gebhart/patrepeval huggingface dataset:
A Synthetic Reaction Network:  Chemical Amplification Using Nonequilibrium Autocatalytic Reactions Coupled in Time (2004)

This article reports a functional chemical reaction network synthesized in a microfluidic device. This chemical network performs chemical 5000-fold amplification and shows a threshold response. It operates in a feedforward manner in two stages: the output of the first stage becomes the input of the second stage. Each stage of amplification is performed by a reaction autocatalytic in Co(2+). The microfluidic network is used to maintain the two chemical reactions away from equilibrium and control the interactions between them in time. Time control is achieved as described previously (Angew. Chem., Int. Ed. 2003, 42, 768) by compartmentalizing the reaction mixture inside plugs which are aqueous droplets carried through a microchannel by an immiscible fluorinated fluid. Autocatalytic reaction displayed sensitivity to mixing; more rapid mixing corresponded to slower reaction rates. Synthetic chemical reaction networks may help understand the function of biochemical reaction networks, the goal of systems biology. They may also find practical applications. For example, the system described here may be used to detect visually, in a simple format, picoliter volumes of nanomolar concentrations of Co(2+), an environmental pollutant.
The Profile of Gene Expression of Human Marrow Mesenchymal Stem Cells (2003)

Mesenchymal stem cells (MSCs) are multipotent precursors present in adult bone marrow, that differentiate into osteoblasts, adipocytes and myoblasts, and play important roles in hematopoiesis. We examined gene expression of these cells by serial analysis of gene expression, and found that collagen I, secreted protein acidic and rich in cysteine (osteonectin), transforming growth factor beta- (TGF-beta) induced, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and matrix metalloproteinase-2 are among the most abundantly expressed genes. Comparison with a library of CD34(+) cells revealed that MSCs had a larger number of expressed genes in the categories of cell adhesion molecule, extracellular and development. The two types of cells share abundant transcripts of many genes, some of which are highly expressed in myeloid progenitors (thymosin-beta 4 and beta 10, fos and jun). Interleukin-11 (IL-11), IL-15, IL-27 and IL-10R, IL-13R and IL-17R were the most expressed genes among the cytokines and their receptors in MSCs, and various interactions can be predicted with the CD34(+) cells. MSCs express several transcripts for various growth factors and genes suggested to be enriched in stem cells. This study reports the profile of gene expression in MSCs and identifies the important contribution of extracellular protein products, adhesion molecules, cell motility, TGF-beta signaling, growth factor receptors, DNA repair, protein folding, and ubiquination as part of their transcriptome.
THE QUENCHING OF SINGLET OXYGEN BY AMINO ACIDS AND PROTEINS (1975)

Abstract— The physical quenching of singlet molecular oxygen ( 1 Δ g ) by amino acids and proteins in D 2 O solution has been measured by their inhibition of the rate of singlet oxygen oxidation of the bilirubin anion. Steady‐state singlet oxygen concentrations are produced by irradiating the oxygenated solution with the 1–06 μm output of a Nd‐YAG laser, which absorbs directly in the electronic transition 1 Δ g + 1 v → 3 Σ g ‐ . The rate of quenching by most of the proteins studied is approximated by the sum of the quenching rates of their amino acids histidine, tryptophan and methionine, which implies that these amino acids in the protein structure are all about equally accessible to the singlet oxygen. The quenching constants differ from those obtained by the ruby‐laser methylene‐blue‐photosensitized method of generating singlet oxygen, or from the results of steady‐state methylene‐blue‐photosensitized oxidation, where singlet oxygen is assumed to be the main reactive species. The singlet oxygen quenching rates in D 2 O, pD 8, are (10 7 ? mol ‐1 s ‐1 ): alanine 0–2, methionine 3, tryptophan 9, histidine 17, carbonic anhydrase 85, lysozyme 150, superoxide dismutase 260, aposuperoxide dismutase 250.
Functional rat bladder regeneration through xenotransplantation of the bladder acellular matrix graft (1998)

The present in vivo and in vitro studies show that BAMG-augmentation cystoplasty can lead to morphological and functional regeneration of the rat bladder, preserving its low-pressure reservoir function. Because BAMG-regenerated bladders show functional innervation that is similar to normal bladders, they can work in coordination with the host bladder components, thus generating adequate intravesical pressure to produce sustained voiding. The decreased antigenicity makes heterologous BAMG transplants feasible without immunosuppression.
Differential activation of Myf5 and MyoD by different Wnts in explants of mouse paraxial mesoderm and the later activation of myogenesis in the absence of Myf5 (1998)

