gebhart/patrepeval huggingface dataset:
Universal primers and PCR of gut contents to study marine invertebrate diets (2005)

Determining the diets of marine invertebrates by gut content analysis is problematic. Many consumed organisms become unrecognizable once partly digested, while those with hard remains (e.g. diatom skeletons) may bias the analysis. Here, we adapt DNA-based methods similar to those used for microbial diversity surveys as a novel approach to study the diets of macrophagous (the deep-sea amphipods Scopelocheirus schellenbergi and Eurythenes gryllus) and microphagous (the bivalve Lucinoma aequizonata) feeders in the deep sea. Polymerase chain reaction (PCR) in conjunction with 'universal' primers amplified portions of the mitochondrial cytochrome c oxidase I (COI) gene for animals ingested by S. schellenbergi and E. gryllus and the 18S rRNA gene for lesser eukaryotes ingested by L. aequizonata. Amplified sequences were combined with sequences from GenBank to construct phylogenetic trees of ingested organisms. Our analyses indicate that S. schellenbergi, E. gryllus and L. aequizonata diets are considerably more diverse than previously thought, casting new light on the foraging strategies of these species. Finally, we discuss the strengths and weaknesses of this technique and its potential applicability to diet analyses of other invertebrates.
Are biogenic emissions a significant source of summertime atmospheric toluene in the rural Northeastern United States? (2009)

Abstract. Summertime atmospheric toluene enhancements at Thompson Farm in the rural northeastern United States were unexpected and resulted in a toluene/benzene seasonal pattern that was distinctly different from that of other anthropogenic volatile organic compounds. Consequently, three hydrocarbon sources were investigated for potential contributions to the enhancements during 2004–2006. These included: (1) increased warm season fuel evaporation coupled with changes in reformulated gasoline (RFG) content to meet US EPA summertime volatility standards, (2) local industrial emissions and (3) local vegetative emissions. The contribution of fuel evaporation emission to summer toluene mixing ratios was estimated to range from 16 to 30 pptv d−1, and did not fully account for the observed enhancements (20–50 pptv) in 2004–2006. Static chamber measurements of alfalfa, a crop at Thompson Farm, and dynamic branch enclosure measurements of loblolly pine trees in North Carolina suggested vegetative emissions of 5 and 12 pptv d−1 for crops and coniferous trees, respectively. Toluene emission rates from alfalfa are potentially much larger as these plants were only sampled at the end of the growing season. Measured biogenic fluxes were on the same order of magnitude as the influence from gasoline evaporation and industrial sources (regional industrial emissions estimated at 7 pptv d−1 and indicated that local vegetative emissions make a significant contribution to summertime toluene enhancements. Additional studies are needed to characterize the variability and factors controlling toluene emissions from alfalfa and other vegetation types throughout the growing season.
HUMAINE: Human Multi-Agent Immersive Negotiation Competition (2020)

Competitions that directly pit software agents against one another have proven to be an effective and entertaining way to advance the state of the art in a multitude of AI domains. Less frequently, human-agent competitions have been held to gauge the relative competence of humans vs. agents, or agents vs. agents as measured indirectly by their performance against humans. We are developing a platform that supports a new type of AI competition that involves both agent-agent and human-agent interactions situated in an immersive environment. In this competition, human buyers haggle (in English) with two life-size AI agents that attempt to sell them various goods. We describe several research challenges that arise in this context, present the platform architecture and accompanying technologies, and report on early experiments with simple agents that establish feasibility and suggest that human participants enjoy the experience.
Polymers Comprising Cholesterol: Synthesis, Self-Assembly, and Applications (2009)

This article reviews the current status of self-assembling liquid crystalline polymers comprising cholesterol. This article will focus on synthesis, structure-property relationships and strategies to direct ordering and packing of meso- and nanostructures of cholesterol polymers in the neat- or melt state and in solution. The applications of these self-assembled structures will be presented.
Protein Misfolding Diseases (2009)

