gebhart/patrepeval huggingface dataset:
Two-Component System That Regulates Methanol and Formaldehyde Oxidation in Paracoccus denitrificans (2001)

A chromosomal region encoding a two-component regulatory system, FlhRS, has been isolated from Paracoccus denitrificans. FlhRS-deficient mutants were unable to grow on methanol, methylamine, or choline as the carbon and energy source. Expression of the gene encoding glutathione-dependent formaldehyde dehydrogenase (fhlA) was undetectable in the mutant, and expression of the S-formylglutathione hydrolase gene (fghA) was reduced in the mutant background. In addition, methanol dehydrogenase was immunologically undetectable in cell extracts of FhlRS mutants. These results indicate that the FlhRS sensor-regulator pair is involved in the regulation of formaldehyde, methanol, and methylamine oxidation. The effect that the FlhRS proteins exert on the regulation of C(1) metabolism might be essential to maintain the internal concentration of formaldehyde below toxic levels.
Dynamics of Electric Field Screening in Semi‐Insulating ZnSe (1991)

Abstract The dynamics of the screening of an external electic field in semi‐insulating ZnSe is studied. It is found that this dynamics exhibits two different regimes depending on the crystal temperature and the conditions of the preliminary illumination: expansion of the single homogeneous depletion layer or formation of numerous space charge layers of alternating sign. All these results are described within a simple model allowing for two types of deep centers with different recharging times.
Phosphorylated Aminoacetal in the Synthesis of New Acyclic, Cyclic, and Heterocyclic Polyphenol Structures (2014)

ABSTRACT New phosphorylated aminoacetal has been synthesized by the Kabachnik–Fields reaction; its reactivity has been studied in acid‐catalyzed condensation with linear polyphenols (2‐methylresorcinol, resorcinol, pyrogallol) and the Mannich reaction with macrocyclic polyphenol (calix[4]resorcinol). It has been determined for the first time that acid‐catalyzed reaction of phosphorus‐containing acetal with resorcinol and its derivatives in ethanol in the presence of hydrochloric acid gives new phosphorylated piperazines in addition to the compounds of diarylmethane series. Condensation of macrocyclic polyphenol (calix[4]resorcinol) with formaldehyde and N ‐((dihexylphosphoryl)methyl)‐2, 2‐dimethoxyethylamine (the Mannich reaction) has resulted in novel tetrasubstituted calixarene containing aminophosphine oxide and acetal groups on the “upper rim” of molecule.
Propagation and radiation behaviour of corrugated feeds. Part 1: Corrugated-waveguide feed (1971)

An investigation of the propagation and radiation behaviour of circular corrugated waveguides is described. Particular attention is given to modes of unity azimuthal dependence because of their importance in antennafeed applications. It is shown that the radiation pattern of a corrugated waveguide exhibits nearly perfect symmetry over a 1.5:1 frequency band, and, when the corrugations are approximately λ/4 deep, the pattern is symmetric and there is no crosspolarised component of radiated field. The attenuation of the dominant HE11 mode is investigated theoretically and is shown to be less than that of the H11mode in a uniform waveguide over at least a 2:1 frequency bandwidth. An important similarity is described between the propagation behaviour of a corrugated waveguide and that of a dielectric rod of low relative permittivity, such as those used in fibre optics and optical waveguides. Finally, the determination of the input voltage standing-wave ratio (v.s.w.r.) at the junction between homogeneous and corrugated waveguides is theoretically and experimentlly studied.
Supplementary methods and figure legends from Combined BTK and PI3Kδ Inhibition with Acalabrutinib and ACP-319 Improves Survival and Tumor Control in CLL Mouse Model (2023)

&lt;p&gt;Supplementary methods and figure legends&lt;/p&gt;
Ultrasound Debridement of Trabeculated Bone (1994)

