gebhart/patrepeval huggingface dataset:
Modeling Oral Multispecies Biofilm Recovery After Antibacterial Treatment (2019)

Abstract Recovery of multispecies oral biofilms is investigated following treatment by chlorhexidine gluconate (CHX), iodine-potassium iodide (IPI) and Sodium hypochlorite (NaOCl) both experimentally and theoretically. Experimentally, biofilms taken from two donors were exposed to the three antibacterial solutions (irrigants), respectively, for 10 minutes. We observe that (a) live bacterial cell ratios decline for a week after the exposure and the trend then reverses beyond the week; after fifteen weeks, live bacterial cell ratios in biofilms fully return to their pretreatment levels; (b) NaOCl is shown as the strongest antibacterial agent for the oral biofilms; (c) multispecies oral biofilms from different donors showed no difference in their susceptibility to all the bacterial solutions. Guided by the experiment, a mathematical model for biofilm dynamics is developed, accounting for multiple bacterial phenotypes, quorum sensing, and growth factor proteins, to describe the nonlinear time evolutionary behavior of the biofilms. The model captures time evolutionary dynamics of biofilms before and after antibacterial treatment very well. It reveals the important role played by quorum sensing molecules and growth factors in biofilm recovery and verifies that the source of biofilms has a minimal effect to their recovery. The model is also applied to describe the state of biofilms of various ages treated respectively by CHX, IPI and NaOCl, taken from different donors. Good agreement with experimental data predicted by the model is obtained as well, confirming its applicability to modeling biofilm dynamics in general.
Extended Regularization Methods for Nonconvergent Model Selection (1992)

Many techniques for model selection in the field of neural networks correspond to well established statistical methods. The method of &amp;apos;stopped training&amp;apos;, on the other hand, in which an oversized network is trained until the error on a further validation set of ex-amples deteriorates, then training is stopped, is a true innovation, since model selection doesn&amp;apos;t require convergence of the training process. In this paper we show that this performance can be significantly enhanced by extending the &amp;apos;non convergent model selection method&amp;apos; of stopped training to include dynamic topology modifications (dynamic weight pruning) and modified complexity penalty term methods in which the weighting of the penalty term is adjusted during the training process. 1
Studies on the Photothermal Effect of PEGylated Fe3O4 Nanoparticles (2017)

We reported the photothermal studies on the PEGylated Fe3O4 nanoparticles. In our study, we prepared a series of PEGylated Fe3O4 nanoparticles with different formulations and found that all the PEGylated Fe3O4 nanoparticles have both the photothermal conversion effect and magnetic hyperthermia. We first tried to illustrate the importance of photothermal effect and magnetic heating in the hyperthermia of Fe3O4 nanoparticles, and describe the relationship between the structures and functions. Among these samples, there were two different structures. One is a similar colloidal nanostructure, while the other is a typical nanoparticle structure. Both of them have the similar ultraviolet-visible absorption spectra, Fourier transform infrared spectra and X-ray diffraction patterns. However, the second nanoparticles have higher photothermal conversion efficiency and magnetic resonance imaging contrast than the first colloidal nanostructures. Moreover, by transmission electron microscopy, we found that when the core diameter was in the range of 19–20 nm, the temperature change was above 28 C by photothermal effect, while the magnetic heating was low. All these results not only help us have more comprehensive understanding of Fe3O4 nanoparticle properties, but also provide a rational theoretical support for applying Fe3O4 nanoparticles as a suitable candidate in the photothermal treatment.
When Cells Suffocate: Autophagy in Cancer and Immune Cells under Low Oxygen (2011)

Hypoxia is a signature feature of growing tumors. This cellular state creates an inhospitable condition that impedes the growth and function of all cells within the immediate and surrounding tumor microenvironment. To adapt to hypoxia, cells activate autophagy and undergo a metabolic shift increasing the cellular dependency on anaerobic metabolism. Autophagy upregulation in cancer cells liberates nutrients, decreases the buildup of reactive oxygen species, and aids in the clearance of misfolded proteins. Together, these features impart a survival advantage for cancer cells in the tumor microenvironment. This observation has led to intense research efforts focused on developing autophagy-modulating drugs for cancer patient treatment. However, other cells that infiltrate the tumor environment such as immune cells also encounter hypoxia likely resulting in hypoxia-induced autophagy. In light of the fact that autophagy is crucial for immune cell proliferation as well as their effector functions such as antigen presentation and T cell-mediated killing of tumor cells, anticancer treatment strategies based on autophagy modulation will need to consider the impact of autophagy on the immune system.
EXPERIMENTAL STUDY OF A PULSATING HEAT PIPE USING FC-72, ETHANOL, AND WATER AS WORKING FLUIDS (2004)

