gebhart/patrepeval huggingface dataset:
Genome Mining Enabled by Biosynthetic Characterization Uncovers a Class of Benzoxazolinate‐Containing Natural Products in Diverse Bacteria (2022)

Abstract Benzoxazolinate is a rare bis‐heterocyclic moiety that interacts with proteins and DNA and confers extraordinary bioactivities on natural products, such as C‐1027. However, the biosynthetic gene responsible for the key cyclization step of benzoxazolinate remains unclear. Herein, we show a putative acyl AMP‐ligase responsible for the last cyclization step. We used the enzyme as a probe for genome mining and discovered that the orphan benzobactin gene cluster in entomopathogenic bacteria prevails across Proteobacteria and Firmicutes. It turns out that Pseudomonas chlororaphis produces various benzobactins, whose biosynthesis is highlighted by a synergistic effect of two unclustered genes encoding enzymes on boosting benzobactin production; the formation of non‐proteinogenic 2‐hydroxymethylserine by a serine hydroxymethyltransferase; and the types I and II NRPS architecture for structural diversity. Our findings reveal the biosynthetic potential of a widespread benzobactin gene cluster.
Kagome Hollow-Core Photonic Crystal Fiber Resonator for Rotation Sensing (2016)

International audience
Epigenetic Modifications: Basic Mechanisms and Role in Cardiovascular Disease (2013 Grover Conference Series) (2014)

Epigenetics refers to heritable traits that are not a consequence of DNA sequence. Three classes of epigenetic regulation exist: DNA methylation, histone modification, and noncoding RNA action. In the cardiovascular system, epigenetic regulation affects development, differentiation, and disease propensity or expression. Defining the determinants of epigenetic regulation offers opportunities for novel strategies for disease prevention and treatment.
SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing (2016)

Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.
Electrostatic methods for measuring the binding of ionic ligands to proteins (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrostatic methods for measuring the binding of ionic ligands to proteinsClarke J. Halfman and Jacinto SteinhardtCite this: Biochemistry 1971, 10, 19, 3564–3569Publication Date (Print):September 14, 1971Publication History Published online1 May 2002Published inissue 14 September 1971https://pubs.acs.org/doi/10.1021/bi00795a012https://doi.org/10.1021/bi00795a012research-articleACS PublicationsRequest reuse permissionsArticle Views38Altmetric-Citations3LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Mikroalgenbioraffinerie – Entwicklung von Zellaufschluss‐ und Extraktionsprozessen zur Kaskadennutzung von Mikroalgenbiomasse (2016)

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Objective sensory testing methods reveal a higher prevalence of olfactory loss in COVID-19–positive patients compared to subjective methods: A systematic review and meta-analysis (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has currently infected over 6.5 million people worldwide. In response to the pandemic, numerous studies have tried to identify causes and symptoms of the disease. Emerging evidence supports recently acquired anosmia (complete loss of smell) and hyposmia (partial loss of smell) as symptoms of COVID-19, but studies of olfactory dysfunction show a wide range of prevalence, from 5% to 98%. We undertook a search of Pubmed/Medline and Google Scholar with the keywords "COVID-19," "smell," and/or "olfaction." We included any study that quantified olfactory loss as a symptom of COVID-19. Studies were grouped and compared based on the type of method used to measure smell loss-subjective measures such as self-reported smell loss versus objective measures using rated stimuli-to determine if prevalence rate differed by method type. For each study, 95% confidence intervals (CIs) were calculated from point estimates of olfactory disturbance rates. We identified 34 articles quantifying anosmia as a symptom of COVID-19, collected from cases identified from January 16 to April 30, 2020. The pooled prevalence estimate of smell loss was 77% when assessed through objective measurements (95% CI of 61.4-89.2%) and 45% with subjective measurements (95% CI of 31.1-58.5%). Objective measures are a more sensitive method to identify smell loss as a result of infection with SARS-CoV-2; the use of subjective measures, while expedient during the early stages of the pandemic, underestimates the true prevalence of smell loss.
Pairwise-Distance-Analysis-Driven Dimensionality Reduction Model with Double Mappings for Hyperspectral Image Visualization (2015)