Activation of myogenesis in newly formed somites is dependent upon signals derived from neighboring tissues, namely axial structures (neural tube and notochord) and dorsal ectoderm. In explants of paraxial mesoderm from mouse embryos, axial structures preferentially activate myogenesis through a Myf5-dependent pathway and dorsal ectoderm preferentially through a MyoD-dependent pathway. Here we report that cells expressing Wnt1 will preferentially activate Myf5 while cells expressing Wnt7a will preferentially activate MyoD. Wnt1 is expressed in the dorsal neural tube and Wnt7a in dorsal ectoderm in the early embryo, therefore both can potentially act in vivo to activate Myf5 and MyoD, respectively. Wnt4, Wnt5a and Wnt6 exert an intermediate effect activating both Myf5 and MyoD equivalently in paraxial mesoderm. Sonic Hedgehog synergises with both Wnt1 and Wnt7a in explants from E8.5 paraxial mesoderm but not in explants from E9.5 embryos. Signaling through different myogenic pathways may explain the rescue of muscle formation in Myf5 null embryos, which do not form an early myotome but later develop both epaxial and hypaxial musculature. Explants of unsegmented paraxial mesoderm contain myogenic precursors capable of expressing MyoD in response to signaling from a neural tube isolated from E10.5 embryos, the developmental stage when MyoD is present throughout the embryo. Myogenic cells cannot activate MyoD in response to signaling from a less mature neural tube. Together these data suggest that different Wnt molecules can activate myogenesis through different pathways such that commitment of myogenic precursors is precisely regulated in space and time to achieve the correct pattern of skeletal muscle development.
Enzyme-Linked Immunosorbent Assay ofCarbamoylphosphate Synthetase I: PlasmaEnzyme in Rat Experimental Hepatitis andIts Clearance (1994)

Carbamoylphosphate synthetase I (CPS I), a urea cycle enzyme, is located almost exclusively in the mitochondria of hepatocytes. The enzyme is unique in that it constitutes about 2-6% of total liver protein and is composed of a large subunit of 160 kD. We developed a sensitive enzyme-linked immunosorbent assay (ELISA) for measurement of the enzyme in plasma using an antibody against the rat enzyme. In galactosamine-induced rat acute hepatitis, plasma concentration of CPS I that was 1-2 micrograms/ml blood before the treatment, increased up to 125 micrograms/ml blood in 24 h after the treatment and decreased to a near control level in 72 h. Plasma concentration of ornithine carbamoyl-transferase (OCT), another urea cycle enzyme, reached a maximum in 24 h and then decreased a little more rapidly than that of CPS I. On the other hand, alanine aminotransferase activity reached a maximum in 36 h and decreased to a normal level in 96 h. In immunoblot analysis, the native CPS I polypeptide of 160 kD and its fragments of 140 and 125 kD were detected 24-48 h after the treatment. When purified rat CPS I and bovine OCT were injected intravenously into rats, the enzymes disappeared from blood roughly exponentially with apparent half-lives of about 67 and 18 min, respectively. Development of an ELISA for human CPS I and determination of the serum enzyme in various liver diseases remain to be performed.
Protection of cats against feline leukemia virus by vaccination with a canarypox virus recombinant, ALVAC-FL (1993)

Two ALVAC (canarypox virus)-based recombinant viruses expressing the feline leukemia virus (FeLV) subgroup A env and gag genes were assessed for their protective efficacy in cats. Both recombinant viruses contained the entire gag gene. ALVAC-FL also expressed the entire envelope glycoprotein, while ALVAC-FL(dl IS) expressed an env-specific gene product deleted of the putative immunosuppressive region. Although only 50% of the cats vaccinated with ALVAC-FL(dl IS) were protected against persistent viremia after oronasal exposure to a homologous FeLV isolate, all cats administered ALVAC-FL resisted the challenge exposure. Significantly, protection was afforded in the absence of detectable FeLV-neutralizing antibodies. These results represent the first effective vaccination of cats against FeLV with a poxvirus-based recombinant vector and have implications that are relevant not only to FeLV vaccine development but also to developing vaccines against other retroviruses, including human immunodeficiency virus.
High performance fully-depleted tri-gate CMOS transistors (2003)

