathy in individuals with diabetes. Further longitudinal assessments in patients with diabetes necessitate further investigation.
Hypoxia and Inflammation (2011)

This review deals with emerging evidence of an association between systemic or local hypoxia and inflammation in a variety of diseases. The evidence points to new ways of treating inflammatory disorders or conditions such as certain cancers with intralesional hypoxia.
Phase II study of the farnesyltransferase inhibitor R115777 in advanced melanoma (CALGB 500104) (2012)

Despite potent target inhibition, R115777 showed no evidence of clinical activity in this cohort of melanoma patients. Inhibition of T cell function by FTIs has potential clinical implications. Clinicaltrials.gov number NCT00060125.
Crystallization of and preliminary X-ray data for an intracellular vitamin A-binding protein from rat liver. (1981)

Crystals of a cellular retinol-binding protein from rat liver have been grown from solutions of polyethylene glycol-6,000 and CdCl2. The crystals are orthorhombic, space group P212121, a = 40.09, b = 47.39, and c = 69.34 A. An asymmetric unit contains 1 molecule. Diffraction has been observed to Bragg spacings of 1.7 A resolution.
Realization of both a single electron transistor and a field effect transistor with an underlapped FDSOI MOSFET geometry (2012)

A dual mode device has been realized with FDSOI MOSFET technology implementing both a single electron transistor (SET) and a field effect transistor (FET). The silicon substrate is used as a back gate to choose between these two functionalities. We show in this paper that the behavior of the device is determined by the position of the electron gas in the silicon mesa: the device is a SET if the electron gas is created by the top gate, and behaves as a FET when the back gate induces a electron gas at the bottom of the silicon mesa. This opens the possibility to design hybrid circuits exploiting both advantages of FETs and SETs.
Layer-by-layer films for tunable and rewritable control of contact electrification (2013)

Charges generated by contact of solid surfaces (contact electrification) can be hazardous or useful depending on the circumstance. This paper describes a process to design a solid surface rationally to either induce or prevent charging during contact electrification; this process coats the surface with polyelectrolytes. It is observed experimentally that a surface coated with a layer of a polymer having multiple, covalently attached positive charges (a “polycation”) develops a positive charge after contacting another surface; a surface coated with a layer of polymer having negative charges (a “polyanion”) develops a negative charge. By coating the surface using layer-by-layer (LBL) deposition, the tendency of the surface to charge either positively or negatively can be switched: adding a layer of polyelectrolyte with charge opposite to the charge on the surface switches the polarity of the surface. Through microcontact printing (μCP), the surface can be stamped to create a mosaic pattern of polycation and polyanion — and importantly, the fraction of the surface area covered with polycation and polyanion can be tuned by using stamps of different patterns. Using poly(diallyldimethylammonium chloride) (PDDA) as the polycation and poly(sodium 4-styrenesulfonate) (PSS) as the polyanion, it is found that for a surface with >75% PSS, the surface charges negatively; with <75% PSS, the surface charges positively. At ∼75% PSS, the surface becomes non-charging. The patterns on the surface can, subsequently, be erased through coating the surface with a uniform layer of polyelectrolyte. After erasing, the surface is rewritable by depositing or patterning the surface with a desired polyelectrolyte.
Na3V2O2(PO4)2F/graphene sandwich structure for high-performance cathode of a sodium-ion battery (2013)

A Na3V2O2(PO4)2F/reduced-graphene-oxide (RGO) sandwich structure has been synthesized by a facile one-step solvothermal method. Cubic Na3V2O2(PO4)2F nanoparticles are homogeneously trapped between conductive RGO sheets during its growth and assembled into a compact sandwich structure, which allows the electrically insulating Na3V2O2(PO4)2F nanoparticles to be wired up to a current collector through the underlying graphene conducting layers. As a sodium-insertion cathode material, the structure exhibits a high reversible capacity of 120 mA h g(-1) at a discharge rate of C/20 with a capacity retention of 100.4 mA h g(-1) at 1 C and an excellent cyclic retention of 91.4% after the 200th cycle at C/10. These results highlight the importance of anchoring Na3V2O2(PO4)2F on a conducting scaffold for maximum utilization of the electrochemically active Na3V2O2(PO4)2F particles in a high-performance sodium-ion battery.
Effects of Guchang Capsule on Dextran Sulphate Sodium‐Induced Experimental Ulcerative Colitis in Mice (2016)

