gebhart/patrepeval huggingface dataset:
Direct Visualization of Spatial and Temporal Patterns of Antimicrobial Action within Model Oral Biofilms (2008)

A microscopic method for noninvasively visualizing the action of an antimicrobial agent inside a biofilm was developed and applied to describe spatial and temporal patterns of mouthrinse activity on model oral biofilms. Three species biofilms of Streptococcus oralis, Streptococcus gordonii, and Actinomyces naeslundii were grown in glass capillary flow cells. Bacterial cells were stained with the fluorogenic esterase substrate Calcien AM (CAM). Loss of green fluorescence upon exposure to an antimicrobial formulation was subsequently imaged by time-lapse confocal laser scanning microscopy. When an antimicrobial mouthrinse containing chlorhexidine digluconate was administered, a gradual loss of green fluorescence was observed that began at the periphery of cell clusters where they adjoined the flowing bulk fluid and progressed inward over a time period of several minutes. Image analysis was performed to quantify a penetration velocity of 4 mum/min. An enzyme-based antimicrobial formulation led to a gradual, continually slowing loss of fluorescence in a pattern that was qualitatively different from the behavior observed with chlorhexidine. Ethanol at 11.6% had little effect on the biofilm. None of these treatments resulted in the removal of biomass from the biofilm. Most methods to measure or visualize antimicrobial action in biofilms are destructive. Spatial information is important because biofilms are known for their structural and physiological heterogeneity. The CAM staining technique has the potential to provide information about the rate of antimicrobial penetration, the presence of tolerant subpopulations, and the extent of biomass removal effected by a treatment.
Sensing touch using resistive graphs (2014)

In early design, instrumenting an object with touch sensing capability, especially one with complex surface geometry, can be problematic. In this paper, we show how resistive graph patterns--or resigraphs--can be used to quickly fabricate multi-touch sensors tailored to an object's shape. In very early ideation, resigraphs can be drawn using conductive ink. In later refinements they can be silk-screened or laser cut from off-the-shelf materials. A resigraph uses a commonly available microprocessor (e.g. Arduino), re-quires only three wires, and enables touch input on non-planar and non-developable surfaces.
Optimized dCas9 Programmable Transcriptional Activators for Plants (2022)

Understanding how gene expression impacts plant development and physiology is important for rationally engineering improved crops. Programmable Transcriptional Activators (PTAs), including CRISPR-Cas activators, have traditionally relied on a limited number of transcriptional activation domains. Usually the VP64 domain, derived from human herpes simplex virus, is fused to a DNA-binding domain to activate target gene expression. We reasoned there was considerable space for PTA improvement by replacing VP64 with a plant-derived activation domain. To address this, we designed, built, and tested a PTA library of 38 putative plant transcriptional activation domains. Domains from HSFA6b, AvrXa10, DOF1, DREB1 , and DREB2 genes function as strong activators in Setaria viridis and Arabidopsis thaliana in protoplast assays and in transgenic plants. Overexpression of multiple endogenous genes ( FT, PAP1, WUS ) reached levels similar to the highly expressed housekeeping gene, PP2A , regardless of basal expression level. Further, these domains were effective in different PTA architectures, including the dCas9-SunTag, dCas9-Moontag, and TALE-SunTag systems. Lastly, we demonstrate the ability of these improved PTAs to map enhancer regions that promote gene expression in plants. This work demonstrates the effective and flexible nature of PTAs to activate target genes in plants, providing tools that can be used to improve agronomically relevant traits of interest.
Chemical Vapor Deposition of Copper from Cu(I) Compounds (1994)

This chapter contains sections titled: Introduction precursOr Design Synthesis and characterization Physical and Chemical Properties Chemical Vapor Deposition Reaction Stoichiometry, Kinetics, and Mechanisms Selectivity Chemical Vapor Deposition of Copper Alloys Etching Summary and Conclusions
Evaluation of the in vivo antitumor activity and in vitro cytotoxic properties of auranofin, a coordinated gold compound, in murine tumor models. (1985)