Fully-depleted (FD) tri-gate CMOS transistors with 60 nm physical gate lengths on SOI substrates have been fabricated. These devices consist of a top and two side gates on an insulating layer. The transistors show near-ideal subthreshold gradient and excellent DIBL behavior, and have drive current characteristics greater than any non-planar devices reported so far, for correctly-targeted threshold voltages. The tri-gate devices also demonstrate full depletion at silicon body dimensions approximately 1.5 - 2 times greater than either single gate SOI or non-planar double-gate SOI for similar gate lengths, indicating that these devices are easier to fabricate using the conventional fabrication tools. Comparing tri-gate transistors to conventional bulk CMOS device at the same technology node, these non-planar devices are found to be competitive with similarly-sized bulk CMOS transistors. Furthermore, three-dimensional (3-D) simulations of tri-gate transistors with transistor gate lengths down to 30 nm show that the 30 nm tri-gate device remains fully depleted, with near-ideal subthreshold swing and excellent short channel characteristics, suggesting that the tri-gate transistor could pose a viable alternative to bulk transistors in the near future.
A complementary gain cell technology for sub-1 V supply DRAMs (1992)

A Complementary Gain (CG) cell concept is proposed and experimentally demonstrated to overcome the scaling limit of the conventional DRAM cell. The CG cell performance is described in comparison with a conventional cell from the viewpoint of factors relevant to gigabit integration, such as supply voltage scalability, minimum storage capacitance, immunity to noise on bitline and cell size. The test CG memory cell operation is successfully demonstrated at a supply voltage below 1V.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Developing Enjoyable Second Language Learning Software Tools (2006)

This chapter attempts to examine computer game theories — ludology and narratology— that explain computer games as play activities and storytelling media. Founded onthis theoretical explanation, a game model that incorporates gameplay and narrativesis presented. From the model, two aspects of learning in the game environment areidentified: gameplay-oriented and narrative-oriented. It is believed that playingcomputer games involves at least one of these types of learning; thus, this game’s naturecan be used in designing engaging educational software. In addition, based onMalone’s theoretical framework on motivational heuristics, there are two methods ofapplying computer games in language learning: extrinsic and intrinsic, depending onthe integration of game designs and learning materials. Then, two cases of language-learning games are scrutinized, using the game model, in order to demonstrate the useof computer games in language learning.
Nicotine induces human neutrophils to produce IL-8 through the generation of peroxynitrite and subsequent activation of NF-κB (2003)

Leukocytosis in tobacco smokers has been well recognized; however, the exact cause has not been elucidated. To test the hypothesis that tobacco nicotine stimulates neutrophils in the respiratory tract to produce IL-8, which causes neutrophilia in vivo, we examined whether nicotine induces neutrophil-IL-8 production in vitro; the causative role of NF-kappaB in its production, in association with the possible production of reactive oxygen intermediates that activate NF-kappaB; and the nicotinic acetylcholine receptors (nAChRs) involved in IL-8 production. Nicotine stimulated neutrophils to produce IL-8 in both time- and concentration-dependent manners with a 50% effective concentration of 1.89 mM. A degradation of IkappaB-alpha/beta proteins and an activity of NF-kappaB p65 and p50 were enhanced following nicotine treatment. The synthesis of superoxide and the oxidation of dihydrorhodamine 123 (DHR) were also enhanced. The NOS inhibitor, nomega-Nitro-l-arginine methyl ester, prevented nicotine-induced IL-8 production, with an entire abrogation of DHR oxidation, IkappaB degradation, and NF-kappaB activity. Neutrophils spontaneously produced NO whose production was not increased, but rather decreased by nicotine stimulation, suggesting that superoxide, produced by nicotine, generates peroxynitrite by reacting with preformed NO, which enhances the NF-kappaB activity, thereby producing IL-8. The nAChRs seemed to be involved in IL-8 production. In smokers, blood IL-8 levels were significantly higher than those in nonsmokers. In conclusion, nicotine stimulates neutrophil-IL-8 production via nAChR by generating peroxynitrite and subsequent NF-kappaB activation, and the IL-8 appears to contribute to leukocytosis in tobacco smokers.
A Versatile Synthesis of Amidines from NitrilesViaAmidoximes (1996)

