gebhart/patrepeval huggingface dataset:
Construction of a water-soluble form of penicillin-binding protein 2a from a methicillin-resistant Staphylococcus aureus isolate (1992)

The mecA gene from methicillin-resistant Staphylococcus aureus 27r, which encodes the membrane-bound penicillin-binding protein 2a (PBP 2a), was cloned, sequenced, and expressed in Escherichia coli. PBP 2a is the major factor that mediates methicillin resistance in staphylococci. The DNA sequence of the mecA gene from strain 27r was greater than 99% identical to the DNA sequence of other S. aureus mecA genes and the mecA gene from Staphylococcus epidermidis. Analysis of the deduced amino acid sequence of PBP 2a from strain 27r revealed a hydrophobic region at the amino terminus that possessed characteristics of an uncleaved signal peptide such as those found in type II integral membrane proteins. Site-specific mutagenesis was used to modify the strain 27r mecA gene to permit removal of the region encoding the putative transmembrane region (amino acids 2 to 22). When it was expressed in E. coli, the modified mecA gene from strain 27r encoded a water-soluble form of PBP 2a that was detectable in the cytoplasm of transformants. The water-soluble form of PBP 2a protein from S. aureus 27r retained the same binding efficiency for beta-lactam antibiotics as the unmodified membrane-bound PBP 2a from S. aureus 27r.
The Cell Wall-Associated Mycolactone Polyketide Synthases Are Necessary but Not Sufficient for Mycolactone Biosynthesis (2013)

Mycolactones are polyketide-derived lipid virulence factors made by the slow-growing human pathogen, Mycobacterium ulcerans. Three unusually large and homologous plasmid-borne genes (mlsA1: 51 kb, mlsB: 42 kb and mlsA2: 7 kb) encode the mycolactone type I polyketide synthases (PKS). The extreme size and low sequence diversity of these genes has posed significant barriers for exploration of the genetic and biochemical basis of mycolactone synthesis. Here, we have developed a truncated, more tractable 3-module version of the 18-module mycolactone PKS and we show that this engineered PKS functions as expected in the natural host M. ulcerans to produce an additional polyketide; a triketide lactone (TKL). Cell fractionation experiments indicated that this 3-module PKS and the putative accessory enzymes encoded by mup045 and mup038 associated with the mycobacterial cell wall, a finding supported by confocal microscopy. We then assessed the capacity of the faster growing, Mycobacterium marinum to harbor and express the 3-module Mls PKS and accessory enzymes encoded by mup045 and mup038. RT-PCR, immunoblotting, and cell fractionation experiments confirmed that the truncated Mls PKS multienzymes were expressed and also partitioned with the cell wall material in M. marinum. However, this heterologous host failed to produce TKL. The systematic deconstruction of the mycolactone PKS presented here suggests that the Mls multienzymes are necessary but not sufficient for mycolactone synthesis and that synthesis is likely to occur (at least in part) within the mycobacterial cell wall. This research is also the first proof-of-principle demonstration of the potential of this enzyme complex to produce tailored small molecules through genetically engineered rearrangements of the Mls modules.
Mathematical Modeling of Mass Transfer during Convective Dehydration of Brown Algae<i>Macrocystis Pyrifera</i> (2008)

The aim of this research was to study and to model the drying kinetics of the brown algae Macrocystis pyrifera at 50, 60, 70, and 80°C. GAB equation showed a good fit on the sorption experimental data. Fick's diffusional model, together with Newton, Henderson-Pabis, Page, modified Page, logarithmic, and Midilli-Kukuc models were applied on the drying kinetics of the alga. The Dwe increased from 5.56 to 10.22 × 10−9 m2/s as temperature increased from 50 to 80°C. Midilli-Kukuc and logarithmic models obtained the best-fit quality for drying curves based on the statistical tests. In consequence, both models are excellent tools for estimating the drying time of this product.
Supplementary table 1 from Redundant Innate and Adaptive Sources of IL17 Production Drive Colon Tumorigenesis (2023)

&lt;p&gt;Supplementary Table S1. List of antibody clones used for flow cytometry analysis.&lt;/p&gt;
The Real-time Distributed Control of the Virgo Interferometric Detector of Gravitational Waves (2007)

