gebhart/patrepeval huggingface dataset:
Total Synthesis and Antibacterial Testing of the A54556 Cyclic Acyldepsipeptides Isolated from <i>Streptomyces hawaiiensis</i> (2014)

The first total synthesis of all six known A54556 acyldepsipeptide (ADEP) antibiotics from Streptomyces hawaiiensis is reported. This family of compounds has a unique mechanism of antibacterial action, acting as activators of caseinolytic protease (ClpP). Assembly of the 16-membered depsipeptide core was accomplished via a pentafluorophenyl ester-based macrolactamization strategy. Late stage amine deprotection was carried out under neutral conditions by employing a mild hydrogenolysis strategy, which avoids the formation of undesired ring-opened depsipeptide side products encountered during deprotection of acid-labile protecting groups. The free amines were found to be significantly more reactive toward late stage amide bond formation as compared to the corresponding ammonium salts, giving final products in excellent yields. A thorough NMR spectroscopic analysis of these compounds was carried out to formally assign the structures and to aid with the spectroscopic assignment of ADEP analogues. The identity of two of the structures was confirmed by comparison with biologically produced samples from S. hawaiiensis. An X-ray crystallographic analysis of an ADEP analogue reveals a conformation similar to that found in cocrystal structures of ADEPs with ClpP protease. The degree of antibacterial activity of the different compounds was evaluated in vitro using MIC assays employing both Gram-positive and Gram-negative strains and a fluorescence-based biochemical assay.
HDAC inhibition decreases <i>XIST</i> expression on female IVP bovine blastocysts (2012)

During initial development, both X chromosomes are active in females, and one of them must be silenced at the appropriate time in order to dosage compensate their gene expression levels to male counterparts. Silencing involves epigenetic mechanisms, including histone deacetylation. Major X chromosome inactivation (XCI) in bovine occurs between hatching and implantation, although in vitro culture conditions might disrupt the silencing process, increasing or decreasing X-linked gene expression. In this study, we aimed to address the roles of histone deacetylase inhibition by trichostatin A (TSA) on female preimplantation development. We tested the hypothesis that by enhancing histone acetylation, TSA would increase the percentage of embryos achieving 16-cell stage, reducing percentage of embryos blocked at 8-cell stage, and interfere with XCI in IVF embryos. We noticed that after TSA treatment, acetylation levels in individual blastomeres of 8-16 cell embryos were increased twofold on treated embryos, and the same was detected for blastocysts. Changes among blastomere levels within the same embryo were diminished on TSA group, as low-acetylated blastomeres were no longer detected. The percentage of embryos that reached the 5th cleavage cycle 118 h after IVF, analyzed by Hoechst staining, remained unaltered after TSA treatment. Then, we assessed XIST and G6PD expression in individual female bovine blastocysts by quantitative real-time PCR. Even though G6PD expression remained unaltered after TSA exposure, XIST expression was eightfold decreased, and we also detected a major decrease in the percentage of blastocysts expressing detectable XIST levels after TSA treatment. Based on these results, we conclude that HDAC is involved on XCI process in bovine embryos, and its inhibition might delay X chromosome silencing and attenuate aberrant XIST expression described for IVF embryos.
Design of Planar Differential Microphone Arrays With Fractional Orders (2019)

Differential microphone arrays (DMAs) often encounter white noise amplification, especially at low frequencies. If the array geometry and the number of microphones are fixed, one can improve the white noise amplification problem by reducing the DMA order. With the existing differential beamforming methods, the DMA order can only be a positive integer number. Consequently, with a specified beampattern (or a kind of beampattern), reducing this order may easily lead to over compensation of the white noise gain (WNG) and too much reduction of the directivity factor (DF), which is not optimal. To deal with this problem, we present in this article a general approach to the design of DMAs with fractional orders. The major contributions of this article include but are not limited to: 1) we first define a directivity pattern that can achieve a continuous compromise between the pattern corresponding to the maximum DMA order and the omnidirectional pattern; 2) by approximating the beamformer's beampattern with the Jacobi-Anger expansion, we present a method to find the proper differential beamforming filter so that its beampattern matches closely the target directivity pattern of fractional orders; and 3) we show how to determine analytically the proper fractional order of the DMA with a given target beampattern when either the value of the DF or WNG is specified, which is useful in practice to achieve the desired beampattern and spatial gain while maintaining the robustness of the DMA system.
Automatic online buffer capacity (alkalinity) measurement of wastewater using an electrochemical cell (2016)