This paper describes a novel strategy for the visualization of hyperspectral imagery based on the analysis of image pixel pairwise distances. The goal of this approach is to generate a final color image with excellent interpretability and high contrast at the cost of distorting a few pairwise distances. Specifically, the principle of equal variance is introduced to divide all hyperspectral bands into three subgroups and to ensure the energy is distributed uniformly between them, as in natural color images. Then, after detecting both normal and outlier pixels, these three subgroups are mapped into three color components of the output visualization using two different mapping (i.e., dimensionality reduction) schemes for the two types of pixels. The widely-used multidimensional scaling (MDS) is used for normal pixels and a new objective function, taking into account the weighting of pairwise distances, is presented for the outlier pixels. The pairwise distance weighting is designed such that small pairwise distances between the outliers and their respective neighbors are emphasized and large deviations are suppressed. This produces an image with high contrast and good interpretability while retaining the detailed information content. The proposed algorithm is compared with several state-of-the-art visualization techniques and evaluated on the well-known AVIRIS hyperspectral images. The effectiveness of the proposed strategy is substantiated both visually and quantitatively.
Phased array GNSS antenna for the FORMOSAT-7/COSMIC-2 radio occultation mission (2012)

Future GNSS remote sensing instruments such as the TriG receiver require more capable antennas than those flown on missions such as COSMIC. To maximize the number of ionospheric and atmospheric profiles, the TriG receiver will be capable of tracking legacy and new GPS signals such as L5, L2C and L1C; GLONASS CDMA and Galileo E1 and E5a. There has been an in-house effort at JPL to develop a set of antennas that would provide excellent Radio Occultations performance as well as navigation and ionospheric profiling. This effort is on-going but near completion for the manufacture and delivery of a set of flight antennas for the FORMOSAT-7/COSMIC-2 mission.
Endovascular Treatment of Anterior Tibial Artery Pseudoaneurysm Following Locking Compression Plating of the Tibia (2007)

Less invasive surgery and interventional radiology are relatively new techniques. This case report describes a patient with a distal tibial fracture that was stabilized using minimally invasive osteosynthesis consisting of a precontoured metaphyseal Locking Compression Plate (LCP). Postoperative radiographs showed good alignment of the bone, and the initial postoperative course was uneventful. At the sixth-week follow-up visit after surgery, the patient presented with a pulsating and tender mass on the lower leg that was palpable subcutaneously. Arteriography showed a pseudoaneurysm of the anterior tibial artery. At the same procedure an endovascular stent was placed, thereby excluding the pseudoaneurysm from the main circulation while keeping the vessel lumen patent. At the time of the last visit, 6 months after the operation, the patient was fully weightbearing with normal function of the ankle but with a nonhealing fracture on the x-ray. The dorsalis pedis pulse was equally strong as on the right side. Endovascular treatment with a covered stent proved to be an effective treatment for the described posttraumatic pseudoaneurysm of the anterior tibial artery. This case illustrates a risk of less invasive fracture surgery and at the same time underlines the value of a multidisciplinary approach to complications in trauma surgery.
Abstract PR18: Leveraging synthetic lethality to target convergent therapeutic resistance (2017)

