gebhart/patrepeval huggingface dataset:
Dialysis membrane-induced neutrophil apoptosis is mediated through free radicals. (2001)

Patients on hemodialysis are prone to infection. Neutrophils are the host's first line of defense against certain invading pathogenic microorganisms. Since apoptotic neutrophils are functionally compromised we examined the effect of dialysis membranes on neutrophil apoptosis. Dialysis patients showed greater (p < 0.001) neutrophil apoptosis when compared with control subjects. Cellulose acetate membranes directly promoted (p < 0.001) neutrophil apoptosis. Cellulose acetate membrane-treated neutrophils exhibited greater apoptosis (p < 0.01) when compared with polysulfone membrane-treated neutrophils. Superoxide dismutase (SOD) partly inhibited the cellulose acetate membrane-induced neutrophil apoptosis, whereas both catalase and dimethylthiourea (DMTU) inhibited the polysulfone membrane-induced neutrophil apoptosis. Similarly, L-NAME, a nitric oxide synthase inhibitor, attenuated both the cellulose acetate and the polysulfone membrane-induced neutrophil apoptosis. In addition, cellulose acetate and monocyte interaction products promoted (p < 0.001) neutrophil apoptosis. These results suggest that dialysis membranes can promote neutrophil apoptosis directly as well as through their interaction with monocytes. The direct effect of dialysis membranes seems to be mediated partly through the generation of reactive oxygen species.
A Meta-Analysis reveals the commonalities and differences in Arabidopsis thaliana response to dofferent viral pathogens (2012)

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The role of 5-methylcytidine in the anticodon arm of yeast tRNAPhe: site-specific magnesium binding and coupled conformational transition in DNA analogs (1992)

The tDNA(Phe)AC, d(CCAGACTGAAGAU13m5C14U15GG), with a DNA sequence similar to that of the anticodon stem and loop of yeast tRNA(Phe), forms a stem and loop structure and has an Mg(2+)-induced structural transition that was not exhibited by an unmodified tDNA(Phe)AC d(T13C14T15) [Guenther, R. H., Hardin, C. C., Sierzputowska-Gracz, H., Dao, V., & Agris, P. F. (1992) Biochemistry (preceding paper in this issue)]. Three tDNA(Phe)AC molecules having m5C14, tDNA(Phe)AC d(U13m5C14U15), d(U13m5C14T15), and d(T13,5C14U15), also exhibited Mg(2+)-induced structural transitions and biphasic thermal transitions (Tm approximately 23.5 and 52 degrees C), as monitored by CD and UV spectroscopy. Three other tDNA(Phe)AC, d(T13C14T15), d(U13C14U15), and d(A7;U13m5C14U15) in which T7 was replaced with an A, thereby negating the T7.A10 base pair across the anticodon loop, had no Mg(2+)-induced structural transitions and only monophasic thermal transitions (Tm of approximately 52 degrees C). The tDNA(Phe)AC d(U13m5C14U15) had a single, strong Mg2+ binding site with a Kd of 1.09 x 10(-6) M and a delta G of -7.75 kcal/mol associated with the Mg(2+)-induced structural transition. In thermal denaturation of tDNA(Phe)AC d(U13m5C14U15), the 1H NMR signal assigned to the imino proton of the A5.dU13 base pair at the bottom of the anticodon stem could no longer be detected at a temperature corresponding to that of the loss of the Mg(2+)-induced conformation from the CD spectrum. Therefore, we place the magnesium in the upper part of the tDNA hairpin loop near the A5.dU13 base pair, a location similar to that in the X-ray crystal structure of native, yeast tRNA(Phe).(ABSTRACT TRUNCATED AT 250 WORDS)
Role of the coagulation system in experimental colitis (2006)

