gebhart/patrepeval huggingface dataset:
Tissue-Engineered Pancreatic Islets: Culturing Rat Islets in the Chitosan Sponge (2001)

Subcutaneous islet transplantation has become an attractive modality. With development of tissue-engineering techniques, it is possible to rectify the disadvantage of poor blood supply in the subcutaneous site by reconstruction of the capillary network. According to reports, the Chitosan sponge (CS) could be used for reconstruction of in vitro capillary-like network and could be used in artificial skin equivalent. In this study, we cultured the islets in CS for future application. CSs, having 200-500 microm pore size, were prepared by freeze-drying method. Rat islets were isolated from the pancreas of Lewis rats (10 weeks old, 280-300 g, male) by collagenase digestion followed by discontinuous dextran gradient centrifugation method. Each 20 islets were seeded equally into the CSs and were cultured for 62 days with various culture media such as RPMI-1640, Dulbecco's modified Eagle's medium (DMEM), and Eagle's MEM. They contained 10% fetal bovine serum (FBS) and 5 ml/L antibiotic-antimycotic mixed stock solution in the culture dishes. Insulin concentration both inside and outside of the islet-seeded CS was measured during culture. Changes in the morphology of islets were also observed in this study. Freshly isolated islets had a loose appearance with an irregular border, and most were seen as a single islet. Occasionally a cluster, consisting of 2-4 islets ranging mainly from 150 to 250 microm in diameter, was observed. Islets cultured in the CSs in different culture media retained initial morphology, which had well-delineated smooth borders for at least 53 days. The insulin release behavior of islets cultured in the CS showed constant secretory capacities for 49 days. After that they exhibited a rapid and definitive decline from the initial insulin release. Until this stage, insulin concentration in the CS was well maintained. The properties were dependent on culture medium used and insulin diffusion released from islets. This experiment is a new study model for establishment of islet culture in a three-dimensional matrix. Also extension of this observation will provide new insights for islet transplantation at the subcutaneous site by a tissue-engineering approach.
Hybrid system for multi-language and multi-environment generation of numerical codes (2001)

The paper presents a hybrid system for automatic generation of numerical procedures for various finite element environments from the same symbolic description. The system consists of two major components. The Mathematica package AceGen is used for the automatic derivation of formulae needed in numerical procedures. An approach, implemented in AceGen, avoids the usual problem of uncontrollable growth of expressions by combining several techniques: symbolic and algebraic capabilities of Mathematica, automatic differentiation technique, automatic code generation, simultaneous optimization of expressions and theorem proving by a stochastic evaluation of the expressions. The Computational Templates package is a collection of prearranged modules for the creation of the finite element templates that enables the generation of multi-language and multi-environment finite element codes.
Unusual dominant course of left circumflex coronary artery with absent right coronary artery (2006)

A single coronary artery is an unusual congenital anomaly where only one coronary artery arises from the aortic trunk by a single coronary ostium, supplying the entire heart. We describe here a rare case with an unusual dominant left circumflex artery and no right coronary artery.

A 43 year old man presented with atypical chest pain. His physical examination was unremarkable except for a blood pressure of 180/100 mm Hg. The ECG showed normal sinus rhythm without any …
Synthesis of a photoaffinity-labelled analogue of 1,25-dihydroxyvitamin D3 (1985)

R. Ray, S. A. Holick and M. F. Holick, J. Chem. Soc., Chem. Commun., 1985, 702 DOI: 10.1039/C39850000702
Wedelolactone, a Naturally Occurring Coumestan, Enhances Interferon-γ Signaling through Inhibiting STAT1 Protein Dephosphorylation (2013)

Signal transducers and activators of transcription 1 (STAT1) transduces signals from cytokines and growth factors, particularly IFN-γ, and regulates expression of genes involved in cell survival/death, proliferation, and migration. STAT1 is activated through phosphorylation on its tyrosine 701 by JAKs and is inactivated through dephosphorylation by tyrosine phosphatases. We discovered a natural compound, wedelolactone, that increased IFN-γ signaling by inhibiting STAT1 dephosphorylation and prolonging STAT1 activation through specific inhibition of T-cell protein tyrosine phosphatase (TCPTP), an important tyrosine phosphatase for STAT1 dephosphorylation. More interestingly, wedelolactone inhibited TCPTP through interaction with the C-terminal autoinhibition domain of TCPTP. We also found that wedelolactone synergized with IFN-γ to induce apoptosis of tumor cells. Our data suggest a new target for anticancer or antiproliferation drugs, a new mechanism to regulate PTPs specifically, and a new drug candidate for treating cancer or other proliferation disorders.
Structure Revision and Cytotoxic Activity of the Scabrosin Esters, Epidithiopiperazinediones from the Lichen <i>Xanthoparmelia scabrosa</i> (1999)

