gebhart/patrepeval huggingface dataset:
Transesterification and Gelation of Polyhydroxy Esters Formed from Diepoxides and Dicarboxylic Acids (1984)

The base-catalyzed addition esterification reaction between an epoxy and a carboxyl group is followed by a transesterification reaction, in which the hydroxy ester is transformed into a diester and 1,2-diol. This reaction is reversible. In the reaction of a diepoxide (diglycidyl ether of bisphenol A) and a dicarboxylic acid (azelaic acid or a carboxyl-terminated polybutadiene), gelation occurs by transesterification; the cross-linking density of the gel increases and reaches a steady value corresponding to the transesterification equilibrium. A statistical theory based on the theory of branching processes has been developed for gelation and network formation by addition esterification and transesterification. A relatively high sol fraction is predicted as a result of simultaneously occurring bond formation and scission. Both the experimental sol fractions and degrees of cross-linking calculated from the elasticity modulus are in good agreement with the theory.
Packets found on an internet (1993)

As part of our security measures, we spend a fair amount of time and effort looking for things that might otherwise be ignored. Apart from assorted attempted penetrations, we have also discovered many examples of anomalous behavior. These range from excessive ICMP messages to nominally-local broadcast packets that have reached us from around the world.
A case for a non‐transgenic animal model of Alzheimer's disease (2005)

Alzheimer's disease (AD) is associated with an early impairment in memory and is the major cause of dementia in the elderly. beta-Amyloid (Abeta) is believed to be a primary factor in the pathogenic pathway leading to dementia. Mounting evidence suggests that this syndrome begins with subtle alterations in synaptic efficacy prior to extensive neuronal degeneration and that the synaptic dysfunction could be caused by diffusible oligomeric assemblies of Abeta. This paper reviews the findings from behavioral analysis, electrophysiology, neuropathology and nootropic drug screening studies involving exogenous administration of Abeta in normal rodent brains. This non-transgenic model of amyloid pathology in vivo is presented as a complementary alternative model to transgenic mice to study the cellular and molecular pathways induced by amyloid, which in turn may be a causal factor in the disruption of cognition. The data reviewed here confirm that the diffusible form of Abeta rapidly induces synaptic dysfunction and a secondary process involving cellular cascades induced by the fibrillar form of amyloid. The time-course of alteration in memory processes implicates at least two different mechanisms that may be targeted with selective therapies aimed at improving memory in some AD patients.
Defects in the Medial Entorhinal Cortex and Dentate Gyrus in the Mouse Model of Sanfilippo Syndrome Type B (2011)

Sanfilippo syndrome type B (MPS IIIB) is characterized by profound mental retardation in childhood, dementia and death in late adolescence; it is caused by deficiency of α-N-acetylglucosaminidase and resulting lysosomal storage of heparan sulfate. A mouse model, generated by homologous recombination of the Naglu gene, was used to study pathological changes in the brain. We found earlier that neurons in the medial entorhinal cortex (MEC) and the dentate gyrus showed a number of secondary defects, including the presence of hyperphosphorylated tau (Ptau) detected with antibodies raised against Ptau in Alzheimer disease brain. By further use of immunohistochemistry, we now show staining in neurons of the same area for beta amyloid, extending the resemblance to Alzheimer disease. Ptau inclusions in the dentate gyrus of MPS IIIB mice were reduced in number when the mice were administered LiCl, a specific inhibitor of Gsk3β. Additional proteins found elevated in MEC include proteins involved in autophagy and the heparan sulfate proteoglycans, glypicans 1 and 5, the latter closely related to the primary defect. The level of secondary accumulations was associated with elevation of glypican, as seen by comparing brains of mice at different ages or with different mucopolysaccharide storage diseases. The MEC of an MPS IIIA mouse had the same intense immunostaining for glypican 1 and other markers as MPS IIIB, while MEC of MPS I and MPS II mice had weak staining, and MEC of an MPS VI mouse had no staining at all for the same proteins. A considerable amount of glypican was found in MEC of MPS IIIB mice outside of lysosomes. We propose that it is the extralysosomal glypican that would be harmful to neurons, because its heparan sulfate branches could potentiate the formation of Ptau and beta amyloid aggregates, which would be toxic as well as difficult to degrade.
RstA-Promoted Expression of the Ferrous Iron Transporter FeoB under Iron-Replete Conditions Enhances Fur Activity in Salmonella enterica (2008)