The VIRGO experiment for the detection of gravitational waves is a big challenge both for physics and for technology, in particular, to satisfy the stringent requirements on the alignment and position of its suspended optical components to keep the detector at its working point, a very complex distributed and supervised control system has been implemented. The current constraints are about 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-10</sup> m RMS for the longitudinal control ( "Locking" ) and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> rad RMS for the angular degrees of freedom ( " Alignment " ). These requirements are satisfied by means of a specially designed hierarchical architecture for the local control system, necessary for managing the hard task of filtering all the environments noises that limit the sensitivity of the interferometer, supervised by a distributed global control system to maintain the detector fully operational. In this paper we described the status of the real - time distributed control system of the Virgo interferometric detector of Gravitational waves, its performances and planned improvements.
Proteomic patterns associated with heterosis Proteins and proteomics (2016)

Heterosis is characterized by higher seed yields, plant biomass or other traits in heterozygotes or hybrids compared with their genetically divergent parents, which are often homozygous. Despite extensive investigation of heterosis and its wide application in crops such as maize, rice, wheat and sorghum, its molecular basis is still enigmatic. In the past century, some pioneers have proposed multigene models referring to the complementation of allelic and gene expression variation, which is likely to be an important contributor to heterosis. In addition, there are potential interactions of epigenetic variation involved in heterosis via novel mechanisms. At the level of gene expression, many recent studies have revealed that the heterosis phenomenon can be deciphered not only at the transcriptional level but also at the proteomic level. This review presents an update on the information supporting the involvement of proteomic patterns in heterosis and a possible future direction of the field. This article is part of a Special Issue entitled: Plant Proteomics — a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
Fast noniterative calibration of an external motion tracking device (2013)

Purpose Prospective motion correction of magnetic resonance (MR) scans commonly uses an external device, such as a camera, to track the pose of the organ of interest. However, in order for external tracking data to be translated into the MR scanner reference frame, the pose of the camera relative to the MR scanner must be known accurately. Here, we describe a fast, accurate, non‐iterative technique to determine the position of an external tracking device de novo relative to the MR reference frame. Theory and Methods The method relies on imaging a sparse object that allows simultaneous tracking of arbitrary rigid body transformations in the reference frame of the magnetic resonance imaging (MRI) machine and that of the external tracking device. Results Large motions in the MRI reference frame can be measured using a sparse phantom with an accuracy of 0.2 mm, or approximately 1/10 of the voxel size. By using a dual quaternion algorithm to solve the calibration problem, a good camera calibration can be achieved with fewer than six measurements. Further refinements can be achieved by applying the method iteratively and using motion correction feedback. Conclusion Independent tracking of a series of movements in two reference frames allows for an analytical solution to the hand‐eye‐calibration problem for various motion tracking setups in MRI. Magn Reson Med 71:1489–1500, 2014. © 2013 Wiley Periodicals, Inc .
MYD88 L265P Promotes Survival of Waldenstrom's Macroglobulinemia Cells by Activation of Bruton's Tyrosine Kinase (2012)