The coordinated gold compound, 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucopyranosato-S-triethyl phosphine gold (auranofin; Ridaura), was evaluated for antitumor activity in a variety of mouse tumor models. Of the 15 tumor models evaluated, auranofin was found to be active only against i.p. P388 leukemia. A number of dose schedules was used to measure activity against P388 with optimal activity observed at 12 mg/kg given daily, i.p., on Days 1 to 5. Auranofin was active against i.p. P388 leukemia only when administered i.p.; the drug was completely inactive when administered i.v., s.c., or p.o. on Days 1 to 5. Evaluation of the effects of auranofin in vitro demonstrated that survival curves for B16 melanoma cells as measured by the clongenic and dye exclusion assays were exponential and monophasic; cell cycle distribution was not altered, and auranofin displayed no preferential cytotoxicity to logarithmic or plateau growth phase cell populations; auranofin inhibited DNA, RNA, and protein synthesis at cytotoxic concentrations but showed no selective effect; the cytotoxic activity and cellular association of gold from auranofin were dose, time, and temperature dependent; and binding of auranofin gold to serum proteins markedly decreased cellular uptake of gold and cytotoxicity of auranofin in vitro.
RO 90-7501 Enhances TLR3 and RLR Agonist Induced Antiviral Response (2012)

Recognition of virus infection by innate pattern recognition receptors (PRRs), including membrane-associated toll-like receptors (TLR) and cytoplasmic RIG-I-like receptors (RLR), activates cascades of signal transduction pathways leading to production of type I interferons (IFN) and proinflammatory cytokines that orchestrate the elimination of the viruses. Although it has been demonstrated that PRR-mediated innate immunity plays an essential role in defending virus from infection, it also occasionally results in overwhelming production of proinflammatory cytokines that cause severe inflammation, blood vessel leakage and tissue damage. In our efforts to identify small molecules that selectively enhance PRR-mediated antiviral, but not the detrimental inflammatory response, we discovered a compound, RO 90-7501 ('2'-(4-Aminophenyl)-[2,5'-bi-1H-benzimidazol]-5-amine), that significantly promoted both TLR3 and RLR ligand-induced IFN-β gene expression and antiviral response, most likely via selective activation of p38 mitogen-activated protein kinase (MAPK) pathway. Our results thus imply that pharmacological modulation of PRR signal transduction pathways in favor of the induction of a beneficial antiviral response can be a novel therapeutic strategy.
Fluorescence fluctuations-based super-resolution microscopy techniques:\n an experimental comparative study (2020)

Fluorescence fluctuations-based super-resolution microscopy (FF-SRM) is an\nemerging field promising low-cost and live-cell compatible imaging beyond the\nresolution of conventional optical microscopy. A comprehensive overview on how\nthe nature of fluctuations, label density, out-of-focus light, sub-cellular\ndynamics, and the sample itself influence the reconstruction in FF-SRM is\ncrucial to design appropriate biological experiments. We have experimentally\ncompared several of the recently developed FF-SRM techniques (namely ESI,\nbSOFI, SRRF, SACD, MUSICAL and HAWK) on widefield fluorescence image sequences\nof a diverse set of samples (namely liposomes, tissues, fixed and living\ncells), and on three-dimensional simulated data where the ground truth is\navailable. The simulated microscopy data showed that the different techniques\nhave different requirements for signal fluctuation to achieve their optimal\nperformance. While different levels of signal fluctuations had little effect on\nthe SRRF, ESI and SACD images, image reconstructions from both bSOFI and\nMUSICAL displayed a substantial improvement in their noise rejection,\nz-sectioning, and overall super-resolution capabilities.\n
Optimal finite-difference operators for arbitrarily sampled data (2020)

ABSTRACT We have developed a general method to obtain the equiripple and the least-squares finite-difference (FD) operator weights to compute arbitrary-order derivatives from arbitrary sample locations. The method is based on the complex-valued Remez exchange algorithm applied to three cost functions: the total error, the relative error, and the group-velocity error. We evaluate the method on three acoustic FD modeling examples. In the first example, we assess the accuracy obtained with the optimal coefficients when propagating acoustic waves through a medium. In the second example, we propagate a wave through an irregular grid. In the final example, we position a source and receiver at arbitrary locations in-between the modeling grid points. In the examples using regular grids, the equiripple solution to the relative cost function performs best. It obtains marginally (4%–10%) better results compared to the second-best option, the least-squares solution for the relative cost function. The least-squares solution for the relative error produced the only stable and accurate results also in the example of modeling on an irregular grid.
Refractive error and preferential looking visual acuity in human infants: a pilot study. (1986)

