gebhart/patrepeval huggingface dataset:
Stable Helical Secondary Structure in Short-Chain N,N′-Linked Oligoureas Bearing Proteinogenic Side Chains Access to both the Bruker ARX 500 facilities of the Service Commun de RMN (Faculté de Chimie, Strasbourg) and the Bruker DRX 600 NMR facilities of the Service Commun de Biophysicochimie des Interactions Moléculaires (Université Henri Poincaré, Nancy I) were deeply appreciated. (2002)

Closely related to the (P)2.614 helix of γ-peptides: Heptamer 1 bearing side chains of Ala, Val, and Tyr adopts a stable 2.5-helical secondary structure in solution that is characterized by a pitch of approximately 5.1 Å and by the simultaneous presence of 12- and 14-membered hydrogen-bonded rings. Thus N,N′-linked oligoureas belong to the growing family of non-natural non-peptide oligomers with defined and predictable secondary structure. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2002/z17991_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Differentiation of liposomal irinotecan from dose-dense non-liposomal irinotecan in patient-derived pancreatic cancer xenograft tumor models. (2020)

e16724 Background: Liposomal irinotecan (ONIVYDE) is approved with 5-fluorouracil/leucovorin for metastatic pancreatic ductal adenocarcinoma (PDAC) post progression on gemcitabine-based therapy. The liposomal formulation prolongs payload residence time in the circulation and tumor lesions, where local conversion to the active metabolite SN-38 is thought to occur. The effect of the liposomal formulation on therapeutic index (TI) was assessed in patient-derived xenograft PDAC models (IM-PAN-001 [untreated tumor] and SA-PAN-077) in severe combined immunodeficiency mice. Methods: Liposomal (2.5, 10 or 50 mg/kg, intravenous [IV] 1 x weekly) and non-liposomal irinotecan (2, 5 or 10 mg/kg, IV 5 x weekly) were administered for 3 weeks (n = 8/group). Maximum tolerated dose (MTD) and clinically-relevant weekly doses (10 mg/kg, liposomal; 33 mg/kg, non-liposomal) of irinotecan were evaluated. TI was the ratio of MTD/lowest dose with anti-tumoral activity; time to reach tumor volume of 600 mm 3 (TTV600) was a proxy for overall survival. Tumor, plasma, gut and bone marrow were sampled for pharmacokinetics and safety assessment; DNA damage was evaluated via pH2AX and 53BP1 IHC. Results: The Table reports results of the more sensitive IM-PAN-001 model: TI of weekly liposomal irinotecan was 4-fold higher than for 5 x weekly non-liposomal irinotecan (TI was narrower for SA-PAN-077). For liposomal vs non-liposomal irinotecan in IM-PAN-001, TTV600 was longer at both MTD and clinically equivalent doses, and tumoral irinotecan levels were higher at MTD. High levels of DNA damage were present in most cancer cells in IM-PAN-001 compared to SA-PAN-077 one week after the last liposomal treatment cycle. Conclusions: In both PDAC models, TI was higher for weekly liposomal vs 5 x weekly non-liposomal irinotecan, suggesting potential benefits of the liposomal formulation in a clinical setting. [Table: see text]
Accuracy of overlay measurements: tool and mark asymmetry effects (1992)

Definitions of centerline and centerline overlay (O/L) are built on the implicit assumptions of certain symmetries. Verification of these symmetries, and the use of redundancies built into the design of O/L measurement marks, can estimate the relative accuracy of O/L measurements, even in the absence of certified reference materials (standards). Verification carried out as of paired comparison is shown to be very effective; in addition, it constitutes the basis for data culling. Several sources of O/L measurement inaccuracy, associated with O/L measurement tools and with O/L measurement marks, are pointed out and some are illustrated using modeling. A simple measure of tool-related inaccuracy, tool-induced shift (TIS), is proposed and utilized as a performance estimate of O/L measurement tools relative to accuracy. Inaccuracies of O/L measurements, caused by O/L measurement tools and marks, on the order of 100 nm, are observed and their causes identified. Examples are given of significant improvements in accuracy. A roadmap toward accurate O/L measurement is outlined. This approach is also applicable to alignment systems.
Fast Patch-based Style Transfer of Arbitrary Style (2016)

