gebhart/patrepeval huggingface dataset:
Selective Ortho Methylation of Nitroheteroaryls by Vicarious Nucleophilic Substitution (2008)

An efficient and scalable three-step one-pot approach to 6-methyl-5-nitroisoquinoline (1) from inexpensive 5-nitroisoquinoline, utilizing the vicarious nucleophilic substitution (VNS) as a key step, is described. The optimized reaction conditions can be applied to a limited number of other aromatic and heteroaromatic nitro compounds. Attempts to understand the observed selectivity in the VNS step led to the discovery of two new reaction pathways under VNS conditions, one leading to an isoxazole and the other resulting in the formal cyclopropanation of an aromatic nitro compound.
Regulated Expression of the Interferon-Induced Protein Kinase p68 (PKR) by Vaccinia Virus Recombinants Inhibits the Replication of Vesicular Stomatitis Virus but Not That of Poliovirus (1996)

A direct antiviral role of the interferon-induced human protein kinase p68 has been shown only against encephalomyocarditis virus (EMCV) and vaccinia virus (VV). To determine if p68 kinase (PKR) has a broad antiviral effect, we have used coinfections between VV recombinants expressing p68 kinase under regulation of the lac I operator/repressor elements of Escherichia coli and two RNA viruses, vesicular stomatitis virus (VSV) and poliovirus. In cells coinfected with VV recombinants and VSV, induction with isopropyl-B-D-thiogalactoside (IPTG) of wild-type p68 kinase or a mutant lacking the dsRNA binding domain resulted in inhibition of both VV and VSV protein synthesis. This inhibition is not observed in cells infected with a catalytically inactive point mutant lys-arg296 of p68 kinase. When cells are coinfected with VV recombinants and poliovirus, induction of active p68 kinase resulted in a decrease in VV proteins but not in poliovirus proteins or poliovirus yields. Immunoblot analysis revealed that p68 kinase was expressed during mixed infections. Our results demonstrate a differential effect of p68 kinase on the replication of VV, VSV, and poliovirus. We suggest that in a particular virus-cell system, the different sensitivity of a virus to p68 kinase is probably due to levels of active enzyme.
Evaluation of antibody–chemokine fusion proteins for tumor-targeting applications (2014)

There is an increasing biotechnological interest in the 'arming' of therapeutic antibodies with bioactive payloads. While many antibody-cytokine fusion proteins have been extensively investigated in preclinical and clinical studies, there are only few reports related to antibody-chemokine fusion proteins ('immunochemokines'). Here, we describe the cloning, expression, and characterization of 10 immunochemokines based on the monoclonal antibody F8, specific to the alternatively spliced extra domain A (EDA) of fibronectin, a marker of angiogenesis. Among the 10 murine chemokines tested in our study, only CCL19, CCL20, CCL21, and CXCL10 could be expressed and isolated at acceptable purity levels as F8-based fusion proteins. The immunochemokines retained the binding characteristics of the parental antibody, but could not be characterized by gel-filtration analysis, an analytical limitation which had previously been observed in our laboratory for the unconjugated chemokines. When radioiodinated preparations of CCL19-F8, CCL20-F8, CCL21-F8, and CXCL10-F8 were tested in quantitative biodistribution studies in tumor-bearing mice, the four fusion proteins failed to preferentially accumulate at the tumor site, while the unconjugated parental antibody displayed a tumor:blood ratio >20:1, 24 h after intravenous (i.v.) administration. The tumor-targeting ability of CCL19-F8 could be rescued only in part by preadministration of unlabeled CCL19-F8, indicating that a chemokine trapping mechanism may hinder pharmacodelivery strategies. While this article highlights expression, analytical, and biodistribution challenges associated with the antibody-based in vivo delivery of chemokines at sites of disease, it provides the first comprehensive report in this field and may facilitate future studies with immunochemokines.
Allelic mRNA expression of X-linked monoamine oxidase a (MAOA) in human brain: dissection of epigenetic and genetic factors (2006)