Abstract Abstract 897 Background: MYD88 is an adapter molecule which promotes Toll-Like Receptor and IL-1 Receptor signaling through the IRAK 1/4/TRAF6/NF-κB pathway. MYD88 L265P is a recently described somatic mutation that is widely expressed (&gt;90%) in patients with Waldenstrom's Macroglobulinemia (Treon et al, NEJM 2012). The signaling pathway by which MYD88 L265P promotes WM growth and survival remains to be fully clarified. We therefore sought to identify pathway(s) responsible for MYD88 L265P pro-survival signaling. Patients and Methods: Primary WM-LPCs were isolated from bone marrow biopsy specimens from WM patients. Normal CD19+ B-cells were isolated from the peripheral blood of healthy donors. Western blot analyses was performed using total and phospho-specific antibodies in the MYD88 L265P expressing WM cell lines BCWM.1 and MCWL-1 following MYD88 knockdown by lentiviral transduction, and/or use of MYD88 or IRAK signal inhibitors. WM cells were also treated with the BTK inhibitor PCI-32765, in the presence or absence of an IRAK1/4 inhibitor. Cell survival was evaluated by Annexin V/PI staining and/or AlamarBlue® or ATPLite® assays after treatments with inhibitors. Synergistic interactions were assessed with CalcuSyn software. Results: Lentiviral knockdown of MYD88 and/or use of an inhibitor of MYD88 homo-dimerization led to decreased survival of MYD88 L265P expressing BCWM.1 and MWCL-1 cells, as well as primary WM LPCs expressing MYD88 L265P. In contrast minimal killing was observed in MYD88 Wild Type (WT) expressing Ramos, MM.1S, or healthy donor CD19+ selected B-cells. Phospho-specific western blot analysis showed decreased IRAK1, NF-kB and STAT3 signaling following inhibition of MYD88 signaling in L265P expressing WM cells. Conversely, use of an IRAK1/4 kinase inhibitor showed reduced tumor cell killing, NF-kB and STAT3 signaling. We therefore performed co-immunopreciptation experiments to identify other MYD88 binding partners in L265P expressing WM cells. These studies identified Bruton's Tyrosine Kinase (BTK) in complex with MYD88, with MYD88 showing more robust binding to phospho-BTK in L265P expressing WM cells. Lentiviral knockdown of MYD88 and/or use of an inhibitor of MYD88 homodimerization led to decreased BTK phosphorylation. Moreover, overexpression by lentiviral transduction of MYD88 L265P showed more robust BTK phosphorylation versus WM cells transduced with MYD88 WT. Lastly, the use of a BTK-inhibitor (PCI-32765) blocked NF-kB and STAT3 signaling, as well as induced WM tumor cell killing that was synergistically enhanced by the presence of an IRAK1/4 kinase inhibitor. Conclusion: MYD88 L265P promotes survival of WM cells by activation of BTK. These studies provide the framework for the investigation of BTK inhibitors in WM, as single agents and in combination with other MYD88 pathway inhibitors. Disclosures: Treon: Onyx: Research Funding; Celgene: Research Funding; Pharmacyclics: Research Funding; Cephalon: Consultancy; Avila: Consultancy.
Interspecies activation correlations reveal functional correspondences between marmoset and human brain areas (2021)

Abstract The common marmoset has enormous promise as a nonhuman primate model of human brain functions. While resting-state functional magnetic resonance imaging (fMRI) has provided evidence for a similar organization of marmoset and human cortices, the technique cannot be used to map the functional correspondences of brain regions between species. This limitation can be overcome by movie-driven fMRI (md-fMRI), which has become a popular tool for non-invasively mapping the neural patterns generated by rich and naturalistic stimulation. Here, we used md-fMRI in marmosets and humans to identify whole-brain functional correspondences between the two primate species. In particular, we describe functional correlates for the well-known human face, body, and scene patches in marmosets. We find that these networks have a similar organization in both species, suggesting a largely conserved organization of higher-order visual areas between New World marmoset monkeys and humans. However, while face patches in humans and marmosets were activated by marmoset faces, only human face patches responded to the faces of other animals. Together, the results demonstrate that md-fMRI is a powerful tool for interspecies functional mapping and characterization of higher-order visual functions.
Decentralised state feedback design for large-scale linear systems subject to input saturation (2010)

This study considers the design of decentralised controllers for large-scale linear systems under actuator saturation. Saturation in the magnitude of the control input is first considered. For the closed-loop system under a saturating decentralised state feedback law, conditions are identified under which an ellipsoid is contractively invariant and thus within the domain of attraction, or the restricted ℒ2 gain from the disturbance to the output is less than or equal to a pre-specified value γ. Based on these conditions, the designs of decentralised state feedback laws that achieve large domains of attraction or low ℒ2 gains can be formulated as optimisation problems with bilinear matrix inequality (BMI) constraints. Numerical algorithms are developed to solve these BMI problems. These developments are also extended to the situation where the inputs are subject to nested saturation, such as simultaneous actuator magnitude and rate saturation. Throughout the study, numerical examples are used to demonstrate the effectiveness of the proposed design method.
Abstract A97: Dclk1 identifies adult pancreatic stem and cancer-initiating cells. (2012)