The Fur protein is a primary regulator that monitors and controls cytoplasmic iron levels. We now report the identification of a regulatory pathway mediated by the Salmonella response regulator RstA that promotes Fur activity. Genome-wide expression experiments revealed that under iron-replete conditions, expression of the RstA protein from a plasmid lowered transcription levels of various genes involved in iron acquisition. The RstA protein controlled iron-responsive genes through the Fur-Fe(II) protein because deletion of the fur gene or iron depletion abrogated RstA-mediated repression of these genes. The RstA protein maintained wild-type levels of the Fur protein but exceptionally activated transcription of the feoAB operon encoding the ferrous iron transporter FeoB by binding directly to the feoA promoter. This FeoB induction resulted in increased ferrous iron uptake, which associates with the Fur protein because lack of RstA-dependent transcriptional activation of the feoA promoter and feoB-deletion abolished repression of the Fur target genes by the RstA protein. Under iron-replete conditions, RstA expression retarded Salmonella growth but enabled the Fur protein to repress the target genes beyond the levels which were simply accomplished by iron.
High-Throughput Multiplex Flow Cytometry Screening for Botulinum Neurotoxin Type A Light Chain Protease Inhibitors (2009)

Given their medical importance, proteases have been studied by diverse approaches and screened for small molecule protease inhibitors. Here, we present a multiplexed microsphere-based protease assay that uses high-throughput flow cytometry to screen for inhibitors of the light chain protease of botulinum neurotoxin type A (BoNTALC). Our assay uses a full-length substrate and several deletion mutants screened in parallel to identify small molecule inhibitors. The use of multiplex flow cytometry has the advantage of using full-length substrates, which contain already identified distal-binding elements for the BoNTALC, and could lead to a new class of BoNTALC inhibitors. In this study, we have screened 880 off patent drugs and bioavailable compounds to identify ebselen as an in vitro inhibitor of BoNTALC. This discovery demonstrates the validity of our microsphere-based approach and illustrates its potential for high-throughput screening for inhibitors of proteases in general.
Targeting the Phosphatidylinositol 3-Kinase Signaling Pathway in Breast Cancer (2011)

The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) network plays a key regulatory function in cell survival, proliferation, migration, metabolism, angiogenesis, and apoptosis. Genetic aberrations found at different levels, either with activation of oncogenes or inactivation of tumor suppressors, make this pathway one of the most commonly disrupted in human breast cancer. The PI3K-dependent phosphorylation and activation of the serine/threonine kinase AKT is a key activator of cell survival mechanisms. The activation of the oncogene PIK3CA and the loss of regulators of AKT including the tumor suppressor gene PTEN are mutations commonly found in breast tumors. AKT relieves the negative regulation of mTOR to activate protein synthesis and cell proliferation through S6K and 4EBP1. The common activation of the PI3K pathway in breast cancer has led to the development of compounds targeting the effector mechanisms of the pathway including selective and pan-PI3K/pan-AKT inhibitors, rapamycin analogs for mTOR inhibition, and TOR-catalytic subunit inhibitors. The influences of other oncogenic pathways such as Ras-Raf-Mek on the PI3K pathway and the known feedback mechanisms of activation have prompted the use of compounds with broader effect at multiple levels and rational combination strategies to obtain a more potent antitumor activity and possibly a meaningful clinical effect. Here, we review the biology of the network, its role in the development and progression of breast cancer, and the evaluation of targeted therapies in clinical trials.
Structure of K-76, a complement inhibitor produced by Stachybotrys complementi nov. Sp. K-76 (1979)

H. Kaise, M. Shinohara, W. Miyazaki, T. Izawa, Y. Nakano, M. Sugawara, K. Sugiura and K. Sasaki, J. Chem. Soc., Chem. Commun., 1979, 726 DOI: 10.1039/C39790000726
HIV-1 Coat Protein Neurotoxicity Prevented by Calcium Channel Antagonists (1990)