Diseases caused by protein misfolding are an emerging pathologic category that are thought to share some basic common mechanisms and display impressive heterogeneity in terms of tissue involvement, age of onset and clinical features. The growing recognition of the impact that protein misfolding has on human diseases is certainly related to the phenomenon of population aging and the expansion of the population in which these diseases are more frequent, but it is also based on a scientific revolution that looks at protein dynamics and relates these data to their potential pathologic implications. The multidisciplinary exchange of knowledge between experts in apparently unrelated diseases, such as sickle cell anemia and Alzheimer’s disease, has helped clarify the pathogenesis of these and many other diseases. The quick expansion of knowledge on the mechanisms of these diseases is priming pharmaceutical research that is now providing the first prototype drugs.
Dynamics of DNA methylation during development (1993)

DNA methylation plays a role in the repression of gene expression in animal cells. In the mouse preimplantation embryo, most genes are unmethylated but a wave of de novo methylation prior to gastrulation generates a bimodal pattern characterized by unmethylated CpG island-containing housekeeping genes and fully modified tissue-specific genes. Demethylation of individual genes then takes place during cell type specific differentiation, and this demodification may be a required step in the process of transcriptional activation. DNA modification is also involved in the maintenance of gene repression on the inactive X chromosome in female somatic cells and the marking of parental alleles at genomically imprinted gene loci.
Quality of Life in Heart Failure with Preserved Ejection Fraction: Importance of Obesity, Functional Capacity, and Physical Inactivity (2020)

RELAX, NCT00763867; NEAT-HFpEF, NCT02053493; INDIE-HFpEF, NCT02742129.
Structure of a fish (rainbow trout) growth hormone gene and its evolutionary implications. (1988)

We have isolated and sequenced a clone from a rainbow trout (Salmo gairdneri) genomic library that carries a gene encoding a fish growth hormone (GH). This gene spans a region of approximately equal to 4 kilobases, nearly twice that of mammalian GH genes. The trout GH gene is comprised of six exons, in contrast with five exons in mammals. The additional intron in the fish gene interrupts translated regions that are analogous to the last exon of its mammalian counterpart. In addition, the alleged internally repeating sequence in mammalian GH, prolactin (Prl), or placental lactogen (PL) is not observed in the predicted polypeptide sequence of fish GH. Direct repeats that flank exons I, III, and V of the mammalian GH, Prl, and PL genes are absent in the fish GH gene. These findings indicate that the rainbow trout GH gene structure does not support the current hypothesis that internally repeated regions in GH, Prl, and PL arose from a small primordial gene.
TDCS: A new mechanism for automatic channel assignment for independent IEEE 802.11 networks (2009)

In the last few years, IEEE 802.11 applications has experienced a significant growth. This expansion creates scenarios where distinct administrators manage wireless networks. These scenarios lack of a unique authority to perform an adequate channel allocation that minimizes the performance degradation generated by medium access sharing and co-channel interference. This work proposes a new dynamic channel selection mechanism that focuses on the restrictions imposed by scenarios with independent IEEE 802.11 networks and adapts faster to the interference pattern variations. Besides, the performance of the new mechanism is evaluated and compared to others through simulations.
Complications of Endoscopic Biliary Sphincterotomy (1996)

The rate of complications after endoscopic biliary sphincterotomy can vary widely in different circumstances and is primarily related to the indication for the procedure and to endoscopic technique, rather than to the age or general medical condition of the patients.
Nucleotides part XXX Chemical synthesis of adenylyl‐(2′ → 5′)‐adenylyl‐(2′ → 5′)‐8‐azidoadenosine, and activation and photoaffinity labelling of RNase L by [<sup>32</sup>P]p5′A2′p5′A2′p5′N<sub>3</sub><sup>8</sup>A (1989)

Abstract The chemical synthesis of adenylyl‐(2′–5′)‐adenylyl‐(2′–5′)‐8‐azidoadenosine ( 15 ) was performed by the phosphotriester approach. Enzymatic phosphorylation of 15 by [γ‐ 32 P]ATP led to the corresponding labelled 5′‐monophosphate 16 . Photoinsertion of 16 took place on UV irradiation by covalent cross linking to a protein of M r 80 K known to be RNase L. Radiobinding and core‐cellulose assays as well as photoaffinity labelling experiments with 16 are described.
Proteasomes Control Caspase-1 Activation in Anthrax Lethal Toxin-mediated Cell Killing (2007)

