gebhart/patrepeval huggingface dataset:
Healing of Tendon Defects Implanted with a Porous Collagen-GAG Matrix: Histological Evaluation (1997)

There is currently no method to restore normal function in tendon injuries that result in a gap. The objective of this study was to evaluate the early healing of tendon defects implanted with a porous collagen–glycosaminoglycan (CG) matrix, previously shown to facilitate the regeneration of dermis and peripheral nerve. A novel animal model that isolates the tendon defect site from surrounding tissue during healing was employed. This model used a silicone tube to entubulate the surgically produced tendon gap of 10 mm, allowing for the evaluation of the effects of the analog of extracellular matrix on healing of tendon, absent the influences of the external environment. The results showed that tendon stumps induced synthesis of a tissue cable inside the silicone tube in both the presence and absence of CG matrix. The presence of the CG matrix, however, altered the process of tendon healing. Tubes filled with CG matrix contained a significantly greater volume of tissue at the time periods of evaluation: 3, 6, and 12 weeks. Granulation tissue persisted for a longer period of time in the lesion site of CG-filled defects, and the amount of dense fibrous tissue increased continuously during the period of study in defects filled with CG matrix. In contrast, the amount of dense fibrous tissue decreased after 6 weeks in originally empty tubes. In tubes that did not contain the CG matrix, the new tissue consisted of dense aggregates of crimped fibers with a wavelength and fiber bundle thickness that were significantly shorter than those in normal tendon, and consistent with the type of scar that is the end result of repair of many connective tissues. Although, CG-filled tubes contained dense fibrous tissue by 12 weeks, the tissue had no crimp. The CG matrix may have prolonged the synthesis of granulation tissue and delayed or prevented the formation of scar.
Antigen Targeting to Human HLA Class II Molecules Increases Efficacy of DNA Vaccination (2016)

It has been difficult to translate promising results from DNA vaccination in mice to larger animals and humans. Previously, DNA vaccines encoding proteins that target Ag to MHC class II (MHC-II) molecules on APCs have been shown to induce rapid, enhanced, and long-lasting Ag-specific Ab titers in mice. In this study, we describe two novel DNA vaccines that as proteins target HLA class II (HLA-II) molecules. These vaccine proteins cross-react with MHC-II molecules in several species of larger mammals. When tested in ferrets and pigs, a single DNA delivery with low doses of the HLA-II-targeted vaccines resulted in rapid and increased Ab responses. Importantly, painless intradermal jet delivery of DNA was as effective as delivery by needle injection followed by electroporation. As an indication that the vaccines could also be useful for human application, HLA-II-targeted vaccine proteins were found to increase human CD4<sup>+</sup> T cell responses by a factor of ×10<sup>3</sup> in vitro. Thus, targeting of Ag to MHC-II molecules may represent an attractive strategy for increasing efficacy of DNA vaccines in larger animals and humans.
Modeling, simulation, and optimization of a front-end system for acetylene hydrogenation reactors (2004)

The modeling, simulation, and dynamic optimization of an industrial reaction system for acetylene hydrogenation are discussed in the present work. The process consists of three adiabatic fixed-bed reactors, in series, with interstage cooling. These reactors are located after the compression and the caustic scrubbing sections of an ethylene plant, characterizing a front-end system; in contrast to the tail-end system where the reactors are placed after the de-ethanizer unit. The acetylene conversion and selectivity profiles for the reactors are optimized, taking into account catalyst deactivation and process constraints. A dynamic optimal temperature profile that maximizes ethylene production and meets product specifications is obtained by controlling the feed and intercoolers temperatures. An industrial acetylene hydrogenation system is used to provide the necessary data to adjust kinetics and transport parameters and to validate the approach.
Plasma etching of III–V semiconductors in CH4/H2/Ar electron cyclotron resonance discharges (1990)