The use of an automatic online electrochemical cell (EC) for measuring the buffer capacity of wastewater is presented. pH titration curves of different solutions (NaHCO3, Na2HPO4, real municipal wastewater, and anaerobic digester liquid) were obtained by conventional chemical titration and compared to the online EC measurements. The results show that the pH titration curves from the EC were comparable to that of the conventional chemical titration. The results show a linear relationship between the response of the online EC detection system and the titrimetric partial alkalinity and total alkalinity of all tested samples. This suggests that an EC can be used as a simple online titration device for monitoring the buffer capacity of different industrial processes including wastewater treatment and anaerobic digestion processes.
Association of Botulinum Neurotoxin Serotypes A and B with Synaptic Vesicle Protein Complexes (2007)

Botulinum neurotoxins (BoNTs) elicit flaccid paralysis through cleavage of SNARE proteins within peripheral neurons. There are seven serotypes of the BoNTs, termed A-G, which differ in the SNARE protein and/or site that is cleaved. BoNTs are single-chain toxins that comprise an N-terminal zinc metalloprotease domain that is disulfide linked to the C-terminal translocation/receptor binding domain. SV2 and synaptotagmin have been identified as receptors for BoNT serotypes A and B, respectively. Using affinity chromatography, BoNTs A and B were observed to bind synaptic vesicle protein complexes in synaptosome lysates. Tandem LC-MS/MS identified SV2, synaptotagmin I, synaptophysin, vesicle-associated membrane protein 2 (VAMP2), and the vacuolar proton pump as components of the BoNT-receptor complex. Density gradient analysis showed that BoNT serotypes A and B exhibited unique interactions with the synaptic vesicle protein complexes. The association of BoNT serotypes A and B with synaptic vesicle protein complexes implicates a physiological role for protein complexes in synaptic vesicle biology and provides insight into the interactions of BoNT and neuronal receptors.
Be Prepared (2012)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTBe PreparedHarry J. ElstonHarry J. ElstonMore by Harry J. ElstonCite this: J. Chem. Health Saf. 2012, 19, 5, 66Publication Date (Web):September 1, 2012Publication History Published online1 September 2012Published inissue 1 September 2012https://pubs.acs.org/doi/10.1016/j.jchas.2012.07.008https://doi.org/10.1016/j.jchas.2012.07.008editorialACS Publications© 2012 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views60Altmetric-Citations-LEARN 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 PDF (38 KB) Get e-Alerts
Müllerian Inhibiting Substance Induces Apoptosis of Human Endometrial Stromal Cells in Endometriosis (2012)

The results support a central role for MIS in endometriosis. Although the precise mechanism of MIS-mediated inhibition of ESC growth has not been fully defined, these data suggest that MIS has activity against ESC in vitro and may also be an effective targeted therapy for endometriosis.
The rheology of suspensions of solid particles (2009)

