gebhart/patrepeval huggingface dataset:
Accumulation of Polychlorinated Dibenzo-<i>p</i>-dioxins and Dibenzofurans in Liver of Control Laboratory Rats (1994)

Polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and biphenyls belong to a class of compounds, the polyhalogenated aromatic hydrocarbons (PHAHs), which are ubiquitous environmental contaminants. Due to the existence of a common mechanism of action, i.e., binding to the Ah receptor, the activity of members of this class of compounds is generally expressed relative to the prototypical 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) as toxic equivalency factors (TEFs). In the present studies we examined the presence of PCDDs and PCDFs in standard laboratory feed and in the liver of untreated rats at three different ages (60, 140, and 200 days) in terms of concentration and in toxic equivalents (TEQs, TEF × concentration). Feed was shown to contain trace amounts of PCDDs and PCDFs and control rat liver was shown to contain several PCDD and PCDF congeners in terms of concentration of congener and concentration of TEQs contributed by that congener. The total concentration of TEQs increased with increasing age in rat liver, going from 20 ppt TEQ at 60 days to 78 ppt TEQ at 200 days of age. This accumulation in dioxin-like activity was due primarily to PCDFs. In particular the congener 2,3,4,7,8-pentachlorodibenzofuran accrued in untreated rat liver accounting for approximately 80% of the total TEQ at 200 days of age. These studies affirm the pervasive presence of PHAHs and suggest prudence in evaluating chronic rat studies in which interference from background levels of PCDDs and PCDFs may be a factor.
Insertion of central venous catheters induces a hypercoagulable state (2012)

In healthy swine and patients with critical illness, a systemic hypercoagulable state occurred after CVC insertion, and this may partially account for an increased risk of venous thromboembolism. However, because the sample size was small and not powered to detect changes in coagulation proteins, no inferences can be made about the mechanism for the hypercoagulable response.
Mitochondria and the Link Between Neuroinflammation and Neurodegeneration (2010)

The innate immune response is thought to exert a dichotomous role in the brain. Indeed, although molecules of the innate immune response can promote repair mechanisms, during neuroinflammatory processes many harmful mediators are also released. Signs of neuroinflammation and neurodegeneration represent a ubiquitous pathological finding during the course of several different neurological diseases. Interestingly, it has been proposed that mitochondria may exert a crucial role in the pathogenesis of both inflammatory and neurodegenerative central nervous system disorders. In this review, we describe the mechanisms by which neuroinflammation and mitochondrial impairment may synergistically trigger a vicious cycle ultimately leading to neuronal death. In particular, we describe the close relationship existing among neuroinflammation, neurodegeneration, and mitochondrial impairment in three different widely-diffused neurological diseases in which these pathogenetic events coexist, namely multiple sclerosis, Parkinson's disease, and Alzheimer's disease.
Modeling study of scattering and absorption properties of tar-ball aggregates (2019)

Atmospheric tar balls (TBs) form an important class of atmospheric brown carbon (BrC) particulates. The morphology of the individual TBs is typically described as amorphous and nearly spherical. However, several studies reported observations of TBs aggregated with other aerosols or agglomerations consisting of up to tens of individual TBs. We use the superposition $T$T-matrix method to compute the scattering matrix elements and optical cross sections for a variety of TB aggregates, each of which is composed of a number of monomers whose sizes follow a lognormal distribution. The results for a TB aggregate can differ fundamentally from those calculated for two simplified models commonly used in climate modeling; viz., the external mixture of TBs and the respective volume-equivalent sphere model. Clustering of individual TBs into an aggregate can either enhance or weaken absorption depending on the wavelength, the monomer size, and how absorptive the BrC material is. In the case of strongly absorptive BrC, aggregation results in enhanced absorption only at 1064 nm, while at 355 and 532 nm TB aggregates become less effective absorbers relative to the corresponding external mixtures. The effect of aggregation is always to increase the single-scattering albedo and asymmetry parameter, sometimes more than tenfold. The significant scattering-matrix differences between a TB aggregate, the "equivalent" external mixture, and the volume-equivalent sphere model demonstrate the failure of the conventional Lorenz-Mie theory to represent the scattering properties of morphologically complex BrC aerosols. We show that TB aggregates can help explain exceptionally strong and spectrally dependent lidar depolarization ratios reported in several recent studies.
Plasmas for organic synthesis and chemical probes for plasma diagnostics (2014)