The scabrosin esters (1){(4), isolated from the lichen Xanthoparmelia scabrosa , were reanalysed by modern one- and two-dimensional n.m.r. spectroscopic methods, including 15N n.m.r. spectroscopy, and single-crystal X-ray structural analysis. This reinvestigation has resulted in the unambiguous structure elucidation and complete spectral assignment of these metabolites and established them to be a family of epidithiopiperazinedione derivatives. A new scabrosin ester, scabrosin butyrate hexanoate (5), has also been isolated and its structure determined, including assignment of absolute configuration. Several scabrosins were found to exhibit potent cytotoxic activity against the murine P815 mastocytomia cell line (IC50 c . 0·5 µM) and the human breast MCF7 carcinoma cell line (IC50 c . nM). Compounds which contain a dithiopiperazinedione moiety have not previously been identified in lichenized fungi.
Single Polymer Chain Elongation of Poly(<i>N</i>-isopropylacrylamide) and Poly(acrylamide) by Atomic Force Microscopy (2000)

The nanomechanical properties of poly(N-isopropylacrylamide) (PNIPAM) and poly(acrylamide) (PAAM) in deionized water and 8 M urea aqueous solution were studied by using an atomic force microscopy based techniquesingle-molecule force spectroscopy (SMFS). Different force−extension traces were obtained in both systems. They could be normalized and superimposed, respectively. The force curves of PNIPAM and PAAM in 8 M urea aqueous solution could be fitted by extended freely jointed chain (FJC) model separately. These facts indicate that single polymer chain stretching was obtained. Moreover, the elasticities of PNIPAM and PAAM in pure water and in 8 M urea aqueous solution were compared. It is worthy to be pointed out that for PAAM in deionized water, a deviation from the extended FJC model at the middle regime (from ∼50 to 450 pN) in the force curve was found. When 8 M urea aqueous solution was used as buffer solution, the deviation disappeared and the force curve could be fitted with extended FJC model. This result may be related to the fact that PAAM could form certain intramolecular hydrogen bonding in water. After the PNIPAM sample was heated to 33 °C, above its LCST, more signals were observed in one stretching. This could be attributed to the fact that polymer chains form more contact points with the glass substrate after thermal treatment. In addition, another way just different from the normal one to do the SMFS experiment was also provided.
Philosophies for engineering computer-based systems (1990)

A sound problem-relevant philosophy is the key to achieving successful implementation of complex computer-based systems and software engineering methods and tools naturally flow from this foundation. The importance of a philosophy is illustrated by considering the development of Simula. Several philosophy-relevant factors are discussed and experiences where philosophies have played a central role in realizing complex real-time applications are described. These experiences relate to telecommunication software, automatic train control and power dispatching.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Biology of <i>Phytophthora infestans</i> at Its Center of Origin (2005)

The central highlands of Mexico are considered to be a center of genetic diversity for both the potato late blight pathogen and for tuber-bearing Solanum spp. Recent work conducted in Mexico and South America sheds new light on the biology and evolution of Phytophthora infestans and other related Phytophthora pathogens. It now appears that Mexican Solanum species, which coevolved with P. infestans and were previously known for providing a source of R-genes, also provide a source of quantitative, rate-reducing resistance that is highly effective, stable, and durable. It is now apparent that Mexico is the center of origin not only of the potato late blight pathogen P. infestans, but also of several related Phytophthora species including P. mirabilis, P. ipomoeae, and possibly P. phaseoli. We close with the hypothesis that these Phytophthora species evolved sympatrically from one ancestral host through adaptive radiation onto their respective four host families.
Diverse effects of the CARD15 and IBD5 loci on clinical phenotype in 630 patients with Crohnʼs disease (2008)