Experimental studies were performed on a pulsating heat pipe (PHP), consisting of a heating section, an adiabatic section, and a condensation section incorporating a heat sink. The capillary tube used in this study has an inside diameter of 1.18 mm and a wall thickness of 0.41 mm. The experiments were conducted under the condition of pure natural convection, for heating powers from 5 to 60 W, fill ratios from 60% to 90%. Three working fluids-FC-72, ethanol, and deionized water--were used. The thermal oscillation of the thin wall surface was recorded by a high-speed data acquisition system. Such thermal oscillation waves are random for some run cases due to the randomly distributed vapor plug and liquid slugs inside the PHP. The thermal oscillation amplitude is much smaller for FC-72, due to its lower surface tension, than for ethanol and water, while the oscillation cycle period for FC-72 is shorter than for the other two fluids, indicating the faster oscillation movement in the channels, possibly due to the lower latent heat of evaporation for FC-72. The unlooped PHP is not helpful for the fluid circulation and the PHP does not work. For the looped PHP, there is a minimum heating power that initiates the PHP working. Such minimum heating power is strongly dependent on the working fluid, and is considerably smaller for FC-72 compared with water. The optimal filling ratio is around 70% for all three working fluids. The looped PHP with water as working fluid provides better overall thermal performance once the heating power is greater than a minimum value. However, FC-72 is suggested to be used for low-heat-flux situations, due to its lower minimum heating power.
Quantitative assessment of the germicidal efficacy of ultrasonic energy (1991)

Propagated (free-field) ultrasonic energy at a frequency of 26 kHz was used to expose aqueous suspensions of bacteria (Escherichia coli, Staphylococcus aureus, Bacillus subtilis, and Pseudomonas aeruginosa), fungus (Trichophyton mentagrophytes), and viruses (feline herpesvirus type 1 and feline calicivirus) to evaluate the germicidal efficacy of ultrasound. There was a significant effect of time for all four bacteria, with percent killed increasing with increased duration of exposure, and a significant effect of intensity for all bacteria except E. coli, with percent killed increasing with increased intensity level. There was a significant reduction in fungal growth compared with that in the controls, with decreased growth with increased ultrasound intensity. There was a significant reduction for feline herpesvirus with intensity, but there was no apparent effect of ultrasound on feline calicivirus. These results suggest that ultrasound in the low-kilohertz frequency range is capable to some degree of inactivating certain disease agents that may reside in water. The physical mechanism of inactivation appears to be transient cavitation.
Reduction of Fecundity and Egg Hatch in Three Stored-Product Phycitid Moths After Repetitive Sublethal Carbon Dioxide Exposures13 (1973)

Three stored-product phycitid moths were exposed 2 hours daily for 6 days to atmospheres containing about 96% CO2, Egg hatch was completely eliminated in the Mediterranean flour moth, Anagasta kuehniella (Zeller), and was less than 2% in the almond moth, Cadra cautella (Walker). Carbon dioxide was slightly less effective in preventing egg hatch in the Indian meal moth, Plodia interpunctella (Hubner). A large reduction in oviposition occurred in all 3 species.
Simulation of helix association in membranes: modeling the glycophorin A transmembrane domain (2002)

A study to predict the transmembrane structure of glycophorin A (GpA), a dimeric membrane protein is presented. The authors have developed a method to study the stability, structure, and energetics of a large number of conformations of pairs of helical proteins. The method employs molecular dynamics simulation to study the association of two helices in vacuum using an automated procedure and can be applied to any amino-acid sequence. The calculations found three conformations of the helical dimer located inside the membrane that form local energy minima of the interaction energy of the helices. Only one of the three conformations, a right-handed supercoil, is compatible with mutagenesis data. Simulations inside a lipid bilayer were performed to further refine the structure of the transmembrane region. The work shows that a combined approach of modeling and mutagenesis can be used to reveal structural information about a protein with known secondary structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Results from CXCR2 Expression in Tumor Cells Is a Poor Prognostic Factor and Promotes Invasion and Metastasis in Lung Adenocarcinoma (2023)

&lt;p&gt;XLSX file - 1MB, List of genes in excel format&lt;/p&gt;
LuxT is a Global Regulator of Low-Cell-Density Behaviors Including Type III Secretion, Siderophore Production, and Aerolysin Production in Vibrio harveyi (2021)

RNA-Sequencing and Numerical Data files for "LuxT is a Global Regulator of Low-Cell-Density Behaviors Including Type III Secretion, Siderophore Production, and Aerolysin Production in Vibrio harveyi".
Control of Multifunctional Prosthetic Hands by Processing the Electromyographic Signal (2002)