Although organic chemistry plays a critical role in many plasma applications, there is\nroom for further cross-fertilization between the two disciplines. Here we explore two\npossible avenues: (1) plasma physics as a new tool for the organic chemist and (2)\norganic compounds as diagnostics for the plasma physicist.
Temperature stabilized wideband optical isolator with 60-dB isolation loss (1988)

A small optical isolator with high-isolation loss usable over a wide wavelength and temperature range is anticipated for a high bit rate of 2-10 Gbit/s for coherent optical communication systems. The isolation loss and its wavelength and temperature dependence are improved by a cascaded optical isolator consisting of two conventional ones as theoretically predicted by Shiraishi and Kawakami.1 Design considerations for the setting of polarizers and the configuration of magnets and the experimental results on the newly developed isolator are discussed.
Bacterial cell wall polymers (peptidoglycan-polysaccharide) cause reactivation of arthritis (1993)

Intraperitoneal (i.p.) injection of peptidoglycan-polysaccharide derived from group A streptococci (PG-APS) causes chronic arthritis with spontaneous remissions and exacerbations. We hypothesized that, following i.p. injection, PG-APS released from hepatic stores mediated spontaneous recurrences of arthritis. We tested whether transplanted livers with large amounts of PG-APS were able to reactivate quiescent arthritis. Saline-loaded (group 1) or PG-APS-loaded (group 2) livers were transplanted into rats which had been injected intra-articularly 10 days earlier with PG-APS in one joint and saline in the other. A comparison was made with the arthritis that occurred in rats injected i.p. with PG-APS which did not receive transplants (group 3). Arthritis was monitored by serial measurement of joint diameters. Transplantation of saline-loaded livers (group 1) caused no reactivation of arthritis. However, transplantation of PG-APS-loaded livers (group 2) reactivated arthritis (P < 0.0001). Injection of PG-APS i.p. (group 3) induced the most-severe arthritis. PG-APS levels in plasma decreased with time, and PG-APS accumulated in the spleen in groups 2 and 3. Plasma and hepatic levels of PG-APS in rats injected i.p. with PG-APS were greater than levels in rats transplanted with PG-APS-loaded livers, which in turn were greater than levels in rats with saline-loaded livers. Plasma tumor necrosis factor did not correlate with recurrence of arthritis. Transplantation with PG-APS-loaded livers induced reactivation of arthritis in preinjured joints. The extent of arthritis was proportional to hepatic PG-APS content. Reactivation of arthritis may be mediated by slow release of liver-sequestered PG-APS or cytokines (not tumor necrosis factor) released by the liver.
A consideration of electro-magnetic-resonant coupling mode in wireless power transmission (2009)

The resonant mode of the wireless power transmission system is discussed to unveil a mechanism of wireless power transmission. We have analyzed electro-magnetic resonance phenomenon by using MoM to calculate input impedance, port currents, transmission efficiency, and near field distribution. We have checked that the system has two resonant frequencies, and the power transmission efficiency is maximized at those frequencies. The magnetic field distribution proves that the system has two different resonant modes. We have also considered far field to find that the higher frequency resonance is better for its high efficiency and low undesired emission.
Deep Learning-based Online Alternative Product Recommendations at Scale (2020)

Alternative recommender systems are critical for ecommerce companies. They guide customers to explore a massive product catalog and assist customers to find the right products among an overwhelming number of options. However, it is a non-trivial task to recommend alternative products that fit customers' needs. In this paper, we use both textual product information (e.g. product titles and descriptions) and customer behavior data to recommend alternative products. Our results show that the coverage of alternative products is significantly improved in offline evaluations as well as recall and precision. The final A/B test shows that our algorithm increases the conversion rate by 12% in a statistically significant way. In order to better capture the semantic meaning of product information, we build a Siamese Network with Bidirectional LSTM to learn product embeddings. In order to learn a similarity space that better matches the preference of real customers, we use co-compared data from historical customer behavior as labels to train the network. In addition, we use NMSLIB to accelerate the computationally expensive kNN computation for millions of products so that the alternative recommendation is able to scale across the entire catalog of a major ecommerce site.
Effect of hyperoxia, hypercapnia, and hypoxia on cerebral interstitial oxygen tension and cerebral blood flow (2001)