Genetic variants at the CARD15 and IBD5 loci have diverse effects on clinical expression in CD. CARD15 mutations are significantly correlated with the presence of granulomas.
Active stromelysin‐3 (MMP‐11) increases MCF‐7 survival in three‐dimensional Matrigel culture via activation of p42/p44 MAP‐kinase (2003)

Abstract Stromelysin‐3 (ST3) has the characteristic structure of matrix metalloproteinases (MMP), but its substrate specificity and pattern of expression differ markedly from that of other MMP family members. ST3 was originally isolated on the basis of its expression in primary breast cancers and has been shown to be overexpressed in virtually all primary carcinomas, suggesting that ST3 participates in the initial development of epithelial malignancies. Recent data using murine models reported that ST3 expression was able to increase tumor take by suppressing cell apoptosis. Our present goal was to set up an in vitro model in which we could study this new function. For this purpose, we analyzed survival of MCF‐7 transfectants expressing either wild‐type or catalytically inactive ST3 (ST3wt or ST3cat‐) in three‐dimensional (3‐D) culture conditions by inclusion in Matrigel. In such conditions, that mimic the in vivo microenvironment, we found a marked decrease in the percentage of cell death when active ST3 was expressed (ST3wt transfectants vs. ST3cat‐ or vector only transfectants) as assessed by FACS and TUNEL analysis. The addition of batimastat, a broad spectrum MMP inhibitor, reversed the increased cell survival in ST3wt transfectants, confirming that ST3 enzymatic activity was required for this effect. Finally, we analyzed the expression of anti‐ and pro‐apoptotic proteins as well as activation of cell survival pathways and we found that ST3‐mediated cell survival was accompanied by activation of both p42/p44 MAPK and AKT. Our data confirm and extend the anti‐apoptotic function of ST3 and provide a useful model to dissect this new role and identify new physiological substrates. © 2003 Wiley‐Liss, Inc.
Low-temperature ohmic Au/Sb contacts to <i>n</i>-type Si (1994)

Au/Sb films annealed at temperatures as low as 370 °C yield ohmic contacts to n-type Si. The contact formation is based on a liquid-phase epitaxy process of Sb-doped Si from Au solution. Measured contact resistivities range around 3×10−2 Ω cm2 and are at least one order of magnitude higher than what is expected from the solid solubility of Sb in Si. The discrepancy stems from local inhomogeneous etching and epitaxial regrowth of the (100)-oriented Si surface by and from the Au solution. Only a small fraction of the macroscopic contact area is doped by Sb and contributes to current transport across the Au/Si(100) interface.
Comparative Studies on Uptake Pathway of Cadmium by Perna viridis (2006)

实验被设计暴露喂过滤器的瓣鳃类 Perna viridisto 不同的污染 Cd 的水环境以便比较 Cd 通过被积累的不同小径。结果证明贻贝能在时间的一个短时期通过海水，食物，沉积和推迟的粒子小径积累 Cd。贻贝“通过海水小径的 Cd 的举起到达最高的集中比通过水藻和沉积小径大约 3 和 9 倍分别地在 7 d 以后。这显示通过海水的 theCd 累积是很有效的。结果也显示举起直接通过贻贝摄取的污染水藻，粒子或沉积是不太重要的什么时候与由通过海水小径的贻贝的 Cd 的举起相比。由海洋的瓣鳃类的简历累积的金属举起小径和机制也在这篇论文被讨论。
A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection (2019)

