gebhart/patrepeval huggingface dataset:
Microbial metabolite deoxycholic acid shapes microbiota against Campylobacter jejuni chicken colonization (2019)

ABSTRACT Despite reducing the prevalent foodborne pathogen Campylobacter jejuni in chickens decreases campylobacteriosis, few effective approaches are available. The aim of this study was to use microbial metabolic product bile acids to reduce C. jejuni chicken colonization. Broiler chicks were fed with deoxycholic acid (DCA), lithocholic acid (LCA), or ursodeoxycholic acid (UDCA). The birds were also transplanted with DCA modulated anaerobes (DCA-Anaero) or aerobes (DCA-Aero). The birds were infected with human clinical isolate C. jejuni 81-176 or chicken isolate C. jejuni AR101. Notably, C. jejuni 81-176 was readily colonized intestinal tract at d16 and reached an almost plateau at d21. Remarkably, DCA excluded C. jejuni cecal colonization at 100, 99.997, and 100% at 16, 21, and 28 days of age. Neither chicken ages of infection nor LCA or UDCA altered C. jejuni AR101 chicken colonization level, while DCA reduced 91% of the bacterium in chickens at d28. Notably, DCA diet reduced phylum Firmicutes but increased Bacteroidetes compared to infected control birds. Importantly, DCA-Anaero attenuated 93% of C. jejuni colonization at d28 compared to control infected birds. In conclusion, DCA shapes microbiota composition against C. jejuni colonization in chickens, suggesting a bidirectional interaction between microbiota and microbial metabolites.
IMPACTS in natural language generation NLG between technology and applications : workshop at Schloss Dagstuhl, Germany July 26-28, 2000 (2001)

Instructional text, because it is a useful and relatively constrained sub-Ianguage, has been a popular target for research-oriented generation systems. This work has demonstrated that existing technology is adequate for generating draft instructions; the problem, as is typical of generation work in general, has been with the acquisition of domain and lexicogrammatical knowledge. This acquisition task is a formidable barrier to the practical use of generation\ntechnology. The Isolde project attempts to address this problem by extracting\nparts of the required knowledge from existing models and by building tools to\ntailor what is extracted into a form suitable for generation.
A Simplified Benchmark for Ambiguous Explanations of Knowledge Graph Link Prediction using Relational Graph Convolutional Networks (2022)

Relational Graph Convolutional Networks (RGCNs) are commonly used on Knowledge Graphs (KGs) to perform black box link prediction. Several algorithms have been proposed to explain their predictions. Evaluating performance of explanation methods for link prediction is difficult without ground truth explanations. Furthermore, there can be multiple explanations for a given prediction in a KG. No dataset exists where observations have multiple ground truth explanations to compare against. Additionally, no standard scoring metrics exist to compare predicted explanations against multiple ground truth explanations. We propose and evaluate a method, including a dataset, to benchmark explanation methods on the task of explainable link prediction using RGCNs.
Coded Caching and Spatial Multiplexing Gain Trade-off in Dynamic MISO Networks (2022)

The global caching gain of multi-antenna coded caching techniques can be also mostly achieved in dynamic network setups, where the cache contents of users are dictated by a central server, and each user can freely join or leave the network at any moment. In the dynamic setup, users are assigned to a limited set of caching profiles and the non-uniformness in the number of users assigned to each profile is compensated during the delivery phase by either adding phantom users for multicasting or serving a subset of users with unicast transmissions. In this paper, we perform a thorough analysis and provide closed-form representations of the achievable degrees of freedom (DoF) in such hybrid schemes, and assess the inherent trade-off between the global caching and spatial multiplexing gains caused by either adding phantom users or serving parts of the data through unicasting.
Enhancing supervisory training signals with environmental reinforcement learning using adaptive dynamic programming and artificial neural networks (2016)

A method for hybridizing supervised learning with adaptive dynamic programming was developed to increase the speed, quality, and robustness of on-line neural network learning from an imperfect teacher. Reinforcement learning is used to modify and enhance the original supervisory signal before learning occurs. This paper describes the method of hybridization and presents a model problem in which a human supervisor teaches a simulated car to drive around a race track. Simulation results show successful learning and improvements in convergence time, error rate, and stability over either component method alone.
DNA-Binding Hemoproteins Tethering Polyamine Interface (2010)

