gebhart/patrepeval huggingface dataset:
Micro- and Nanoengineering Approaches to Control Stem Cell-Biomaterial Interactions (2011)

As our population ages, there is a greater need for a suitable supply of engineered tissues to address a range of debilitating ailments. Stem cell based therapies are envisioned to meet this emerging need. Despite significant progress in controlling stem cell differentiation, it is still difficult to engineer human tissue constructs for transplantation. Recent advances in micro- and nanofabrication techniques have enabled the design of more biomimetic biomaterials that may be used to direct the fate of stem cells. These biomaterials could have a significant impact on the next generation of stem cell based therapies. Here, we highlight the recent progress made by micro- and nanoengineering techniques in the biomaterials field in the context of directing stem cell differentiation. Particular attention is given to the effect of surface topography, chemistry, mechanics and micro- and nanopatterns on the differentiation of embryonic, mesenchymal and neural stem cells.
Glucosylation of Human Collagen (1982)

Many of She debilities that characterize the aging syndrome can be explained by cross-linking of macromol-ecules such as collagen. And several of the characteristic complications of diabetes mellitus resemble age-like changes in collagen-rich tissues. In this laboratory, studies of human collagen that is not the site of lesions have revealed an age-related decrease in susceptibility to collagenase digestion and increased glucosylation of tendon collagen, both markedly increased in diabetes. An age-related decrease in solubility and an increase in glucosylation of skin collagen, both also markedly increased in diabetes, were also observed. Glucosylation of skin collagen was less than that of tendon, possibly because of the greater turnover of skin collagen. Collagen alterations in diabetes were most apparent in samples from younger adult subjects. Samples from older diabetics gave values within the range of nondiabetics, suggesting that the degree to which collagen can be cross-linked or glucosyiated is limited, and that limits may be attained at earlier ages in diabetes. The association between glucosylation and cross-linking of collagen suggests that glucosylation may cause cross-linking, as has been shown to occur in albumin and eye lens protein. Both the cross-linking of collagen occurring in maturation and glucosylation of protein involve the -amino group of lysine. If blood glucose is high during periods of collagen synthesis, namely during growth or fi-brosis, it is conceivable that lysine and hydroxylysine are glucosyiated rather than deaminated to form normal cross-links, and that an abnormal collagen forms that plays a role in the complications of diabetes. Control of diabetes during periods of collagen synthesis would then be a critical factor in preventing subsequent complications. Epidemiologie studies of collagen properties, bearing on questions about the roles of genetic factors and control of diabetes in alterations in collagen and in complications of diabetes, would be feasible by the use Of skin biopsies.
Glycosylated DOTA−α-Melanocyte-Stimulating Hormone Analogues for Melanoma Targeting: Influence of the Site of Glycosylation on in Vivo Biodistribution (2009)

α-Melanocyte-stimulating hormone (α-MSH) is known to bind to the melanocortin receptor 1 (MC1R) which is overexpressed on melanotic and amelanotic melanoma cells. α-MSH analogues are potential candidates for specific targeting of melanoma metastases. Several linear and cyclic radiolabeled MSH peptides have been designed and tested in the past, showing both high affinity for the MC1R in vitro and good incorporation in tumor xenografts in vivo. However, considerable kidney reabsorption of the radiopeptides could not be avoided. With the aim to increase the tumor-to-kidney ratio, we synthesized six glycosylated derivatives of NAPamide, an α-MSH octapeptide analogue with high tumor selectivity and coupled them to the chelator DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid). The peptides were evaluated in vitro for MC1R binding and bioactivity and, after labeling with 111In, for in vitro cellular uptake and in vivo tissue distribution in mice carrying B16F1 melanoma tumors. The glycopeptides showed excellent binding affinities in the low nanomolar to subnanomolar range using both murine and human melanoma cell lines. However, five glycopeptides displayed lower selectivity in vivo than the parent DOTA−NAPamide, because of either a lower tumor uptake or a higher kidney uptake. In particular C-terminal extension of the amide group by a galactosyl moiety increased the kidney retention dramatically. By contrast, an N-terminally positioned galactose residue in DOTA−Gal-NAPamide improved the tumor-to-kidney ratio (4−48 h AUC of 1.34) by a factor of about 1.2 as compared to the parent DOTA−NAPamide (4−48 h AUC of 1.11), thus serving as new lead compound for MC1R-targeting molecules.
Calculation of Static Pressure Gradients in Gas Wells (1945)

