gebhart/patrepeval huggingface dataset:
Mineral and Matrix Changes in Brtl/+Teeth Provide Insights into Mineralization Mechanisms (2013)

The Brtl/+ mouse is a knock-in model for osteogenesis imperfecta type IV in which a Gly349Cys substitution was introduced into one COL1A1 allele. To gain insight into the changes in dentin structure and mineral composition in these transgenic mice, the objective of this study was to use microcomputed tomography (micro-CT), scanning electron microscopy (SEM), and Fourier transform infrared imaging (FTIRI) to analyze these structures at 2 and 6 months of age. Results, consistent with the dental phenotype in humans with type IV OI, showed decreased molar volume and reduced mineralized tissue volume in the teeth without changes in enamel properties. Increased acid phosphate content was noted at 2 and 6 months by FTIRI, and a trend towards altered collagen structure was noted at 2 but not 6 months in the Brtl/+ teeth. The increase in acid phosphate content suggests a delay in the mineralization process, most likely associated with the defect in the collagen structure. It appears that in the Brtl/+ teeth slow maturation of the mineralized structures allows correction of altered mineral content and acid phosphate distribution.
Pressure-Regulated Ventilator Splitting (PReVentS) – A COVID-19 Response Paradigm from Yale University (2020)

Abstract In the current COVID-19 crisis, the US and many countries in the world are suffering acute shortages of modern ventilators to care for desperately ill patients. Since modern ICU ventilators are powerful devices that can deliver very high gas flow rates and pressures, multiple physicians have attempted to ventilate more than one patient on a single ventilator – so-called “vent splitting”. Early applications of this approach have utilized simple concatenations of ventilator tubing and T-pieces, to provide flow to more than one patient. Additional approaches using custom flow splitters – sometimes made using 3D printing technologies – have also advanced into the clinic with FDA approval. However, heretofore there has been less progress made on controlling individual ventilatory pressures for patients with severe lung disease. Given the inherent variability and instability of lung compliance amongst patients with COVID-19, there remains an important need to provide a means of extending ventilator usefulness to more than one patient, but in a way that provides more tailored pressures that can be titrated over time. In this descriptive report, we provide the basis for a ventilator circuit that can support two patients with individualized peak inspiratory and end-expiratory pressures. The circuit is comprised of exclusively “off the shelf” materials and is inexpensive to produce. The circuit can be used with typical ICU ventilators, and with anesthesia ventilators used in operating rooms. Inspiratory and end-expiratory pressures for each patient can be titrated over time, without changes for one patient affecting the ventilation parameters of the other patient. Using in-line spirometry, individual tidal volumes can be measured for each patient. This Pressure-Regulated Ventilator Splitting (PReVentS) Yale University protocol operates under a pressure-control ventilatory mode, and may function optimally when patients are not triggering breaths from the ventilator. This method has been tested thus far only in the laboratory with mock lungs, and has not yet been deployed in animals or in patients. However, given the novelty and potential utility of this approach, we deemed it appropriate to provide this information to the broader critical care community at the present time. In coming days and weeks, we will continue to characterize and refine this approach, using large animal models and proof-of-principle human studies.
Isolation of Differentially Expressed cDNAs During Ferret Tracheal Development: Application of Differential Display PCR (1996)

The technique of differential display polymerase chain reaction (DD-PCR) was used to identify cDNA sequences, which are temporally expressed during ferret tracheal airway development. Such differentially expressed cDNAs may ultimately prove to be useful markers in elucidating mechanisms of epithelial differentiation and submucosal gland development in the airway. Using two sets of oligonucleotide primers 15 differentially amplified cDNAs were isolated by comparative reverse transcriptase (RT) PCR of 6-h and 3-day postnatal tracheal poly-A mRNA. In situ hybridization was used to assess the reliability of this method and confirm the differential mRNA expression patterns of cloned cDNAs. Results of in situ hybridization analysis demonstrated that 10 of the 15 cDNA sequences gave a temporally regulated pattern of expression, which was concordant with that of the differential display. Furthermore, sequence analysis of the 15 isolated cDNAs revealed that the majority of clones were amplified from two inverted decamer primers. These findings demonstrate the lack of poly-T priming in the differential display reaction, which suggests that this method may yield substantially more information regarding the coding sequence of cloned genes. In support of this observation, 6 of the 15 cDNA sequences contained one complete open reading frame. Although the majority of cDNAs demonstrated no homology to sequence data bases at the DNA or amino acid level, clone FT-4, which demonstrated a differential expression pattern limited to 3-day tracheal time points, was composed of a 10-amino acid repeat domain that was structurally similar to neuropeptide anthoRFamide and barley D hordein seed protein. A second interesting clone, FT-3, demonstrated an infrequent pattern of expression within a subset of epithelial cells limited to early developmental time points (6 h) and was dramatically reduced by 3 days postnatally. Several additional clones with no homologies to previously cloned genes demonstrated expression patterns that were also temporally regulated throughout tracheal development. Although the function of these temporally regulated genes has not been determined, these genes may ultimately prove to be useful markers of cellular differentiation during tracheal development.
Perovskite Supported Catalysts for the Selective Oxidation of Glycerol to Tartronic Acid (2022)