Guchang capsule (GC) is a Chinese materia medica standardized product extracted from 15 Chinese traditional medical herbs and it has been clinically used in the treatment of intestinal disease. In this study, in order to extend the research of GC in intestinal disease, we were aiming to evaluate potential effects of GC on dextran sulphate sodium- (DSS-) induced murine experimental colitis and to elucidate the underlying mechanisms. GC treatment attenuated DSS-induced body weight loss and reduced the mortality. Moreover, GC treatment prevented DSS-induced colonic pathological damage; meanwhile it inhibited proinflammatory cytokines production in colon tissues. In vitro, GC significantly reduced LPS-induced proinflammatory cytokines production via inhibiting the activation of NF-κB in macrophage cells, and the expressions of several long noncoding RNAs (lncRNAs) which were reported in regulating NF-κB signaling pathway were obviously affected by adding GC into culture medium. In conclusion, our data suggested that administration of GC exhibits therapeutic effects on DSS-induced colitis partially through regulating the expression of NF-κB related lncRNAs in infiltrating immune cells.
Solvent inhibition in the liquid-phase catalytic oxidation of 1,4-butanediol: understanding the catalyst behaviour from NMR relaxation time measurements (2016)

Solvent inhibition over surfaces affects behaviour and performances of heterogeneous catalysts.
A Magneto-optic Polarization Readout Model (1985)

Information stored on magneto-optic disks is typically read using a linearly polarized laser beam whose state of polarization is altered by the Faraday and/or polar Kerr effects upon reflection from the recording medium. Polarization sensitive optics are used to convert these media induced polarization changes into irradiance variations at photodetectors. Because the magneto-optic polarization effects are small (typically less than one degree of polarization rotation in the reflected beam) it is essential that the optical system introduce little additional polarization change if the recorded signal is to be recovered faithfully. This paper describes a polarization model that is used to predict the effects that real optical elements will have on the readout signals, noise, and ultimately, the signal to noise ratio of a magneto-optic recording system.
An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors (2017)

The non-receptor tyrosine kinase Src is a key signalling hub for upregulating the function of N-methyl D-aspartate receptors (NMDARs). Src is anchored within the NMDAR complex via NADH dehydrogenase subunit 2 (ND2), a mitochondrially encoded adaptor protein. The interacting regions between Src and ND2 have been broadly identified, but the interaction between ND2 and the NMDAR has remained elusive. Here we generate a homology model of ND2 and dock it onto the NMDAR via the transmembrane domain of GluN1. This interaction is enabled by the evolutionary loss of three helices in bilaterian ND2 proteins compared to their ancestral homologues. We experimentally validate our model and demonstrate that blocking this interaction with an ND2 fragment identified in our experimental studies prevents Src-mediated upregulation of NMDAR currents in neurons. Our findings establish the mode of interaction between an NMDAR accessory protein with one of the core subunits of the receptor.
Neutronics and safety analysis of pellet bed reactor for nuclear thermal propulsion (1993)

The Pellet Bed Reactor for Nuclear Thermal Propulsion is modeled using the TWODANT discrete ordinance code to determine a reactor point design based on the selection of a fuel fraction in and a diameter of the pellets, dimensions of the reactor core, maximum fuel temperature, and sub‐criticality during a water flooding accident. A total excess reactivity of approximately $1.25 (or keff of 1.01), an order of magnitude higher than that estimated at BOM for 15 hours of full power, steady‐state operation of the PeBR, is considered. Besides calculating the dimensions of the reactor core to satisfy the excess reactivity at BOM, the results of the neutronics calculations include estimates of the radial and axial fission power density profiles in the PeBR core. These results, in conjunction with a 1‐D, steady‐state thermal hydraulics analysis are used to select the operation and design characteristics of the PeBR point design, namely: (a) core radius and height of 38.4 cm and 120 cm, respectively, (b) pellet matrix fraction of 0.5, (c) total reactor mass of 3500 kg, excluding those of the radiation shield, the propulsion nozzle, external structure for the propellant flow into the core, and the drive mechanisms of the control drums in the radial reflector, (d) power density of 10 and 15 MW/l for a reactor thermal power of 1000 MW and 1500 MW, submersion calculations show that with all safety rods removed from the core, the 16 control drums are insufficient to maintain the reactor sub‐critical. However, when the 8, B4C safety rods are inserted into the reactor, it is possible to maintain the submerged PeBR point design $7.5 sub‐critical (keff=0.94).
A numerical approach to the evaluation of uncertainty in nonconventional measurements on power systems (2002)