Abstract Our laboratory uses genomic and pharmacological methods to define the pathways of resistance to targeted anticancer therapies. Toward this end, we recently developed a technique in which engineered lentiviral cDNAs encoding activators of major oncogenic signaling pathways are introduced into cells and then profiled to identify those capable of conferring resistance to drugs. In parallel, we have also developed analogous loss-of-function screening approaches based on CRISPR/Cas9 gene editing, and have used these approaches to map the pathways supporting intrinsic resistance to targeted therapies. Using these tools in conjunction with data and mouse models derived from human tumors, we recently discovered that major pathways of resistance frequently converge onto common downstream effectors, the targeting of which can forestall resistance. Here, I will describe the discovery of common resistance effectors in JAK2-driven myeloproliferative neoplasms, EGFR-driven colorectal cancers, and BRAF-driven melanomas. Focusing particularly on melanoma, I will describe the discovery that major pathways of resistance converge to activate the transcription factor c-MYC (MYC). MYC expression and gene signatures were suppressed following initial drug treatment, then rebounded during tumor progression in each member of a large panel of human patients, independent of the upstream pathway driving resistance. MYC suppression using either genetic approaches or BET bromodomain inhibition was sufficient to both resensitize diverse BRAFi/MEKi-resistant models and delay resistance in treatment naïve models. Although direct pharmacological inhibition of MYC remains difficult, the BRAFi/MEKi-resistant, MYC-activated state harbors synthetic lethal signaling and metabolic dependencies, including those involving SRC family and c-KIT tyrosine kinases and glucose, glutamine, and serine pathways, that can be targeted to create combination therapies that uniquely select against resistance evolution. Citation Format: Kris C. Wood. Leveraging synthetic lethality to target convergent therapeutic resistance [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR18.
Plant material features responsible for bamboo's excellent mechanical performance: a comparison of tensile properties of bamboo and spruce at the tissue, fibre and cell wall levels (2014)

The superior tensile properties of bamboo fibres and fibre bundles are mainly a result of amplified cell wall formation, leading to a densely packed tissue, rather than being based on specific cell wall properties. The material optimization towards extremely compact fibres with a multi-lamellar cell wall in bamboo might be a result of a plant growth strategy that compensates for the lack of secondary thickening growth at the tissue level, which is not only favourable for the biomechanics of the plant but is also increasingly utilized in terms of engineering products made from bamboo culms.
[Hormonal regulation of gene transcription--specificity and regulation of the hormonal response and results of its dysfunction]. (2000)

Nuclear hormone receptors act as ligand activated transcription factors. Hormonal response in vivo is, however, modulated at various levels beyond the mere activation of hormone receptors by their respective ligands. There is a great variability of particular arrangements of HRE and receptors of the TR/RAR subfamily use extensive dimerization to produce a particular dimer with optimal affinity for HRE in question. Hormonal response is mediated by complex hormone responsive units (HRU), which integrate HRE together with other regulatory sequences. Some hormone responsive genes may themselves code transcription factors or other regulatory proteins, underlying delayed primary and secondary responses. In addition to transcription activation, nuclear receptors enter repressive interactions with unrelated transcription factors like AP-1 or NF-kappa B. Genes for coding nuclear receptors are subjected to homologous downregulation. Functioning of nuclear receptors might be modulated by phosphorylation, which can underly ligand-independent activation. Nuclear receptors are mutated and/or disregulated in various pathologies, like hormone resistance syndromes of cancer.
Facile Access to 5′‐S‐(4,4′‐Dimethoxytrityl)‐2′,5′‐Dideoxyribonucleosides via Stable Disulfide Intermediates (2015)

Thionucleosides represent an important class of modified nucleos(t)ides that have found distinct applications in the chemical biology of synthetic oligonucleotides, but the use of these compounds is substantially lessened by the instability or high reactivity of the sulfhydryl group. This unit describes a protocol for the synthesis of 2',5'-dideoxy-5'-thioribonucleoside disulfides by utilizing Mitsunobu reaction conditions on 3'-O-levulinyl-2'-deoxyribonucleosides in the presence of thiobenzoic acid followed by facile hydrolysis and in situ oxidation of the resulting 5'-thiolated nucleosides using methanolic ammonia. The utility of these disulfides has been demonstrated as stable precursors for the synthesis of 5'-thio-modified 2'-deoxynucleosides. To validate the potential of the methodology, 5'-S-(4,4'-dimethoxytrityl)-2',5'-dideoxythymidine phosphoramidite has been synthesized by in situ cleavage of the disulfide linkage of 2',5'-dideoxy-5'-thiothymidine disulfide followed by protection with a dimethoxytriphenyl (DMT) group and 3'-phosphitylation using 2-cyanoethyl N,N-diisopropylchlorophosphoramidite.
EVNERT Program: Testing of Adaptive HQ-Liner for Aft Noise Control (2008)