Activation of caspase-1 through the inflammasome protein Nalp1b controls anthrax lethal toxin (LT)-induced necrosis in murine macrophages. In this study we analyzed physiological changes controlled by caspase-1 in LT-treated murine macrophages. The caspase-1 inhibitor Boc-D-cmk blocked caspase-1 activity and membrane impairment in LT-treated cells. To determine the relationship between caspase-1 activation and membrane integrity, we added Boc-D-cmk to J774A.1 macrophages at different time points following LT exposure. Remarkably, Boc-D-cmk rescued LT-treated macrophages, even when added at the peak of caspase-1 activation. Late addition of the caspase-1 inhibitor reversed the losses of plasma membrane integrity and metabolic activity in these cells. Similar results were obtained with the proteasome inhibitor MG132, one of the most potent inhibitors of LT toxicity. LT-treated macrophages displaying evidence of membrane impairment recovered upon the addition of MG132, mirroring the Boc-D-cmk response. Strikingly, late addition of proteasome inhibitors also abrogated caspase-1 activity in LT-treated macrophages. Proteasomal control of caspase-1 activity and membrane impairment, however, was restricted to LT-induced cytolysis, because proteasome inhibitors did not block caspase-1 activation and cell death triggered by lipopolysaccharide and nigericin. Our findings indicate that proteasome inhibitors do not target caspase-1 directly but instead control an upstream event in LT-treated macrophages leading to caspase-1 activation. Taken together, caspase-1-mediated necrosis appears to be tightly controlled and differentially regulated by proteasomes depending on the source of caspase-1 induction.
In situ neutron scattering study of structural transitions in fibrin networks under shear deformation (2011)

Small angle neutron scattering (SANS) is used to decipher the origin of the strain hardening in biopolymer networks by directly measuring the structural response of a fibrin gel to simple shear deformation. A special Couette shear cell is used to systematically probe the structural properties of a fibrin clot over strain values in the range of γ = 1–170%. The SANS results indicate that the strain hardening response of coarse fibrin gels occurs in two distinct regions having different structural and mechanical signatures that are separated by an intermediate strain softening regime. At low strains (γ < 10%) there is a measurable increase in the shear modulus upon the application of shear strain but there are no significant changes to the clot structure. At higher strain values (γ > 30%), a second strain-hardening regime is directly correlated to significant fiber alignment. The mean diameter of the fibers determined directly from two-dimensional fits to the anisotropic scattering data is found to decrease monotonically in the high-strain regime. The results suggest that the non-linear mechanical properties of fibrin clots are the result of a reduction of lateral entropic fluctuations at low strains and a transition between bending and stretching at higher strain values.
Mechanistic and epidemiologic considerations in the evaluation of adverse birth outcomes following gestational exposure to statins (2004)

The cholesterol-lowering "statin" drugs are contraindicated in pregnancy, but few data exist on their safety in human gestation. We reviewed case reports for patterns suggesting drug-related effects on prenatal development and considered a variety of mechanisms by which such effects, if confirmed, might occur. This uncontrolled case series included all FDA reports of statin exposures during gestation, as well as others from the literature and from manufacturers. Exposures and outcomes were reviewed and were tabulated by individual drug. Age-specific rates of exposure to each drug among women of child-bearing age were estimated. Of 214 ascertained pregnancy exposures, 70 evaluable reports remained after excluding uninformative cases. Among 31 adverse outcomes were 22 cases with structural defects, 4 cases of intrauterine growth restriction, and 5 cases of fetal demise. There were two principal categories of recurrent structural defects: cerivastatin and lovastatin were associated with four reports of severe midline CNS defects; simvastatin, lovastatin, and atorvastatin were all associated with reports of limb deficiencies, including two similar complex lower limb defects reported following simvastatin exposure. There were also two cases of VACTERL association among the limb deficiency cases. All adverse outcomes were reported following exposure to cerivastatin, simvastatin, lovastatin, or atorvastatin, which are lipophilic and equilibrate between maternal and embryonic compartments. None were reported following exposure to pravastatin, which is minimally present in the embryo. Statins reaching the embryo may down-regulate biosynthesis of cholesterol as well as many important metabolic intermediates, and may have secondary effects on sterol-dependent morphogens such as Sonic Hedgehog. The reported cases display patterns consistent with dysfunction of cholesterol biosynthesis and Sonic Hedgehog activity. Controlled studies are needed to investigate the teratogenicity of individual drugs in this class.
Adsorption of Cadmium from Aqueous Solutions by Vermiculite (2003)