The use of digital signal processing techniques allows measuring any quantity mathematically defined. However, the application of the rules endorsed by the ISO "Guide to the expression of uncertainty in measurement" to evaluate the measurement uncertainty can turn into a difficult task, for instance, when quantities different from those usually measured to characterize the operation of power systems must be determined. In this paper, a numerical approach is proposed to easily tackle this task. Contrary to the closed-form approach, which allows to evaluate the output uncertainty by analytically solving the uncertainty propagation law, as prescribed by the ISO Guide, the method proposed numerically finds the uncertainty by applying a recursive algorithm. First, first the validity of the numerical approach is proved in the case of the spectral analysis of a periodic signal, which is the first step for nonconventional measurement. Then, the approach is used to evaluate the uncertainty in the measurement of the harmonic losses of a power transformer supplying nonsinusoidal load currents. The results confirm that these losses can be accurately determined from the difference between two powers measured as correlated quantities at the transformer output terminals.
Determination of the capture radii of magnetite bearing hydroxide flocs in magnetic filtration (1998)

Magnetic filtration may be applied in water technology for the separation of flocs which are formed in a flocculation tank together with magnetite as an additive. The capture radius is an important mathematical quantity to calculate the performance of such filters in advance. Thus, the capture radii of magnetite bearing copper hydroxide flocs were measured with a direct visual evaluation of the floc trajectories in the neighborhood of a single magnetized wire. For this purpose, an experimental setup was assembled, which allowed the observation and the measurement of the trajectories. With the image processing system used, it was possible to observe flocs larger than 30 /spl mu/m and the flow velocity was limited to a maximum value of 20 mm/s. Capture radii were calculated by the established single-wire theory under the assumption of potential and creeping flow conditions. It has been proved that further information on the solids content of the flocs, which strongly influences the floc susceptibility, was necessary to obtain an agreement between the experimental data and the theoretical predictions. By introducing a flee size dependent solids content into the single-wire theory, measured by means of sedimentation analysis, an accurate description of the observed capture radii was possible.
Supersonic Shear Wave Imaging to Assess Arterial Nonlinear Behavior and Anisotropy: Proof of Principle via Ex Vivo Testing of the Horse Aorta (2014)

Supersonic shear wave imaging (SSI) is a noninvasive, ultrasound-based technique to quantify the mechanical properties of bulk tissues by measuring the propagation speed of shear waves (SW) induced in the tissue with an ultrasound transducer. The technique has been successfully validated in liver and breast (tumor) diagnostics and is potentially useful for the assessment of the stiffness of arteries. However, SW propagation in arteries is subjected to different wave phenomena potentially affecting the measurement accuracy. Therefore, we assessed SSI in a less complex ex vivo setup, that is, a thick-walled and rectangular slab of an excised equine aorta. Dynamic uniaxial mechanical testing was performed during the SSI measurements, to dispose of a reference material assessment. An ultrasound probe was fixed in an angle position controller with respect to the tissue to investigate the effect of arterial anisotropy on SSI results. Results indicated that SSI was able to pick up stretch-induced stiffening of the aorta. SW velocities were significantly higher along the specimen's circumferential direction than in the axial direction, consistent with the circumferential orientation of collagen fibers. Hence, we established a first step in studying SW propagation in anisotropic tissues to gain more insight into the feasibility of SSI-based measurements in arteries.
Learning seasonal phytoplankton communities with topic models (2017)

In this work we develop and demonstrate a probabilistic generative model for phytoplankton communities. The proposed model takes counts of a set of phytoplankton taxa in a timeseries as its training data, and models communities by learning sparse co-occurrence structure between the taxa. Our model is probabilistic, where communities are represented by probability distributions over the species, and each time-step is represented by a probability distribution over the communities. The proposed approach uses a non-parametric, spatiotemporal topic model to encourage the communities to form an interpretable representation of the data, without making strong assumptions about the communities. We demonstrate the quality and interpretability of our method by its ability to improve performance of a simplistic regression model. We show that simple linear regression is sufficient to predict the community distribution learned by our method, and therefore the taxon distributions, from a set of naively chosen environment variables. In contrast, a similar regression model is insufficient to predict the taxon distributions directly or through PCA with the same level of accuracy.