Introduction: Despite recent progress in the detection and management of pancreatic cancer it remains and almost uniformly lethal disease. Pancreatic ductal adenocarcinoma (PDAC) currently ranks as the fourth leading cause of cancer-related death in the U.S. and has the highest case mortality rate of all major cancers. While genetically engineered mouse models have yielded valuable insights into the genetic hallmarks of the disease, they have failed to identify the cell of origin in pancreatic cancer. Adult tissue stem cells are attractive candidates for cancer initiating cells. However, the existence of adult pancreatic stem or progenitor cells is a point of considerable debate. Doublecortin-like kinase 1 protein (Dclk1) has been proposed as a marker of gastrointestinal and pancreatic stem cells although formal lineage tracing was not performed. Furthermore, it was demonstrated that Dclk1 cells expand in the setting of tissue injury, metaplasia and hyperplasia. Aim: To clarify the role of Dclk1 in the pancreatic organ homeostasis and pancreatic cancer we have generated Dclk1 BAC transgenic mouse lines (Dclk1-CreERT) expressing tamoxifen-inducible Cre recombinase under the control of Dclk1 gene regulation. Results: Genetic lineage tracing revealed that Dclk1 marks rare ductal and centroacinar cells. Interestingly, Dclk1 cells are not derived from p48-labled pancreatic progenitor cells. Dclk1 cells are very long lived and give rise to ductal and acinar tissue over time and participate in organ regeneration after caerulein-induced pancreatitis. Furthermore, Dclk1 cells were found to be expanded in murine and human PanINs. Selective expression of mutant KRas in Dclk1 cells causes rapid development of mPanINs (1 month) and invasive pancreatic ductal adenocarcinoma (2-3 months) in adult mice without the need for tissue injury or additional mutations. Conclusions: Dclk1 marks rare adult pancreatic stem cells. These cells take part in organ homeostasis and regeneration. Furthermore, Dclk1 cells expand in the setting of malignant transformation. Finally, Dclk1 cells are potent cancer initiating cells. We propose that Dclk1 might identify a novel type of pancreatic stem cell and a potential cell of origin in pancreatic cancer. Citation Format: Christoph B. Westphalen, Michael Quante, Daniel L. Worthley, Samuel Asfaha, Courtney Houchen, Randal May, Helen Remotti, Kenneth P. Olive, Timothy C. Wang. Dclk1 identifies adult pancreatic stem and cancer-initiating cells. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Progress and Challenges; Jun 18-21, 2012; Lake Tahoe, NV. Philadelphia (PA): AACR; Cancer Res 2012;72(12 Suppl):Abstract nr A97.
Honey bee brood ring-test: method for testing pesticide toxicity on honeybee brood in laboratory conditions (2010)

International audience
Perturbation of the interactions of calmodulin with GRK5 using a natural product chemical probe (2019)

G protein-coupled receptor (GPCR) kinases (GRKs) are responsible for initiating desensitization of activated GPCRs. GRK5 is potently inhibited by the calcium-sensing protein calmodulin (CaM), which leads to nuclear translocation of GRK5 and promotion of cardiac hypertrophy. Herein, we report the architecture of the Ca<sup>2+</sup>·CaM-GRK5 complex determined by small-angle X-ray scattering and negative-stain electron microscopy. Ca<sup>2+</sup>·CaM binds primarily to the small lobe of the kinase domain of GRK5 near elements critical for receptor interaction and membrane association, thereby inhibiting receptor phosphorylation while activating the kinase for phosphorylation of soluble substrates. To define the role of each lobe of Ca<sup>2+</sup>·CaM, we utilized the natural product malbrancheamide as a chemical probe to show that the C-terminal lobe of Ca<sup>2+</sup>·CaM regulates membrane binding while the N-terminal lobe regulates receptor phosphorylation and kinase domain activation. In cells, malbrancheamide attenuated GRK5 nuclear translocation and effectively blocked the hypertrophic response, demonstrating the utility of this natural product and its derivatives in probing Ca<sup>2+</sup>·CaM-dependent hypertrophy.
Spontaneous Bacterial Keratitis in CD36 Knockout Mice (2010)