Abstract Benzamidines were prepared conveniently from benzonitriles in good yield via catalytic hydrogenation of intermediate benzamidoximes in acetic acid/acetic anhydride.
Design Parameters and Current Fabrication Approaches for Developing Bioinspired Dry Adhesives (2007)

The attachment pads of some beetles, spiders, flies, and geckos are covered by a dense array of long hairs with characteristic geometries. This curious surface topography allows them to firmly attach to and easily release from almost any kind of surface. In a technological context, such reversible adhesion could enable robots to walk along walls or ceilings, or lead to new medical devices, disposable plasters, reusable adhesive tapes, etc. Artificial fibrillar surfaces mimicking nature's design have been recently fabricated, but their adhesion performance is still far from that of natural systems. This review describes the progress in this field during the last few years and discusses the issues pending for the future.
Characterization and magnetic properties of core/shell structured Fe/Au nanoparticles (2004)

Au-coated Fe nanoparticles have been prepared by using a reverse micelle method through reduction of an aqueous solution. Characterizations have been carried out over time to probe the oxidation of Fe. Immediately after synthesis, the samples exhibit metallic conduction and a negative magnetoresistance, consistent with the presence of α-Fe. The temperature dependence of magnetization displays a maximum at a blocking temperature of around 150 K. After a period of 1 month, the samples exhibit insulating behavior, indicating the oxidation of the Fe core. Mössbauer spectroscopy indicates the presence of an α-Fe component and a broad distribution of local environments.
ChemInform Abstract: PYRROLES AND RELATED COMPOUNDS PART 26, PYRROLE BETA‐KETO‐ESTERS (1974)

Abstract Zahlreiche Versuche zur Synthese von Pyrrol‐β‐ketoestern (als Modell‐ bzw. Zwischer Verbindungen bei der Chlorophyllsynthese) werden durchgeführt.
Split-Brain Autoencoders: Unsupervised Learning by Cross-Channel Prediction (2017)

We propose split-brain autoencoders, a straightforward modification of the traditional autoencoder architecture, for unsupervised representation learning. The method adds a split to the network, resulting in two disjoint sub-networks. Each sub-network is trained to perform a difficult task - predicting one subset of the data channels from another. Together, the sub-networks extract features from the entire input signal. By forcing the network to solve crosschannel prediction tasks, we induce a representation within the network which transfers well to other, unseen tasks. This method achieves state-of-the-art performance on several large-scale transfer learning benchmarks.
Allele-specific expression and total expression levels of imprinted genes during early mouse development: implications for imprinting mechanisms. (1995)

Genomic imprinting determines the monoallelic expression of a small number of genes during at least later stages of development. To obtain information necessary for the elucidation of imprinting mechanisms, we assessed the allele-specific expression and total expression level of four imprinted genes during early stages of development of normal F1 hybrid mice utilizing quantitative allele-specific reverse transcription-PCR (RT-PCR) single-nucleotide primer extension assays. The Igf2r and Snrpn genes were activated by the early 4-cell stage and exhibited biallelic and monoallelic expression, respectively, throughout preimplantation development. Thus, with respect to different imprinted genes, epigenetic systems determining monoallelic expression are not uniform in their time of establishment. Biallelic expression of Igf2r was observed in single blastomeres, discounting the possibility of random allelic inactivation at this stage. The closely linked H19 and Igf2 genes were activated after the blastocyst stage and often exhibited biallelic and monoallelic expression respectively in tissues of pregastrulation postimplantation-stage embryos, rather than reciprocal monoallelic modes as observed at later stages. This raises the possibility that imprinting of H19 is involved only in the maintenance and not in the initiation of monoallelic expression of Igf2. Monoallelic expression of Snrpn was observed in each blastomere at the 4-cell stage, demonstrating that the germ line, which exhibits biallelic expression of imprinted genes, must be derived from cells in which imprinting was once manifest.
Performance issues of enterprise level web proxies (1997)