Artistic style transfer is an image synthesis problem where the content of an image is reproduced with the style of another. Recent works show that a visually appealing style transfer can be achieved by using the hidden activations of a pretrained convolutional neural network. However, existing methods either apply (i) an optimization procedure that works for any style image but is very expensive, or (ii) an efficient feedforward network that only allows a limited number of trained styles. In this work we propose a simpler optimization objective based on local matching that combines the content structure and style textures in a single layer of the pretrained network. We show that our objective has desirable properties such as a simpler optimization landscape, intuitive parameter tuning, and consistent frame-by-frame performance on video. Furthermore, we use 80,000 natural images and 80,000 paintings to train an inverse network that approximates the result of the optimization. This results in a procedure for artistic style transfer that is efficient but also allows arbitrary content and style images.
Isolation and Structural Characterization of a New Minor Penta β-D-Glucopyranosyl Diterpene from Stevia rebaudiana Bertoni (2014)

From the commercial extract of the leaves of Stevia rebaudiana Bertoni, a new minor ent-kaurane diterpene glycoside having five β-D-glucopyranosyl units has been isolated. The chemical structure of the new compound was characterized as 13-[(2-O-β-D-glucopyranosyl-β-D-glucopyranosyl)oxy] ent-kaur-16-en-19-oic acid-(2-O-β-D-glucopyranosyl-6-O-β-D-glucopyranosyl-β-D-glucopyranosyl) ester (1) on the basis of extensive 1D (1H & 13C) and 2D NMR (TOCSY, HMQC, and HMBC), and High Resolution (HR) mass spectroscopic data as well as hydrolysis studies.
Using genetic programming to predict financial data (2003)

This paper presents the application of genetic programming (GP) to the prediction of price data in the Japanese stock market. The goal of this task is to choose the best stocks when making an investment and to decide when and how many stocks to sell or buy. There have been several applications of genetic algorithms (GAs) to financial problems, such as portfolio optimization, bankruptcy prediction, financial forecasting, fraud detection and scheduling. GP has also been applied to many problems in time-series prediction. However, relatively few studies have been made for the purpose of predicting stock market data by means of GP. This paper describes how successfully GP is applied to predicting stock data so as to gain a high profit. Comparative experiments are conducted with neural networks to show the effectiveness of the GP-based approach.
Design of an Indoor Self-Positioning System for the Visually Impaired - Simulation with RFID and Bluetooth in a Visible Light Communication System (2007)

After a public experiment of the indoor guidance system using FLC (fluorescent light communication), we found that FLC provides a promising medium for the installation of a guidance system for the visually impaired. However, precise self-positioning was not satisfactorily achieved. In this article, we propose a new self-positioning method, one that uses a combination of RFID (Radio-frequency identification), Bluetooth and FLC. We analyzed the situation and developed a model that combined the three communication modes. Then we performed a series of experiments and get some results in the first step.
Polyalkylcyanoacrylates as colloidal drug carriers. (1988)

A considerable amount of energy has been spent in creating new colloidal drug delivery systems that are acceptable for general systemic use. Among these new systems, nanoparticles made with biodegradable polymers are gaining more and more interest. The aim of this paper is to describe the preparation and characterization of these nanoparticles and their in vivo behavior and to show the possibilities of using them in various fields of human medicine. The interaction of polyalkylcyanoacrylate nanoparticles with cells in culture is also discussed, as well as the possibility of improving the specificity of the carrier by coating it with monoclonal antibodies.
Brachial Plexus Injury During Open Heart Surgery - Controlled Prospective Study (2005)

There are no reports in the literature of routine preoperative and postoperative electrophysiological studies in large patient groups to evaluate brachial plexus injury during open heart surgery. It is known that heart surgery sometimes causes partial brachial plexus injury, especially in the lower trunk. However, these peripheral nerve problems are usually not considered clinically important and are not investigated. Patients undergoing open heart surgery must be closely followed up for peripheral nerve injury during the postoperative period.
K+ channel types targeted by synthetic OSK1, a toxin fromOrthochirus scrobiculosusscorpion venom (2004)