The assessment of cerebral interstitial oxygen tension (piO2) can provide valuable information regarding cerebrovascular physiology and brain function. Compartment-specific cerebral piO2 was measured by 19F NMR following the infusion of an oxygen-sensitive perfluorocarbon directly into the interstitial and ventricular space of the in vivo rat brain. 19F T1 measurements were made and cerebral piO2 were obtained through in vitro calibrations. The effects of graded hyperoxia, hypercapnia, and hypoxia on piO2 and cerebral blood flow (CBF) were investigated. Under normoxia (arterial pO2 ∼ 120 mm Hg), piO2 was ∼30 mm Hg and jugular venous pO2 was ∼50 mm Hg. During hyperoxia (arterial pO2 = 90–300 mm Hg), piO2 increased linearly with the arterial pO2. Following hypercapnia (arterial pCO2 = 20–60 mm Hg), the piO2 increased sigmoidally with increasing CBF. With hypoxia (arterial pO2 = 30–40 mm Hg), CBF increased ∼56% and piO2 decreased to ∼15 mm Hg. The hypoxia-induced CBF increase was effective to some extent in compensating for the reduced piO2. This methodology may prove useful for investigating cerebral piO2 under pathologically or functionally altered conditions. Magn Reson Med 45:61–70, 2001. © 2001 Wiley-Liss, Inc.
Structural and Physicochemical Characteristics of Tetrabutylammonium Tetrahalogenoferrates(III), [(C<sub>4</sub>H<sub>9</sub>)<sub>4</sub>N][FeBr<sub>4−n</sub>Cl<sub>n</sub>] (2006)

Abstract A series of tetrahalogenoferrates(III), [FeBr 4−n Cl n ] − (n=0‐4) stabilized with the tetrabutylammonium cation, of general formula [(C 4 H 9 ) 4 N][FeBr 4−n Cl n ], has been synthesized. The crystal and molecular structure of [(C 4 H 9 ) 4 N][FeCl 4 ] was determined. The iron cation adopts slightly distorted tetrahedral coordination with two opposite angles smaller than tetrahedral one, two equal to tetrahedral and two larger than tetrahedral. The bond valences were computed. The total valence of iron atom is equal to 3.08. In the structure can be found only one hydrogen bond C(1)–H···Cl. Except mentioned there are no unusually intermolecular short contacts between ions existing in the structure. All [(C 4 H 9 ) 4 N][FeBr 4−n Cl n ] (n=0‐4) compounds are isostructural in solid state. On the basis of conductometric measurements, relative stabilities of the anions have been estimated in methanol (MeOH), dimethyl sulfoxide (DMSO), acetone (AC), acetonitrile (AN) and dichloromethane (CH 2 Cl 2 ) representing both polar (including amphiprotic and aprotic) as well as non‐polar solvents. Further, the dissociation constants of the compounds were calculated from the expanded Pitt's conductivity equation. The results of the conductometric measurements were supported by electronic spectra.
Heterogeneous hyperactivity and distribution of ischemic lesions after focal cerebral ischemia in Mongolian gerbils (2006)

Various types of poststroke hyperactivity exist in humans, but studies of each mechanism using animal models are scarce. We aimed to analyze the heterogeneity of postischemic hyperlocomotion and to identify the ischemic lesions responsible for postischemic hyperlocomotion in rodent models of focal ischemia. Mongolian gerbils underwent right common carotid artery occlusion (CCAO) for 10 or 20 min. At 24 h, 2 days, and 7 days postischemia, we performed quantitative and qualitative locomotor analysis and correlated these results with the extent of ischemic lesions. Intermittent explosive hyperlocomotion was induced transiently in a 10-min CCAO group at 24 h after ischemia and continual unexplosive hyperlocomotion persisted for 7 days in the 20-min CCAO animals. Selective neuronal death, confined to the hippocampal cornu ammonis 1 (CA1), was observed in the 10-min CCAO group and widespread cortical and basal ganglia infarction was observed in the 20-min CCAO group. Amyloid precursor protein was transiently observed in the hippocampus at 24 h postischemia in the 10-min CCAO animals, while it was widely distributed over the ischemic regions throughout the 7 days postischemia in the 20-min CCAO animals. Incidence maps and correlation analysis revealed hippocampal neuronal death of the CA1 sector and widespread hemispheric infarction, including the cortex, as the region responsible for the 10-min and 20-min CCAO-induced hyperactivity, respectively. Two distinct types of locomotor hyperactivity were observed that varied with regard to the distribution of the ischemic lesion, that is, hippocampal neuronal death and widespread infarction involving the cortex. These two types of locomotor hyperactivity appear to be models of the different types of poststroke hyperactivity seen in stroke patients.
Haptic cooperation between people, and between people and machines (2006)

