gebhart/patrepeval huggingface dataset:
Characterization of Fungal FAD-Dependent AA3_2 Glucose Oxidoreductases from Hitherto Unexplored Phylogenetic Clades (2021)

The CAZy auxiliary activity family 3 (AA3) comprises FAD-dependent enzymes belonging to the superfamily of glucose-methanol-choline (GMC) oxidoreductases. Glucose oxidase (GOx; EC 1.1.3.4) and glucose dehydrogenase (GDH; EC 1.1.5.9) are part of subfamily AA3_2 and catalyze the oxidation of β-D-glucose at its anomeric carbon to D-glucono-1,5-lactone. Recent phylogenetic analysis showed that AA3_2 glucose oxidoreductases can be grouped into four major clades, GOx I and GDH I-III, and in minor clades such as GOx II or distinct subclades. This wide sequence space of AA3_2 glucose oxidoreductases has, however, not been studied in detail, with mainly members of GOx I and GDH I studied biochemically or structurally. Here, we report the biochemical characterization of four fungal glucose oxidoreductases from distinct, hitherto unexplored clades or subclades. The enzyme from <i>Aureobasidium subglaciale</i>, belonging to the minor GOx II clade, showed a typical preference for oxygen and glucose, confirming the correct annotation of this clade. The other three enzymes exhibited strict dehydrogenase activity with different substrate specificities. GDH II from <i>Trichoderma virens</i> showed an almost six-fold higher catalytic efficiency for maltose compared to glucose. The preferred substrate for the two GDH III enzymes from <i>Rhizoctonia solani</i> and <i>Ustilago maydis</i> was gentiobiose, a β(1→6) disaccharide, as judged from the catalytic efficiency. Overall, the newly studied AA3_2 glucose oxidoreductases showed a much broader substrate spectrum than the archetypal GOx from <i>Aspergillus niger</i>, which belongs to clade GOx I.
Passive and Active Hybrid Integrated EMI Filters (2006)

Two new planar integrated EMI filter structures which reduce the filter volume and which are based on standard PCB process technology are presented in this paper. First, a passive integrated EMI filter is presented, which results in a volume reduction of 25% compared to the discrete solution. However, this filter requires a planar ferrite core for the CM inductor. In order to eliminate the ferrite core and reduce the filter volume further (-40% vs. discrete filter) a passive integrated structure is combined with an active EMI filtering circuit. The transfer function, the volume and the losses of the discrete and the two integrated filters, which are designed for a 600W PFC converter, are compared.
Discovering functional and inclusion dependencies in relational databases (1992)

We consider the problem of discovering the functional and inclusion dependencies that a given database instance satisfies. This technique is used in a database design tool that uses example databases to give feedback to the designer. If the examples show deficiencies in the design, the designer can directly modify the examples. the tool then infers new dependencies and the database schema can be modified, if necessary. the discovery of the functional and inclusion dependencies can also be used in analyzing an existing database. the problem of inferring functional dependencies has several connections to other topics in knowledge discovery and machine learning. In this article we discuss the use of examples in the design of databases, and give an overview of the complexity results and algorithms that have been developed for this problem. © 1992 John Wiley & Sons, Inc.
AC WebWorks: MS/MS: Multimedia shopping for a mass spec. (2000)

ADVERTISEMENT RETURN TO ISSUEPREVDepartmentsNEXTAC WebWorks: MS/MS: Multimedia shopping for a mass spec.How to use the Internet to research a mass spectrometer purchase.Kermit K. MurrayCite this: Anal. Chem. 2000, 72, 5, 225 A–229 APublication Date (Web):March 1, 2000Publication History Published online1 March 2000Published inissue 1 March 2000https://pubs.acs.org/doi/10.1021/ac002763ahttps://doi.org/10.1021/ac002763anewsACS Publications. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views203Altmetric-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 (5 MB) Get e-Alertsclose SUBJECTS:Mass spectrometry Get e-Alerts
Infrared and skin: Friend or foe (2015)

In the last decade, it has been proposed that the sun's IR-A wavelengths might be deleterious to human skin and that sunscreens, in addition to their desired effect to protect against UV-B and UV-A, should also protect against IR-A (and perhaps even visible light). Several studies showed that NIR may damage skin collagen content via an increase in MMP-1 activity in the same manner as is known for UVR. Unfortunately, the artificial NIR light sources used in such studies were not representative of the solar irradiance. Yet, little has been said about the other side of the coin. This article will focus on key information suggesting that IR-A may be more beneficial than deleterious when the skin is exposed to the appropriate irradiance/dose of IR-A radiation similar to daily sun exposure received by people in real life. IR-A might even precondition the skin – a process called photoprevention – from an evolutionary standpoint since exposure to early morning IR-A wavelengths in sunlight may ready the skin for the coming mid-day deleterious UVR. Consequently IR-A appears to be the solution, not the problem. It does more good than bad for the skin. It is essentially a question of intensity and how we can learn from the sun.
In vivo imaging of microvasculature using optical coherence tomography (2010)