OSK1 (alpha-KTx3.7) is a 38-residue toxin cross-linked by three disulphide bridges that was initially isolated from the venom of the Asian scorpion Orthochirus scrobiculosus. OSK1 and several structural analogues were produced by solid-phase chemical synthesis, and were tested for lethality in mice and for their efficacy in blocking a series of 14 voltage-gated and Ca2+-activated K+ channels in vitro. In the present paper, we report that OSK1 is lethal in mice by intracerebroventricular injection, with a LD50 (50% lethal dose) value of 2 microg/kg. OSK1 blocks K(v)1.1, K(v)1.2, K(v)1.3 channels potently and K(Ca)3.1 channel moderately, with IC50 values of 0.6, 5.4, 0.014 and 225 nM respectively. Structural analogues of OSK1, in which we mutated positions 16 (Glu16-->Lys) and/or 20 (Lys20-->Asp) to amino acid residues that are conserved in all other members of the alpha-KTx3 toxin family except OSK1, were also produced and tested. Among the OSK1 analogues, [K16,D20]-OSK1 (OSK1 with Glu16-->Lys and Lys20-->Asp mutations) shows an increased potency on K(v)1.3 channel, with an IC50 value of 0.003 nM, without loss of activity on K(Ca)3.1 channel. These data suggest that OSK1 or [K16,D20]-OSK1 could serve as leads for the design and production of new immunosuppressive drugs.
Signal transduction pathways in the induction of 2',5'-oligoadenylate synthetase gene expression by interferon alpha/beta. (1989)

Treatment of quiescent BALB/c mouse 3T3 cells with murine interferon alpha/beta (IFN-alpha/beta) (1000 units/ml) leads to the appearance at 4 hr of 1.7-kilobase 2',5'-oligoadenylate (2',5'-OAS)mRNA as detected by Northern blot analysis. This mRNA accumulates for at least 18 hr. Two protein kinase C activators, 1,2-dioctanoyl glycerol and phorbol 12-myristate 13-acetate, suppress, whereas the calcium ionophore ionomycin enhances, the IFN-alpha/beta-induced expression of 2',5'-OAS mRNA. The 8-bromo and dibutyryl analogs of cAMP and the adenylate cyclase activator forskolin did not affect the induction of 2',5'-OAS mRNA by IFN-alpha/beta. In the absence of IFN-alpha/beta, the above agents used either singly or in combinations, did not induce 2',5'-OAS mRNA expression nor did platelet-derived growth factor (1-2 units/ml), fibroblast growth factor (6-100 ng/ml), or bovine serum (10-20%). Bovine serum also did not affect 2',5'-OAS mRNA induction by IFN-alpha/beta. The poly(ADP)-ribose synthetase inhibitor 3-aminobenzamide suppressed IFN-alpha/beta-induced 2',5'-OAS gene expression. These results suggest that in quiescent BALB/c 3T3 cells (i) the 2',5'-OAS gene is not responsive to the three major signal transduction pathways activated by diacylglycerol, Ca2+, and cAMP; (ii) induction of the 2',5'-OAS gene by IFN-alpha/beta is decreased by activation of the protein kinase C pathway but enhanced by elevation of intracellular [Ca2+].
Granulocyte-macrophage colony-stimulating factor (GM-CSF) is expressed in mouse skin in response to tumor-promoting agents and modulates dermal inflammation and epidermal dark cell numbers (1994)

In mouse dorsal skin multistage carcinogenesis models, tumor promotion can be mediated by chemical agents, but also by wounding or abrasion of the epidermis, suggesting that endogenous growth factors mediate this process. Granulocyte-macrophage colony-stimulating factor (GM-CSF) is one such factor that has been reported to be produced by keratinocytes in vitro, and has been suggested both to stimulate keratinocyte proliferation, and also to be a chemoattractant for neutrophils and macrophages. In this study we examined the expression and function of GM-CSF in mouse skin following the application of tumor-promoting agents. Both single and multiple applications of 12-O-tetradecanoylphorbol-13-acetate (TPA) resulted in accumulation of GM-CSF mRNA in the epidermis. Various phorbol and non-phorbol ester tumor promoters were found to induce increases in epidermal GM-CSF mRNA levels commensurate with their relative tumor promoting capabilities. Fluocinolone acetonide (FA) and tosyl phenylalanine chloromethyl ketone (TPCK), inhibitors of tumor promotion, inhibited tumor promoter-mediated GM-CSF accumulation, whereas all-trans-retinoic acid (RA) enhanced the TPA-induced increase. The retinoic acid analogue RO-109359 which, unlike RA, does not have tumor promoting activity per se, inhibited the TPA-induced increase in epidermal GM-CSF mRNA levels. When an antibody specific to GM-CSF was administered prior to TPA, the promoter-induced dermal inflammation and increase in epidermal dark cell number were reduced, yet promoter-induced epidermal hyperplasia was not. These findings implied that elevation of GM-CSF levels plays an important role in chemically-mediated mouse skin tumor promotion and principally via effects on promoter-induced inflammation and increased epidermal dark cell number.
The association of psychedelic use and opioid use disorders among illicit users in the United States (2017)