Haptic interaction between people and machines might benefit from an understanding of haptic communication between one person and another. We recently reported results showing that two people performing a physically shared dyadic task can outperform either person alone, even when the perception of each participant is that the other is a hindrance. Evidently a dyad quickly negotiates a more efficient motion strategy than is available to individuals. This negotiation must take place through a haptic channel of communication, and it is apparently at a level below the awareness of the participants. Here we report results on the motion strategy that emerged. By recording forces and motions we show that the dyads "specialized" temporally such that one member took on early parts of the motion and the other late parts. Tests in which one participant's contribution was surreptitiously replaced by a motor did not elicit a similar cooperative response from the remaining human participant, showing that the language of haptic communication between people must be rather subtle
Phytotoxicity of Fumonisins and Rfzated Compounds (1993)

AbstractThe fumonisins and AAL-toxin are related long-chain alkylamines with propane carboxylic acid moieties. The fumonisins, especially fumonisin B1 (FB1), were initially described as mammalian toxins; however, they are also potent phytotoxins. The fumonisins have a spectrum of susceptible plant species similar to that of AAL-toxin. The aminopentol derivatives of the B fumonisins are generally less toxic than the parent compounds, while the A series of fumonisins (acetylated forms) are essentially inactive. AAL-toxin was first thought to be host-specific for certain tomato cultivars, but now is known to affect many weed and crops species. Monocotyledonous species are less affected than dicotyledonous species. Tomatoes with the asc/asc genotype, jimsonweed, black nightshade, and duckweeds are the most susceptible species tested thus far. FB, causes toxicity on contact with plant tissue and at sites distal from wounds, demonstrating xylem mobility. AAL-toxin is an important virulence factor for infection of certain susceptible tomato cultivars by Alternaria altemata f. sp. lycopersici. Ultrastructural studies show that FB1 and AAL-toxin both cause rapid plasma membrane disruption. Both FBI and AAL-toxin are thought to interfere with plasma membrane function through disruption of sphingolipid metabolism by inhibition of sphinganine (sphingosine) N-acyltransferase (ceramide synthase), the same mechanism of toxicity as in animals. As in animals, high levels of ceramide synthase precursors accumulate in fumonisin-and AAL-toxin-treated plants. In addition, high concentrations of long chain sphingoid bases applied to plants cause phytotoxicity symptoms similar to those of fumonisins and AAL-toxin. Thus, the phytotoxicity of fumonisins and AAL-toxin are likely to be due to the accumulation of phytotoxic sphingolipid intermediates.
Dendritic cells: Understanding immunogenicity (2007)

The impetus for the discovery of dendritic cells in 1972 was to understand immunogenicity, the capacity of an antigenic substance to provoke immunity. During experiments to characterize "accessory" cells that enhanced immunity, we spotted unusual stellate cells in mouse spleen. They had a distinct capacity to form and retract processes or dendrites and were named dendritic cells (DC). DC proved to be different from other cell types and to be peculiarly immunogenic when loaded with antigens. When Langerhans cells were studied, immunogenicity was found to involve two steps: antigen presentation by immature DC and maturation to elicit immunity. Antigen-bearing DC were also immunogenic in vivo and were therefore termed "nature's adjuvants". Several labs then learned to generate large numbers of DC from progenitors, which accelerated DC research. Tolerogenicity via DC, including the control of foxp3(+) suppressor T cells, was recently discovered. Two areas of current research that I find intriguing are to identify mechanisms for antigen uptake and processing, and for the control of different types of immunity and tolerance. These subjects should be studied in vivo with clinically relevant antigens, so that the activities of DC can be better integrated into the prevention and treatment of disease in patients.
Thermisch induzierte Reaktionen von Imidazolderivaten, IV. Die Kinetik der thermischen Umlagerung von 2,4,4‐Thriaryl‐5‐mathylthio‐4<i>H</i>‐imidazolen (1974)