Abstract The derivations of three methods of computing the static pressure gradientsin natural gas wells have been presented to show the assumptions made. Chartswere developed from which the pressure gradients may be read when the well-headpressure, the well fluid gravity, depth, and the average well temperature aregiven. A chart for estimating the well fluid gravity from the condensatecontent and separator gas gravity is included. The effect of the increasedaverage well temperature after flow on the calculation of the static pressuregradient is discussed. Introduction Reservoir pressures have been calculated from well-head pressures for gaswells for many years. As the pressure measurements become more accurate, theneed for a reliable calculation of the static pressure gradient often arises.This paper will develop the several methods for computing the pressure gradientin gas wells and make a comparison between them. The method of calculating static pressure gradients in common use is Eq. I(ref. I) or its counterpart which includes a factor for the deviation of thegas from the ideal gas law. An alternate method is to compute the average density of the gas in the welland multiply by the well depth in a manner similar to that used for liquidgradients. Derivation of Formulas A static pressure gradient is a special case of the general fluid-flowequation. Consider a pound of fluid flowing in a vertical column from point Ito point 2, Fig. I. T.P. 1814
Characterization of a gamma-carboxyglutamic acid-containing protein from bone. (1976)

A gamma-carboxyglutamic acid-containing protein has been purified from the calcified tissues of several vertebrates. The presence of three-gamma-carboxyglutamic acid residues in the bovine protein was established by alkaline hydrolysis and amino acid analysis, a method based upon studies with synthetic gamma-carboxyglutamic acid. The identity of gamma-carboxyglutamic acid in the bovine protein was established by mass spectroscopy on the unknown amino acid isolated from alkaline hydrolysates.
Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment (2014)

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.
Thick Airfoils With Blunt Trailing Edge for Wind Turbine Blades (2010)

This paper addresses the primary concerns regarding the aerodynamic performance characteristics of thick airfoils with blunt trailing edges (or so-called flatback airfoils) and the utilization of these section shapes in the design of rotor blades for utility-scale wind turbines. Results from wind tunnel and computational fluid dynamic studies demonstrate the favorable impact of the blunt trailing edge on the aerodynamic performance characteristics including higher maximum lift coefficient and reduced sensitivity of lift to premature boundary layer transition. The negative effect of the blunt trailing edge on drag can be partially mitigated through simple trailing edge treatments such as splitter plates. Studies on the effect of these section shapes on wind turbine rotor performance show that at attached flow conditions this inboard blade modification does not adversely affect rotor torque output. Blade system design studies involving the collective optimization of aerodynamic performance, structural strength and weight, and manufacturing complexity demonstrate the overall favorable impact of the flatback concept.
1910 annual spring catalogue / (1910)

The large, well formed flowers, borne on long and strong peduncles, last a long time in a cut state and furnish fine material for bouquets and decorative purposes.The colors vary from pure white through
17.6% stabilized efficiency in low-temperature processed planar perovskite solar cells (2015)

Compact TiO<sub>2</sub> is replaced by a low-temperature solution-processed TiO<sub>X</sub>/60-PCBM layer for electron extraction in perovskite solar cells with high steady conversion efficiencies.
Isolation and characterization of SGE1: a yeast gene that partially suppresses the gal11 mutation in multiple copies. (1993)

Recessive mutations of GAL11 in Saccharomyces cerevisiae cause pleiotropic defects that include weak fermentation of galactose, alpha-specific sterility and slow growth on nonfermentable carbon sources. Recent experiments suggest that Gal11P functions as a "co-activator" that links transcriptional activators, such as Gal4p and Grf1p/Rap1p/Tuf1p, with the basic transcription machinery. In the present experiments we isolated a gene, SGE1, that suppresses gal11 for growth on ethidium bromide/galactose agar when the gene was present in two or more copies. The other gal11 phenotypes were not suppressed by SGE1 in the multiple-copy state. Multiple copies of SGE1 increased expression of galactose-inducible genes in gal11 yeast, presumably at the level of transcription. When SGE1 was disrupted in wild-type yeast, the expression of galactose-inducible genes decreased to 50-60% of the wild-type level, presumably due to effect on transcription. Complete DNA sequence analysis revealed that SGE1 encodes a predicted protein of 543 amino acids. SGE1-specific mRNA of 1.8 kilonucleotides was detected by Northern analysis along the direction of the open reading frame. The gene mapped near RAD56, at the right end of chromosome 16.
Endothelial Cell-Specific Transcriptional Targeting from a Hybrid Long Terminal Repeat Retrovirus Vector Containing Human Prepro-Endothelin-1 Promoter Sequences (1999)