A pVNTR repeat polymorphism located in the promoter region of the X-linked MAOA gene has been associated with mental disorders. To explore the effect of polymorphisms and epigenetic factors on mRNA expression, we have measured allelic expression imbalance (AEI) in female human brain tissue, employing two frequent marker single nucleotide polymorphisms (SNPs) in exon 8 (T890G) and exon 14 (C1409T) of MAOA. This approach compares one allele against the other in the same subject. AEI ratios ranged from 0.3 to 4 in prefrontal cortex, demonstrating the presence of strong cis-acting factors in mRNA expression. Analysis of CpG methylation in the MAOA promoter region revealed substantial methylation in females but not in males. MAOA methylation ratios for the three- and four-repeat pVNTR alleles of MAOA did not correlate with X-chromosome inactivation ratios, determined at the X-linked androgen receptor locus, suggesting an alternative process of dosage compensation in females. The extent of allelic MAOA methylation was highly variable and correlated with AEI (R2=0.5 and 0.7 at two CpG loci), indicating that CpG methylation regulates gene expression. Genetic factors appeared also to contribute to the AEI ratios. Genotyping of 13 MAOA polymorphisms in female subjects showed strong association with a haplotype block spanning from the pVNTR to the marker SNP. Therefore, allelic mRNA expression is affected by genetic and epigenetic events, both with the potential to modulate biogenic amine tone in the CNS.
2012-18: The financial coaching advice model: An exploration into how it satisfies expectations of quality advice (Working paper) (2012)

For 20 years, the financial planning sector in Australia has been transitioning from a sales-orientated force to a profession of qualified and skilled practitioners. Today, the potential for professional financial planning advice to benefit Australians financially, economically and psychologically is recognised by government. Financially, these benefits include increased savings, less interest expense through faster debt reduction, higher investment returns and appropriate levels of insurance. Economically, a more financially literate society has the potential for less reliance on an already burdened social security. Psychologically, the benefits include the peace of mind that comes from an individual being confident in financial matters. However despite this level of recognition and development, national surveys have reported that only a small percentage of the population actually seek professional financial advice. The factors attributing to these low percentages included the gaps in financial literacy limiting an individual's engagement in financial matters and consumer's current mistrust of the financial advice business models that remain dominated by commission-driven product sales. These deficiencies have led some financial planning firms to break from financial product sales as the primary advice model and focus on financial coaching. Exploratory interviews with the practitioners and clients of a selected financial planning firm have generated insightful discussion into how a financial coaching advice model is achieving the financial, economic and psychological benefits recognised by government as the potential outcomes of professional financial advice. The aim of this paper is to present the findings from that discussion and demonstrate the opportunities embedded within a financial coaching advice model. It is argued this discussion offers a foundation for future research direction in an area currently unattended in academic literature.
Constructive influence of the induced electron pairing on the Kondo state (2016)

Superconducting order and magnetic impurities are usually detrimental to each other. We show, however, that in nanoscopic objects the induced electron pairing can have constructive influence on the Kondo effect originating from the effective screening interactions. Such situation is possible at low temperatures in the quantum dots placed between the conducting and superconducting reservoirs, where the proximity induced electron pairing cooperates with the correlations amplifying the spin-exchange potential. The emerging Abrikosov-Suhl resonance, which is observable in the Andreev conductance, can be significantly enhanced by increasing the coupling to superconducting lead. We explain this intriguing tendency within the Anderson impurity model using: the generalized Schrieffer-Wolff canonical transformation, the second order perturbative treatment of the Coulomb repulsion, and the nonperturbative numerical renormalization group calculations. We also provide hints for experimental observability of this phenomenon.
3 % Thermal Load Measured in Tandem-pumped Ytterbium-doped Fiber Amplifier (2014)

A tandem-pumped Yb-doped fiber with a quantum defect of 2% generates 3% of heat. We believe this is a record-low thermal load and the first calorimetric measurement of the heat from a fiber core.
Gas transport properties in (6FDA‐RTIL)‐(6FDA‐MDA) block copolyimides (2015)