In vivo imaging technologies drive the development of improved cancer therapies by revealing critical aspects of the complex pathophysiology of solid tumors in small animal models. The abnormal vascular function, which predicts tumor malignant potential and presents broad barriers to effective treatment, has been studied at the subcellular size scale using multiphoton (MP) microscopy, and at significantly larger size scales using ultrasound, ¿CT and ¿MRI. However, limited in vivo imaging approaches exist to study the vascular function at the network level, i.e., with sufficient resolution to discern smaller vessels while maintaining a field of view and penetration depth large enough to reveal interconnectivity and inhomogeneities across the tumor and surrounding tissue. One promising technology operating at this size scale is optical frequency domain imaging (OFDI) using Doppler-methods to detect blood flow.
Crystalline H-aggregate nanoparticles for detecting dopamine release from M17 human neuroblastoma cells (2022)

Crystalline H-aggregate nanoparticles of a cyanine dye were developed as a highly efficient photo-induced electron transfer probe for the detection of dopamine, which shows that the dopamine release from cells was enhanced by nicotine stimulation.
Improved low-k dielectric properties using He/H2 plasma forresist removal (2008)

Aurora ELK low-k films, deposited using a PECVD porogen-based
process, were treated with 35 s of He/H2 downstream-plasma
(DSP) at varied temperatures of 25 C, 200 C, 300 C and 350 C.
The plasma modifications were investigated using various
physical-chemical methods. Results showed that extended He/H2
DSP plasma exposure at elevated temperature may lead to k-value
reduction due to porosity increase without hydrophilisation of
the modified layer. Improvement in dielectric constant is
accompanied by a small reduction of mechanical strength. The
porosity increase was related to removal of porogen residues
formed during the ultra-violet (UV) curing. The porogen residue
removal signature was reflected in the optical properties in
the UV range and the C-depth profile of the investigated low-k
material.
A Mouse Model of Celiac Disease (2022)

The design and use of mouse models that reproduce key features of human diseases are critical to advance our understanding of the pathogenesis of autoimmune diseases and to test new therapeutic strategies. Celiac disease is a unique organ-specific autoimmune-like disorder occurring in genetically susceptible individuals carrying HLA-DQ2 or HLA-DQ8 molecules who consume gluten. The key histological characteristic of the disease in humans is the destruction of the lining of the small intestine, a feature that has been difficult to reproduce in immunocompetent animal models. This unit describes the DQ8-D<sup>d</sup> -villin-IL-15 transgenic mouse model of CeD, which was engineered based on the knowledge acquired from studying CeD patients' intestinal samples, and which represents the first animal model that develops villous atrophy in an HLA- and gluten-dependent manner without administration of any adjuvant. We provide detailed protocols for inducing and monitoring intestinal tissue damage, evaluating the cytotoxic properties of intraepithelial lymphocytes that mediate enterocyte lysis, and assessing the activation of the enzyme transglutaminase 2, which contributes to the generation of highly immunogenic gluten peptides. Detailed protocols to prepare pepsin-trypsin digested gliadin (PT-gliadin) or chymotrypsin-digested gliadin (CT-gliadin), which allow antibody detection against native or deamidated gluten peptides, are also provided in this unit. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Induction of celiac-like disease in DQ8-D<sup>d</sup> -villin-IL-15tg mice Basic Protocol 2: Histological assessment of villous atrophy Support Protocol 1: Morphometric assessment of villous/crypt ratio Support Protocol 2: Evaluation of epithelial cells renewal Support Protocol 3: Evaluation of the density of intraepithelial lymphocytes Basic Protocol 3: Analysis of cytotoxic intraepithelial lymphocytes Basic Protocol 4: Transglutaminase 2 activation and measurement of antibodies against native and deamidated gluten peptides Support Protocol 4: Preparation of CT-gliadin Support Protocol 5: Preparation of PT-gliadin.
Nonmydriatic Retinal Image Review at Time of Endocrinology Visit Results in Short-Term HbA1c Reduction in Poorly Controlled Patients with Diabetic Retinopathy (2011)