Coat protein gp120 from the human immunodeficiency virus type-1 (HIV-1) increased intracellular free calcium and injured rodent retinal ganglion cells and hippocampal neurons in culture. Highly purified recombinant gp120 envelope protein produced these effects in a dose-dependent fashion at picomolar concentrations. Immunoprecipitation with antibody to gp120, but not with control immunoglobulin-containing serum, depleted solutions of the viral envelope protein and also prevented both the rise in intracellular calcium and neuronal toxicity. The gp120-induced increase in intracellular calcium was abrogated by transiently lowering extracellular calcium or by adding the dihydropyridine calcium channel antagonist nimodipine (100 nM). Calcium channel antagonists also prevented gp120-induced neuronal injury. In addition, intracellular stores appeared to contribute substantially to the increase in calcium elicited by gp120. Since increases in intracellular calcium have been associated with neurotoxicity, it is possible that an injurious effect of gp120 on neurons might be related to this mechanism and that treatment with calcium channel antagonists may prove useful in mitigating HIV-1-related neuronal injury.
Tumor Necrosis Factor-α (1997)

These studies demonstrate that exogenous TNF-alpha exacerbates focal ischemic injury and that blocking endogenous TNF-alpha is neuroprotective. The specificity of the action(s) of TNF-alpha was demonstrated by antagonism of its effects with specific anti-TNF-alpha tools (ie, mAb and sTNF-RI). TNF-alpha toxicity does not appear to be due to a direct effect on neurons or modulation of neuronal sensitivity to glutamate or oxygen radicals and apparently is mediated through nonneuronal cells. These data suggest that inhibiting TNF-alpha may represent a novel pharmacological strategy to treat ischemic stroke.
Magnetic Cell Separation:  Characterization of Magnetophoretic Mobility (2003)

Magnetic cell separation has become a popular technique to enrich or deplete cells of interest from a heterogeneous cell population. One important aspect of magnetic cell separation is the degree to which a cell binds paramagnetic material. It is this paramagnetic material that imparts a positive magnetophoretic mobility to the target cell, thus allowing effective cell separation. A mathematical relationship has been developed to correlate magnetic labeling to the magnetophoretic mobility of an immunomagnetically labeled cell. Four parameters have been identified that significantly affect magnetophoretic mobility of an immunomagnetically labeled cell: the antibody binding capacity (ABC) of a cell population, the secondary antibody amplification (psi), the particle-magnetic field interaction parameter (DeltachiV(m)), and the cell diameter (D(c)). The ranges of these parameters are calculated and presented along with how the parameters affect the minimum and maximum range of magnetophoretic mobility. A detailed understanding of these parameters allows predictions of cellular magnetophoretic mobilities and provides control of cell mobility through selection of antibodies and magnetic particle conjugates.
Adjuvant-Enhanced Antibody Responses in the Absence of Toll-Like Receptor Signaling (2006)

Innate immune signals mediated by Toll-like receptors (TLRs) have been thought to contribute considerably to the antibody-enhancing effects of vaccine adjuvants. However, we report here that mice deficient in the critical signaling components for TLR mount robust antibody responses to T cell-dependent antigen given in four typical adjuvants: alum, Freund's complete adjuvant, Freund's incomplete adjuvant, and monophosphoryl-lipid A/trehalose dicorynomycolate adjuvant. We conclude that TLR signaling does not account for the action of classical adjuvants and does not fully explain the action of a strong adjuvant containing a TLR ligand. This may have important implications in the use and development of vaccine adjuvants.
Cytochrome P-450 in Human Liver Microsomes: High-Performance Liquid Chromatographic Isolation of Three Forms and Their Characterization1 (1988)

Three forms of cytochrome P-450, designated as P-450-HM1, P-450-HM2, and P-450-HM3, were isolated from human liver microsomes using high-performance liquid chromatography (HPLC) techniques. Each purified preparation showed a single protein band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). From the results of SDS-PAGE, the molecular weights of P-450-HM1, P-450-HM2, and P-450-HM3 were estimated to be 51,000, 54,000, and 52,000, respectively. The oxidized absolute spectra of these three forms of cytochrome P-450 showed Soret absorption peaks at around 417 nm, indicating that these forms were in the low spin state. In a reconstituted system, P-450-HM1 showed the highest catalytic activities of nifedipine and (S)- or (R)-nilvadipine oxidases. The same form showed higher activities of testosterone 6 beta-hydroxylase and progesterone 6 beta- and 16 alpha-hydroxylases. P-450-HM2 showed high N-demethylase activities for benz-phetamine and aminopyrine, and also showed the highest activity of testosterone 16 beta-hydroxylase among the three forms, while it did not show detectable activities of testosterone 6 beta-hydroxylase and progesterone 6 beta- and 16 alpha-hydroxylases. Anti-P-450-HM1 immunoglobulin G (IgG), but not anti-P-450-HM2 IgG, inhibited the activities of testosterone 6 beta-hydroxylase and nifedipine and nilvadipine oxidases in human liver microsomes. Anti-P-450-HM1 IgG was also inhibitory against progesterone 6 beta- and 16 alpha-hydroxylases.(ABSTRACT TRUNCATED AT 250 WORDS)
Nanoimprint Lithography for Hybrid Plastic Electronics (2003)