ABSTRACT This article reports synthesis and structure property studies of block copolyimides synthesized using diamino room temperature ionic liquids (RTIL) as diamine monomers. Specifically, polyimide oligomers of different lengths were synthesized using 2,2‐bis (3,4‐carboxylphenyl) hexafluoropropane dianhydride (6FDA) and diamino RTIL (1,3‐di(3‐aminopropyl) imidazolium bis[(trifluoromethyl) sulfonyl] imide). These oligomers were copolymerized with 6FDA and m ‐phenylenediamine (MDA) using in situ polymerization to form (6FDA‐RTIL)‐(6FDA‐MDA) block copolyimides. The impact of the length and relative concentration of 6FDA‐RTIL oligomer in the copolymer on the resulting thermal, physical, and gas transport properties was monitored. As the concentration of the 6FDA‐RTIL segments increased, the backbone of the block copolyimides became more flexible resulting in a decrease in the glass transition temperature ( T g ) and an increase in the density. The permeabilities of the RTIL containing copolyimides were consistently lower than those of the base polyimide, 6FDA‐MDA, with some increase in selectivities. Interestingly, the permeabilities of films produced with the low molecular weight oligomers were very different than those produced with same composition of the high molecular weight oligomers. This may be indicative of very different morphologies within these copolyimides. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133 , 43077.
Entropy-based Classification of 'Retweeting' Activity on Twitter (2011)

Twitter is used for a variety of reasons, including information dissemination, marketing, political organizing and to spread propaganda, spamming, promotion, conversations, and so on. Characterizing these activities and categorizing associated user generated content is a challenging task. We present a information-theoretic approach to classification of user activity on Twitter. We focus on tweets that contain embedded URLs and study their collective `retweeting' dynamics. We identify two features, time-interval and user entropy, which we use to classify retweeting activity. We achieve good separation of different activities using just these two features and are able to categorize content based on the collective user response it generates. We have identified five distinct categories of retweeting activity on Twitter: automatic/robotic activity, newsworthy information dissemination, advertising and promotion, campaigns, and parasitic advertisement. In the course of our investigations, we have shown how Twitter can be exploited for promotional and spam-like activities. The content-independent, entropy-based activity classification method is computationally efficient, scalable and robust to sampling and missing data. It has many applications, including automatic spam-detection, trend identification, trust management, user-modeling, social search and content classification on online social media.
Involvement of histone hyperacetylation in triggering DNA fragmentation of rat thymocytes undergoing apoptosis (1996)

The treatment of rat thymocytes with trichostatin A and sodium butyrate, which are inhibitors of histone deacetylase, resulted in an increase in DNA fragmentation in a concentration-dependent manner. A significant increase in DNA fragmentation induced by these compounds was observed after a lag time of 2 h. Analysis of the fragmented DNA revealed the production of approximately 50 kb DNA fragments and DNA ladders, the biochemical hallmarks of apoptotic cell death. Judging from a laser scanning microscopic analysis, the inhibitors of histone deacetylase induced nuclear condensation, the morphological feature of apoptosis. Biochemical and morphological analyses demonstrated that trichostatin A and sodium butyrate induced thymocyte apoptosis. Furthermore, hyperacetylation of nuclear histones was observed in thymocytes treated with the inhibitors of histone deacetylase. These effects of sodium butyrate and trichostatin A were seen 0.5 and 1 h, respectively, after incubation of the cells. These results thus indicate that hyperacetylation of nucleosomal histones precedes DNA fragmentation in thymocytes undergoing apoptosis induced by trichostatin A and sodium butyrate.
A comparison of the inflammatory potential of particulates derived from two composite materials (1997)