The human hand is a complex system, with a large number of degrees of freedom (DoFs), sensors embedded in its structure, actuators and tendons, and a complex hierarchical control. Despite this complexity, the efforts required to the user to carry out the different movements is quite small (albeit after an appropriate and lengthy training). On the contray, prosthetic hands are just a pale replication of the natural hand, with significantly reduced grasping capabilities and no sensory information delivered back to the user. Several attempts have been carried out to develop multifunctional prosthetic devices controlled by electromyographic (EMG) signals (myoelectric hands), harness (kinematic hands), dimensional changes in residual muscles, and so forth, but none ofthese methods permits the "natural" control of more than two DoFs. This article presents a review of the traditional methods used to control artificial hands by means of EMG signal, in both the clinical and research contexts, and introduces what could be the future developments in the control strategy of these devices.
A Robust Infrared Transducer of an Ultra-Large-Scale Array (2020)

A robust micro-electro-mechanical systems (MEMS) infrared thin film transducer of an ultra-large-scale array was proposed and fabricated on a 4-inch silicon wafer. The silicon substrate and micro cavities were introduced. This novel transducer had excellent mechanical stability, time response, and state-of-the-art pixel scale. It could bear a load of 1700 g and its load pressure was improved by more than 5.24 times and time constant decreased by 50.7% compared to the traditional soft infrared thin film transducer. The array scale of its pixels exceeded 2k × 2k. The simulation and measured results of the transient temperature and radiation intensity were well consistent. Illuminated by a 532 nm laser with a frequency of 50 Hz and 50% duty cycle, the thermal decay time of the proposed transducer was 6.0 ms. A knife-edge image was utilized for spatial resolution test and the full width at half maximum (FWHM) of the proposed transducer was 24% smaller than the traditional soft one. High-resolution infrared images were generated using the proposed robust transducer. These results proved that the robust transducer was promising in infrared image generation.
Self-discrepancies and emotional vulnerability: How magnitude, accessibility, and type of discrepancy influence affect. (1986)

Two studies examined whether the type of emotional change experienced by individuals is influenced by the magnitude and accessibility of the different types of self-discrepancies they possess. In both studies, subjects filled out a measure of self-discrepancy a few weeks prior to the experimental session. Subjects were asked to list up to 10 attributes each for different self-states--their actual self, their ideal self (their own or others' hopes and goals for them), and their ought self (their own or others' beliefs about their duty and obligations). Magnitude of self-discrepancy was calculated by comparing the attributes in the actual self to the attributes in either the ideal self or the ought self, with the total number of attribute pairs that matched being subtracted from the total number of attribute pairs that mismatched. In Study 1, subjects were asked to imagine either a positive event or a negative event and were then given a mood measure and a writing-speed task. Subjects with a predominant actual:ideal discrepancy felt more dejected (e.g., sad) and wrote more slowly in the negative event condition than in the positive event condition, whereas subjects with a predominant actual:ought discrepancy, if anything, felt more agitated (e.g., afraid) and wrote more quickly in the negative event condition. In Study 2, subjects were selected who were either high in both kinds of discrepancies or low in both. Half of the subjects in each group were asked to discuss their own and their parents' hopes and goals for them (ideal priming), and the other half were asked to discuss their own and their parents' beliefs concerning their duty and obligations (ought priming). For high-discrepancy subjects, but not low-discrepancy subjects, ideal priming increased their dejection whereas ought priming increased their agitation. The implications of these findings for identifying cognitive-motivational factors that may serve as vulnerability markers for emotional problems is discussed.
Macintosh Design to Production: The Definitive Guide (1995)

Desktop professionals turn out everything from newsletters to glossy, full-page magazines. However, many of these designers know little about the entire publishing process. This can lead to restarts, communication problems and lost time and revenues. Designed to solve this problem, this book offers helpful hints and techniques for bridging the gap between design and production.
Anion-Controlled Assembly of Porphyrin−Bicyclic Guanidine Conjugates (2001)

[reaction: see text] Cationic porphyrins 1-3 bearing one, two, and four bicyclic guanidines form highly ordered chiral assemblies in aqueous solutions. The chirality is controlled by the type of the anionic counterpart and results from a spontaneous process. The chiral assemblies of 1-3 relate structurally to the complexes of achiral porphyrins with helical DNA. However, the presence of a chiral template (DNA, poly L-Glu were tested) is not necessary for formation of these specific chiral porphyrin assemblies.
E-048 moya moya syndrome: evaluation and treatment in patients with inflammatory conditions causing a puff of smoke (2015)