Abstract Artificial prosthetic groups tethering a polyamine moiety at the terminal of two peripheral heme–propionate side chains as a molecular interface were inserted into apocytochrome b562 to provide positively charged reconstituted hemoproteins, which exhibit a strong binding with double-stranded DNA.
Comprehensive DNA methylation analysis of benign and malignant adrenocortical tumors (2012)

The molecular pathogenesis of benign and malignant adrenocortical tumors (ACT) is incompletely clarified. The role of DNA methylation in adrenocortical tumorigenesis has not been analyzed in an unbiased, systematic fashion. Using the Infinium HumanMethylation27 BeadChip, the DNA methylation levels of 27,578 CpG sites were investigated in bisulfite-modified DNA from 6 normal adrenocortical tissue samples, 27 adrenocortical adenomas (ACA), and 15 adrenocortical carcinomas (ACC). Genes involved in cell cycle regulation, apoptosis, and transcriptional regulation of known or putative importance in the development of adrenal tumors showed significant and frequent hypermethylation. Such genes included CDKN2A, GATA4, BCL2, DLEC1, HDAC10, PYCARD, and SCGB3A1/HIN1. Comparing benign versus malignant ACT, a total of 212 CpG islands were identified as significantly hypermethylated in ACC. Gene expression studies of selected hypermethylated genes (CDKN2A, GATA4, DLEC1, HDAC10, PYCARD, SCGB3A1/HIN1) in 6 normal and 16 neoplastic adrenocortical tissues (10 ACA and 6 ACC), displayed reduced gene expression in benign and malignant ACT versus normal adrenocortical tissue. Treatment with 5-aza-2'-deoxycytidine of adrenocortical cancer H-295R cells increased expression of the hypermethylated genes CDKN2A, GATA4, DLEC1, HDAC10, PYCARD, and SCGB3A1/HIN1. In conclusion, the current study represents the first unbiased, quantitative, genome-wide study of adrenocortical tumor DNA methylation. Genes with altered DNA methylation patterns were identified of putative importance to benign and malignant adrenocortical tumor development.
Small-sized Er,Yb: glass planar waveguide laser amplifier pumped by a laser diode bar (2018)

We developed a small-sized Er,Yb:glass planar waveguide laser amplifier pumped by a laser diode bar with the butt joint configuration, toward the application of the wind sensing coherent lidar (light detection and ranging). We demonstrate the signal amplification operation and the output power of 3.2W in continuous-wave mode.
Genes drive organisms and slippery slopes (2022)

The bioethical debate about using gene drives to alter or eradicate wild populations has focused mostly on issues concerning short-term risk assessment and management, governance and oversight, and public and community engagement, but has not examined big-picture- 'where is this going?'-questions in great depth. In other areas of bioethical controversy, big-picture questions often enter the public forum via slippery slope arguments. Given the incredible potential of gene drive organisms to alter the Earth's biota, it is somewhat surprising that slippery slope arguments have not played a more prominent role in ethical and policy debates about these emerging technologies. In this article, we examine a type of slippery slope argument against using gene drives to alter or suppress wild pest populations and consider whether it has a role to play in ethical and policy debates. Although we conclude that this argument does not provide compelling reasons for banning the use of gene drives in wild pest populations, we believe that it still has value as a morally instructive cautionary narrative that can motivate scientists, ethicists, and members of the public to think more clearly about appropriate vs. inappropriate uses of gene drive technologies, the long-term and cumulative and emergent risks of using gene drives in wild populations, and steps that can be taken to manage these risks, such as protecting wilderness areas where people can enjoy life forms that have not been genetically engineered.
Gas Adsorption Properties of Woodceramics (2005)