Nonmydriatic imaging and discussion of retinal findings during an endocrinologist visit may contribute, at least in the short term, to improved glycemic control in patients with DR and elevated HbA1c.
Droplet and cluster formation in freely falling granular streams (2011)

Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream's macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gaslike jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams.
Supplemental Table 3 from A Chemical Genetics Approach for the Functional Assessment of Novel Cancer Genes (2023)

&lt;p&gt;Supplemental Table 3: List of alternatively spliced genes identified in response to SF3B1 mutant&lt;/p&gt;
Direct top-down ordering of diblock copolymers through nanoimprint lithography (2011)

International audience
Dynamic axial-position control of a laser-trapped particle by wave-front modification (2003)

The axial position of a laser-trapped particle has been controlled by modification of the wave front by means of a membrane deformable mirror. The mirror gives wave-front modulation in terms of Zernike polynomials. By modulation of the Zernike defocus term we can modulate the particle position under conditions of laser trapping. A polystyrene particle of 1-µm diameter was moved along the optical axis direction for a distance of 2370 nm in minimum steps of 55.4 nm. We also demonstrated particle oscillation along the optical axis by changing the focal position in a sinusoidal manner. From the frequency dependency of the amplitude of particle oscillation we determined the spring constant as 91.7 nN/m.
Differential modulation of neurons in the rostral ventromedial medulla by neurokinin-1 receptors (2011)

The rostral ventromedial medulla (RVM) is part of descending circuitry that modulates nociceptive processing at the level of the spinal cord. RVM output can facilitate pain transmission under certain conditions such as inflammation, and thereby contribute to hyperalgesia. Evidence suggests that substance P and activation of neurokinin-1 (NK-1) receptors in the RVM are involved in descending facilitation of nociception. We showed previously that injection of NK-1 receptor antagonists into the RVM attenuated mechanical and heat hyperalgesia produced by intraplantar injection of capsaicin. Furthermore, intraplantar injection of capsaicin excited ON cells in the RVM and inhibited ongoing activity of OFF cells. In the present studies, we therefore examined changes in responses of RVM neurons to mechanical and heat stimuli after intraplantar injection of capsaicin and determined the role of NK-1 receptors by injecting a NK-1 receptor antagonist into the RVM prior to capsaicin. After capsaicin injection, excitatory responses of ON cells and inhibitory responses of OFF cells evoked by mechanical and heat stimuli applied to the injected, but not contralateral, paw were increased. Injection of the NK-1 antagonist L-733,060 did not alter evoked responses of ON or OFF cells but attenuated the capsaicin-evoked enhanced responses of ON cells to mechanical and heat stimuli with less of an effect on the enhanced inhibitory responses of OFF cells. These data support the notion that descending facilitation from RVM contributes to hyperalgesia and that NK-1 receptors, presumably located on ON cells, play an important role in initiating descending facilitation of nociceptive transmission.
Model driven embedded systems (2004)

Summary form only given. We are now at a stage in the development of embedded systems where the complexity of the software development and the software itself needs to be managed not via code but via models. This move to a more abstract representation of the system brings many new challenges to primarily the methodology and the style of system development. The Object Management Group's (OMG) model driven architecture (MDA) is an initiative towards fully model based software development. The advantages of taking a (or even the) model driven approach is that we can abstract from the system at many levels and take advantage of well known "large scale software" techniques.
Tunicate Gonadotropin-Releasing Hormone (GnRH) Peptides Selectively Activate Ciona intestinalis GnRH Receptors and the Green Monkey Type II GnRH Receptor (2005)

In vertebrates, GnRH binds to its receptor and stimulates predominantly G(q/11)-mediated signal transduction in gonadotropes. However, little is known about the GnRH receptor and its signaling pathway in tunicates, a group that arose before the vertebrates. Although tunicates have had duplications of a few genes in the last 600 million years, the early vertebrates had duplications of the full genome. Also unknown is the nature of GnRH signaling in the tunicate, which lacks both a pituitary gland and sex steroids. However, we know that tunicates have GnRH peptides because we previously reported six GnRH peptides encoded within the tunicate genome of Ciona intestinalis. Here we clone and sequence cDNAs for four putative GnRH receptors from C. intestinalis. These are the only invertebrate GnRH receptors found to date. Each Ciona GnRH receptor was expressed in COS-7 cells, incubated with each of the six C. intestinalis GnRHs and assayed for a signaling response. GnRH receptors 1, 2, and 3 responded to Ciona GnRH peptides to stimulate intracellular cAMP accumulation. In contrast, only GnRH receptor 1 activated inositol phosphate turnover in response to one of the Ciona GnRHs. The green monkey type II GnRH receptor cDNA was tested as a comparison and a positive control. In conclusion, the four GnRH receptors encoded within the C. intestinalis genome were all transcribed into messenger RNA, but only three of the Ciona GnRH receptors were biologically active in our assays. The Ciona GnRH receptors almost exclusively activated the cAMP pathway.
La Química médica en el desarrollo de las Sociedades. Biodiversidad y Productos naturales (2001)