Growing evidence indicates that there is significant “cross‐talk” between inflammatory and coagulation pathways. While patients with inflammatory bowel disease exhibit an increased incidence of thrombosis, it remains unclear whether the coagulation cascade contributes to the intestinal inflammation. The objective of this study was to determine whether tissue factor (TF) contributes to leukocyte/platelet‐endothelial adhesion, tissue injury, and disease severity in experimental murine colitis induced by feeding C57Bl/6 mice 3% dextran sodium sulfate (DSS) in drinking water for 6 days. Some mice were treated with a monoclonal antibody (mAb) against murine tissue factor (muTF‐mAb) two times (20mg/kg, ip) during the 6 days of DSS ingestion. Colitis was assessed by a disease activity index (DAI) and histology. Intravital fluorescence microscopy was used to quantify leukocyte and platelet adhesion in venules. In untreated mice, DSS resulted in an increased DAI, colon shortening, an increased colon weight/length ratio, and a profound increase in the number of adherent leukocytes and platelets in colonic venules. All of these responses to DSS were significantly attenuated in DSS mice treated with muTF‐mAb. These findings support a link between the coagulation and inflammatory pathways in experimental colitis and implicate tissue factor as a major pro‐inflammatory agent in this model. (Supported by DK65649)
124 CCR6 Ligands Inhibit HIV in Highly Susceptible CD4+CCR6+ T Cells by Inducing APOBEC3G Expression (2011)

CD4+CCR6+ T cells are highly susceptible to infection by both R5 and X4 isolates of HIV, as compared to CD4+CCR6- cells. We had shown that two CCR6 ligands (hBD2 and hBD3) inhibit HIV infection. We hypothesized that CCR6 mediates a novel type of antiretroviral activity. We observed that treatment with CCR6 ligands hBD2, -3, and MIP3α resulted in HIV inhibition and decreased abundance of early products of reverse transcription, which are abrogated by treating cells with PTx, an inhibitor of Gi proteins that are associated to signal transduction mediated by chemokine receptors. We found that expression of the cellular protein APOBEC3G is increased concomitantly with treatment with CCR6 ligands and with decrement of early reverse transcription products. Treatment of cells with a specific siRNA targeting APOBEC3G abrogates HIV inhibition, demonstrating the central role of APOBEC3G in the effects of CCR6 ligands. Induction of APOBEC3G by CCR6 ligands is also abrogated by treatment with pertussis toxin, indicating the requirement of intracellular signaling in this effect. We found that expression of CCR6 ligands is lower in HIV infected subjects than in controls. Our findings show that CCR6-induced antiviral activity can be a target for novel approaches to treatment and prevention of HIV infection, since CCR6 is expressed on cells most relevant to HIV infection, including CD4+CCR5+ memory T cells, Th17 cells, DC, and activated macrophages.
ChemInform Abstract: Ascidiatrienolide A is a 10‐Membered Lactone. (1993)

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.
Binary Batch Codes With Improved Redundancy (2020)

A primitive k-batch code encodes a string x of length n into a stringy of length N, such that each multiset of k symbols from x has k mutually disjoint recovering sets from y. In this paper, we discuss new constructions of binary primitive batch codes. First, we develop novel explicit and random coding constructions of linear primitive batch codes based on finite geometries. Second, a new explicit coding construction of binary primitive batch codes based on bivariate lifted multiplicity codes is provided. For any k = n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ε</sup> with ε ∈ (0, 0.47) \ {1/5, 1/4}, our proposed codes have a better trade-off between the redundancy and the parameters k, n than previously known batch codes.
The National Ignition Facility modular Kirkpatrick-Baez microscope (2016)

Current two-dimensional X-ray imaging at the National Ignition Facility (NIF) uses time resolved pinhole cameras with ∼10-25 μm pinholes. This method has limitations in the smallest resolvable features that can be imaged with reasonable photon statistics for inertial confinement fusion (ICF) applications. ICF sources have a broadband self-emission spectrum that causes the pinhole images obtained, through thin foil filters, to contain a similarly broadband spectrum complicating the interpretation of structure in the source. In order to study phenomena on the scale of ∼5 μm, such as dopant mix in the ICF capsule, a narrow energy band, higher spatial resolution microscope system with improved signal/noise has been developed using X-ray optics. Utilizing grazing incidence mirrors in a Kirkpatrick-Baez microscope (KBM) configuration [P. Kirkpatrick and A. V. Baez, J. Opt. Soc. Am. 38, 766-774 (1948)], an X-ray microscope has been designed and fielded on NIF with four imaging channels. The KBM has ∼12 × magnification, <8 μm resolution, and higher throughput in comparison to similar pinhole systems. The first KBM mirrors are coated with a multilayer mirror to allow a "narrow band" energy response at 10.2 keV with ΔE ∼ 3 keV. By adjusting the mirror coating only, the energy response can be matched to the future experimental requirements. Several mirror packs have been commissioned and are interchangeable in the diagnostic snout.
The human endothelin-1 gene (EDN1) encoding a peptide with potent vasoactive properties maps distal to HLA on chromosome arm 6p in close linkage to D6S89 (1993)