Experience with psychedelic drugs is associated with decreased risk of opioid abuse and dependence. Conversely, other illicit drug use history is largely associated with increased risk of opioid abuse and dependence. These findings suggest that psychedelics are associated with positive psychological characteristics and are consistent with prior reports suggesting efficacy in treatment of substance use disorders.
Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi (2018)

In industry, filamentous fungi have a prominent position as producers of economically relevant primary or secondary metabolites. Particularly, the advent of genetic engineering of filamentous fungi has led to a growing number of molecular tools to adopt filamentous fungi for biotechnical applications. Here, we summarize recent developments in fungal biology, where fungal host systems were genetically manipulated for optimal industrial applications. Firstly, available inducible promoter systems depending on carbon sources are mentioned together with various adaptations of the Tet-Off and Tet-On systems for use in different industrial fungal host systems. Subsequently, we summarize representative examples, where diverse expression systems were used for the production of heterologous products, including proteins from mammalian systems. In addition, the progressing usage of genomics and functional genomics data for strain improvement strategies are addressed, for the identification of biosynthesis genes and their related metabolic pathways. Functional genomic data are further used to decipher genomic differences between wild-type and high-production strains, in order to optimize endogenous metabolic pathways that lead to the synthesis of pharmaceutically relevant end products. Lastly, we discuss how molecular data sets can be used to modify products for optimized applications.
Sequential logic and random access memory (RAM): a molecular approach (2011)

Since it was first suggested that molecules could be used for information processing, there has been a significant effort to generate systems that behave according to various logic schemes. Here we will summarize and discuss various approaches that serve one common goal: constructing a (bio)-molecular flip–flop. This logic circuit is at the core of random access memory (RAM) and is one of the pillars of sequential logic. We will highlight the concept underlying various approaches towards flip–flops and we will discuss how these constitute and expand the field of molecular logic. This multi-disciplinary approach results in various schemes that range from all photonic systems to transition metal complexes and hybrid nanoparticle/protein-based systems on solid supports.
Smart Memories Polymorphic Chip Multiprocessor (2015)

The Stanford Smart Memories polymorphic chip-multipro-cessor architecture was conceived as a unified multipurpose hardware architecture base, capable of supporting a vari-ety of programming models and per-application optimiza-tions [17]. Backing the architectural claims, our team of PhD students set out to implement this challenging design in silicon, targeting 90nm technology. Now, with 55M tran-sistors covering 61mm2, this is one of the most complex chips ever fabricated in academia.
Quantitative phase microscopy with asynchronous digital holography (2007)

We demonstrate a new method of measuring quantitative phase in imaging of biological materials. This method, asynchronous digital holography, employs knowledge of a moving fringe created by acousto-optic modulators to execute phase-shifting interferometry using two near-simultaneous interferograms. The method can be used to obtain quantitative phase images of dynamic biological samples on millisecond time scales. We present results on a standard sample, and on live cell samples.
SpFGFR, a New Member of the Fibroblast Growth Factor Receptor Family, Is Developmentally Regulated during Early Sea Urchin Development (1996)