Abstract Exceptional selectivity of LaMnO 3 perovskite supported Au catalysts for the oxidation of glycerol to the dicarboxylate tartronic acid is reported. Through using monometallic Au, Pt or bimetallic Au:Pt nanoparticles the tartronic acid yield could be altered significantly, with a maximum yield of 44% in 6 h with Au/LaMnO 3 and 80% within 24 h. These LaMnO 3 supported catalysts were compared with conventionally TiO 2 supported catalysts, which at comparable reaction conditions produced lactic acid, via a dehydration pathway, in high yield and a maximum tartronic acid yield of only 9% was observed. The LaMnO 3 catalysts produced minimal lactic acid regardless of the supported metal, showing that the support structure influences the prevalence of dehydration and oxidation pathways. The choice of metal nanoparticle influenced product selectivity along the oxidation pathway for both LaMnO 3 and TiO 2 supported catalysts. Au catalysts exhibited a higher selectivity to tartronic acid, whereas AuPt catalysts produced glyceric acid and Pt catalysts produced predominantly C–C scission products. Graphical Abstract
Configuring intracortical microelectrode arrays and stimulus parameters to minimize neuron loss during prolonged intracortical electrical stimulation (2021)

Neuron loss due to stimulation was minimal at Q = 2 Ncp, but at 8 Ncp, 20%-50% of neurons within 250 μm of the stimulated microelectrodes were lost, compared to unstimulated microelectrodes. Loss was greatest in tissue facing electrode sites. Stimulation-induced loss was similar for neurons labeled for NeuN and for inhibitory neurons expressing parvalbumin. Correlation between neuron loss and QD was not significant. Electrodes in the medullary pyramidal tract recorded neuronal activity evoked by stimulation in the cerebral cortex. The pyramidal neurons were activated by intracortical stimulation of 2 nC/phase. 140 h of microstimulation at 2 nC/phase and 50 Hz induced minimal neuron loss.
The usefulness of diffusion‐weighted readout‐segmented EPI and fast spin echo with BLADE (PROPELLER) k‐space sampling: A comparison with single‐shot EPI for diffusion‐weighted imaging in ischemic stroke patients (2016)

ABSTRACT We evaluated the value of diffusion‐weighted readout‐segmented EPI (DW rs‐EPI) and diffusion‐weighted fast spin echo images with BLADE (PROPELLER) k ‐space sampling (DW BLADE) in patients with ischemic stroke through intra‐individual comparisons with diffusion‐weighted single‐shot EPI (DW ss‐EPI). Forty‐four patients with acute ischemic stroke who had undergone three different types of diffusion weighted imaging (DWI) ( b = 1000 s/mm 2 ) were included. Two reviewers assessed the three types of DWI for diagnostic confidence based on a five‐point confidence score (CS). The inter‐ and intra‐observer agreements for the CS were assessed. The DWI signal ratio to the contralateral normal area and the apparent diffusion coefficient (ADC) of DWI lesions were compared. The CSs of the three DWI methods were significantly different ( P &lt; 0.001). A post hoc analysis showed a significantly higher CS with DW rs‐EPI than with DW ss‐EPI ( P = 0.022). There were significant increases in the CSs for DW rs‐EPI compared to DW ss‐EPI, for patients who underwent DWI within 24 h of symptom onset, and for patients with DWI lesions ≤ 50 mm 2 . The inter‐observer and intra‐observer agreements of the CS were good. DW rs‐EPI increased the diagnostic confidence of ischemic stroke compared to DW ss‐EPI, particularly for patients with small lesions and for those who underwent DWI within 24 h of symptom onset. DW BLADE showed a similar level of diagnostic confidence to DW ss‐EPI. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 216–224, 2016
Aminated glycidyl methacrylates as a support media for goethite nanoparticle enabled hybrid sorbents for arsenic removal: From copolymer synthesis to full-scale system modeling (2016)

