gebhart/patrepeval huggingface dataset:
Engineering of Klebsiella oxytoca for the Production of 2,3-Butanediol from High Concentration of Xylose (2021)

Klebsiella oxytoca is widely used for the biological production of 2,3-butanediol (2,3-BDO), a promising platform chemical with a broad range of applications. Here, to improve cell growth and production of 2,3-BDO under high concentration of xylose (100 g/L), we engineered K. oxytoca using an adaptive laboratory evolution and a biosensor-derived high throughput screening strategy. First, we developed a XylR-dependent xylose biosensor for the detection of intracellular xylose, and K. oxytoca containing the xylose biosensor was used for adaptive laboratory evolution in 100 g/L xylose. Cells were isolated by FACS screening, and the isolated strain (KO8S16) showed much improved cell growth with high xylose consumption rate (1.35 g/L/h) and 2,3-BDO productivity (0.53 g/L/h) compared with the wild-type strain. Through whole genome resequencing, it was revealed that a mutation in OmpR (a response regulator of osmotic stress) allowed to withstand high concentrations of xylose. Finally, fed-batch cultivation was performed by feeding high concentration of xylose, and K. oxytoca successfully produced 2,3-BDO at a concentration as high as 57.5 g/L by consuming 238.13 g/L xylose in 47 h.
Extrinsic giant magnetoresistance in chromium (IV) oxide, CrO2 (1998)

Polycrystalline CrO2 is shown to exhibit a giant magnetoresistance (GMR) at low temperatures. A rapid decrease in the GMR with increasing temperature is correlated with a decrease in the intergranular resistance. Single-crystal CrO2 is a half-metallic ferromagnet, as the data are interpreted to reflect two types of charge carriers, crossing a grain boundary: those that tunnel between conduction bands of adjacent grains and those that hop after residing at a localized state for a time long compared to a spin relaxation time.
Effect of age, castration, and testosterone replacement on the development and restoration of canine benign prostatic hyperplasia (1986)

An experiment was designed to test the effect of castration and testosterone replacement on the development of benign prostatic hyperplasia (BPH) in young and on the restoration of BPH in old beagles. Twenty beagles were divided by age into young (1.5-2.5-yr) and old (6.0-8.5-yr) groups. Each of these groups was further divided randomly into two additional groups of age-matched, intact, untreated control and castrate beagles. The latter were then treated with testosterone-filled Silastic implants designed to clamp serum testosterone at concentrations similar to those observed in adult beagles for 7 months beginning 5 months after castration. Histopathologic characterization of each prostate was completed on biopsy material obtained at the beginning and end of the experiment. Prostate weights were determined each month for 12 months via a noninvasive two-dimensional X-ray procedure. Testosterone treatment for 7 months allowed BPH to develop in young and restored BPH in old beagles. These results suggest that testosterone in the adult beagle acts permissively to allow BPH to develop in the prostate of the aging dog. Some other testicular product may be required for the continued growth of BPH in aged beagles.
TiN@TiO2Core–Shell Nanoparticles as Plasmon‐Enhanced Photosensitizers: The Role of Hot Electron Injection (2020)

Abstract Metal–semiconductor heterostructures have attracted a lot of attention due to their ability to enhance photovoltaic and photocatalytic processes via plasmonic effects. Thus far, most of the proposed heterostructures are designed with noble metals and the potential of alternative plasmonic materials, such as titanium nitride (TiN), is not yet well explored. In this work, TiN@TiO 2 core–shell nanoparticles (NPs) are synthesized and proposed as plasmon‐enhanced photosensitizers for efficient singlet oxygen generation, with the focus on the role of hot electron injection. Excitation of dilute TiN@TiO 2 NP dispersions by a 700 nm femtosecond‐pulsed laser effectively converts ground‐state oxygen into singlet oxygen ( 1 O 2 ), driven primarily by hot electrons generated during plasmon decay at the TiN–TiO 2 interface and injected into the TiO 2 layer. Analytical calculations reveal the unique advantages of TiN–TiO 2 heterostructures in hot‐electron‐mediated photocatalysis. Considering the chemical inertness and low cost of TiN, TiN@TiO 2 NPs hold great potential as plasmonic photosensitizers for photodynamic therapy and other photocatalytic applications at red‐to‐near‐infrared wavelengths.
Synthesis and Investigation of Nematic Liquid Crystals with Flexoelectric Properties (2005)