For many applications, specificity of gene expression by recombinant retroviral vectors is necessary. We wished to obtain transcriptional targeting in endothelial cells as part of an antivasculature approach to cancer treatment and have achieved specificity by using the promoter for human prepro-endothelin-1. In particular, we have inserted this heterologous promoter within the 3' long terminal repeat (LTR), replacing all viral upstream transcriptional regulatory sequences, to generate a hybrid LTR with precise fusion at the TATA box for initiation of transcription at the viral start site. Reverse transcription and integration resulted in duplication of this hybrid promoter in the 5' LTR of the provirus for transcription of the internal transgene. An important feature of our vectors is the absence of a selectable marker gene or additional promoters to avoid potential complications of silencing or interference and because selection will be inappropriate for clinical application. This vector design showed endothelial cell specificity of beta-galactosidase expression when tested on a panel of human cell lines and primary breast microvascular endothelial cells, matching the specificity of expression of the endogenous promoter. Such simplified vectors exhibiting transcriptional specificity are likely to be useful for the development of a gene therapy approach to targeting tumor vasculature.
Activation of PPARs<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>α</mml:mi></mml:math>,<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>β</mml:mi></mml:math>/<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>δ</mml:mi></mml:math>, and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>γ</mml:mi></mml:math>Impairs TGF-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>β</mml:mi></mml:math>1-Induced Collagens' Production and Modulates the TIMP-1/MMPs Balance in Three-Dimensional Cultured Chondrocytes (2010)

Background and Purpose. We investigated the potency of Peroxisome Proliferators-Activated Receptors (PPARs) α, β/δ, and γ agonists to modulate Transforming Growth Factor-β1 (TGF-β1-) induced collagen production or changes in Tissue Inhibitor of Matrix Metalloproteinase- (TIMP-) 1/Matrix Metalloproteinase (MMP) balance in rat chondrocytes embedded in alginate beads. Experimental Approach. Collagen production was evaluated by quantitative Sirius red staining, while TIMP-1 protein levels and global MMP (-1, -2, -3, -7, and -9) or specific MMP-13 activities were measured by ELISA and fluorigenic assays in culture media, respectively. Levels of mRNA for type II collagen, TIMP-1, and MMP-3 & 13 were quantified by real-time PCR. Key Results. TGF-β1 increased collagen deposition and type II collagen mRNA levels, while inducing TIMP-1 mRNA and protein expression. In contrast, it decreased global MMP or specific MMP-13 activities, while decreasing MMP-3 or MMP-13 mRNA levels. PPAR agonists reduced most of the effects of TGF-β1 on changes in collagen metabolism and TIMP-1/MMP balance in rat in a PPAR-dependent manner, excepted for Wy14643 on MMP activities. Conclusions and Implications. PPAR agonists reduce TGF-β1-modulated ECM turnover and inhibit chondrocyte activities crucial for collagen biosynthesis, and display a different inhibitory profile depending on selectivity for PPAR isotypes.
A bacterial type III secretion-based protein delivery tool for broad applications in cell biology (2015)

Methods enabling the delivery of proteins into eukaryotic cells are essential to address protein functions. Here we propose broad applications to cell biology for a protein delivery tool based on bacterial type III secretion (T3S). We show that bacterial, viral, and human proteins, fused to the N-terminal fragment of the Yersinia enterocolitica T3S substrate YopE, are effectively delivered into target cells in a fast and controllable manner via the injectisome of extracellular bacteria. This method enables functional interaction studies by the simultaneous injection of multiple proteins and allows the targeting of proteins to different subcellular locations by use of nanobody-fusion proteins. After delivery, proteins can be freed from the YopE fragment by a T3S-translocated viral protease or fusion to ubiquitin and cleavage by endogenous ubiquitin proteases. Finally, we show that this delivery tool is suitable to inject proteins in living animals and combine it with phosphoproteomics to characterize the systems-level impact of proapoptotic human truncated BID on the cellular network.
Total Synthesis of Indole and Dihydroindole Alkaloids. VIII. Studies on the synthesis of bisindole alkaloids in the vinblastine‐vincristine series. The chloroindolenine approach (1975)

Abstract Studies on the syntheses of 18′‐epi‐4′‐deoxo‐4′‐epivinblastine (IX, R = CO 2 CH 3 ; R 1 = H), 18′‐decarbomethoxy‐18′‐epi‐4′‐deoxo‐4′‐epivinblastine (IX, R = R 1 = H) and related analogues are described. The synthetic method employs a coupling reaction involving chloroindolenine derivatives of the cleavamine series (for example, III) with vindoline (V) under acidic conditions. The complete structures, including absolute configuration, of the resulting dimers are established by a combination of chemical and spectroscopic techniques, including X‐ray analysis.
Fast quasi-adiabatic gas cooling: an experiment revisited (2012)