A clinical pilot study comparing refractive error and preferential looking (PL) visual acuity in infants 2 to 12 months of age is described. The PL visual acuity of 30 normal infants without significant visual disorders was assessed using the Acuity Card Procedure. Near retinoscopy was used to determine refractive error. Infants of this sample had monocular PL visual acuities similar to those established by McDonald et al. in a laboratory setting. Statistical analysis of the data for this sample of infants showed that refractive error did not change systematically from 2 to 12 months of age. We have found that results obtained with the Acuity Card Procedure in a clinical setting agree with infant visual acuity as described in the research literature. Refractive error did not correlate with changes in PL visual acuity in infants 2 to 12 months of age.
Photonic Wires of Nanometric Dimensions. Electronic Energy Transfer in Rigid Rodlike Ru(bpy)32+-(ph)n-Os(bpy)32+Compounds (ph = 1,4-Phenylene;n= 3, 5, 7) (1999)

We have synthesized nine rodlike compounds of nanometric dimension with general formula [M(bpy)3-(ph)n-M‘(bpy)3]4+ (M = M‘ = Ru(II); M = M‘ = Os(II); M = Ru(II), M‘ = Os(II); bpy = 2,2‘-bipyridine; ph = 1,4-phenylene; n = 3, 5, 7; the central phenylene unit bears two alkyl chains for solubility reasons; the metal-to metal distance is 4.2 nm for the longest spacer). The absorption spectra and the luminescence properties (emission spectra, quantum yields, and excited-state lifetimes) of the nine dinuclear complexes have been investigated in acetonitrile solution at 293 K and in butyronitrile rigid matrix at 77 K. The results obtained have been compared with those found for the separated chromophoric units ([Ru(bpy)3]2+, [Os(bpy)3]2+, and oligophenylene derivatives). The absorption spectrum of each dinuclear complex is essentially equal to the sum of the spectra of the component species, showing that intercomponent electronic interactions are weak. In the homodinuclear compounds, the strong fluorescence of the oligophenylene spacers is completely quenched by energy transfer to the metal-based units, which exhibit their characteristic metal-to-ligand charge-transfer (MLCT) phosphorescence. In the heterodinuclear compounds, besides complete quenching of the fluorescence of the oligophenylene spacers, a quenching of the phosphorescence of the [Ru(bpy)3]2+ chromophoric unit and a parallel sensitization of the phosphorescence of the [Os(bpy)3]2+ chromophoric unit are observed, indicating the occurrence of electronic energy transfer. The rate of the energy-transfer process from the [Ru(bpy)3]2+ to the [Os(bpy)3]2+ unit is practically temperature independent and decreases with increasing length of the oligophenylene spacer (in acetonitrile solution at 293 K, ken = 6.7 × 108 s-1 for n = 3; ken = 1.0 × 107 s-1 for n = 5; ken = 1.3 × 106 s-1 for n = 7). It is shown that such an energy-transfer process takes place via a Dexter-type mechanism (superexchange interaction) with an attenuation coefficient of 0.32 per Å and 1.5 per interposed phenylene unit.
Crystal Structures of and Displacive Transitions in OsN2, IrN2, RuN2 and RhN2. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Bruton's tyrosine kinase inhibitor BMS-986142 in experimental models of rheumatoid arthritis enhances efficacy of agents representing clinical standard-of-care (2017)