Given the plethora of techniques available for debridement of contaminated bone, no single method can be considered ideal. Ultrasound has been shown to be less traumatic and more effective for debridement of contaminated soft tissue than either abrasive scrubbing or high-pressure jet irrigation. Using the distal femur and condyle of 23 freshly sacrificed adult Sprague-Dawley rats, this study was undertaken to compare ultrasonication to traditional debridement techniques in (1) their effectiveness in decontaminating trabeculated bone, (2) the subsequent effect of each treatment on bone cell function as measured by protein synthesis, and (3) the direct mechanical effects of each technique on the integrity of the bone structure itself. Ultrasonic debridement was found to be as effective as high-pressure jet irrigation or surgical scrubbing in debridement of contaminated trabeculated bone (no significant statistical difference). Overall activated bone cell function 24 hours after each debridement technique also was found to be equivalent (no significant statistical difference). However, electron microscopy reveals radical structural alterations of the bone after high-pressure jet irrigation or abrasive scrubbing that are not seen with ultrasound debridement. Acutely, the devastating effects of abrasive scrubbing and high-pressure jet irrigation leave an exposed bone matrix not only devoid of any cells but also honeycombed with interstices for entrapment of bacteria and other contaminants. All three debridement methods leave the deeper bone cells viable, but only ultrasound maintains the integrity of the directly involved bone trabeculum to reduce contamination, prevent colonization, and decrease possible infection. (Plast. Reconstr. Surg. 93: 561, 1994.)
NGMA-4. Creation of a MADR brain tumor single-cell atlas for examination of inter-/intratumor heterogeneity and the results of genetic perturbations in a diverse array of brain tumor subtypes (2021)

Abstract We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a (aka H3.3) mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M mutant human glioma. Moreover, we have generated novel models of H3.3 WT glioma, H3.3 G34R glioma, and supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of phenotypic fidelity and we now compare these models on a single-cell level with our previous models, mouse single-cell RNA glioma datasets from other studies, and human tumor cell transcriptomes. Our multi-omics approach includes integration of ChIP-seq/Cut&amp;Tag datasets, single-cell ATAC, and single-cell Cut&amp;Tag datasets. Moreover, we have engineered a novel methodology for inducible gain- and loss-of function perturbation studies in vivo. Using ETS transcription factors as a proof-of-principle, we overlay these genetic perturbations on the glioma atlas to examine the gene networks altered by precise molecular manipulations. We hope that these combined approaches will enable researchers to discover disease mechanisms with increased resolution and test therapeutics in credentialed pre-clinical disease models.
Hedonic Taste in Drosophila Revealed by Olfactory Receptors Expressed in Taste Neurons (2008)

Taste and olfaction are each tuned to a unique set of chemicals in the outside world, and their corresponding sensory spaces are mapped in different areas in the brain. This dichotomy matches categories of receptors detecting molecules either in the gaseous or in the liquid phase in terrestrial animals. However, in Drosophila olfactory and gustatory neurons express receptors which belong to the same family of 7-transmembrane domain proteins. Striking overlaps exist in their sequence structure and in their expression pattern, suggesting that there might be some functional commonalities between them. In this work, we tested the assumption that Drosophila olfactory receptor proteins are compatible with taste neurons by ectopically expressing an olfactory receptor (OR22a and OR83b) for which ligands are known. Using electrophysiological recordings, we show that the transformed taste neurons are excited by odor ligands as by their cognate tastants. The wiring of these neurons to the brain seems unchanged and no additional connections to the antennal lobe were detected. The odor ligands detected by the olfactory receptor acquire a new hedonic value, inducing appetitive or aversive behaviors depending on the categories of taste neurons in which they are expressed i.e. sugar- or bitter-sensing cells expressing either Gr5a or Gr66a receptors. Taste neurons expressing ectopic olfactory receptors can sense odors at close range either in the aerial phase or by contact, in a lipophilic phase. The responses of the transformed taste neurons to the odorant are similar to those obtained with tastants. The hedonic value attributed to tastants is directly linked to the taste neurons in which their receptors are expressed.
Estudo da composição química das raízes de Citrus sinensis x Citrus limonia e avaliação da atividade microbiana de piranocumarinas frente a bactéria Xylella fastidiosa (2019)