The initiation of an immune response is dependent on the activation and maturation of dendritic cells after sensing pathogen associated molecular patterns by pattern recognition receptors. However, the response needs to be balanced as excessive pro-inflammatory cytokine production in response to viral or stress-induced pattern recognition receptor signaling has been associated with severe influenza A virus (IAV) infection. Here, we use an inhibitor of Toll-like receptor (TLR)3, a single-stranded oligonucleotide (ssON) with the capacity to inhibit certain endocytic routes, or a TLR3 agonist (synthetic double-stranded RNA PolyI:C), to evaluate modulation of innate responses during H1N1 IAV infection. Since IAV utilizes cellular endocytic machinery for viral entry, we also assessed ssON's capacity to affect IAV infection. We first show that IAV infected human monocyte-derived dendritic cells (MoDC) were unable to up-regulate the co-stimulatory molecules CD80 and CD86 required for T cell activation. Exogenous TLR3 stimulation did not overcome the IAV-mediated inhibition of co-stimulatory molecule expression in MoDC. However, TLR3 stimulation using PolyI:C led to an augmented pro-inflammatory cytokine response. We reveal that ssON effectively inhibited PolyI:C-mediated pro-inflammatory cytokine production in MoDC, notably, ssON treatment maintained an interferon response induced by IAV infection. Accordingly, RNAseq analyses revealed robust up-regulation of interferon-stimulated genes in IAV cultures treated with ssON. We next measured reduced IAV production in MoDC treated with ssON and found a length requirement for its anti-viral activity, which overlapped with its capacity to inhibit uptake of PolyI:C. Hence, in cases wherein an overreacting TLR3 activation contributes to IAV pathogenesis, ssON can reduce this signaling pathway. Furthermore, concomitant treatment with ssON and IAV infection in mice resulted in maintained weight and reduced viral load in the lungs. Therefore, extracellular ssON provides a mechanism for immune regulation of TLR3-mediated responses and suppression of IAV infection <i>in vitro</i> and <i>in vivo</i> in mice.
Modeling dispersion and radiation characteristics of conductor-backed CPW with finite ground width (2003)

Dispersion and radiation properties of the conductor-backed coplanar waveguide (CPW) with finite ground planes are analyzed and modeled. A frequency-domain finite-difference method using the perfectly matched layer absorbing boundary condition is used as reference. Based on these results, a closed-form description is derived and implemented into an existing quasi-static CPW model. This leads to a comprehensive and efficient CPW description accounting for all relevant effects from conductor loss to high-frequency dispersion. Additionally, design rules to avoid parasitic radiation effects are given.
Trace Eyeblink Conditioning Increases CA1 Excitability in a Transient and Learning-Specific Manner (1996)

Time-dependent, learning-related changes in hippocampal excitability were evaluated by recording from rabbit CA1 pyramidal neurons in slices prepared at various times after acquisition of trace eyeblink conditioning. Increased excitability (reduced postburst afterhyperpolarizations and reduced spike-frequency adaptation) was seen as early as 1 hr after acquisition to behavioral criterion, was maximal in neurons studied 24 hr later, and returned to baseline within 7 d, whereas behavioral performance remained asymptotic for months. Neurons were held at -67 mV to equate voltage-dependent effects. No learning-related effects were observed on input resistance, action-potential amplitude or duration, or resting membrane potential. The excitability changes were learning-specific, because they were not seen in neurons from very slow learning (exhibited < 30% conditioned responses after 15 training sessions) or from pseudoconditioned control rabbits. Neurons from rabbits that displayed asymptotic behavioral performance after long-term retention testing (an additional training session 14 d after learning) were also indistinguishable from control neurons. Thus, the increased excitability of CA1 neurons was not performance- or memory-dependent. Rather, the time course of increased excitability may represent a critical window during which learning-specific alterations in postsynaptic excitability of hippocampal neurons are important for consolidation of the learned association elsewhere in the brain.
SUPERBASE-INDUCED GENERATION OF PHOSPHIDE AND PHOSPHINITE IONS AS APPLIED IN ORGANIC SYNTHESIS (1991)

Abstract A series of new direct reactions of red phosphorus (or white) with organyl halides, alkenes and acetylenes have been developed. Reactions occur in superbasic systems, such as alkali metal hydroxide-dipolar aprotic complexing solvent (DMSO, HMPA) or under phase-transfer conditions to afford earlier inaccessible triorganylphosphines and -phosphine oxides including unsaturated ones in good yields.
Harnessing Deformation to Switch On and Off the Propagation of Sound (2015)

A new class of architected materials is designed to control the propagation of sound. The proposed system comprises an array of elastomeric helices in background air and is characterized by frequency ranges of strong wave attenuation (bandgaps) in the undeformed configuration. Upon axially stretching the helices, such bandgaps are suppressed, enabling the design of a new class of acoustic switch.
Interfacial adhesion of fluoropolymer composites to commercial copper foils subjected to aqueous photolithographic processes (2002)