Bruton's tyrosine kinase (BTK) regulates critical signal transduction pathways involved in the pathobiology of rheumatoid arthritis (RA) and other autoimmune disorders. BMS-986142 is a potent and highly selective reversible small molecule inhibitor of BTK currently being investigated in clinical trials for the treatment of both RA and primary Sjögren's syndrome. In the present report, we detail the in vitro and in vivo pharmacology of BMS-986142 and show this agent provides potent and selective inhibition of BTK (IC50 = 0.5 nM), blocks antigen receptor-dependent signaling and functional endpoints (cytokine production, co-stimulatory molecule expression, and proliferation) in human B cells (IC50 ≤ 5 nM), inhibits Fcγ receptor-dependent cytokine production from peripheral blood mononuclear cells, and blocks RANK-L-induced osteoclastogenesis. Through the benefits of impacting these important drivers of autoimmunity, BMS-986142 demonstrated robust efficacy in murine models of rheumatoid arthritis (RA), including collagen-induced arthritis (CIA) and collagen antibody-induced arthritis (CAIA). In both models, robust efficacy was observed without continuous, complete inhibition of BTK. When a suboptimal dose of BMS-986142 was combined with other agents representing the current standard of care for RA (e.g., methotrexate, the TNFα antagonist etanercept, or the murine form of CTLA4-Ig) in the CIA model, improved efficacy compared to either agent alone was observed. The results suggest BMS-986142 represents a potential therapeutic for clinical investigation in RA, as monotherapy or co-administered with agents with complementary mechanisms of action.
Phenotypic Polarization of Activated Astrocytes: The Critical Role of Lipocalin-2 in the Classical Inflammatory Activation of Astrocytes (2013)

Astrocytes provide structural and functional support for neurons, as well as display neurotoxic or neuroprotective phenotypes depending upon the presence of an immune or inflammatory microenvironment. This study was undertaken to characterize multiple phenotypes of activated astrocytes and to investigate the regulatory mechanisms involved. We report that activated astrocytes in culture exhibit two functional phenotypes with respect to pro- or anti-inflammatory gene expression, glial fibrillary acidic protein expression, and neurotoxic or neuroprotective activities. The two distinct functional phenotypes of astrocytes were also demonstrated in a mouse neuroinflammation model, which showed pro- or anti-inflammatory gene expression in astrocytes following challenge with classical or alternative activation stimuli; similar results were obtained in the absence of microglia. Subsequent studies involving recombinant lipocalin-2 (LCN2) protein treatment or Lcn2-deficient mice indicated that the pro- or anti-inflammatory functionally polarized phenotypes of astrocytes and their intracellular signaling pathway were critically regulated by LCN2 under in vitro and in vivo conditions. Astrocyte-derived LCN2 promoted classical proinflammatory activation of astrocytes but inhibited IL-4-STAT6 signaling, a canonical pathway involved in alternative anti-inflammatory activation. Our results suggest that the secreted protein LCN2 is an autocrine modulator of the functional polarization of astrocytes in the presence of immune or inflammatory stimuli and that LCN2 could be targeted therapeutically to dampen proinflammatory astrocytic activation and related pathologies in the CNS.
Handset antenna design for FM reception (2008)

A passive internal handset antenna for FM reception is presented. Several prototypes have been simulated and tested showing the interesting potential of this solution to eliminate the long cable 1 meter length used at the present time in some mobiles phones.
Graded composition and valence states in self-forming barrier layers at Cu–Mn/SiO2 interface (2010)

A self-forming diffusion barrier (SFB) layer was formed at Cu–Mn/SiO2 interface. Spatial variation of the chemical composition and valence state of the elements in the SFB was investigated in a subnanometer resolution using electron energy loss spectroscopy and transmission electron microscopy. The SFB was found to have a layered structure with graded compositions of nanocrystalline MnO and amorphous MnSiO3. The valence state of Mn was found to be +2 in the MnO layer and gradually increased to +3 in the MnSiO3 layer. The reported dielectric constant of the SFB could be explained by the observed composition and microstructure.
.alpha.-Keto dianion precursors via conjugate additions to cyclic .alpha.-bromo enones (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.alpha.-Keto dianion precursors via conjugate additions to cyclic .alpha.-bromo enonesConrad J. Kowalski, Ann E. Weber, and Kevin W. FieldsCite this: J. Org. Chem. 1982, 47, 26, 5088–5093Publication Date (Print):December 1, 1982Publication History Published online1 May 2002Published inissue 1 December 1982https://doi.org/10.1021/jo00147a008RIGHTS & PERMISSIONSArticle Views1796Altmetric-Citations81LEARN 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 InReddit PDF (860 KB) Get e-Alertsclose Get e-Alerts
Multi-layer planar micro-coils chip as actuators and heaters for biological applications (2012)