A cultura de citros encontra-se disseminada em todo o territorio nacional, possuindo grande importância economica e social para varios estados brasileiros 1 . O genero Citrus pertence a familia Rutaceae 2 e e caracterizado pela presenca de cumarinas, limonoides, flavonoides e alcaloides derivados do acido antranilico 3,4 . Dentre as cumarinas, sao relatados quatro subtipos, que incluem as cumarinas simples, furanocumarinas, piranocumarinas e pironas substituidas 5 . Estas substâncias contribuem para a adaptacao de plantas aos estresses bioticos ou abioticos e sao consideradas protetores de plantas contra fitopatogenos e insetos 6 . As piranocumarinas sao substâncias majoritarios nas raizes de citros e de acordo com estudos anteriores, podem estar atuando no mecanismo de defesa da planta contra as bacterias Xylella fastidiosa 7 , causadora do Clorose Variegada dos Citros (CVC) e Candidatus liberibacter 8 , causadora do huanglonbing (HLB). O objetivo deste estudo e isolar e identificar as substâncias presentes em raizes de Citrus sinensis x Citrus limonia e realizar ensaios de atividade microbiana de piranocumarinas frente a bacteria X. fastidiosa . A analise do perfil quimico do extrato hexânico das raizes de C. sinensis x C. limonia foi realizada em HRMS-qTOF, em modo de ionizacao ESI-MS [M + H] + e permitiu a identificacao das cumarinas; suberosina m/z 245,0813; xantiletina m/z 229,0859; seselina m/z 229,0861; ostol m /z 245,0825; xantoxantiletina m/ z 259,0973; suberenol m/z = 261,1120 e do limonoide; limonina m/z 471,2008. Foi realizado o fracionamento destes extratos hexânicos das raizes de citros, utilizando cromatografia em coluna de silica. A partir das analises de RMN H 1 das 6 fracoes obtidas, verificou-se que a fracao F3 apresentou sinais que caracterizam a classe estrutural das piranocumarinas: xantiletina (1) e seselina (2). Foi possivel observar sinais com δ 7,83 d , 7,38 d , 6,76 d, 6,23, 5,81 e 1,47 s e os sinais com δ 7,85 d . 6,83 d , 6,24 d e 5,87 d e 1,48 s, que correspondem as substâncias (1) e (2), respectivamente. Afim de purificar estas substâncias, a fracao F3 foi submetida a uma nova etapa de fracionamento, empregando cartuchos de SPE C-18 e as bandas correspondentes as substâncias de interesse foram analisadas e coletadas em HPLC-DAD preparativo, com modo isocratico de eluicao. As substâncias coletadas foram identificadas atraves de experimentos em RMN de 1 H, COSY, HMBC e HSQC. Apos o isolamento das piranocumarinas (1) e (2), a avaliacao da atividade microbiana destes compostos frente a bacteria Xylella fastidiosa , foi realizada utilizando a metodologia com resazurina para a determinacao da concentracao inibitoria minima (CIM). A xantiletina (1) e a seselina (2), apresentaram um CIM de 34,24 μM, indicando que estas piranocumarinas possuem um grande potencial inibitorio, sugerindo que as mesmas podem estar diretamente associadas ao mecanismo de defesa dos citros frente ao CVC.
Acyloxyacyl Hydrolase Regulates Microglia-Mediated Pelvic Pain Through Toll-Like Receptor-4 (2021)

ABSTRACT Interstitial cystitis/bladder pain syndrome (IC/BPS) is a devastating condition of chronic pelvic pain and urinary dysfunction. We have shown that mice deficient for the lipase acyloxyacyl hydrolase (AOAH) develop pelvic allodynia and exhibit symptoms and comorbidities consistent with IC/BPS, as well as gut dysbiosis. Microglia are resident immune cells of the central nervous system (CNS) that respond to changes in the gut microbiome, and studies have linked microglial activation to neuropathic pain. Additionally, microglia express toll-like receptors (TLRs), including TLR4, which are activated by microbial components. We have previously shown that AOAH-deficient mice exhibit increased gut permeability, suggesting a possible mechanism of microglial TLR4 activation via translocation of microbial products across the intestinal barrier to the brain. Here, we assessed the role of AOAH and TLR4 in microglial activation and pelvic pain. AOAH immunoreactivity co-localized with the microglial marker P2YR12 but not astrocytes, suggesting a functional role for AOAH in microglia. Pharmacologic ablation of CNS microglia with PLX5622 resulted in decreased pelvic allodynia in AOAH-deficient mice and resurgence of pelvic pain upon drug washout. Aligned with microglial activation, we observed altered cytokine abundance in Aoah −/− cortex that was reduced in Aoah/Tlr4 −/− cortex. Consistent with our hypothesis of TLR4 activation by gut microbes, we observed microbiome-dependent activation of cultured BV2 microglial cells. Skeletal analyses revealed that AOAH-deficient mice have an activated microglia morphology in brain regions associated with neuropathic pain, independent of TLR4. Compared to Aoah −/− mice, Aoah/Tlr4 −/− mice exhibited decreased pelvic pain and microglial cytokine expression. Together, these findings demonstrate differential roles for AOAH and TLR4 in microglial activation and pelvic pain and thus identify novel therapeutic targets for IC/BPS.
Porous Organic Cage Nanocrystals by Solution Mixing (2011)