To achieve short mass transfer zones that enable arsenic removal under high hydraulic loading rates and short empty bed contact times needed for small point-of-use packed bed applications, hybrid media was developed and tested. Cross-linked macroporous glycidyl methacrylate copolymer support media was synthetized, amino modified and in-situ impregnated by goethite nanoparticles via an oxidative deposition in a hydrophilic/hydrophobic (water/xylene) system. The media properties were characterized via scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDS), X-ray diffraction (XRD), and surface area analysis. Arsenic removal capabilities of the hybrid goethite impregnated media were evaluated by conducting batch sorption tests, developing isotherms and simulating the breakthrough curve with a pore surface diffusion model (PSDM), after being verified by a short bed column (SBC) test. The high porous media (e p ≈ 0.7) contained ∼16% of iron and exhibited Freundlich adsorption capacity parameter of K ≈ 369 (µg g −1 )(L µg −1 ) 1/n and Freundlich intensity parameter of 1/n ≈ 0.54. Without engaging in taxing pilot scale testing, the PSDM was able to provide a good prediction of the media's capacity and intraparticle mass transport properties under high hydraulic loading rates.
Chiral Supraparticles for Controllable Nanomedicine (2019)

Chirality is ubiquitous in nature and hard-wired into every biological system. Despite the prevalence of chirality in biological systems, controlling biomaterial chirality to influence interactions with cells has only recently been explored. Chiral-engineered supraparticles (SPs) that interact differentially with cells and proteins depending on their handedness are presented. SPs coordinated with d-chirality demonstrate greater than threefold enhanced cell membrane penetration in breast, cervical, and multiple myeloma cancer cells. Quartz crystal microbalance with dissipation and isothermal titration calorimetry measurements reveal the mechanism of these chiral-specific interactions. Thermodynamically, d-SPs show more stable adhesion to lipid layers composed of phospholipids and cholesterol compared to l-SPs. In vivo, d-SPs exhibit superior stability and longer biological half-lives likely due to opposite chirality and thus protection from endogenous proteins including proteases. This work shows that incorporating d-chirality into nanosystems enhances uptake by cancer cells and prolonged in vivo stability in circulation, providing support for the importance of chirality in biomaterials. Thus, chiral nanosystems may have the potential to provide a new level of control for drug delivery systems, tumor detection markers, biosensors, and other biomaterial-based devices.
A power-scalable linearized model for RF power amplifiers starting from S-parameter measurements (2009)

A method is proposed to estimate the dasiabest linear approximationpsila of RF power amplifiers excited by spectrally rich signals under variable input power levels. Since the input-output behavior of these amplifiers is not only a function of the frequency, but also of the input power, a 2-dimensional model that linearizes the behavior will be needed. The proposed method estimates a 2D rational model in the frequency variable jomega and the input power P. The proposed approach is suitable for the experimental characterization of existing RF power amplifiers.
Distributed Symbolic Bounded Property Checking (2006)

In this paper we describe an algorithm for distributed, BDD-based bounded property checking and its implementation in the verification tool SymC. The distributed algorithm verifies larger models and returns results faster than the sequential version. The core algorithm distributes partitions of the state set to computation nodes after reaching a threshold size. The nodes proceed with image computation on the nodes asynchronously. The main scalability problem of this scheme is the overlap of state set partitions. We present static and dynamic overlap reduction techniques.
Production of 5-hydroxymethylfurfural and furfural by dehydration of biomass-derived mono- and poly-saccharides (2007)

Furan derivatives, such as 5-hydroxymethylfurfural (HMF) and furfural, obtained from renewable biomass-derived carbohydrates have potential to be sustainable substitutes for petroleum-based building blocks used in production of fine chemicals and plastics. We have studied the production of HMF and furfural by dehydration of fructose, glucose and xylose using a biphasic reactor system, comprised of reactive aqueous phase modified with DMSO, combined with an organic extracting phase consisting of a 7 : 3 (w/w) MIBK–2-butanol mixture or dichloromethane (DCM). Experiments with the MIBK–2-butanol mixture were conducted at a temperature of 443 K using mineral acid catalysts (HCl, H2SO4 and H3PO4) at a pH from 1.0 to 2.0, whereas experiments with DCM as the extracting solvent were conducted at 413 K and did not require the use of an acid catalyst. The modifiable nature of the biphasic system allowed us to identify preferred DMSO and pH levels for each sugar to maximize the HMF selectivity at high sugar conversions, leading to selectivities of 89%, 91%, and 53% for dehydration of fructose, xylose, and glucose, respectively. Using these reaction conditions for each monosaccharide unit, we can process the corresponding polysaccharides, such as sucrose (a disaccharide of glucose and fructose), inulin (a polyfructan), starch (a polyglucan), cellobiose (a glucose dimer) and xylan (a xylose polysaccharide), with equally good selectivities at high conversions. In addition, we show that the biphasic reactor system can process high feed concentrations (10 to 30 wt%) along with excellent recycling ability. By processing these highly functionalized polysaccharides, that are inexpensive and abundantly available, we eliminate the need to obtain simple carbohydrate molecules by acid hydrolysis as a separate processing step.
Risk of Cardiovascular and All-Cause Mortality in Individuals With Diabetes Mellitus, Impaired Fasting Glucose, and Impaired Glucose Tolerance (2007)