Gas adsorption properties of woodceramics prepared from cedar (Cryptomeria japonica, abbreviated as CE), apple waste (AP), and chicken waste (CH) were studied. Depending on the starting material, woodceramics differed in physisorption properties as evaluated by specific surface area (SSA) obtained by BET (Brunauer–Emmett–Teller) method, in pore structure and size, and in chemical adsorption properties for perfumery substances. CH and AP yielded lower SSA as compared with CE, however, they showed higher gas selectivity for oxygen vs nitrogen gas molecules. The adsorption ability of CE on perfumery essential oil components was evaluated for the first time using the rapid measuring method for VOCs; i.e., the adsorption capacity of cedar-based woodceramics for perfumery materials (essential oil extracts: carvone, pulegone, geraniol, citronellol, menthone, nerol, and citral) was examined. CE showed particularly strong affinity with geraniol and citral, in which more than 99.9% of the compounds were adsorbed. About 99.7–99.8% of pulegone and menthone, 99.0% of nerol, 97.9% of carvone, and 94.0% of citronellol were adsorbed by CE. The adsorption affinity was also influenced by the particle size; particles coarser than 4.0 mm in size showed stronger adsorption.
Study of high throughput EUV mask pattern defect inspection technologies using multibeam electron optics (2021)

Using a POC tool, we are continuing a feasibility study for an EUV mask pattern inspection tool having multibeam electron optics with D2D and D2DB functions. In this paper, we will discuss our technologies in addition to our latest results on our POC tool.
Hepcidin knockout mice spontaneously develop chronic pancreatitis owing to cytoplasmic iron overload in acinar cells (2016)

Iron is both an essential and a potentially toxic element, and its systemic homeostasis is controlled by the iron hormone hepcidin. Hepcidin binds to the cellular iron exporter ferroportin, causes its degradation, and thereby diminishes iron uptake from the intestine and the release of iron from macrophages. Given that hepcidin-resistant ferroportin mutant mice show exocrine pancreas dysfunction, we analysed pancreata of aging hepcidin knockout (KO) mice. Hepcidin and Hfe KO mice were compared with wild-type (WT) mice kept on standard or iron-rich diets. Twelve-month-old hepcidin KO mice were subjected to daily minihepcidin PR73 treatment for 1 week. Six-month-old hepcidin KO mice showed cytoplasmic acinar iron overload and mild pancreatitis, together with elevated expression of the iron uptake mediators DMT1 and Zip14. Acinar atrophy, massive macrophage infiltration, fatty changes and pancreas fibrosis were noted in 1-year-old hepcidin KO mice. As an underlying mechanism, 6-month-old hepcidin KO mice showed increased pancreatic oxidative stress, with elevated DNA damage, apoptosis and activated nuclear factor-κB (NF-κB) signalling. Neither iron overload nor pancreatic damage was observed in WT mice fed iron-rich diet or in Hfe KO mice. Minihepcidin application to hepcidin KO mice led to an improvement in general health status and to iron redistribution from acinar cells to macrophages. It also resulted in decreased NF-κB activation and reduced DNA damage. In conclusion, loss of hepcidin signalling in mice leads to iron overload-induced chronic pancreatitis that is not seen in situations with less severe iron accumulation. The observed tissue injury can be reversed by hepcidin supplementation. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Discoidin Domain Receptor 1 is a therapeutic target for neurodegenerative diseases (2020)

The role of Discoidin Domain Receptors (DDRs) is poorly understood in neurodegeneration. DDRs are upregulated in Alzheimer's and Parkinson's disease (PD), and DDRs knockdown reduces neurotoxic protein levels. Here we show that potent and preferential DDR1 inhibitors reduce neurotoxic protein levels in vitro and in vivo. Partial or complete deletion or inhibition of DDR1 in a mouse model challenged with α-synuclein increases autophagy and reduces inflammation and neurotoxic proteins. Significant changes of cerebrospinal fluid microRNAs that control inflammation, neuronal injury, autophagy and vesicular transport genes are observed in PD with and without dementia and Lewy body dementia, but these changes are attenuated or reversed after treatment with the DDR1 inhibitor, nilotinib. Collectively, these data demonstrate that DDR1 regulates autophagy and reduces neurotoxic proteins and inflammation and is a therapeutic target in neurodegeneration.
Subclinical hepatic encephalopathy: proton MR spectroscopic abnormalities. (1994)

H-1 MR spectroscopy allows accurate diagnosis of SCHE, and the results suggest an important role for myo-inositol in psychomotor and visuopractic functions.
Adsorption of Chitosan onto Poly(D,L‐lactic acid) Particles: A Physico‐Chemical Investigation (2005)