We present here a simple method for the bottom-up fabrication of microporous organic particles with surface areas in the range 500–1000 m2 g–1. The method involves chiral recognition between prefabricated, intrinsically porous organic cage molecules that precipitate spontaneously upon mixing in solution. Fine control over particle size from 50 nm to 1 μm can be achieved by varying the mixing temperature or the rate of mixing. No surfactants or templates are required, and the resulting organic dispersions are stable for months. In this method, the covalent synthesis of the cage modules can be separated from their solution processing into particles because the modules can be dissolved in common solvents. This allows a “mix and match” approach to porous organic particles. The marked solubility change that occurs upon mixing cages with opposite chirality is rationalized by density functional theory calculations that suggest favorable intermolecular interactions for heterochiral cage pairings. The important contribution of molecular disorder to porosity and surface area is highlighted. In one case, a purposefully amorphized sample has more than twice the surface area of its crystalline analogue.
A portable cell-based optical detection device for rapid detection of Listeria and Bacillus toxins (2005)

A mammalian cell-based optical biosensor was built to detect pathogenic <i>Listeria</i> and <i>Bacillus</i> species. This sensor measures the ability of the pathogens to infect and induce cytotoxicity on hybrid lymphocyte cell line (Ped-2E9) resulting in the release of alkaline phosphatase (ALP) that can be detected optically using a portable spectrophotometer. The Ped-2E9 cells were encapsulated in collagen gel matrices and grown in 48-well plates or in specially designed filtration tube units. Toxin preparations or bacterial cells were introduced and ALP release was assayed after 3-5 h. Pathogenic <i>L. monocytogenes </i> strains or the listeriolysin toxins preparation showed cytotoxicity ranging from 55% - 92%. Toxin preparations (~20 &#956;g/ml) from <i>B. cereus </i>strains showed 24 - 98% cytotoxicity. In contrast, a non-pathogenic <i>L. innocua </i>(F4247) and a <i>B. substilis </i>induced only 2% and 8% cytotoxicity, respectively. This cell-based detection device demonstrates its ability to detect the presence of pathogenic <i>Listeria</i> and <i>Bacillus</i> species and can potentially be used onsite for food safety or in biosecurity application.
Cathodes manufacturing processes for high-rate Li/SOCl/sub 2/ batteries (1983)

Influence of type of carbon black, wetting agent, teflon content (up to 50 %), and carbon paste processing on cathodes characteristics and performances were evaluated. Single cell tests at 30 mA/cm/sup 2/ indicated that high cathode efficiencies could be achieved with various cathode formulations, even with a teflon content of 50 %. Discharge performances on glassy carbon cathodes and analysis of pores size distribution in the porous cathode provided baselines for the interpretation of the above-mentioned results as well as a better understanding of carbon cathode behaviour in Li/SOCl/sub 2/ cells.
Inhibition of T cell antigen receptor-dependent phosphorylation of CD4 in human immunodeficiency virus type 1 infected cells. (1992)

Inhibitory effects of human immunodeficiency virus (HIV) on T lymphocyte function have been linked to perturbation of signaling through the T cell antigen receptor-CD3 complex. Comparative biochemical analyses of signaling responses were performed in T cells that were either uninfected or chronically infected with the HIV-1/IIIB strain. Stimulation with antibodies to CD3 triggered both Ca2+ accumulation and phosphoinositide hydrolysis responses that were equivalent in uninfected and infected cells. Treatment with anti-CD3 or with phorbol diester also stimulated serine phosphorylation of CD4 molecules in uninfected T cells. However, phosphorylation of CD4 was not observed after anti-CD3 treatment in HIV-infected T cells despite normal phosphorylation responses to phorbol diester. Identical results were obtained using a T cell line that was infected with an env (gp160/120-) HIV-1 defective variant. These studies indicate that infection with HIV-1 inhibits the activation of protein kinase associated with the T cell receptor-CD3 complex by a mechanism which is independent of viral env protein components.
Citalopram for agitation in Alzheimer's disease: Design and methods (2012)

The authors believe the design elements in CitAD are important features to be included in trials assessing the safety and efficacy of psychotropic medications for clinically significant agitation in AD.
Inference with path resolution and semantic graphs (1987)