We have investigated the etch rates, residual lattice damage, surface morphologies, and chemistries of InP, InGaAs, AlInAs, and GaAs plasma etched in electron cyclotron resonance (ECR) CH4/H2/Ar discharges. The etch rates of InP and InGaAs increase linearly with additional rf biasing of the substrate, and are approximately a factor of 2 faster than for GaAs. Under our conditions the etch rate of Al0.52Ga0.48As is very low (∼25 Å min−1) even for the addition of 100 V rf bias. In all of these materials the residual damage layer remaining after dry etching is very shallow (∼20 Å) as evidenced from Schottky barrier height and photoluminescence measurements combined with wet chemical etching. InP shows significant P depletion with the addition of rf biasing during the ECR etching while GaAs retains a near-stoichiometric surface. Hydrogen passivation of shallow donors in n-type GaAs occurs to a depth of ∼3000 Å during exposure to the CH4/H2/Ar discharge for long periods (60 min). The surface morphologies in the In-based materials become roughened for etching with the addition of rf biasing while GaAs displays smooth, residue-free surfaces under these conditions.
ORGANIC MEMRISTOR DEVICES FOR LOGIC ELEMENTS WITH MEMORY (2012)

Memristors are promising next-generation memory candidates that are nonvolatile, possess low power requirements and are capable of nanoscale fabrication. In this article, we physically realize and describe the use of organic memristors in designing stateful boolean logic gates for the AND OR and NOT operations. The output of these gates is analog and dependent on the length of time that suitable charge is applied to the inputs, displaying a learning property. Results may be also interpreted in a traditional binary manner through the use of a suitable thresholding function at the output. The memristive property of the gate allows for the production of analog outputs that vary based on the charge-dependent nonvolatile state of the memristor. We provide experimental results of physical fabrication of three types of logic gate. A simulation of a one-bit full adder comprised of memristive logic gates is also included, displaying varying response to two distinct input patterns.
Analysis of the Female Gametophyte Transcriptome of Arabidopsis by Comparative Expression Profiling (2005)

The extensive data on the transcription of the plant genome are derived primarily from the sporophytic generation. There currently is little information on genes that are expressed during female gametophyte development in angiosperms, and it is not known whether the female gametophyte transcriptome contains a major set of genes that are not expressed in the sporophyte or whether it is primarily a subset of the sporophytic transcriptome. Because the embryo sac is embedded within the maternal ovule tissue, we have utilized the Arabidopsis (Arabidopsis thaliana) mutant sporocyteless that produces ovules without embryo sacs, together with the ATH1 Arabidopsis whole-genome oligonucleotide array, to identify genes that are preferentially or specifically expressed in female gametophyte development. From analysis of the datasets, 225 genes are identified as female gametophyte genes, likely a lower limit as stringent criteria were used for the analysis, eliminating many low expressed genes. Nearly 45% of the identified genes were not previously detected by sporophytic expression profiling, suggesting that the embryo sac transcriptome may contain a significant fraction of transcripts restricted to the gametophyte. Validation of six candidate genes was performed using promoterbeta-glucuronidase fusions, and all of these showed embryo sac-specific expression in the ovule. The unfiltered expression data from this study can be used to evaluate the possibility of female gametophytic expression for any gene in the ATH1 array, and contribute to identification of the functions of the component of the Arabidopsis genome not represented in studies of sporophytic expression and function.
Neurocontroller for unknown systems using simultaneous perturbation (2003)

Describes a neurocontroller via the simultaneous perturbation learning rule to control an unknown plant. When we apply a direct inverse control scheme by a neural network, the neural network must learn an inverse system of the objective unknown plant. When we use a kind of gradient method as a learning rule of the neural network, the Jacobian of the plant is required. On the other hand, our control scheme described here does not require information about the plant Jacobian, because the simultaneous perturbation method estimates the gradient using only values of the error defined by output of the plant and its desired one. A regulation problem for a flexible beam is handled to confirm the feasibility of the method.
Human 'pregnancy-associated endometrial α1-globulin', an insulin-like growth factor-binding protein: immunohistological localization in the decidua and placenta during pregnancy employing monoclonal antibodies (1989)