Purpose.: CD36 is a Class B scavenger receptor that is constitutively expressed in the corneal epithelium and has been implicated in many homeostatic functions, including the homeostasis of the epidermal barrier. The aim of this study is to determine (1) whether CD36 is required for the maintenance of the corneal epithelial barrier to infection, and (2) whether CD36-deficient mice present with an increased susceptibility to bacterial keratitis. Methods.: The corneas of CD36−/−, TSP1−/−, TLR2−/−, and C57BL/6 WT mice were screened via slit lamp microscopy or ex vivo analysis. The epithelial tight junctions and mucin layer were assessed via LC-biotin and Rose Bengal staining, respectively. Bacterial quantification was performed on corneal buttons and GFP-expressing Staphylococcus aureus was used to study bacterial binding. Results.: CD36−/− mice develop spontaneous corneal defects that increased in frequency and severity with age. The mild corneal defects were characterized by a disruption in epithelial tight junctions and the mucin layer, an infiltrate of macrophages, and increased bacterial binding. Bacterial quantification revealed high levels of Staphylococcus xylosus in the corneas of CD36−/− mice with severe defects, but not in wild-type controls. Conclusions.: CD36−/− mice develop spontaneous bacterial keratitis independent of TLR2 and TSP1. The authors conclude that CD36 is a critical component of the corneal epithelial barrier, and in the absence of CD36 the barrier breaks down, allowing bacteria to bind to the corneal epithelium and resulting in spontaneous keratitis. This is the first report of spontaneous bacterial keratitis in mice.
Individual health discount rate in patients with ulcerative colitis (2010)

The accepted discount rate of 5% grossly underestimates UC patients' preference for long-term over short-term risk. This might explain UC patients' frequent choice of the long-term risks of immunosuppressive medical therapy over the short-term risks of colectomy.
The development of dendronized polymers containing phosphorescent iridium(III) complexes for solution-processable OLED Devices (2014)

Polymers containing pendant phosphorescent iridium(III) complexes encapsulated within carbazole-based dendrons were prepared using Ring Opening Metathesis Polymerization (ROMP). Their design and synthesis are discussed and their photophysical and optoelectronic properties are presented in the context of applications within flexible lighting modules.
Density Functional Theory Study on the Initial Step of the Permanganate Oxidation of Substituted Alkynes (2004)

The initial step of the oxidation of alkynes by permanganate has been studied by DFT (B3LYP/6-311+G(d,p)) calculations. The influence of electron-withdrawing as well as electron-donating substituents was explored. The singlet and triplet potential energy hypersurfaces (PES) for a concerted [3 + 2] and a stepwise [2 + 2] mechanism were investigated. The crossing point between the singlet and triplet PES has been identified. The reaction proceeds via a [3 + 2] mechanism on the singlet PES with free energy activation barriers (ΔG298) between 18.4 and 28.9 kcal/mol, while the lowest lying identified state is a reactive triplet intermediate. Available experimental and computed data are in good agreement. For the [2 + 2] case a reaction on the triplet surface would be preferred over the singlet, but both pathways lay well above the [3 + 2] pathway.
Davis–Beirut Reaction: Alkoxide versus Hydroxide Addition to the Key <i>o</i>-Nitrosoimine Intermediate (2018)

Reaction options, alkoxide vs hydroxide vs amine addition to the key intermediate (o-nitrosoimine) generated in the Davis-Beirut reaction of an o-nitrobenzylamine substrate, are reported to explain the nucleophilic addition selectivity of this one-pot indazole-forming process. The hydroxide addition/deprotection pathway as well as the fate of the resulting o-nitrosobenzaldehyde were both uncovered with several o-nitrobenzylamine substrates, and design elements required for an efficient double Davis-Beirut reaction, inspired by new mechanistic insights, were defined.
Unsupervised Clustering using Multi-Resolution Perceptual Grouping (2007)

Clustering is a common operation for data partitioning in many practical applications. Often, such data distributions exhibit higher level structures which are important for problem characterization, but are not explicitly discovered by existing clustering algorithms. In this paper, we introduce multi-resolution perceptual grouping as an approach to unsupervised clustering. Specifically, we use the perceptual grouping constraints of proximity, density, contiguity and orientation similarity. We apply these constraints in a multi-resolution fashion, to group sample points in high dimensional spaces into salient clusters. We present an extensive evaluation of the clustering algorithm against state-of-the-art supervised and unsupervised clustering methods on large datasets.
Parameter estimation and uncertainty quantification of reservoir and geomechanical modeling of surface uplift at In Salah Algeria. (2020)

Abstract not provided.