We determined the precise genetic location of the human endothelin-1 gene (EDN1), which encodes a peptide with extremely potent vasoactive properties and is apparently involved in a spectrum of diseases ranging from hypertension to asthma. Analyzing the segregation of a four-allele EDN1 polymorphism in 40 CEPH families including 480 individuals, we detected significant linkage of EDN1 to DNA markers spanning the telomeric half of chromosome arm 6p. EDN1 was closest to the highly polymorphic nucleotide-repeat marker D6S89 at a theta = 0.06 with the highest pairwise LOD score Zmax = 31.2. Subsequent multipoint analysis placed EDN1 at 8 cM distal to D6S89; EDN1 was flanked at its telomeric site at a 13-cM distance by the gene encoding the A subunit of blood clotting factor XIII (F13A1). Furthermore, EDN1 was located at approximately 34-36 cM distal to the HLA region defined by HLA-A, -B, and -DRB1, and 31 cM proximal to the most telomeric marker D6S7. This location of EDN1 on the primary genetic map is strongly supported with odds of 2.7 x 10(12):1 against the next best alternative.
Structure–mechanical property correlations in mechanochromic luminescent crystals of boron difluoride dibenzoylmethane derivatives (2015)

The structure and mechanical properties of crystalline materials of three boron difluoride dibenzoylmethane (BF2dbm) derivatives were investigated to examine the correlation, if any, among mechanochromic luminescence (ML) behaviour, solid-state structure, and the mechanical behaviour of single crystals. Qualitative mechanical deformation tests show that the crystals of BF2dbm( (t) Bu)2 can be bent permanently, whereas those of BF2dbm(OMe)2 exhibit an inhomogeneous shearing mode of deformation, and finally BF2dbmOMe crystals are brittle. Quantitative mechanical analysis by nano-indentation on the major facets of the crystals shows that BF2dbm( (t) Bu)2 is soft and compliant with low values of elastic modulus, E, and hardness, H, confirming its superior suceptibility for plastic deformation, which is attributed to the presence of a multitude of slip systems in the crystal structure. In contrast, both BF2dbm(OMe)2 and BF2dbmOMe are considerably stiffer and harder with comparable E and H, which are rationalized through analysis of the structural attributes such as the intermolecular interactions, slip systems and their relative orientation with respect to the indentation direction. As expected from the qualitative mechanical behaviour, prominent ML was observed in BF2dbm( (t) Bu)2, whereas BF2dbm(OMe)2 exhibits only a moderate ML and BF2dbmOMe shows no detectable ML, all examined under identical conditions. These results confirm that the extent of ML in crystalline organic solid-state fluorophore materials can be correlated positively with the extent of plasticity (low recovery). In turn, they offer opportunities to design new and improved efficient ML materials using crystal engineering principles.
Devices with Embedded Channels (2015)

Micro- and nanoresonators with embedded channels are attractive because they unite high mechanical quality factors normally associated only with vacuum environments with the ability to analyze samples in the liquid phase. This chapter first gives a general introduction to the theory of microfluidic resonators and the different types of measurements that can be conducted with these versatile devices. The effects of fluid density and flow are considered first, followed by a brief account of the influence of fluid viscosity. Next, the sensitivity to localized mass changes is described. Such localized loading commonly arises in both surface based measurements and in the detection of micro-particles and nanoparticles bymass. The chapter also describes the technology for fabricating and packaging embedded channel resonators. Finally, it presents a short overview of the applications with examples from the current literature.
Steering Angle Assisted Vehicular Navigation Using Portable Devices in GNSS-Denied Environments (2019)