The results of the static engine tests for evaluation of the adaptive HQ-Liner concept for aft-fan noise control on the Honeywell turbofan engine Tech977 are presented in this paper. The tests were part of the NASA/Honeywell EVNERT program to evaluate the performance of innovative noise control technologies for the commercial aviation industry. The HQ-Liner concept incorporates the capabilities of typical acoustic liners, which are known to effectively reduce broadband noise, and HQ tubes, that have demonstrated potential to reduce BPF tone. Additionally, the concept of adaptation is based on shifting the resonance frequencies of the HQ tube in order to target the BPF tone at several operating power settings. The system tested was designed by Virginia Polytechnic Institute & State University, with collaboration from Goodrich Corporation and Lord Corporation, and it was fabricated by a combined effort between Goodrich and Lord. The experiments were conducted at the Honeywell San Tan static test facility in Arizona. The HQ tubes were tested with and without the liner and for both passive and adaptive configurations. The baseline configurations were defined as the hard wall (no acoustic treatment), the current production liner mounted on the engine (customer liner), and the newly designed liner for implementation with the HQ tubes. The results show that all HQ-Liner cases performed superior to the customer liner. The adaptation effects were clearly observed on the BPF tone results, but it did not appear to provide sufficient contribution to affect the regulation metrics. As a result, the HQ tubes (passive or adaptive) did not provide significant additional contribution with respect to the newly designed liner to justify implementation.
Two Memristor SPICE Models and Their Applications in Microwave Devices (2014)

This paper presents two simple SPICE circuit models of the memristor using two different kinds of integrators. These models expand and simplify the previous methods of solving the memristor's modeling equations presented by Hewlett-Packard Lab. The behaviors of the two memristor models are investigated when they are excited by a sinusoidal voltage source. Both models satisfy the general features of memristive systems such as having a zero-crossing property in the form of an i-v Lissajous figure. In order to explore the unique characteristics and applications of the memristor in microwave devices, first we incorporate the memristor in a microstrip transmission line as a load. We do the analysis using a finite-difference time-domain simulator integrated with a nonlinear SPICE circuit solver. Furthermore, we design a reconfigurable microstrip bandpass filter based on a memristor-loaded resonator, and utilize a memristor as a carrier-wave modulator connecting the microstrip patch antenna to the ground.
Endogenous mono-ADP-ribosylation of the free Gβγ prevents stimulation of phosphoinositide 3-kinase-γ and phospholipase C-β2 and is activated by G-protein-coupled receptors (2002)

We have recently demonstrated that the beta subunit of the heterotrimeric G-proteins is endogenously mono-ADP-ribosylated in intact cells. The modified betagamma heterodimer loses its ability to inhibit calmodulin-stimulated type 1 adenylate cyclase and, remarkably, is de-ADP-ribosylated by a cytosolic hydrolase that completes an ADP-/de-ADP-ribosylation cycle of potential physiological relevance. In the present study, we show that this ADP-ribosylation might indeed be a general mechanism for termination of betagamma signalling, since the ADP-ribosylated betagamma subunit is also unable to activate both phosphoinositide 3-kinase-gamma and phospholipase C-beta2. Moreover, we show that beta subunit ADP-ribosylation is induced by G-protein-coupled receptor activation, since hormone stimulation of Chinese-hamster ovary plasma membranes leads to increases in beta subunit labelling. This occurs when betagamma is in its active heterodimeric conformation, since full inhibition of this modification can be achieved by binding of GDP-alphai3 to the betagamma heterodimer. Taken together, these findings delineate a pathway that arises from the activation of a G-protein-coupled receptor and leads to the inhibition of betagamma activity through its reversible mono-ADP-ribosylation.
Relationships between body roundness with body fat and visceral adipose tissue emerging from a new geometrical model (2013)