We describe the cloning of a new fibroblast growth factor receptor, SpFGFR1, that is differentially regulated at the level of transcript abundance during sea urchin embryogenesis. Sequence representing the conserved tyrosine kinase domain was obtained by reverse transcription-polymerase chain reaction using degenerate primers, and the entire open reading frame was obtained by standard cDNA library screening methods. SpFGFR contains a series of domains characteristic of FGFRs: three immunoglobulin-like motifs, an acid box, a transmembrane domain, a relatively long juxtamembrane sequence, a split tyrosine kinase domain, and two conserved intracellular tyrosine residues. Alternative splicing of SpFGFR generates two variants (Ig3L and Ig3S), which differ by insertion in the center of the Ig3 domain of 34 extra amino acids, encoded by an additional exon. Transcripts encoding both variants accumulate when morphogenesis begins with mesenchyme cell ingression and gastrulation. SpFGFR transcripts accumulate in all cell types of the embryo, although in situ hybridization shows that they are somewhat enriched in cells of oral ectoderm and endoderm. Transcripts encoding the Ig3S variant, whose structure resembles more closely that of vertebrate receptors, are enriched in endomesoderm, suggesting that the SpFGFR variants could play distinct roles in the sea urchin embryo.
Regulation of Wnt Signaling and Embryo Patterning by an Extracellular Sulfatase (2001)

The developmental signaling functions of cell surface heparan sulfate proteoglycans (HSPGs) are dependent on their sulfation states. Here, we report the identification of QSulf1, the avian ortholog of an evolutionarily conserved protein family related to heparan-specific N-acetyl glucosamine sulfatases. QSulf1 expression is induced by Sonic hedgehog in myogenic somite progenitors in quail embryos and is required for the activation of MyoD, a Wnt-induced regulator of muscle specification. QSulf1 is localized on the cell surface and regulates heparan-dependent Wnt signaling in C2C12 myogenic progenitor cells through a mechanism that requires its catalytic activity, providing evidence that QSulf1 regulates Wnt signaling through desulfation of cell surface HSPGs.
Serological response over time to recombinant Neospora caninum antigens in cattle after a neosporosis-induced abortion (1997)

Recombinant Neospora caninum tachyzoite antigens were evaluated in an enzyme-linked immunosorbent assay (ELISA) for recognition by serum antibodies (Ab) from Neospora-infected cattle. Serum samples were obtained every 2 to 3 weeks for 8 to 15 months from 10 cows with histories of Neospora-associated abortion. Serum samples were also obtained from offspring of these animals and from a large number of cows that had aborted a fetus, due to infection by Neospora or other organisms, at various times during gestation. All 10 cows had positive ELISA Ab titers to both recombinant N. caninum tachyzoite antigens after abortion, during subsequent gestation, and after parturition. In three cows, there was a noticeable peak in Ab titers early in gestation. Calves born to Neospora-infected cows also had positive titers of Ab to the recombinant tachyzoite antigens, and these titers remained elevated for at least 4 months after birth. A portion of the serum immunoglobulin in calves may have been derived from colostrum of infected cows. A calf born from a seronegative mother had a positive ELISA titer only after being fed colostrum from a seropositive cow. However, precolostral titers in calves born from Neospora-infected cows were high at birth, suggesting that the parasite was transmitted to the fetus via the placenta and induced a humoral immune response therein. The recombinant tachyzoite antigens were also useful for corroborating clinical diagnoses of Neospora-induced abortion. A significant difference (P < 0.05) between anti-recombinant antigen Ab titers in cows that aborted due to Neospora and those in cows that aborted from other causes was found.
A new group of potent inducers of differentiation in murine erythroleukemia cells. (1976)

This report identifies a group of compounds, polymethylene bisacetamides (acetylated diamines), which are potent inducers of erythroid differentiation in murine erythroleukemia cells. A known inducing agent, N-methylacetamide, was dimerized through varying numbers of methylenes in an attempt to increase the local effective concentration at adjacent target sites. The simple dimer was no more effective than N-methylacetamide alone; introduction of five to eight methylenes between acetamide groups substantially increased the effectiveness of these compounds. The hexamethylene bisacetamide was active between 0.5 mM and 5 mM; the percentage of cells induced and the rate at which they were recruited to differentiation was dependent upon the concentration of inducer within this range. At 5 mM hexamethylene bisacetamide essentially the entire population (greater than 99%) was induced to a pathway of erythroid differentiation which was greater differentiation of the cultured cells than with any inducer yet tested.