This document has been prepared by the IUPAC Medicinal Chemistry section and is backed by a large number of scientists, many of whom have had direct involve-ment and whose names appear at the end of the article. This work discusses the role that the discovery of new medicinal agents has in the development of societies as well as in the conservation of biodiversity in terms of the work carried out on natural products. Also included are several recommendations for countries which are presently in search of their own scientific and technological development in medicinal agents. The IUPAC Medicinal Chemistry section would appreciate the collaboration of the scientific societies in every country to aid in the diffusion of this document.
Inter-layer grating coupler on double-layer silicon nanomembranes (2013)

We present an adhesive bonding process to fabricate on-chip, double-layer, single crystalline silicon nanomembranes. Inter-layer coupling efficiency of 25% with 35 nm 3dB bandwidth is demonstrated using subwavelength nanostructure based grating couplers.
Mass Spectrometric Identification of Mtb81, a Novel Serological Marker for Tuberculosis (2000)

We have used serological proteome analysis in conjunction with tandem mass spectrometry to identify and sequence a novel protein, Mtb81, which may be useful for the diagnosis of tuberculosis (TB), especially for patients coinfected with human immunodeficiency virus (HIV). Recombinant Mtb81 was tested by an enzyme-linked immunosorbent assay to detect antibodies in 25 of 27 TB patients (92%) seropositive for HIV as well as in 38 of 67 individuals (57%) who were TB positive alone. No reactivity was observed in 11 of 11 individuals (100%) who were HIV seropositive alone. In addition, neither sera from purified protein derivative (PPD)-negative (0 of 29) nor sera from healthy (0 of 45) blood donors tested positive with Mtb81. Only 2 of 57 of PPD-positive individuals tested positive with Mtb81. Sera from individuals with smear-positive TB and seropositive for HIV but who had tested negative for TB in the 38-kDa antigen immunodiagnostic assay were also tested for reactivity against Mtb81, as were sera from individuals with lung cancer and pneumonia. Mtb81 reacted with 26 of 37 HIV+TB+ sera (70%) in this group, compared to 2 of 37 (5%) that reacted with the 38-kDa antigen. Together, these results demonstrate that Mtb81 may be a promising complementary antigen for the serodiagnosis of TB.
Viral Activation of Interleukin-15 (IL-15): Characterization of a Virus-Inducible Element in the IL-15 Promoter Region (2000)

We identified an interferon regulatory factor motif (IRF-E) upstream of an NF-kappaB binding site in the interleukin-15 (IL-15) promoter. Since these two motifs are part of the virus-inducible enhancer region of the beta interferon promoter, we speculated that there might be similar responses of these two genes to stimuli such as viruses. To test this hypothesis, L929 cells were infected with Newcastle disease virus (NDV), which led to the induction of IL-15 mRNA and protein expression. Using IL-15 promoter-reporter deletion constructs, a virus-inducible region, encompassing IRF-E, NF-kappaB, and a 13-nucleotide sequence flanked by these two motifs, was mapped to the -295-to--243 position relative to the transcription initiation site. Using cotransfection studies, it was demonstrated that all three motifs were essential to achieve the maximum promoter activity induced by IRF-1 and NF-kappaB expression plasmids. The presence of a virus-inducible region in the IL-15 promoter suggests a role for IL-15 as a component of host antiviral defense mechanisms.
Antibacterial Activities of Indole and Its Related Compounds against Pseudomonas solanacearum(III). In Vivo Assay for Antibacterial Activity of Indole Derivatives Using Detached Tomato Leaves and Genetically Marked Pathogen. (1992)

[in Japanese]
Digital Noise-tolerant Silicon Nanophotonic Switch (2010)

Error-free switching performance of a digital electro-optic silicon switch based on multi-stage Mach-Zehnder lattice is demonstrated. Robust crosstalk levels of lower than −15dB are obtained for drive-voltage noise levels exceeding 300mV while maintaining error-free operation.