Recently, land vehicle navigation, and especially by the use of low-cost sensors, has been the object of a huge level of research interest. Consumer Portable Devices (CPDs) such as tablets and smartphones are being widely used by many consumers all over the world. CPDs contain sensors (accelerometers, gyroscopes, magnetometer, etc.) that can be used for many land vehicle applications such as navigation. This paper presents a novel approach for estimating steering wheel angles using CPD accelerometers by attaching CPDs to the steering wheel. The land vehicle change of heading is then computed from the estimated steering wheel angle. The calculated change of heading is used to update the navigation filter to aid the onboard Inertial Measurement Unit (IMU) through the use of an Extended Kalman Filter (EKF) in GNSS-denied environments. Four main factors that may affect the steering wheel angle accuracy are considered and modeled during steering angle estimations: static onboard IMU leveling, inclination angle of the steering wheel, vehicle acceleration, and vehicle inclination. In addition, these factors are assessed for their effects on the final result. Therefore, three methods are proposed for steering angle estimation: non-compensated, partially-compensated, and fully-compensated methods. A road experimental test was carried out using a Pixhawk (PX4) navigation system, iPad Air, and the OBD-II interface. The average Root Mean Square Error (RMSE) of the change of heading estimated by the proposed method was 0.033 rad/s. A navigation solution was estimated while changes of heading and forward velocity updates were used to aid the IMU during different GNSS signal outages. The estimated navigation solution is enhanced when applying the proposed updates to the navigation filter by 91% and 97% for 60 s and 120 s of GNSS signal outage, respectively, compared to the IMU standalone solution.
Assigning Keywords to Automatically Extracted Personal Cliques from Social Networks (2015)

In Twitter and other microblogging services, users often have large social networks formed around cliques (communities) such as friends, coworkers or former classmates. However, the membership of each user in multiple cliques makes it difficult to process information and interact with other clique members. We address this problem by automatically dividing the social network of a Twitter user into personal cliques and assigning keywords to each clique to identify the common ground of its members. In this way, the user can understand the structure of their social network and interact with the members of each clique independently. Our proposed method improves clique annotation by not only extracting keywords from the tweet history of the clique members, but individually weighting the extracted keywords of each member according to the relevance of their tweets for the clique. The keyword weight is influenced by two factors. The first factor is calculated based on the number of connections of a user within the clique, and the second factor depends on whether the user publishes personal information or information of general interest. We developed the prototype of a Twitter client with clique management functionality and conducted an experiment in which on average 46.96% of the keywords extracted from our proposed method were relevant for the cliques as opposed to 38.31% for the baseline method.
Action potential morphology heterogeneity in the atrium and its effect on atrial reentry: a two-dimensional and quasi-three-dimensional study (2006)

Atrial fibrillation (AF) is believed to be perpetuated by recirculating spiral waves. Atrial structures are often characterized with action potentials of varying morphologies; however, the role of the structure-dependent atrial electrophysiological heterogeneity in spiral wave behaviour is not well understood. The purpose of this study is to determine the effect of action potential morphology heterogeneity associated with the major atrial structures in spiral wave maintenance. The present study also focuses on how this effect is further modulated by the presence of the inherent periodicity in atrial structure. The goals of the study are achieved through the simulation of electrical behaviour in a two-dimensional atrial tissue model that incorporates the representation of action potentials in various structurally distinct regions in the right atrium. Periodic boundary conditions are then imposed to form a cylinder (quasi three-dimensional), thus allowing exploration of the additional effect of structure periodicity on spiral wave behaviour. Transmembrane potential maps and phase singularity traces are analysed to determine effects on spiral wave behaviour. Results demonstrate that the prolonged refractoriness of the crista terminalis (CT) affects the pattern of spiral wave reentry, while the variation in action potential morphology of the other structures does not. The CT anchors the spiral waves, preventing them from drifting away. Spiral wave dynamics is altered when the ends of the sheet are spliced together to form a cylinder. The main effect of the continuous surface is the generation of secondary spiral waves which influences the primary rotors. The interaction of the primary and secondary spiral waves decreased as cylinder diameter increased.
Up‐Regulation and Redistribution of Bax in Ultraviolet B‐Irradiated Melanocytes (2000)