We present data for the rheology of suspensions of monodisperse particles of varying aspect ratio, from oblate to prolate, and covering particle volume fractions ϕ from dilute to highly concentrated. Rheology is characterized by fitting the experimental data to the model of Herschel & Bulkley (Herschel & Bulkley 1926 Kolloid Z. 39 , 291–300 ( doi:10.1007/BF01432034 )) yielding three rheometric parameters: consistency K (cognate with viscosity); flow index n (a measure of shear-thinning); yield stress τ 0 . The consistency K of suspensions of particles of arbitrary aspect ratio can be accurately predicted by the model of Maron & Pierce (Maron & Pierce 1956 J. Colloid Sci. 11 , 80–95 ( doi:10.1016/0095-8522(56)90023-X )) with the maximum packing fraction ϕ m as the only fitted parameter. We derive empirical relationships for ϕ m and n as a function of average particle aspect ratio r p and for τ 0 as a function of ϕ m and a fitting parameter τ *. These relationships can be used to predict the rheology of suspensions of prolate particles from measured ϕ and r p . By recasting our data in terms of the Einstein coefficient, we relate our rheological observations to the underlying particle motions via Jeffery’s (Jeffery 1922 Proc. R. Soc. Lond. A 102 , 161–179 ( doi:10.1098/rspa.1922.0078 )) theory. We extend Jeffery’s work to calculate, numerically, the Einstein coefficient for a suspension of many, initially randomly oriented particles. This provides a physical, microstructural explanation of our observations, including transient oscillations seen during run start-up and changes of rheological regime as ϕ increases.
Sensing with Polarized LIDAR in Degraded Visibility Conditions Due to Fog and Low Clouds (2021)

LIDAR (Light Detection and Ranging) sensors are one of the leading technologies that are widely considered for autonomous navigation. However, foggy and cloudy conditions might pose a serious problem for a wide adoption of their use. Polarization is a well-known mechanism often applied to improve sensors' performance in a dense atmosphere, but is still not commonly applied, to the best of our knowledge, in self-navigated devices. This article explores this issue, both theoretically and experimentally, and focuses on the dependence of the expected performance on the atmospheric interference type. We introduce a model which combines the well-known LIDAR equation with Stocks vectors and the Mueller matrix formulations in order to assess the magnitudes of the true target signal loss as well as the excess signal that arises from the scattering medium radiance, by considering the polarization state of the E-M (Electro-Magnetic) waves. Our analysis shows that using the polarization state may recover some of the poor performance of such systems for autonomous platforms in low visibility conditions, but it depends on the atmospheric medium type. This conclusion is supported by measurements held inside an aerosol chamber within a well-controlled and monitored artificial degraded visibility atmospheric environment. The presented analysis tool can be used for the optimization of design and trade-off analysis of LIDAR systems, which allow us to achieve the best performance for self-navigation in all weather conditions.
Dynamics of an innate myeloid cell response to acute CNS viral infection (162.16) (2011)

Abstract Viral infections of central nervous system (CNS) often trigger an inflammatory response that gives rise to a wide range of pathological outcomes. The CNS is equipped with an elaborate network of innate immune sentinels that routinely serve as first responders to these infections. The meninges and perivascular spaces are inhabited by specialized macrophages, and the brain parenchyma contains microglia - the most abundant CNS myeloid cell. To gain novel insights into how myeloid cells respond to an acute CNS viral infection, we utilized genomics and two-photon imaging approaches to study a pure innate response to LCMV infection. This was accomplished by monitoring temporal gene expression patterns and myeloid cell dynamics in the brains of CX3CR1-GFP mice lacking LCMV-specific T cells. Two-photon imaging studies revealed that CNS myeloid sentinels responded significantly to acute infection by sequestering DsRed-labeled virus. Microglia but not peripheral myeloid cells proliferated following acute infection and responded directly to viral antigen by reducing process complexity, suggesting a localized response to the presence of virus. However, at the genomic level, acute infection triggered massive changes in CNS gene expression with the majority of genes being linked to innate viral control and the type I interferon system. These data suggest that localized detection of virus by CNS myeloid sentinels can translate into engagement of an extensive anti-viral program.
Hallucinated Humans as the Hidden Context for Labeling 3D Scenes (2013)

For scene understanding, one popular approach has been to model the object-object relationships. In this paper, we hypothesize that such relationships are only an artifact of certain hidden factors, such as humans. For example, the objects, monitor and keyboard, are strongly spatially correlated only because a human types on the keyboard while watching the monitor. Our goal is to learn this hidden human context (i.e., the human-object relationships), and also use it as a cue for labeling the scenes. We present Infinite Factored Topic Model (IFTM), where we consider a scene as being generated from two types of topics: human configurations and human-object relationships. This enables our algorithm to hallucinate the possible configurations of the humans in the scene parsimoniously. Given only a dataset of scenes containing objects but not humans, we show that our algorithm can recover the human object relationships. We then test our algorithm on the task of attribute and object labeling in 3D scenes and show consistent improvements over the state-of-the-art.
Emerging Procedures in Narrative Assessment (2008)