We have previously shown that pregnancy-associated endometrial alpha 1-globulin, a small molecular weight insulin-like growth factor-binding protein (IGF-BP), is quantitatively the major secretory protein product of the decidualized endometrium during human pregnancy. In the present study, employing monoclonal antibodies raised against this protein in an immunohistological technique, the cellular localization of the protein has been examined in the decidua and placenta during pregnancy. During the first trimester the protein was principally associated with the decidual cell in the decidualized decidua compacta region of the endometrium with both cytoplasmic and extracellular matrix-associated staining patterns being detected. No extensive staining was observed in the placenta. At term the protein was localized in similar cells in the placental bed and endometrium associated with the amniochorion but not in the placenta. These studies suggest that the decidual cell represents the major source of IGF-BP during pregnancy and have relevance to the origin of amniotic fluid IGF-BP and the paracrine role of the decidual cell in the control of trophoblast growth.
<title>Mechanism of laser-induced solubility reduction of dental enamel</title> (1997)

Several studies in our laboratories have demonstrated that CO<SUB>2</SUB> laser treatment of dental enamel can inhibit subsequent caries-like progression from 10-75 percent compared to controls. The present study tested the hypothesis that laser radiation at specific wavelengths is absorbed by the mineral, converted efficiently to heat at the surface, causing thermal decomposition of the carbonated apatite enamel crystals to a less soluble form. Samples of enamel 5 X 5 mm were examined before and after laser irradiation by specular reflectance FTIR. Sample surfaces were irradiated by pulsed CO<SUB>2</SUB> laser at 9.3, 9.6, 10.3 or 10.6 micrometers , 100 microsecond(s) pulse duration, 25 pulses per spot, with fluences of 0-6 J/cm<SUP>2</SUP>. In separate experiments surface temperatures were measured dependent, and fluence dependent, with total loss occurring with 9.6 micrometers irradiation occurred at 4 J/cm<SUP>2</SUP>. Optimum inhibition of caries progression following 9.6 micrometers irradiation occurred at 4 J/cm<SUP>2</SUP>. We conclude that irradiation of dental enamel by specific wavelengths and fluences of CO<SUB>2</SUB> laser light alters the chemical composition of the crystals, decomposing the CO<SUB>3</SUB> component, thereby markedly reducing the reactivity.
A binary single-key-lock system for access control (1989)

A binary coding method was invented and has been applied to the single-key-lock (SKL) system which achieves access control by associating with each accesser only one key and with each resource only one lock. The new system is called the binary single-key-lock (BSKL) system. In both the SKL and BSKL systems, through operations on the single-key-lock pair, the control information can be revealed. On the basis of the new binary coding method, and because binary operations are much faster, better performance for such an access control system can be achieved. The increased extensibility of the modification is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Advancing of Zinc Oxide Nanoparticles for Biomedical Applications (2018)

Zinc oxide nanoparticles (ZnO NPs) are used in an increasing number of industrial products such as rubber, paint, coating, and cosmetics. In the past two decades, ZnO NPs have become one of the most popular metal oxide nanoparticles in biological applications due to their excellent biocompatibility, economic, and low toxicity. ZnO NPs have emerged a promising potential in biomedicine, especially in the fields of anticancer and antibacterial fields, which are involved with their potent ability to trigger excess reactive oxygen species (ROS) production, release zinc ions, and induce cell apoptosis. In addition, zinc is well known to keep the structural integrity of insulin. So, ZnO NPs also have been effectively developed for antidiabetic treatment. Moreover, ZnO NPs show excellent luminescent properties and have turned them into one of the main candidates for bioimaging. Here, we summarize the synthesis and recent advances of ZnO NPs in the biomedical fields, which will be helpful for facilitating their future research progress and focusing on biomedical fields.
The PARN Deadenylase Targets a Discrete Set of mRNAs for Decay and Regulates Cell Motility in Mouse Myoblasts (2012)