<h3>Title</h3> Evaluation of Angiographic appearances of Moya Moya variants and their treatment options <h3>Purpose</h3> To familiarize the viewer with many of the different disease entities known to cause the Moya Moya angiographic phenotype and help the viewer to identify additional salient imaging findings elsewhere in the body that may help with more precise diagnosis. <h3>Approach/methods</h3> 1. Review relevant anatomy of the intracranial arterial circulation. 2. Describe the Moya Moya disease findings. 3. Describe several of the known diseases that cause Moya Moya appearance on angiography and give imaging examples of each by angiographic studies. 4. Imaging examples of pathognomonic findings in each disease entity.5. Review of imaging features that correlate with symptomatic disease where treatment is indicated. 6. Discussion of past and current treatment modalities including intracranial angioplasty, stenting and surgical bypass options. <h3>Findings/discussion</h3> The “puff of smoke” imaging findings described for moya moya can be seen with the classic Moya Moya disease which was first described in Japanese families in the 1950’s. Since that time, we have identified other disease that has similar presentations such as neurofibromatosis, lupus erytmatosis and fibromuscular dysplasia. Evaluating perfusion in asymptomatic patients as well as stroke burden in symptomatic patients have been used to guide need for treatment. Treatment of this condition has been traditionally medical with aspirin as well as surgical through bypass surgery. Endovascular stent angioplasty has been utilized for intracranial stenosis associated with Moya Moya disease although evidence for its efficacy is thin in the current literature. After SAMMPRIS and COSS trial, evidence for benefit from intracranial stents or surgical bypass for intracranial atherosclerotic disease has come into question. Surgical bypass or intracranial angioplasty may offer additional treatment options for Moya Moya disease type patients in the future. <h3>Conclusion</h3> By describing the angiographic patterns associated with Moya Moya phenomenon as well as associated symptoms we hope to elucidate the nuances of angiographic appearances in this broad clinical setting which may help narrow the differential diagnosis.. We will also discuss the treatment options and the current level of evidence for endovascular or surgical treatment. <h3>Disclosures</h3> R. Shastri: None. N. Chaudhary: None. A. Pandey: None. C. Roark: None. B. Thompson: None. J. Gemmete: None.
Multilinear algebra and parallel programming (1990)

The authors study the use of multilinear algebra in designing and implementing algorithms for linear computations. In particular, they discuss their experience in using these techniques on the Cray Y-MP and to implement Strassen's matrix multiplication algorithm on the Encore Multimax. It is concluded that the formulation of numerical algorithms in terms of the constructs of multilinear algebra, especially the tensor product, together with the coding methods presented, simplifies the writing of the programs for implementing these algorithms. By making the implementation process simpler and more mechanical, one can more easily experiment with and monitor the coding of these algorithms and thereby find better implementations. >
Editorial: Proteoglycans in the Tumor Microenvironment (2022)

The Proteoglycans (PGs) family consists of core proteins covalently attached to glycosaminoglycans (GAGs) belonging to different classes: heparan sulfates/heparin, chondroitin/dermatan sulfates, and keratan sulfate. A last family of GAGs includes the molecule hyaluronan, which is the only one not bound to a protein core nor chemically modified by sulfates. Even if hyaluronan is a unique chemical structure, it can be present within the extracellular matrix (ECM) at various molecular weights with different biological activity.
Nature of Supramolecular Complexes Controlled by the Structure of the Guest Molecules: Formation of Octa Acid Based Capsuleplex and Cavitandplex (2009)

Factors that govern inclusion of organic molecules within octa acid (OA), a synthetic deep cavity cavitand, have been delineated by examining the complexation behavior of a number of organic molecules with varying dimensions and functionalities with OA. The formation of two types of complexes has been noted: the one which we call cavitandplex is a partially open complex in which a part of the guest molecule remains exposed to water, and the other termed capsuleplex is formed through assembly of two OA molecules. In capsuleplex, the guest is protected from water. Generally, guest molecules that possess ionic head groups form cavitandplex, and all others form capsuleplex. Capsuleplex may contain one or two guest molecules within the capsule. Small organic molecules (<10 A in length) may form both 2:1 and 2:2 capsuleplex, while longer ones (>12 A) preferentially form 2:1 capsuleplex. Extensive 1H NMR experiments have been carried out to characterize host-guest complexes. In the absence of the guest, OA tends to aggregate in water. The extent of aggregation depends on the concentration of OA and the presence of salts in solution. We expect the information obtained from this study to be of great value in predicting the nature of complexes with a given guest and facilitating appropriate guest chosen by researchers.
Research on Supersonic Turbulent Separated and Reattached Flows. (1975)

Abstract : Basic research programs are reported with fundamental applications to supersonic flight. The experimental studies made use of the unique capabilities of the high Reynolds number Mach 3 facility. The experimental programs concentrated on phenomena associated with incipient separation and separation of turbulent boundary layers over a large Reynolds number range. The reattachment phenomena of a shear layer was also studied in great depth.
Coated Glass for Energy Efficient Buildings : Spectral Selectivity, Angular Dependence and Time Variability, in Functional Glasses (2013)

Coated Glass for Energy Efficient Buildings : Spectral Selectivity, Angular Dependence and Time Variability, in Functional Glasses