Three commercial copper foils containing various degrees of surface roughness and a chemically similar surface treatment were laminated to a fluoropolymer composite and also subjected to water-based photolithographic and stripping processes. Surface analysis performed on the processed foils indicated that the highly basic pH of the stripping process was effective in removing zinc oxide, a component of the surface treatments on these foils. Morphologically, however, the surfaces did not seem to change. Ninety degree peel measurements of the resulting interfaces with and without a photoresist processes showed that the resulting practical adhesion seemed to be mainly controlled by mechanical interlocking and to a lesser amount, by chemical factors. When 50 /spl mu/m wide lines were subjected to the photolithographic process and a full fabrication sequence, adhesion variability seemed to be affected by interfacial attack of the fluoropolymer/metal foil interface by the alkaline medium of stripping and other process chemicals. Reliable interfacial adhesion of narrow lines is only possible when process parameters have been optimized.
Conformational changes induced by integration host factor at origin gamma of R6K and copy number control (1991)

We have investigated the role of integration host factor (IHF) in the replication of plasmid R6K by studying the maintainance of the plasmid in a strain of Escherichia coli that lacks both subunits of IHF and in an isogenic wild type strain and found that all three origins, alpha, beta, and gamma, were functional in the absence of IHF; however, loss of IHF reduced the copy number of those replicons initiating solely from ori gamma by 5-fold. Concomitant loss of direct repeats within the origin that bind the R6K replication initiator protein, Pi, resulted in a further reduction in copy number. Using gel mobility shift analysis, we showed that IHF bound specifically only to one site within the A/T rich region of the minimal origin adjacent to the Pi binding sites. The origin region possessed no intrinsic DNA curvature although IHF induced a strong bend upon binding. Combination footprinting with different orders of addition of Pi and IHF suggested that there was no cooperativity between the two proteins with regard to DNA binding. Hydroxyl-radical footprinting revealed hypersensitive asymmetric periodic cleavage sites within the origin region in the presence of IHF that extended over 200 base pairs and a localized perturbation of cleavage chemistry. The presence of periodic cleavages was dependent upon the presence of the wild type R6K origin sequence and was not observed when the IHF binding site was positioned adjacent to a heterologous sequence. We observed that the conformational changes induced by IHF upon binding to the R6K origin were negatively correlated with the observed decrease in copy number, and therefore, origin conformation altered by protein-DNA interaction may play an important role in the regulation of replication initiation.
Wittig Reaction by Using DBU as a Base (2003)

Abstract The reaction of methyltriphenylphosphonium bromide with DBU in refluxing dichloromethane or toluene afforded methylenetriphenylphosphorane, which further reacted with benzaldehydes to give styrenes in good yields. Semistabilized ylide, benzylidenetriphenylphosphorane was also synthesized by using DBU, which reacted with aldehydes to afford olefins in nearly quantitative yields.
Characteristics and Mechanisms of Locomotion Induced by Intraspinal Microstimulation and Dorsal Root Stimulation in Spinal Cats (2007)

Intraspinal microstimulation (ISMS) through a single microelectrode can induce locomotion in cats spinalized at T(13) 1 wk before (untrained) or after 3-5 wk of treadmill training. Here we study the optimal parameters of ISMS and the characteristics of locomotion evoked. ISMS was applied in the dorsal region of segments L(3)-S(1) at different lateralities (midline to 2.5 mm) and after an intravenous injection of clonidine (noradrenergic agonist). Kinematics and electromyographic recordings were used to characterize locomotion. ISMS could induce a bilateral locomotor pattern similar to that obtained with perineal stimulation, and the characteristics of locomotion varied according to the spinal segment stimulated. Mechanisms by which ISMS could evoke locomotion were then investigated by stimulating, inactivating, or lesioning different spinal structures. Dorsal root stimulation (DRS), just like ISMS, could evoke a variety of ipsi- and bilateral nonlocomotor movements as well as locomotor responses. This suggests that sensory afferent pathways are involved in the production of locomotion by ISMS. Microinjections of yohimbine (noradrenergic antagonist) in L(3) and L(4) segments or a complete second spinal lesion at L(3)-L(4) abolished all locomotor activity evoked by ISMS applied at more caudal segments. Progressive dorsoventral spinal lesions at L(3) or L(4) and restricted ventral lesions at L(4) further suggest that the integrity of the ventral or ventrolateral funiculi as well as the L(3)-L(4) segments are critical for the induction of locomotion by ISMS at L(5) to S(1) or by DRS at these caudal segments.