Abstract Summary: Particles of poly( D , L ‐lactic acid) (PLA) obtained by emulsification‐diffusion were surface‐modified by adsorption of chitosan. Thus, positively charged biodegradable carriers were obtained as potential carriers for DNA. Various physico‐chemical parameters, susceptible to impact the elaboration of such colloids, were investigated. External parameters were the ionic strength and the nature of the buffer; pH was fixed at 4.5 in order to ensure the ionisation of both counterparts. Internal parameters were the molar mass of chitosan and its degree of acetylation (DA). Kinetically, the adsorption of chitosan was spontaneous. Adsorption isotherms of chitosan were established using two different assays for chitosan, one based on the formation of a covalent bond, and the other on the formation of an ion pair. Two adsorption regimes were evidenced in ammonium acetate buffer. The amount of adsorbed chitosan increased with its molar mass up to a limit due to steric hindrance and with the DA. The latter effect could be explained by a reduction of the molecular dimensions of chitosan with DA. On storing, desorption of chitosan was dependent on the molar mass of the polysaccharide and, to a lesser extent, on the DA. Complexation isotherm of chitosan onto PLA particles. image Complexation isotherm of chitosan onto PLA particles.
Supplementary Methods, Figures 1-4, Tables 1-5 from The mRNA-Destabilizing Protein Tristetraprolin Is Suppressed in Many Cancers, Altering Tumorigenic Phenotypes and Patient Prognosis (2023)

Supplementary Methods, Figures 1-4, Tables 1-5 from The mRNA-Destabilizing Protein Tristetraprolin Is Suppressed in Many Cancers, Altering Tumorigenic Phenotypes and Patient Prognosis
ChemInform Abstract: Anomalous threo‐Diastereoselectivity in Allylic Silane‐ or Stannane‐ Aldehyde Condensation Reactions: New Interpretation of the Antiperiplanar vs. Synclinal Problem on the Transition‐State Conformations. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Synthesis and characterization of tubular amphiphilic networks with controlled pore dimensions for insulin delivery (2000)

Abstract A convenient laboratory process for the preparation of thin-walled (∼0.02 cm) tubular amphiphilic membranes has been developed. The membranes are suitable for implantation and isolation of pancreatic islets from immune responses. The process involves the simultaneous free radical copolymerization/crosslinking of dimethyl acrylamide (DMAAm) and methacrylate ditelechelic polyisobutylene (MA-PIB-MA) in narrow-bore (∼4 mm inner diameter) glass tubes horizontally rotating in a thermostated oven. The pore sizes of the membranes can be controlled by the length, i.e. molecular weight, of the hydrophilic poly(dimethyl acrylamide) (PDMAAm) segment (M c,hydrophilic). Pore sizes, M c,hydrophilic's, and molecular weight cut-off (MWCO) ranges of designed amphiphilic membranes were characterized in terms of Stokes (or viscosity) radii (R s) and the relationships between these parameters were evaluated. Membranes were designed to allow the rapid diffusion of molecules such as insulin (M n = 5733 g/mol, R s = 1.34 nm) but to be opaque to serum albumin (M n > 66 000 g/mol, R s > 3.62 nm) and larger proteins such as immunoglobulins. The diffusion coefficients (D) and permeabilities (P) of tubular and flat-sheet amphiphilic membranes have been compared and were found to be similar. Membrane pore size dimensions of the tubular devices were determined by the out-diffusion of commercially available protein markers of known molecular weights (M n = 6500-66 000 g/mol) and dimensions (Rs = 1.50-3.62 nm). It was found that the minimum Mc,hydrophilic or Rs that still allows the diffusion of insulin is ∼ 800 g/mol or ∼ 1.34nm, respectively, and that the maximum Mc,hydrophilic or Rs that prevents the ingress of antibodies is ∼ 5000 g/mol or ∼ 3.62 nm, respectively. According to diffusion experiments, the presence or absence of lightly crosslinked 1% calcium alginate does not affect the rate of diffusion of glucose and insulin through our tubules. These membranes are being used in vivo for encapsulating islet cells for implantation to correct type 1 diabetes. Keywords: Amphiphilic membranesamphiphilic networksimmunoisolation of isletsinsulin diffusionartificial pancreas
The stereospecific assignment of H5' and H5'' in RNA using the sign of two-bond carbon-proton scalar couplings (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe stereospecific assignment of H5' and H5'' in RNA using the sign of two-bond carbon-proton scalar couplingsJennifer V. Hines, Gabriele Varani, Stacy M. Landry, and Ignacio Tinoco Jr.Cite this: J. Am. Chem. Soc. 1993, 115, 23, 11002–11003Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ja00076a073https://doi.org/10.1021/ja00076a073research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations29LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
SPARC: Parameters of Electrical Excitation and Block of the Rat Vagus Nerve (2020)