BRI, a new shape measure, is a predictor of %body fat and %VAT and can be applied as a visual tool for health status evaluations.
Discovery of 3-Amino-2-Hydroxypropoxyisoflavone Derivatives as Potential Anti-HCV Agents (2018)

Synthesis and anti-hepatitis C virus (anti-HCV) effects of certain 3-amino-2-hydroxy-propoxy isoflavone derivatives, <b>6a</b>⁻<b>i</b>, were described. The known 3-(3,4-dimethoxyphenyl)-7-(oxiran-2-ylmethoxy)-4<i>H</i>-chromen-4-one (<b>5</b>) was reacted with substituted amines to give the desired isoflavone derivatives, <b>6a</b>⁻<b>i</b>. Among them, 7-{3-[(3,4-dimethoxy-phenethyl)amino]-2-hydroxypropoxy}-3-(3,4-dimethoxyphenyl)-4<i>H</i>-chromen-4-one (<b>6b</b>) was the most active, exhibiting approximately 2-fold higher anti-HCV effects than standard antiviral drug ribavirin (EC<sub>50</sub> of 6.53 vs. 13.16 μM). In addition, compound <b>6b</b> was less cytotoxic than ribavirin. The selectivity index (SI) of <b>6b</b> is approximately 2.6-fold higher than ribavirin. The compounds <b>6e</b>, <b>6h</b>, and <b>6i</b> were also found to possess higher anti-HCV effects than ribavirin. Compound <b>6b</b> was found to inhibit the HCV RNA expression in Ava5 cells in a dose-dependent manner; furthermore, we found that the antiviral mechanism of compounds <b>6b</b>, <b>6e</b>, <b>6h</b>, and <b>6i</b> gave rise to induction of HO-1 expression. With the HO-1 promoter-based analysis, we found compounds <b>6b</b>, <b>6e</b>, <b>6h</b>, and <b>6i</b> induced HO-1 expression through increasing Nrf-2 binding activity. Taken together, compound <b>6b</b> may serve as a potential lead compound for developing novel anti-HCV agents.
Lipoprotein Transport: Greasing the Machines of Outer Membrane Biogenesis (2018)

The Gram-negative outer membrane (OM) is a potent permeability barrier against antibiotics, limiting clinical options amid mounting rates of resistance. The Lol transport pathway delivers lipoproteins to the OM. All the OM assembly machines require one or more OM lipoprotein to function, making the Lol pathway central for all aspects of OM biogenesis. The Lol pathways of many medically important species clearly deviate from the Escherichia coli paradigm, perhaps with implications for efforts to develop novel antibiotics. Moreover, recent work reveals the existence of an undiscovered alternate route for bringing lipoproteins to the OM. Here, lipoprotein transport mechanisms, and the quality control systems that underpin them, is re-examined in context of their diversity.
A performance comparison between cricket bat designs (2011)

Seven cricket bats, four standard and three significantly different designs, were tested for a set of mechanical properties: equivalent bending stiffness, moment of inertia, and freely-suspended vibration. These properties are known to be related to the performance of the cricket bats in terms of pick up weight, vibrations imparted to the batsman, and energy imparted to the cricket ball. The aim of this work was to determine whether these novel designs improve the bat’s performance parameters. Intuitively correctly, results showed that by redistributing the mass of the bat further away from the rotational axis the moment of inertia increases. This results in an increase of the ball’s rebound speed after collision. Carbon fibres inserted in the handle of the bat were found to improve its vibrational performance and provide the advantage of having a stiffer blade combined with a relatively less-stiff handle, which is an optimum for imparting maximum energy to the ball.