The present study involves an investigation of a low-cost adsorbent, vermiculite for the removal of cadmium from aqueous solutions. The effects of pH and contact time on the adsorption process were examined. The optimum pH for adsorption was found to be 6. Residual cadmium concentration reached equilibrium in four hours and the rate of cadmium adsorption by vermiculite was rapid in the first hour of the reaction time. Ho's pseudo second order model best described the reaction rate. Batch adsorption experiments conducted at room temperature (22±1°C) showed that the adsorption pattern followed the Freundlich isotherm model. The maximum removal of cadmium obtained from batch studies was 96%. Thomas model was used to describe the adsorption data from column studies. Overall, the results showed that vermiculite could be considered as a potential adsorbent for cadmium removal from aqueous solutions.
The Treatment of Temporomandibular Disorders Through Repositioning Splint Therapy: A Follow-up Study (1998)

The purpose of this study was to investigate the effectiveness of repositioning splint therapy as a conservative treatment modality for TMD patients. The treatment sequence of 160 randomly sampled TMD patients was monitored in order to assess different aspects of the patients' response to splint therapy. Included among these aspects were the pretreatment symptoms; the treatment duration required for initial and final alleviation of symptoms; the number of patients requiring surgery; and the particular appliance and its wear pattern utilized to maintain the treatment results. The treatment success was based on the remission of symptoms including but not limited to pain to palpation, headaches, earaches, jaw locking, and joint noises. Eighty-nine and four tenths percent (89.4%) of the patients experienced a complete remission of symptoms and did not require any surgical intervention. The average time for initial improvement was 22.3 days, while the average time for complete remission of symptoms was 4.3 months. The results of the study indicate that repositioning splint therapy is an effective treatment modality for the conservative treatment of temporomandibular disorders.
Potent Bivalent Inhibition of Human Tryptase-? by a Synthetic Inhibitor (2003)

Human tryptase-beta (HTbeta) is a unique serine protease exhibiting a frame-like tetramer structure with four active sites directed toward a central pore. Potent inhibition of HTbeta has been attained using CRA-2059. This compound has two phenylguanidinium head groups connected via a linker capable of spanning between two active sites. The properties of the CRA-2059:HTbeta interaction were defined in this study. Tight-binding reversible inhibition was observed with an inhibition constant (Ki) of 620 pM, an association rate constant of 7x10(7) M(-1) s(-1) and a relatively slow dissociation rate constant of 0.04 s(-1). Bivalent inhibition was demonstrated by displacement of p-aminobenzamidine from the primary specificity pocket with a stoichiometry, [CRA-2059]0/[HTbeta]0, of 0.5. The potency of the bivalent interaction was illustrated by CRA-2059 inhibition of HTbeta, 24% or 53% inhibited by pre-incubation with an irreversible inhibitor. Two interactions were observed consistent with mono- and bi-valent binding; the Ki value for bivalent inhibition was at least 10(4)-fold lower than that for monovalent inhibition. Comparison of the affinities of CRA-2059 and phenylguanidine for HTbeta finds an approximate doubling of the free energy change upon bivalent binding. This doubling suggests that the linker portion minimally hinders the binding of CRA-2059 to HTbeta. The potency of CRA-2059 is thus attributable to effective bivalent binding.
Mismatch-stimulated killing. (1986)

DNA duplexes with or without mismatches and with or without adenine-methylated GATC sequences were prepared from separated strands of bacteriophage lambda DNA and used to transfect Escherichia coli. Unmethylated heteroduplexes containing one or more repairable mismatches transfect cells with a functioning mismatch repair system less efficiently than they transfect cells deficient in mismatch repair. No difference is observed when the duplexes contain no mismatch or a poorly repaired mismatch or when the heteroduplexes are fully or hemimethylated. These results and the phenotypes of E. coli dam mutants suggest that the E. coli mismatch repair system may introduce double-strand breaks in unmethylated DNA at or near repairable mismatches.
Breast tissue classification using x-ray scattering measurements and multivariate data analysis (2007)