The well-known experiment of the rapid expansion and cooling of the air contained in a bottle is performed with a rapidly responsive, yet very cheap thermometer. The adiabatic, low temperature limit is approached quite closely and measured with our apparatus. A straightforward theoretical model for this process is also presented and discussed. Both the experimental setup and the associated theoretical interpretation of the cooling phenomenon are suited for a standard general physics course at undergraduate level.
Phospholipid Hydrolysis Caused by<i>Clostridium perfringens</i>α-Toxin Facilitates the Targeting of Perfringolysin O to Membrane Bilayers (2010)

Clostridium perfringens causes gas gangrene and gastrointestinal disease in humans. These pathologies are mediated by potent extracellular protein toxins, particularly α-toxin and perfringolysin O (PFO). While α-toxin hydrolyzes phosphatidylcholine and sphingomyelin, PFO forms large transmembrane pores on cholesterol-containing membranes. It has been suggested that the ability of PFO to perforate the membrane of target cells is dictated by how much free cholesterol molecules are present. Given that C. perfringens α-toxin cleaves the phosphocholine headgroup of phosphatidylcholine, we reasoned that α-toxin may increase the number of free cholesterol molecules in the membrane. Our present studies reveal that α-toxin action on membrane bilayers facilitates the PFO−cholesterol interaction as evidenced by a reduction in the amount of cholesterol required in the membrane for PFO binding and pore formation. These studies suggest a mechanism for the concerted action of α-toxin and PFO during C. perfringens pathogenesis.
Electrochemical Detection of Circadian Redox Rhythm in Cyanobacterial Cells via Extracellular Electron Transfer (2015)

Recent research on cellular circadian rhythms suggests that the coupling of transcription-translation feedback loops and intracellular redox oscillations is essential for robust circadian timekeeping. For clarification of the molecular mechanism underlying the circadian rhythm, methods that allow for the dynamic and simultaneous detection of transcription/translation and redox oscillations in living cells are needed. Herein, we report that the cyanobacterial circadian redox rhythm can be electrochemically detected based on extracellular electron transfer (EET), a process in which intracellular electrons are exchanged with an extracellular electrode. As the EET-based method is non-destructive, concurrent detection with transcription/translation rhythm using bioluminescent reporter strains becomes possible. An EET pathway that electrochemically connected the intracellular region of cyanobacterial cells with an extracellular electrode was constructed via a newly synthesized electron mediator with cell membrane permeability. In the presence of the mediator, the open circuit potential of the culture medium exhibited temperature-compensated rhythm with approximately 24 h periodicity. Importantly, such circadian rhythm of the open circuit potential was not observed in the absence of the electron mediator, indicating that the EET process conveys the dynamic information regarding the intracellular redox state to the extracellular electrode. These findings represent the first direct demonstration of the intracellular circadian redox rhythm of cyanobacterial cells.
High-throughput techniques for the evaluation of fire retardancy (2006)

As new flame retardant (FR) approaches are developed they must be evaluated with conventional FR additives, processing additives, stabilizers, and fillers. In most cases this is done in a number of polymers, and a variety of processing conditions also must be optimized. Thus the development of new FR methods is a multi-parameter problem. A full-factorial approach to developing the structure–property relationships of interest requires numerous experiments and is prohibitively labor intensive; additional methods in which the composition space can be rapidly sampled and evaluated are necessary. Several new high throughput approaches are described herein which have been correlated with conventional flammability tests.
Intrauterine insemination: a first-step procedure in the algorithm of male subfertility treatment (1995)

Despite the widespread clinical use of intrauterine insemination (IUI) in the treatment of male subfertility, its therapeutic value remains unclear. The objective of this review was to determine why its efficacy has not been consistently documented in the literature and to give strong evidence supporting the therapeutic merit of ovarian stimulation/IUI in male subfertility treatment. Because (i) this technique is much easier to perform and less expensive than assisted reproduction methods, and seems to be reasonably effective in controlled studies of a male subfertility treatment, and (ii) we may expect that financial resources available for the health care of infertility patients will be limited in the future, we believe that ovarian stimulation/IUI must become the first-line treatment in most cases of male factor subfertility, provided that the multiple gestation incidence can be reduced to an acceptable level.
A numerical simulation study for the zone refining processes of cadmium and tellurium (2008)

This article presents the results of a three-dimensional numerical simulation study carried out for a three-zone refiner system. Firstly, an overall thermal analysis was performed to study the effects of changes in the size of the ZR system. A complete mass, heat, and momentum transport model was then developed for this system, and the fluid flow and impurity concentration distributions in a single molten zone were studied. A parametric study was also carried out to obtain the most favourable freezing interfaces and molten zone sizes. The flow field in the molten zone was studied to determine its effect on impurity transport.