There is growing interest in bioelectronic medicines, where diseases are treated through electrical stimulation and block of the peripheral autonomic nervous system. Given the widespread connections of the vagus nerve from the brainstem to most truncal organs, applications include treating epilepsy, depression, obesity, heart failure, and rheumatoid arthritis. However, designing and programming the parameters of bioelectronic medicines require understanding the biophysical responses of small myelinated and unmyelinated autonomic fibers. Using in vivo electrophysiology, we quantified strength‐duration properties, activity‐dependent slowing (ADS), and responses to kilohertz frequency (KHF) signals for rapidly conducting (&gt;2 m/s) and slowly conducting (&lt;2 m/s) fibers in the rat vagus nerve. We stimulated the cervical vagus nerve and recorded compound action potential (CAP) input‐output curves from the abdominal vagus nerve for pulse widths from 20 to 1000 μs. Thresholds were largest for the slowest fibres (0.5 to 1 m/s), especially at shorter pulse widths. Fits to the data using standard strength‐duration equations were qualitatively similar, but the estimates of chronaxie and rheobase varied substantially. ADS describes the slowed conduction in peripheral axons resulting from persistent low frequency activity. Using a novel cross‐correlation CAP‐based analysis method, we measured ADS of ~2.3% after 3 min of 2 Hz stimulation, approximately constant across fiber conduction speeds. This is comparable to that reported for sympathetic efferents in somatic nerves, but much smaller than ADS in cutaneous nociceptors. We found greater ADS with higher stimulation frequency and non‐monotonic changes in conduction speed in select cases. KHF signals can block neural conduction in peripheral axons, and we used CAP recordings to quantify the effects of KHF signals from 10 to 80 kHz on small autonomic fibers. Block thresholds were higher for more slowly conducting fibers, and block thresholds increased monotonically with frequency, in contrast to published findings indicating that block thresholds of unmyelinated axons vary non‐monotonically with frequency. Further, there are varied reports on the time for recovery of neural conduction after KHF block; we found that the carryover effect could last tens of seconds following 25 s of KHF signal. The quantification of mammalian autonomic nerve responses to conventional and kilohertz frequency signals provides essential information for development of bioelectronic medical devices and for understanding mechanisms of action. Support or Funding Information This work was supported by Fulbright Canada (15122811), the Natural Sciences and Engineering Research Council of Canada (PGS M‐425353‐2012 and PGS D3‐437918‐2013), and Duke University (University Scholars Program, James B. Duke Fellowship, and Pratt School of Engineering Faculty Discretionary Fund).
Electronic Structure of Metallophthalocyanines, MPc (M = Fe, Co, Ni, Cu, Zn, Mg) and Fluorinated MPc (2021)

We compute the electronic structure and optical excitation energies of metal-free and transition-metal phthalocyanines (H<sub>2</sub>Pc and MPc for M = Fe, Co, Ni, Cu, Zn, Mg) using density functional theory with optimally tuned range-separated hybrid functionals (OT-RSH). We show that the OT-RSH approach provides photoemission spectra in quantitative agreement with experiments as well as optical band gaps within 10% of their experimental values, capturing the interplay of localized d-states and delocalized π-π* states for these organometallic compounds. We examine the tunability of MPcs and H<sub>2</sub>Pc through fluorination, resulting in quasi-rigid shifts of the molecular orbital energies by up to 0.7 eV. Our comprehensive data set provides a new computational benchmark for gas-phase phthalocyanines, significantly improving upon other density-functional-theory-based approaches.