In this paper, a multi-functional of multi-layer planar micro-coils chip is demonstrated to play as actuators and heaters. For playing as actuators, the micro-coil generate local magnetic field with applied current of 15 mA to quickly manipulated magnetic beads to center of micro-coil within one minute. For functioning as heaters, the micro-coil heater can be quickly heated up to denatured temperature of 95 °C with input power of 50.5 mW, and its heating and cooling rate are 19.7 and 11.8 °C/s, respectively. For the typical 25 polymerase chain reaction (PCR) cycles, it took only 770 seconds. To further shrink and optimize the multi-layer planar micro-coils chip can be possibly used to manipulate single cell with magnetic beads to specific region and analyze its gene sequence by using single cell PCR technique.
RTHP-23. Cs131 IMPLANTS FOR SALVAGE THERAPY OF RECURRENT HIGH GRADE GLIOMAS (HGG) (2016)

We report our initial experience using Cs131 brachytherapy seeds in the adjuvant setting after resection of recurrent HGG. Thirteen patients with recurrent HGG status post resection, external beam radiation and chemotherapy, were treated using surgical resection and placement of Cs 131 brachytherapy seeds. Average age at the time of implant was 60 years (range 36-80). Nine and four patients had WHO Grade 4 and 3 respectively. Eleven and two patients had cerebral and cerebellar tumors respectively. Cs 131seeds (range of 9-38) were used to deliver 60 Gy at 5 mm from the tumor bed after surgical resection. Overall Survival was calculated from the time of implant till the time of death. Treatment failure was defined radiographically by area of new Gadolinium enhancement on follow up MRI. Serial imaging, perfusion scans or both were used to differentiate recurrence from post therapy changes. Failure was considered to be local if it happened within 2 cm of the implant bed and distant if beyond 2 cm from the implant bed. At the time of analysis; six patients were alive. Median overall survival for the whole group and the living patients was 5.2 months (range: 0.13 to 23.45 months and 0.53 to 23.45 months for the whole group and living patients respectively). Two patients died in the immediate postoperative period of unrelated operative complications and were excluded from the treatment failure analysis. One of the remaining 11 patients had local failure at 6 months. Three patients had distant intracranial failure at 6, 8 and 9 months. No patient had wound complications or radiation necrosis that required surgical intervention. We report the first experience using Cs131 brachytherapy in patients with recurrent HGG. Cs 131 implant may be considered a safe and effective treatment in this group of patients with limited salvage options.
High-carbon fullerene based spin-on organic hardmask (2018)

Irresistible Materials has previously introduced the HM340 series of fullerene based spin-on carbon, and reported on material characterization, including very high carbon content and high thermal stability. The materials have a low Ohnishi number providing high etch durability and the low hydrogen level allows for high-resolution etching without wiggling. Here we present further investigation of the spin-on-carbon, and demonstrate the flexibility of the platform. Film carbon content can be easily varied from as high as 95% (suitable for high durability etches) to as low as 80% (for instance to use as a sacrificial etch material). We present characterisation of the optical properties of the materials, and process and formulation developments. Work to vary the curing temperature between 200 and 300&deg;C, and to reduce cure times to 90 seconds or less has been successfully undertaken. Alternative casting solvents have been investigated and work to achieve spin coatable film thickness ranges from less than 50 nm to significantly more than 500nm is described. and spin-coatable film thickness ranges from less than 50 nm to significantly more than 500nm are described. Results from initial planarisation trials are presented together with initial results from on-going work on spin-on carbon formulations that exceed 95% carbon content.
Anticancer efficacy of KRASG12C inhibitors is potentiated by PAK4 inhibitor KPT9274 in preclinical models of KRASG12C mutant pancreatic and lung cancers (2023)

KRASG12C inhibitors demonstrate limited durable response in patients with KRASG12C mutations. In this study, combining PAK4 inhibitor KPT9274 with KRASG12C inhibitors has resulted in potent antitumor effects in preclinical cancer models of PDAC and NSCLC. Our results bring forward a novel combination therapy for cancer patients that do not respond or develop resistance to KRASG12C inhibitor treatment.