In order to develop total joint prostheses with moduli of elasticity close to bone while retaining excellent strength characteristics, composite materials are being developed. Composites consist of graphite fibers embedded in a polymer matrix. We studied the inflammatory potential of particulates derived from two composites with different matrix components, polysulfone (PFS) and polyetherketoneketone (PEKK), in the rat subcutaneous air pouch model. Neat components of the composites were studied separately in the air pouch. Particulates also were studied in culture using the macrophage cell line RAW 264.7, adherent synovial cells (ASC), and human polymorphonuclear neutrophils (PMNs). Particles derived from the PEKK-containing composite material consistently were less inflammatory than the PFS composite-derived particles, as measured by PMN infiltration, neutral metalloprotease activity, tumor necrosis factor (TNF) activity, and prostaglandin E2 (PGE2) accumulation. Results from the neat materials confirmed the findings in the composite-derived material. PEKK composite-derived material produced less TNF from macrophage cultures, but there were no significant differences noted in PGE2 production from ASC or in superoxide anion generation from PMNs. Particles from both PSF and PEKK produced minimal inflammatory responses in the rat subcutaneous air pouch. PEKK elicited a response virtually the same as the saline control and significantly less than that produced by particles of PSF.
Architecting connectivity for fine-grained 3-D vertically integrated circuits (2015)

Conventional CMOS technology is reaching fundamental scaling limits, and interconnection bottleneck is dominating IC power and performance. Migrating to 3-D integrated circuits, though promising, has eluded us due to inherent customization and manufacturing requirements in CMOS that are incompatible with 3-D organization. Skybridge, a fine-grained 3-D IC fabric technology was recently proposed towards this aim, which offers a paradigm shift in technology scaling and design. In this paper we present specifically architected core Skybridge structures to enable fine-grained connectivity in 3-D intrinsically. We develop predictive models for interconnect length distribution for Skybridge, and use them to quantify the benefits in terms of expected reduction in interconnect lengths and repeater counts when compared to 2-D CMOS in 16nm node. Our estimation indicates up to 10x reduction in longest global interconnect length vs. 16nm 2-D CMOS, and up to 2 orders of magnitude reduction in the number of repeaters for a design consisting of 10 million logic gates. These results show great promise in alleviating interconnect bottleneck due to a higher degree of connectivity in 3-D, leading to shorter global interconnects and reduced power and area overhead due to repeater insertion.
Helping Patients Decide Whether to Participate in Clinical Trials (2007)

Case "I've been feeling miserable lately, and I haven't been able to eat much at all," Mr. Brooks said, wincing as he shifted on the exam table. "Well, end-stage colon cancer is a pretty nasty disease," Dr. Winston, his primary care physician of 15 years, replied softly. "And I understand from your chart that the masses in your liver and lungs haven't gotten any smaller since your last round of chemo."
Proviral rearrangements and overexpression of a new cellular gene (nov) in myeloblastosis-associated virus type 1-induced nephroblastomas. (1992)

Histological and anatomopathological studies performed on 152 independent myeloblastosis-associated virus type 1 (MAV1)-induced nephroblastomas allowed us to precisely define the chronology of tumor development in chickens. Three tumors representing increasing developmental stages were used to construct genomic libraries and to study both the state of proviral genomes and the sites of MAV1 integration in genomic DNA. We established that increasing levels of proviral rearrangement, eventually leading to the elimination of infectious MAV genomes, were associated with tumor progression and that 22 individual tumors, representative of different developmental stages, did not contain any common MAV1 integration site. Cloning of cellular fragments flanking the MAV1-related proviruses in tumor DNA showed that each one of eight nephroblastomas tested expressed a high level of an as yet unidentified cellular gene (nov) whose transcription is normally arrested in adult kidney cells. Cloning of the normal nov gene established that in one tumor, fused long terminal repeat-truncated nov mRNA species were expressed, indicating that at least in that case, the high level of nov expression was under the control of the MAV long terminal repeat promoter. The normal nov gene encodes a putative 32-kDa secreted polypeptide, which is a member of a new family of proteins likely to be involved in cell growth regulation. We also showed that the expression of an amino-terminal-truncated nov product in chicken embryo fibroblasts was sufficient to induce their transformation.
Antimicrobial resistance in selected bacteria from poultry (2008)