Ultraviolet B (UVB) radiation may activate or deteriorate cultured human epidermal melanocytes, depending on the doses and culture conditions. It is also reported that cultured human epidermal melanocytes derived from different pigmentary phenotypes showed different responses to UVB radiation. In this study, we examined whether apoptosis of melanocytes can be induced by physiologic doses of UVB irradiation using cultured human epidermal melanocytes derived from oriental males of skin types III and IV. Propidium iodide staining for DNA condensation and flow cytometric analyses demonstrated the apoptotic cell death of melanocytes following UVB irradiation (0–30 mJ/cm 2 ). The levels of p53, Bax, and Bcl‐2, determined by immunoblotting, revealed a dose‐dependent increase in p53 and Bax, but the level of Bcl‐2 remained unchanged. Confocal microscopic examination showed that Bax moved from a diffuse to a punctate distribution after UVB irradiation. However, there were no changes in the pattern of distribution of Bcl‐2. These data suggest that the high constitutional level of Bcl‐2 may protect melanocytes from UVB‐induced injury, and that apoptotic death of melanocytes may be induced by the elevation and redistribution of Bax.
Structure, Stability and Biological Properties of a N‐terminally Truncated form of Recombinant Human Interleukin‐6 Containing a Single Disulfide Bond (1995)

A mutant species of the 185-residue chain of human interleukin-6 lacking 22-residues at its N-terminus and with a Cys-->Ser substitution at positions 45 and 51 was produced in Escherichia coli. The 163-residue protein des-(A1-S22)-[C45S, C51S]interleukin-6, containing a single disulfide bridge, formed inclusion bodies. Mutant interleukin-6 was solubilized in 6 M guanidine hydrochloride, subjected to oxidative refolding and purified to homogeneity by ammonium sulfate precipitation and hydrophobic chromatography. The purity of the mutant species was established by electrophoresis, isoelectrofocusing and reverse-phase HPLC and its structural identity was checked by N-terminal sequencing of both the intact protein and several of its proteolytic fragments. Electrospray mass spectrometry analysis of mutant interleukin-6 gave a molecular mass of 18,695 +/- 2 Da in excellent agreement with the calculated value. Circular dichroic, fluorescence emission and second-derivative ultraviolet absorption spectra indicated that mutant interleukin-6 maintains the overall secondary and tertiary structure, as well as stability characteristics, of the recombinant wild-type human interleukin-6. The urea-induced unfolding of mutant interleukin-6, monitored by circular dichroic measurements in the far-ultraviolet region, occurs as a highly cooperative process with a midpoint of denaturation at 5.5 M urea. The data of the reversible unfolding of mutant interleukin-6 mediated by urea were used to calculate a value of 20.9 +/- 0.4 kJ.mol-1 for the thermodynamic stability of the protein at 25 degrees C in the absence of denaturant. The biological activity of mutant interleukin-6 was evaluated in vitro by the hybridoma proliferation assay, and in vivo by measuring thrombopoiesis in monkeys. Dose/response effects of the mutant were comparable or even higher than those of the wild-type protein. Overall the results of this study show that mutant interleukin-6 is a biologically active cytokine, which could find practical use as a therapeutic agent.
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq (2023)

Adipogenesis is key to maintaining organism-wide energy balance and healthy metabolic phenotype, making it critical to thoroughly comprehend its molecular regulation in humans. By single-nuclei RNA-sequencing (snRNA-seq) of over 20,000 differentiating white and brown preadipocytes, we constructed a high-resolution temporal transcriptional landscape of human white and brown adipogenesis. White and brown preadipocytes were isolated from a single individual's neck region, thereby eliminating inter-subject variability across two distinct lineages. These preadipocytes were also immortalized to allow for controlled, in vitro differentiation, allowing sampling of distinct cellular states across the spectrum of adipogenic progression. Pseudotemporal cellular ordering revealed the dynamics of ECM remodeling during early adipogenesis, and lipogenic/thermogenic response during late white/brown adipogenesis. Comparison with adipogenic regulation in murine models Identified several novel transcription factors as potential targets for adipogenic/thermogenic drivers in humans. Among these novel candidates, we explored the role of TRPS1 in adipocyte differentiation and showed that its knockdown impairs white adipogenesis in vitro. Key adipogenic and lipogenic markers revealed in our analysis were applied to analyze publicly available scRNA-seq datasets; these confirmed unique cell maturation features in recently discovered murine preadipocytes, and revealed inhibition of adipogenic expansion in humans with obesity. Overall, our study presents a comprehensive molecular description of both white and brown adipogenesis in humans and provides an important resource for future studies of adipose tissue development and function in both health and metabolic disease state.