This article summarizes norm-referenced and criterion-referenced measures of narration and introduces a new criterion-referenced narrative scoring system called the Index of Narrative Complexity (INC). The INC was designed to be used as a progress-monitoring tool. A preliminary study of the use of this scoring system is reported that yielded evidence suggesting that the INC can be scored consistently, yields similar scores across five elicitation formats, is sensitive to change after intervention, and correlates highly with the Test of Narrative Language (Gillam & Pearson, 2004). These results support the use of the INC as a clinical tool for evaluating the outcomes of narrative intervention.
Alternative Splicing of the Drosophila<i>Dscam</i>Pre-mRNA Is Both Temporally and Spatially Regulated (2001)

The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene encodes an axon guidance receptor that can express 38,016 different mRNAs by virtue of alternative splicing. The Dscam gene contains 95 alternative exons that are organized into four clusters of 12, 48, 33, and 2 exons each. Although numerous Dscam mRNA isoforms can be synthesized, it remains to be determined whether different Dscam isoforms are synthesized at different times in development or in different tissues. We have investigated the alternative splicing of the Dscam exon 4 cluster, which contains 12 mutually exclusive alternative exons, and found that Dscam exon 4 alternative splicing is developmentally regulated. The most highly regulated exon, 4.2, is infrequently used in early embryos but is the predominant exon 4 variant used in adults. Moreover, the developmental regulation of exon 4.2 alternative splicing is conserved in D. yakuba. In addition, different adult tissues express distinct collections of Dscam mRNA isoforms. Given the role of Dscam in neural development, these results suggest that the regulation of alternative splicing plays an important role in determining the specificity of neuronal wiring. In addition, this work provides a framework to determine the mechanisms by which complex alternative splicing events are regulated.
Hirseins inhibit melanogenesis by regulating the gene expressions of Mitf and melanogenesis enzymes (2009)

Previously, we reported that Thymelaea hirsuta extract has antimelanogenesis effect on B16 murine melanoma cells. The extract was subjected to fractionation, and hirsein A (HA) and hirsein B (HB) were discovered and tested for their ability to regulate melanogenesis in B16 cells. Western blot (WB) analysis was carried out to determine the expression of tyrosinase. Moreover, to elucidate the possible mechanism behind melanogenesis regulation, real-time PCR using primers for Mitf, Tyr, Trp1 and Dct genes, and protein kinase C (PKC) activity assay were carried out. Results clearly show that 0.1 mum HA and HB significantly reduced the melanin content. This reduction in melanin content was accompanied by reduced tyrosinase expression as detected by WB analysis. There was also a significant decrease in the expression level of Mitf gene in HA- and HB-treated cells. HA down-regulated the expressions of Tyr, Trp1 and Dct, whereas HB down-regulated only those of Trp1 and Dct. Interestingly, HB-treated cells had lower kinase activity than HA-treated cells indicating a possible difference in the activities of the compounds but with the same mechanism of melanogenesis regulation. We report for the first time that HA and HB can down-regulate melanogenesis by down-regulating Mitf gene expression, leading to reduced expressions of Tyr, Trp1 and Dct. The hirseins were also able to reduce the kinase activity, suggesting the possible involvement of PKC in the overall ability of the hirseins to down-regulate melanogenesis.
How effective is the influenza vaccine in preventing influenza in adults? (2020)

Weeks, Jeffrey DO, MBA; Clements, Ernestine DO, MPH; Iles, Ashley MD; Hicks, Casey MD; Hurst, Daniel J. PhD Author Information
Temperature compensation of liquid FBAR sensors (2007)