Enterprise level web proxies relay world-wide web traffic between private networks and the Internet. They improve security, save network bandwidth, and reduce network latency. While the performance of web proxies has been analyzed based on synthetic workloads, little is known about their performance on real workloads. In this paper we present a study of two web proxies (CERN and Squid) executing real workloads on Digital's Palo Alto Gateway. We demonstrate that the simple CERN proxy architecture outperforms all but the latest version of Squid and continues to outperform cacheless configurations. For the measured load levels the Squid proxy used at least as many CPU, memory, and disk resources as CERN, in some configurations significantly more resources. At higher load levels the resource utilization requirements will cross and Squid will be the one using fewer resources. Lastly we found that cache hit rates of around 30% had very little effect on the requests service time.
Cells Isolated from Umbilical Cord Tissue Rescue Photoreceptors and Visual Functions in a Rodent Model of Retinal Disease (2006)

Progressive photoreceptor degeneration resulting from genetic and other factors is a leading and largely untreatable cause of blindness worldwide. The object of this study was to find a cell type that is effective in slowing the progress of such degeneration in an animal model of human retinal disease, is safe, and could be generated in sufficient numbers for clinical application. We have compared efficacy of four human-derived cell types in preserving photoreceptor integrity and visual functions after injection into the subretinal space of the Royal College of Surgeons rat early in the progress of degeneration. Umbilical tissue-derived cells, placenta-derived cells, and mesenchymal stem cells were studied; dermal fibroblasts served as cell controls. At various ages up to 100 days, electroretinogram responses, spatial acuity, and luminance threshold were measured. Both umbilical-derived and mesenchymal cells significantly reduced the degree of functional deterioration in each test. The effect of placental cells was not much better than controls. Umbilical tissue-derived cells gave large areas of photoreceptor rescue; mesenchymal stem cells gave only localized rescue. Fibroblasts gave sham levels of rescue. Donor cells were confined to the subretinal space. There was no evidence of cell differentiation into neurons, of tumor formation or other untoward pathology. Since the umbilical tissue-derived cells demonstrated the best photoreceptor rescue and, unlike mesenchymal stem cells, were capable of sustained population doublings without karyotypic changes, it is proposed that they may provide utility as a cell source for the treatment of retinal degenerative diseases such as retinitis pigmentosa.
Prevention of insulin self-aggregation by a protic ionic liquid (2012)

The self-aggregation and thermal instability of insulin (In) was considerably controlled in the presence of ammonium-based protic ionic liquids (PILs). The thermal stability of In in PILs was observed using fluorescence and absorption spectroscopy of the Tyr environment of the biomolecule. Additionally, from circular dichroism (CD) measurements, we observed the shift in the wavelength towards lower values in the presence of PILs, which indicates the formation of monomers of In, further evidently supported by dynamic light scattering (DLS) measurements. Surprisingly, it is the monomeric form of the In that exists in the active form. For the first time, ammonium-based PILs have been shown to be novel solvents for In, which prevent it from associating into an inactive form and also stabilizes In against thermal influence.
Natural killer-like nonspecific tumor cell lysis mediated by specific ligand-activated Vα14 NKT cells (1998)

We have recently identified alpha-galactosylceramide (alpha-GalCer) as a specific ligand for an invariant Valpha14/Vbeta8.2 T cell receptor exclusively expressed on the majority of Valpha14 NKT cells, a novel subset of lymphocytes. Here, we report that alpha-GalCer selectively activates Valpha14 NKT cells resulting in prevention of tumor metastasis. The effector mechanisms of the ligand-activated Valpha14 NKT cells seem to be mediated by natural killer (NK)-like nonspecific cytotoxicity. Indeed, the cytotoxic index obtained by alpha-GalCer-activated Valpha14 NKT cells was reduced by the addition of cold target tumor cells or by treatment with concanamycin A, which inhibits activation and secretion of perforin, but not by mAbs against molecules involved in the NKT cell recognition and conventional cytotoxicity, such as CD1d, Vbeta8, NK1. 1, Ly49C, Fas, or Fas ligand. These results suggest that the ligand-activated Valpha14 NKT cells kill tumor cells directly through a CD1d/Valpha14 T cell receptor-independent, NK-like mechanism.
C-Reactive Protein Levels and Outcomes after Statin Therapy (2005)

Patients who have low CRP levels after statin therapy have better clinical outcomes than those with higher CRP levels, regardless of the resultant level of LDL cholesterol. Strategies to lower cardiovascular risk with statins should include monitoring CRP as well as cholesterol.