The merger of nanoscale devices with flexible, low cost plastics could enable a broad spectrum of electronic and photonic applications, although difficulties in processing plastics at the nanoscale have limited exploration of this potential. Here we describe the use of room temperature nanoimprint lithography for the general fabrication of nanometer- through millimeter-scale patterns on polymer substrates. Specifically, we demonstrate the patterning of arrays of nanoscale source−drain electrode pairs with continuous interconnects to the millimeter length scale, and the fabrication of hundred-nanometer gate features hierarchically patterned over large areas. These patterned plastic substrates have also been used in conjunction with semiconductor nanowires to assemble field-effect transistors.
Influence of Genotype and Ensiling of Corn Grain on In Situ Degradation of Starch in the Rumen (1998)

This trial was conducted to determine the influence of genotype and ensiling of corn grain on the rate and extent of ruminal starch degradation. Two cultivars of corn that differed in texture of the endosperm, dent (Zea mays ssp. indentata) or flint (Zea mays ssp. indentura) were harvested at 30% whole-plant dry matter (DM). After separation from stover and cob, the kernels were coarsely chopped and ensiled or not ensiled. Grains were oven-dried at 40 degrees C and either ground through a 3-mm sieve or left unground. Ruminal DM and starch degradabilities were determined using the in situ technique. The proportion of starch lost through the pores of the bag without degradation was also determined. Mean ruminal DM and starch degradabilities were higher for ground grains than for chopped grains, which could be related to the proportion of DM and starch lost through the pores of the bag. For unensiled, chopped grain, ruminal starch degradability was higher for dent corn than for flint corn (72.3% vs. 61.6%). The ensiling process increased ruminal starch degradability, averaging 5.8 percentage units. The difference in ruminal starch degradability between dent corn and flint corn remained constant whether the corn was unensiled or ensiled (10.7 vs. 11.6 percentage units).
Design, analysis, and performance evaluation for BICM-ID with square QAM constellations in Rayleigh fading channels (2001)

We consider bit-interleaved coded modulation with iterative decoding (BICM-ID) for bandwidth-efficient transmission over Rayleigh fading channels. We propose the design criteria that utilize a large Hamming distance inherited in a low-rate code and a new labeling technique designed specifically for fading channels. This results in a large coding gain over noniterative coded modulation and performance close to that of "turbo" coded modulation with less complexity. We also show that BICM-ID designed for fading channels usually has a very good performance over the additive white Gaussian noise (AWGN) channel while the converse is difficult to achieve. When combined with signal space diversity, diversity order can be improved to twice the diversity order of conventional BICM-ID; therefore, the code complexity can further be reduced while maintaining the same level of performance. Specifically, with the bandwidth efficiency of 2 bits/s/Hz over Rayleigh fading channels, a bit error rate (BER) of 10/sup -6/ can be achieved with 16-QAM, a four-state rate 1/2 code at E/sub b//N/sub 0/ of about seven dB. We also derive performance bounds for BICM-ID with and without signal space diversity over Rayleigh fading channels, which can be easily extended for other types of fading channels.
A low loss, 5.5 GHz-20 GHz monolithic balun (2002)

A low-loss monolithic Marchand balun has been designed and fabricated using polyimide as the inter-metal dielectric. The measured return loss is less than -10 dB from 5.5 GHz to 28 GHz. The balun loss is less than 0.7 dB over the 6 GHz to 21 GHz operating band. This is the lowest loss ever reported for such a balun. The excellent loss is the result of using a relatively thick polyimide layer (10 /spl mu/m) as the inter-metal dielectric. This balun has been applied to HBT and pHEMT amplifiers with second harmonic components suppressed >40 dB, even in compression, demonstrating very good push-pull operation.
HermesC: Low-Power Wireless Neural Recording System for Freely Moving Primates (2009)