A graphical representation of quantifier-free predicate calculus formulas in negation normal form and a new rule of inference that employs this representation are introduced. The new rule, path resolution , is an amalgamation of resolution and Prawitz analysis. The goal in the design of path resolution is to retain some of the advantages of both Prawitz analysis and resolution methods, and yet to avoid to some extent their disadvantages. Path resolution allows Prawitz analysis of an arbitrary subgraph of the graph representing a formula. If such a subgraph is not large enough to demonstrate a contradiction, a path resolvent of the subgraph may be generated with respect to the entire graph. This generalizes the notions of large inference present in hyperresolution, clash-resolution, NC-resolution, and UR-resolution. A class of subgraphs is described for which deletion of some of the links resolved upon preserves the spanning property.
QCM Analysis for Two‐Step Adsorption of Albumin and Fibronectin on Zirconia Surface (2021)

The adsorption of proteins on the dental implant surface is the first step in the key role of osseointegration. Many types of proteins exist in the living body and compete for adsorption on the material surface. As an implant material, partially stabilized zirconia (ZrO 2 ) is currently an attractive alternative to titanium to overcome the shortcomings of titanium implants. In this study, we investigated the two‐step adsorption of fibronectin (Fn) and bovine serum albumin (Alb) on the ZrO 2 surface using a 27‐MHz quartz crystal microbalance (QCM) method. A ZrO 2 sensor was employed for the QCM measurements. Two‐step adsorptions were performed as follows. (1) Fn‐Alb series: first, the Fn solution was injected into the phosphate‐buffered saline (PBS) solution, followed by the Alb solution. (2) Alb‐Fn series: first, the Alb solution was injected, followed by the Fn solution. The decrease in frequency was monitored for 60 minutes after each protein injection. The adsorbed amounts of Fn or Alb were calculated by observing the decrease in frequency, and the apparent reaction rate, k obs , was obtained through the curve fitting of frequency shift against the adsorption time. No significant difference was observed in the adsorbed amounts of Fn and Alb between the Fn‐Alb and Alb‐Fn series ( P &gt; 0.05). The k obs , rate of protein adsorption, in the second step was significantly slower than that in the first step for both Fn and Alb adsorption ( P &lt; 0.05). There was no clear correlation between the amount of protein adsorbed on the ZrO 2 sensor and the surface topography. It was concluded that the amount of protein adsorbed on the ZrO 2 surface was not influenced by the two‐step adsorption series, but the adsorption rate of proteins in the second step was affected by the first‐step protein adsorption.
Expression of Toll-Like Receptor 4 Contributes to Corneal Inflammation in Experimental Dry Eye Disease (2012)

Purpose. To investigate the corneal expression of toll-like receptor (TLR) 4 and determine its contribution to the immunopathogenesis of dry eye disease (DED). Methods. Seven to 8-week-old female C57BL/6 mice were housed in a controlled environment chamber and administered scopolamine to induce experimental DED. Mice received intravenous TLR4 inhibitor (Eritoran) to block systemic TLR4-mediated activity. The expression of TLR4 by the corneal epithelium and stroma was evaluated using real-time polymerase chain reaction and flow cytometry. Corneal fluorescein staining (CFS) was performed to evaluate clinical disease severity. The corneal expression of proinflammatory cytokines (IL-1β, IL-6, TNF, and CCL2), corneal infiltration of CD11b(+) antigen-presenting cells, and lymph node frequency of mature MHC-II(hi) CD11b(+) cells were assessed. Results. The epithelial cells of normal corneas expressed TLR4 intracellularly; however, DED significantly increased the cell surface expression of TLR4. Similarly, flow cytometric analysis of stromal cells revealed a significant increase in the expression of TLR4 proteins by DED-induced corneas as compared with normal corneas. DED increased the mRNA expression of TLR4 in corneal stromal cells, but not epithelial cells. TLR4 inhibition decreased the severity of CFS and significantly reduced the mRNA expression of IL-1β, IL-6, and TNF. Furthermore, TLR4 inhibition significantly reduced the corneal infiltration of CD11b(+) cells and the lymph node frequency of MHC-II(hi) CD11b(+) cells. Conclusions. These results suggest that DED increases the corneal expression of TLR4 and that TLR4 participates in the inflammatory response to ocular surface desiccating stress.