PARN is one of several deadenylase enzymes present in mammalian cells, and as such the contribution it makes to the regulation of gene expression is unclear. To address this, we performed global mRNA expression and half-life analysis on mouse myoblasts depleted of PARN. PARN knockdown resulted in the stabilization of 40 mRNAs, including that encoding the mRNA decay factor ZFP36L2. Additional experiments demonstrated that PARN knockdown induced an increase in Zfp36l2 poly(A) tail length as well as increased translation. The elements responsible for PARN-dependent regulation lie within the 3' UTR of the mRNA. Surprisingly, changes in mRNA stability showed an inverse correlation with mRNA abundance; stabilized transcripts showed either no change or a decrease in mRNA abundance. Moreover, we found that stabilized mRNAs had reduced accumulation of pre-mRNA, consistent with lower transcription rates. This presents compelling evidence for the coupling of mRNA decay and transcription to buffer mRNA abundances. Although PARN knockdown altered decay of relatively few mRNAs, there was a much larger effect on global gene expression. Many of the mRNAs whose abundance was reduced by PARN knockdown encode factors required for cell migration and adhesion. The biological relevance of this observation was demonstrated by the fact that PARN KD cells migrate faster in wound-healing assays. Collectively, these data indicate that PARN modulates decay of a defined set of mRNAs in mammalian cells and implicate this deadenylase in coordinating control of genes required for cell movement.
Comparison of modified New York City medium with Martin-Lewis Medium for recovery of Neisseria gonorrhoeae from clinical specimens (1980)

A modified formulation of New York City medium was comparatively evaluated with Martin-Lewis medium for the recovery of Neisseria gonorrhoeae from clinical specimens. A total of 240 strains of gonococci were recovered from 1,250 specimens collected from walk-in patients attending a sexually transmitted disease clinic. N. gonorrhoeae was cultivated on both of these media from 182 clinical specimens with an additional 58 gonococcal strains isolated on either of the media. Of these discrepant gonococcal isolates, 27 strains were recovered on only modified New York City medium, whereas the remaining 31 strains were recovered on only Martin-Lewis agar. The differences in these isolation rates were not statistically significant. The overall results showed that modified New York City and Martin-Lewis media were comparable in their ability to grow gonococci from clinical material. Since modified New York City medium is capable of supporting the growth of N. gonorrhoeae, Mycoplasma pneumoniae, and urogenital mycoplasmas and inhibiting the growth of commensal microorganisms, it is possible that it may have considerable application as a multifunctional plating medium within the clinical laboratory.
HYDROGENATION OF D-GLUCOSE TO D-MANNITOL USING RANEY NICKEL CATALYST (2009)

Hydrogenation of D-glucose in the presence of Raney nickel as a catalyst was employed for the preparation of D-mannitol. The effects of the reaction time (15-115 min), reaction temperature (15-65 oC), and catalyst to D-glucose ratio (3-11 %) on the yield of D-mannitol were studied. The experimental design of Box-Wilson method was adopted to find a useful relationship between the effecting variables and the D-mannitol yield. The experimental data collected by this design was successively fitted to a second order polynomial mathematical model. The analysis of variance shows that the reaction time had the greatest effect on the yield of D-mannitol among other variables. An optimum operating conditions of 115 min reaction time, 50 ˚C reaction temperature, and 3 % catalyst to D-glucose ratio gave 14.01 % D-mannitol yield, 81.34 % D-sorbitol yield, and 94.9 % D-glucose conversion. D-Mannitol of purity 99.7 % was obtained after its separation from D-sorbitol, the second product of the hydrogenation process, using the fractional crystallization method
The polychromatic <i>Helitron</i> landscape of the maize genome (2009)

Maize Helitron transposons are intriguing because of their notable ability to capture gene fragments and move them around the genome. To document more extensively their variability and their contribution to the remarkable genome structure variation of present-day maize, we have analyzed their composition, copy number, timing of insertion, and chromosomal distribution. First, we searched 2.4 Gb of sequences generated by the Maize Genome Sequencing Project with our HelitronFinder program. We identified 2,791 putative nonautonomous Helitrons and manually curated a subset of 272. The predicted Helitrons measure 11.9 kb on average and carry from zero to nine gene fragments, captured from 376 different genes. Although the diversity of Helitron gene fragments in maize is greater than in other species, more than one-third of annotated Helitrons carry fragments derived from just one of two genes. Most members in these two subfamilies inserted in the genome less than one million years ago. Second, we conducted a BLASTN search of the maize sequence database with queries from two previously described agenic Helitrons not detected by HelitronFinder. Two large subfamilies of Helitrons or Helitron-related transposons were identified. One subfamily, termed Cornucopious, consists of thousands of copies of an approximately 1.0-kb agenic Helitron that may be the most abundant transposon in maize. The second subfamily consists of >150 copies of a transposon-like sequence, termed Heltir, that has terminal inverted repeats resembling Helitron 3' termini. Nonautonomous Helitrons make up at least 2% of the maize genome and most of those tested show +/- polymorphisms among modern inbred lines.
Three-Dimensional Morphology and Platelet Adhesion on Pyrolytic Carbon Heart Valve Materials (1995)