Neural prosthetic systems have the potential to restore lost functionality to amputees or patients suffering from neurological injury or disease. Current systems have primarily been designed for immobile patients, such as tetraplegics functioning in a rather static, carefully tailored environment. However, an active patient such as amputee in a normal dynamic, everyday environment may be quite different in terms of the neural control of movement. In order to study motor control in a more unconstrained natural setting, we seek to develop an animal model of freely moving humans. Therefore, we have developed and tested HermesC-INI3, a system for recording and wirelessly transmitting neural data from electrode arrays implanted in rhesus macaques who are freely moving. This system is based on the integrated neural interface (INI3) microchip which amplifies, digitizes, and transmits neural data across a approximately 900 MHz wireless channel. The wireless transmission has a range of approximately 4 m in free space. All together this device consumes 15.8 mA and 63.2 mW. On a single 2 A-hr battery pack, this device runs contiguously for approximately six days. The smaller size and power consumption of the custom IC allows for a smaller package (51 x 38 x 38 mm (3)) than previous primate systems. The HermesC-INI3 system was used to record and telemeter one channel of broadband neural data at 15.7 kSps from a monkey performing routine daily activities in the home cage.
ERWEITERTE MOEGLICHKEITEN DER ASPHALTWIEDERVERWENDUNG IN TRAGSCHICHTEN (1989)

Ein grosser Teil des ausgebauten Asphalts wird seinem Wert entsprechend nicht wiederverwendet, da der vorgeschriebene Grenzwert fuer den zulaessigen Anteil im bituminoesen Mischgut fuer Tragschichten nach den ZTVT dies nicht zulaesst. Die Zugabe von Ausbauasphalt ist bei Mischgut fuer bituminoese Tragschichten bei Kaltzugabe auf 30 Prozent, bei Erwaermung bis zu 60 Prozent zulaessig. Bei einer durchschnittlichen Grenze von 50 Prozent haetten sich in den drei Jahren Autobahnbau in Hessen von 380.000 Tonnen wiederverwendbarem Ausbauasphalt nur 125.000 Tonnen Ausbauasphalt verwenden lassen, so dass ein stattlicher Rest uebrig bleibt, fuer den innerhalb des Konzeptes der Strassenerhaltung ein zusaetzlicher Absatzmarkt gefunden werden muss. Untersuchungen ueber einen hoeheren Zugabewert sind im Gange. Bei den Versuchsstrecken wurde auf die Frostschutzschicht verzichtet und eine ausschliesslich aus Asphaltgranulat bestehende Schicht von 12 oder 14 Zentimetern direkt auf dem Erdplanum eingebaut. Aus Versuchen mit Einbautemperaturen zwischen 100 und 140 Grad Celsius konnte ein ausreichender Verdichtungsgrad erzielt werden. Asphalttragschichten im Heisseinbau mit bis zu 100 Prozent Asphaltgranulat verhielten sich wie die konventionellen Asphaltarten im Strassenbau. Dies gilt nur fuer den Heisseinbau. Fuer Asphalttragschichten mit Asphaltgranulat wird durch Vermischen mit Bitumenemulsion ein kalteinbaufaehiges Mischgut hergestellt, das Erfolg verspricht.
Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain (2014)

The imprinted Kcnq1 domain contains a differentially methylated region (KvDMR) in intron 11 of Kcnq1. The Kcnq1ot1 non-coding RNA emerges from the unmethylated paternal KvDMR in antisense direction, resulting in cis-repression of neighboring genes. The KvDMR encompasses the Kcnq1ot1 promoter, CTCF sites and other DNA elements, whose individual contribution to regulation of the endogenous domain is unknown. We find that paternal inheritance of a deletion of the minimal Kcnq1ot1 promoter derepresses the upstream Cdkn1c gene. Surprisingly, Kcnq1ot1 transcripts continue to emerge from alternative sites, evidence that silencing depends, not on the ncRNA, but on the promoter sequence. Detailed analyses of Kcnq1ot during cardiogenesis show substantial chromatin reorganization coinciding with discontinuous RNA production in both wild-type and mutant mice, with loss of imprinting. We show that CTCF binds to both methylated and unmethylated alleles of the KvDMR. Furthermore, we report a multitude of enhancers within the Kcnq1ot1 region, and present conformational dynamics of a novel heart enhancer engaged in Kcnq1 expression. Our results have important implications on tissue-specific imprinting patterns and how transcriptional mechanisms compete to maximize the expression of vital genes, in addition to shifting our perception on the role of the long ncRNA in regulating this imprinted domain.