In this work we demonstrate a practically complete temperature compensation of the second harmonic shear mode in a composite Al/AlN/Al/SiO2 thin film bulk acoustic resonator (FBAR) in the temperature range 25 °C–95 °C. The main advantages of this mode are its higher Q value in liquids as well as its higher frequency and hence higher resolution for sensor applications. For comparative reasons the non-compensated fundamental shear mode is also included in these studies. Both modes have been characterized when operated both in air and in pure water. Properties such as Q value, electromechanical coupling, dissipation and sensitivity are studied. An almost complete temperature compensation of the second harmonic shear mode was observed for an oxide thickness of 1.22 µm for an FBAR consisting of 2 µm thick AlN and 200 nm thick Al electrodes. Thus, the measured temperature coefficient of frequency (TCF) in air for the non-compensated fundamental shear mode (1.25 GHz) varied between −31 and −36 ppm °C−1 over the above temperature range while that of the compensated second harmonic shear mode (1.32 GHz) varied between +2 ppm °C−1 and −2 ppm °C−1 over the same temperature interval. When operated in pure water the former type shows a Q value and coupling coefficient, k2t, around 180 and 2%, respectively, whereas for the second harmonic these are 230 and 1.4%, respectively.
Common Traps and Coping Strategies During Job Hunting of College Students (2014)

College students’ problem of job hunting has drawn increasing attention from the society. How to avoid traps in job hunting and safeguard one’s legal rights and interests becomes a compulsory lesson for graduates. This paper lists the features of common traps in job hunting under the current situation, and approaches to avoid these traps are also proposed.
Discrete Chebyshev transform. A natural modification of the DCT (2002)

Although the discrete cosine transform (DCT) is widely used for feature extraction in pattern recognition, it is shown that it converges slowly for most theoretically smooth functions. A modification of the DCT is described, based on a change of variable, which changes it to a new transform, called the discrete Chebyshev transform (DChT), which converges very rapidly for the same smooth functions. Although this rapid convergence is largely destroyed by the noise in real experimental data, the discrete Chebyshev transform is still generally better than the DCT when the sampling of the data can be selected at nonequidistant points. The improvement over the DCT gives a theoretical explanation for improved speech recognition obtained using Mel feature cepstral coefficients. These choose the sampling frequencies of a DCT to correspond to the human perception of pitch. It is shown that this sampling is similar to the sampling used in the discrete Chebyshev transform.
Human α-defensin regulates smooth muscle cell contraction: a role for low-density lipoprotein receptor–related protein/α2-macroglobulin receptor (2002)

We have previously identified alpha-defensin in association with medial smooth muscle cells (SMCs) in human coronary arteries. In the present paper we report that alpha-defensin, at concentrations below those found in pathological conditions, inhibits phenylephrine (PE)-induced contraction of rat aortic rings. Addition of 1 microM alpha-defensin increased the half-maximal effective concentration (EC(50)) of PE on denuded aortic rings from 32 to 630 nM. The effect of alpha-defensin was dose dependent and saturable, with a half-maximal effect at 1 microM. alpha-Defensin binds to human umbilical vein SMCs in a specific manner. The presence of 1 microM alpha-defensin inhibited the PE-mediated Ca(++) mobilization in SMCs by more than 80%. The inhibitory effect of alpha-defensin on contraction of aortic rings and Ca(++) mobilization was completely abolished by anti-low-density lipoprotein receptor-related protein/alpha(2-)macroglobulin receptor (LRP) antibodies as well as by the antagonist receptor-associated protein (RAP). alpha-Defensin binds directly to isolated LRP in a specific and dose-dependent manner; the binding was inhibited by RAP as well as by anti-LRP antibodies. alpha-Defensin is internalized by SMCs and interacts with 2 intracellular subtypes of protein kinase C (PKC) involved in muscle contraction, alpha and beta. RAP and anti-LRP antibodies inhibited the binding and internalization of alpha-defensin by SMCs and its interaction with intracellular PKCs. These observations suggest that binding of alpha-defensin to LRP expressed in SMCs leads to its internalization; internalized alpha-defensin binds to PKC and inhibits its enzymatic activity, leading to decreased Ca(++) mobilization and SMC contraction in response to PE.