Low-temperature isotropic pyrolytic carbon (LTIC) is the preferred material for mechanical heart valve prosthetics due to its durability and good thromboresistance, although thromboembolic complications remain a significant clinical problem. LTlC morphology has been previously studied using scanning (SEM) and transmission electron microscopy (TEM), and scanning tunneling microscopy (STM). However, these microscopies have limitations with imaging rough surfaces. In this study, LTIC valve leaflets from CarboMedics, Inc. and St. Jude Medical, Inc. were prepared and polished exactly as used in clinical prosthetics, and examined at magnifications up to macromolecular resolution using stereo-pair low-voltage SEM (LV -SEM). LV -SEM reveals that LTIC leaflets have a complex topography of 10 nm to 1 ~m features, with height differences of 100- 500 nm occurring over lateral distances of 10-50 nm. Compared to previous reports using conventional SEM and STM, LV -SEM shows a much rougher surface. In contrast to studies that have reported minimal platelet interaction with LTIC, very ex tensive adhesion and spreading were observed. That our observations are different from previous reports may be ex plained by the physics of SEM image formation at low and conventional (higher) accelerating voltages. Due to the low atomic density of LTIC and platelets, obscuration of small features due to specimen coatings, and since platelets closely follow LTIC's three-dimensional contours, the surface sensitivity of conventional SEM is unable to provide sufficient contrast to image either the material topography or thin adherent platelets. These results suggest that the ex tent of platelet interaction on L TIC vascular prosthetics may have been previously underestimated .
The Effect of Charge on Cellular Uptake and Phototoxicity of Polylysine Chlorin<i><sub>e6</sub></i>Conjugates (1997)

The effect of charge on the cellular uptake, localization and phototoxicity of conjugates between chlorin(e6) (ce6) and poly-L-lysine was studied in vitro. These conjugates (average MW 35-55 kDa) were synthesized to have polycationic, polyanionic or neutral charges. Two human cell lines (A431 epidermoid carcinoma cells and EA.hy926 hybrid endothelial cells) were studied and the cellular uptake of ce6 delivered by the conjugates of varying charge and free ce6 was measured at conjugate ce6 equivalent concentrations up to 0.4 microM. Uptake was time and concentration dependent and temperature dependent in the case of neutral and anionic conjugates. Relative uptake at 6 h for A431 cells was 73:15:4:1 and for EA.hy926 cells was 63:11:3:1 for cationic, anionic, neutral and free ce67 respectively, but EA.hy926 cells took up 1.5-2 times as much ce6 from all the conjugates as A431 cells. Localization as studied by fluorescence microscopy indicated that the cationic conjugate was in aggregates bound to the plasma membrane, while the other forms were internalized in organelles and membranes. Phototoxicity was measured by 3-(4,5-dimethylthiazol-2-yl)-diphenyltetrazolium bromide (MTT) assay after irradiation with 5-20 J cm2 of 666 nm light. In contrast to the uptake, the order of phototoxicity for both cell types per mole of ce6 uptake per cell was neutral >> anionic > cationic > free ce6. Polymeric ce6 conjugates bearing positive, negative and neutral charges may have different tissue-localizing properties and could play a role in photodynamic therapy.
(E)-Selective Horner–Wadsworth–Emmons reaction of aldehydes with bis-(2,2,2-trifluoroethyl)phosphonoacetic acid (2003)

The stereoselective Horner-Wadsworth-Emmons reaction of aldehydes with bis-(2,2,2trifluoroethyl)phosphonoacetic acid utilizing i-PrMgBr afforded (E)-,-unsaturated carboxylic acids as the major products. bis-(2,2,2-Trifluoroethyl)phosphonoacetic acid was prepared by enzymatic hydrolysis of the corresponding methyl ester with porcine liver esterase.