This paper reviews the present state of antimicrobial resistance (AMR) in the zoonotic bacteria Salmonella, Campylobacter jejuni and Campylobacter coli, and in Escherichia coli from chickens and turkeys. For Salmonella, the frequencies and patterns of AMR vary depending on time, region, serovar, the particular farm, layers versus broilers, and the antimicrobial agent. There is usually a higher frequency of AMR in Salmonella from turkeys compared with Salmonella from chickens. Clonal and horizontal transmission of AMR occur and there is concern about the spread of transmissible plasmids that encode extended spectrum cephalosporinases. Resistance to fluoroquinolones is generally low. For Campylobacter, resistance to tetracycline is usually at moderate to high frequency, resistance to quinolones/fluoroquinolones varies from low to high, and resistance to macrolides is usually low. There are high levels of fluoroquinolone resistance in some countries. Avian pathogenic E. coli are often highly resistant, especially to tetracycline, streptomycin, and sulfonamides. Plasmid-mediated resistance is common. High levels of resistance to ciprofloxacin have been reported from China. Commensal E. coli from poultry have similar patterns of resistance but at lower frequencies. Integron associated resistance occurs commonly in Salmonella and E. coli but has not been detected in Campylobacter.
Le rôle du Carbon Capture Utilization and Storage (CCUS) dans la transition énergétique (2022)

International audience
Impact of low-precision deep regression networks on single-channel source separation (2017)

Recent work on developing training methods for reduced precision Deep Convolutional Networks show that these networks can perform with similar accuracy to full precision networks when tested on a classification task. Reduced precision networks decrease the demand on the memory and computational power capabilities of the computing platform. This paper investigates the impact of reduced precision deep Recurrent Neural Networks (RNNs) when trained on a regression task, in this case, a monaural source separation task. The effect of reduced precision nets is explored for two popular recurrent network architectures: Vanilla RNNs and RNNs using Long-Short Term Memory (LSTM) units. The results show that the performance of the networks as measured by blind source separation metrics and speech intelligibility tests on two datasets, show very little decrease even when the weight precision goes down to 4 bits.
Toward establishing minimum requirements for extracellular electron transfer in Geobacter sulfurreducens (2017)

The highly redundant pathways for extracellular electron transfer in Geobacter sulfurreducens must be simplified for this microorganism to serve as an effective chassis for applications such as the development of sensors and biocomputing. Five homologs of the periplasmic c-type cytochromes, PpcA-E, offer the possibility of multiple routes of electron transfer across the periplasm. The presence of a large number of outer membrane c-type cytochromes allows G. sulfurreducens to adapt to disruption of an electron transfer pathway in the outer membrane. A strain in which genes for all five periplasmic cytochromes, PpcA-E, were deleted did not reduce Fe(III). Introducing ppcA under the control of an IPTG-inducible system in the quintuple deletion strain yielded a strain that reduced Fe(III) only in the presence of IPTG. A strain lacking known major outer membrane cytochromes, OmcB, OmcE, OmcS and OmcT, and putative functional homologs of OmcB, did not reduce Fe(III). Introduction of omcB in this septuple deletion strain restored the ability to reduce Fe(III). These results demonstrate that it is possible to trim redundancy from the extracellular electron transfer pathways in G. sulfurreducens in order to construct strains with defined extracellular electron transfer routes.
23.3 A 3nW fully integrated energy harvester based on self-oscillating switched-capacitor DC-DC converter (2014)

Recent advances in low-power circuits have enabled mm-scale wireless systems [1] for wireless sensor networks and implantable devices, among other applications. Energy harvesting is an attractive way to power such systems due to limited energy capacity of batteries at these form factors. However, the same size limitation restricts the amount of harvested power, which can be as low as 10s of nW for mm-scale photovoltaic cells in indoor conditions. Efficient DC-DC up-conversion at such low power levels (for battery charging) is extremely challenging and has not yet been demonstrated.