Abstract Die thermische Umlagerung der Titelsubstanzen 1a – d in die 2,4,5‐Triarylimidazole 2 in verschiedenen Lösungsmitteln und bei verschiedenen Temperaturen folgt einem Geschwindigkeitsgesetz 1. Ordnung. Der Einfluß des p ‐Substituenten der wandernden Arylgruppe ändert sich nicht linear mit den Hammett‐Brownschen σ + ‐Werten. Das Lösungsmittel hat praktisch keinen Einfluß auf die Umlagerungsgeschwindigkeit von 1c . Die Aktivierungsparameter der Umlagerung 1c → 2c werden angegeben.
Integrating a spatial reasoner with a resolution theorem-prover (1997)

Some spatial reasoning systems use images to solve problems, rather than making formal logical inferences. However, an open question is how to use these systems in contexts where some nonspatial information is also involved. We present a hybrid reasoning method in which we extend the capabilities of a spatial reasoner by integrating it with a resolution theorem-prover. We prove that the hybrid system is refutation-complete, in the sense that, if a domain theory is unsatisfiable, perhaps only because all of its models entail unrealizable images, then our algorithm will halt. We discuss how our approach differs from other hybrid reasoning algorithms in the way it manages the interaction between sub-systems. Introduction Recently there has been a resurgence of interest in spatial or diagrammatic reasoning (Glasgow, Narayanan, &amp; Chandrasekaran 1995). Among the various spatial reasoning systems that have been proposed, there are two basic types of approaches: axiomatic and image-based. In ...
Extending ribosomal protein identifications to unsequenced bacterial strains using matrix‐assisted laser desorption/ionization mass spectrometry (2005)

A protocol has been developed that allows protein identifications using available DNA-based or protein sequences from a reference strain of a bacterial species to be extended to bacterial strains for which no prior DNA-based or protein sequence information exists. The protocol is predicated on careful isolation of a specific sub-cellular group of proteins. In this study, ribosomal proteins were chosen due to their high relative abundance and similarity in copy number per cell. After isolation of ribosomal proteins, MALDI-MS is used to acquire accurate protein molecular weights. An iterative comparison of reference protein molecular weights and identities is made to the resulting data, allowing for the straightforward identification of ribosomal proteins from any non-reference strains. This approach can reveal differences between proteins at the amino acid or post-translational level. The protocol was developed, validated and applied to ribosomal proteins from three strains of the extreme thermophile Thermus thermophilus. This approach revealed that nearly 60% of the ribosomal proteins from all three strains are identical. The extension of protein identification to additional bacterial strains can be useful in phylogenetic studies as well as in biomarker identification.
Programmable single and multiplex base-editing in <i>Bombyx mori</i> using RNA-guided cytidine deaminases (2018)

ABSTRACT Standard genome editing tools (ZFN, TALEN and CRISPR/Cas9) edited genome depending on DNA double strand breaks (DSBs). A series of new CRISPR tools that convert cytidine to thymine (C to T) without the requirement for DNA double-strand breaks were developed recently, which have changed this status and have been quickly applied in a variety of organisms. Here, we demonstrate that CRISPR/Cas9-dependent base editor (BE3) converts C to T with a high frequency in the invertebrate Bombyx mori silkworm. Using BE3 as a knock-out tool, we inactivated exogenous and endogenous genes through base-editing-induced nonsense mutations with an efficiency of up to 66.2%. Furthermore, genome-scale analysis showed that 96.5% of B. mori genes have one or more targetable sites being knocked out by BE3 with a median of 11 sites per gene. The editing window of BE3 reached up to 13 bases (from C1 to C13 in the range of gRNA) in B. mori . Notably, up to 14 bases were substituted simultaneously in a single DNA molecule, with a low indel frequency of 0.6%, when 32 gRNAs were co-transfected. Collectively, our data show for the first time that RNA-guided cytidine deaminases are capable of programmable single and multiplex base-editing in an invertebrate model.