This study utilized two radiation scatter interactions in order to differentiate malignant from non-malignant breast tissue. These two interactions were Compton scatter, used to measure the electron density of the tissues, and coherent scatter to obtain a measure of structure. Measurements of these parameters were made using a laboratory experimental set-up comprising an x-ray tube and HPGe detector. The breast tissue samples investigated comprise five different tissue classifications: adipose, malignancy, fibroadenoma, normal fibrous tissue and tissue that had undergone fibrocystic change. The coherent scatter spectra were analysed using a peak fitting routine, and a technique involving multivariate analysis was used to combine the peak fitted scatter profile spectra and the electron density values into a tissue classification model. The number of variables used in the model was refined by finding the sensitivity and specificity of each model and concentrating on differentiating between two tissues at a time. The best model that was formulated had a sensitivity of 54% and a specificity of 100%.
Origin of dark counts in In0.53Ga0.47As∕In0.52Al0.48As avalanche photodiodes operated in Geiger mode (2005)

A dark count rate in InP-based single photon counting avalanche photodiodes is a limiting factor to their efficacy. The temperature dependence of the dark count rate was studied to understand its origin in In0.53Ga0.47As∕In0.52Al0.48As separate-absorption-charge-multiplication avalanche photodiodes. The dark count rate was observed to be a very weak function of temperature in the range from 77Kto300K. Various mechanisms for dark count generation were considered. Simulations of band-to-band tunneling in the In0.52Al0.48As multiplication layer were found to agree well with the experimental temperature dependence of dark count rate at various excess biases. To reduce tunneling-induced dark counts, a suitable design change to the detector structure is proposed.
Quantitative Estimation of Retinal Nerve Fiber Layer Height in Glaucoma and the Relationship with Optic Nerve Head Topography and Visual Field (1997)

Retinal nerve fiber layer height measures were reduced substantially in patients with glaucoma compared with age-matched healthy subjects. Retinal nerve fiber layer height was correlated strongly with topographic optic disc parameters and visual field changes in patients with glaucoma.
Semantic network analysis for evidence evaluation: The threat anticipation initiative (2011)

Semantic network analysis offers a computational method for discovery, pattern matching, and reasoning with large amounts of unstructured, semi-structured and structured information. The Threat Anticipation Platform replaces more cumbersome and computationally complex forms of semantic inference with metrics on graph representations of labeled, directed semantic networked data to identify the degree of evidence within multiple data sources for specified hypotheses about potential events.
Routing in ad hoc networks - a wireless perspective (2004)

Traditionally, the routing problem is addressed at the network layer, an approach that has been extended to the wireless realm. In wireless multihop networks, however, strict layer-base protocol design leads to substantial inefficiencies. This paper addresses the routing problem for large wireless ad hoc networks from a fundamental point of view, not constrained by particular protocol implementations or layered architectures, but taking into account the properties of the wireless channel. First, an analytical channel model is presented that is based on Rayleigh fading. It demonstrates how noise and interference effects can be separated, and how each interfering transmission affects the packet reception probability. Second, the distribution of node distances in networks with uniformly randomly placed nodes is derived. These two ingredients are used to discuss the benefits of different routing strategies. In particular, short-hop and long-hop routing schemes are compared. Further, cooperative strategies such as multipath routing and cooperative diversity are briefly discussed as techniques that are enabled by the broadcast nature of the wireless channel.
Temperature-dependence of the growth orientation of atomic layer growth MgO (1992)

High-quality MgO thin films deposited on Si(111) substrates by atomic layer growth (ALG) are formed by a hydrolysis surface reaction of Mg(C2H5)2 and H2O. The growth orientation of MgO changes from (111) to (100), when the temperature of the silicon substrate changes from 600 to 900 °C. The growth orientation difference of MgO grown by ALG is rationalized in terms of the surface diffusion coefficients on MgO.