This study emphasizes the strong association between abnormal glucose metabolism and mortality, and it suggests that this condition contributes to a large number of CVD deaths in the general population. CVD prevention may be warranted in people with all categories of abnormal glucose metabolism.
Helical Semiquinones: Proof of Chirality by ENDOR Spectroscopy (1991)

Diastereomers of paramagnetic Sn semiquinone complexes of type 1 (the P,S isomer is shown on the right) can be distinguished at 213 K by ENDOR spectroscopy; this finding establishes unequivocally the helicity of 4,5-disubstituted phenanthrene semiquinones. The activation barrier for racemization of the phenanthrene moiety (coalescence temperature of 240 K) is appreciably lower that those of the corresponding quinones; it is also strongly dependent on the charge of the complex.
High-resolution microelectromechanical scanners for miniaturized dual-axes confocal microscopes (2005)

In this paper we present scanning micromirrors, actuated by self-aligned, bidirectional, vertical electrostatic combdrives, for dual-axes confocal microscopy. The fabrication process, which is based on Deep Reactive Ion Etching (DRIE) of Silicon-on-insulator (SOI) wafers with two silicon device layers, requires only three lithography steps for one-dimensional scanners, while an additional two lithography steps must be performed to create two-dimensional scanners. Only front side processing is required and the two oxide layers of the double SOI wafers provide efficient and reliable etch stops. These features combined with the fact that the combs are self aligned, enable high-speed, high-resolution microscanners with stable and reliable operation as required for endoscopic implementations of confocal microscopes.
Analysis of the effect of mechanical strength of the resist film on pattern collapse behavior using atomic force microscope (2006)

Recently, pattern collapse is becoming one of the critical issues in semiconductor manufacturing and many works have been done to solve this issue<sup>1</sup>) <sup>2</sup>). Since pattern collapse occurs when outer force onto the resist pattern such as surface tension, impact of rinse solution, etc. surpasses the resistance of the resist pattern such as mechanical strength, adhesion force between resist and substrate, it is considered effective for improvement of pattern collapse to control resist film properties by track process, i.e., optimization of the mechanical properties of the resist film and enhancement of the adhesion force between resist and substrate<sup>3</sup>) <sup>-5</sup>). In this study, we focused on the mechanical strength of the resist film and examined how post applied bake (PAB) condition affects the pattern collapse behavior. From ellipsometry measurement, it was found that increasing PAB time and temperature resulted in thickness reduction and refractive index increase, which suggested that the density of the resist film became high. Then we analyzed the mechanical strength of the resist film with the tip indentation method using atomic force microscope. It was found that the hardness of the resist film was affected by PAB conditions and regardless of PAB condition, hardened layer existed beneath the film surface. Finally, we carried out the measurements of loads to collapse 180nm resist dot patterns using the direct peeling with atomic force microscope tip (DPAT) method. Loads ranged from 600 to 2000nN overall and essentially increased as seen for indentation measurements when PAB temperature or time was increased, except some critical conditions. Through these evaluations using AFM, we succeeded in quantitatively evaluate the mechanical properties of the resist films processed with various PAB conditions. It was found that PAB condition obviously impacts on the hardness of the resist film and it is closely related to pattern collapse load.
Computational design of genes encoding completely overlapping protein domains: Influence of genetic code and taxonomic rank (2020)

Abstract Overlapping genes (OLGs) with long protein-coding overlapping sequences are often excluded by genome annotation programs, with the exception of virus genomes. A recent study used a novel algorithm to construct OLGs from arbitrary protein domain pairs and concluded that virus genes are best suited for creating OLGs, a result which fitted with common assumptions. However, improving sequence evaluation using Hidden Markov Models shows that the previous result is an artifact originating from dataset-database biases. When parameters for OLG design and evaluation are optimized we find that 94.5% of the constructed OLG pairs score at least as highly as naturally occurring sequences, while 9.6% of the artificial OLGs cannot be distinguished from typical sequences in their protein family. Constructed OLG sequences are also indistinguishable from natural sequences in terms of amino acid identity and secondary structure, while the minimum nucleotide change required for overprinting an overlapping sequence can be as low as 1.8% of the sequence. Separate analysis of datasets containing only sequences from either archaea, bacteria, eukaryotes or viruses showed that, surprisingly, virus genes are much less suitable for designing OLGs than bacterial or eukaryotic genes. An important factor influencing OLG design is the structure of the standard genetic code. Success rates in different reading frames strongly correlate with their code-determined respective amino acid constraints. There is a tendency indicating that the structure of the standard genetic code could be optimized in its ability to create OLGs while conserving mutational robustness. The findings reported here add to the growing evidence that OLGs should no longer be excluded in prokaryotic genome annotations. Determining the factors facilitating the computational design of artificial overlapping genes may improve our understanding of the origin of these remarkable genetic constructs and may also open up exciting possibilities for synthetic biology.