We describe the synthesis and characterization of a series of model nematic liquid crystals with transverse dipole moments used to study the flexoelectric effect in guest−host mixtures with commercial liquid crystal host. The flexoelectric coefficicent of the mixtures, containing only 10% by weight of the dopant, are up to 6 times higher than those of the pure hosts. The length, bend angle, and dipole moments of the molecules are systematically varied to investigate any correlations with the flexoelectric effect. We find that the flexoelectric coefficients increase with molecular length, are inversely correlated with the bend angle, and are independent of the dipole moment of the dopant. Although these findings seem to contradict predictions from dipolar flexoelectric theories, they can be reconciled by considering the properties of both the guest and host in the mixture. Thiophenes and dimesogens show particularly large flexoelectric effects. This work should inform the molecular design of new materials with enhanced flexoelectric properties.
Data from iRGD-guided Tumor-penetrating Nanocomplexes for Therapeutic siRNA Delivery to Pancreatic Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Pancreatic cancer is one of the leading causes of cancer-related death, with 5-year survival of 8.5%. The lack of significant progress in improving therapy reflects our inability to overcome the desmoplastic stromal barrier in pancreatic ductal adenocarcinoma (PDAC) as well as a paucity of new approaches targeting its genetic underpinnings. RNA interference holds promise in targeting key mutations driving PDAC; however, a nucleic acid delivery vehicle that homes to PDAC and breaches the stroma does not yet exist. Noting that the cyclic peptide iRGD mediates tumor targeting and penetration through interactions with α&lt;sub&gt;v&lt;/sub&gt;β&lt;sub&gt;3/5&lt;/sub&gt; integrins and neuropilin-1, we hypothesized that “tandem” peptides combining a cell-penetrating peptide and iRGD can encapsulate siRNA to form tumor-penetrating nanocomplexes (TPN) capable of delivering siRNA to PDAC. The use of directly conjugated iRGD is justified by receptor expression patterns in human PDAC biopsies. In this work, we optimize iRGD TPNs with polyethylene glycol (PEG)-peptide conjugates for systemic delivery to sites of disease. We show that TPNs effectively knockdown siRNA targets in PDAC cell lines and in an immunocompetent genetically engineered mouse model of PDAC. Furthermore, we validate their tumor-penetrating ability in three-dimensional organoids and autochthonous tumors. In murine therapeutic trials, TPNs delivering anti-&lt;i&gt;Kras&lt;/i&gt; siRNA significantly delay tumor growth. Thus, iRGD TPNs hold promise in treating PDAC by not only overcoming physical barriers to therapy, but by leveraging the stroma to achieve knockdown of the gold-standard genetic target. Moreover, the modular construction of this delivery platform allows for facile adaptation to future genetic target candidates in pancreatic cancer. &lt;i&gt;Mol Cancer Ther; 17(11); 2377–88. ©2018 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data (2009)

The immune system is essential to body defense and maintenance. Specific antibodies to foreign invaders function in body defense, and it has been suggested that autoantibodies binding to self molecules are important in body maintenance. Recently, the autoantibody repertoires in the bloods of healthy mothers and their newborns were studied using an antigen microarray containing hundreds of self molecules. It was found that the mothers expressed diverse repertoires for both IgG and IgM autoantibodies. Each newborn shares with its mother a similar repertoire of IgG antibodies, which cross the placental but its IgM repertoire is more similar to those of other newborns. Here, we took a system-level approach and analyzed the correlations between autoantibody reactivities of the previous data and extended the study to new data from newborns at birth and a week later, and from healthy young women. For the young women, we found modular organization of both IgG and IgM isotypes into antigen cliques-subgroups of highly correlated antigen reactivities. In contrast, the newborns were found to share a universal congenital IgM profile with no modular organization. Moreover, the IgG autoantibodies of the newborns manifested buds of the mothers' antigen cliques, but they were noticeably less structured. These findings suggest that the natural autoantibody repertoire of humans shows relatively little organization at birth, but, by young adulthood, it becomes sorted out into a modular organization of subgroups (cliques) of correlated antigens. These features revealed by antigen microarrays can be used to define personal states of autoantibody organizational motifs.
Topoisomerase II Inhibitors Influence Simian Virus 40 Chromatin Structure in vivo Accompanied with Inhibition of Replication, Transcription and Changes in DNA Supercoiling (1988)

The association of topoisomerase II enzymes with papovavirus-chromatin has been described recently. We used cells infected with simian virus 40 (SV40) to investigate the in vivo effect of the topoisomerase II inhibitors nalidixic acid and novobiocin on the viral chromatin template. Blocking of topoisomerases inhibits DNA and RNA synthesis. The block with the inhibitors resulted in a conversion of a 95- to 75-svedberg chromatin to a 180- to 150-svedberg component accompanied with a variation in the topological linking number of the DNA. The condensed chromatin fractions (180-150 S) from inhibited cells resemble encapsidation intermediates and their DNA has a linking number as the DNA extracted from purified virions. Moreover, the virion DNA has a higher superhelical density compared to intracellular chromatin isolated from untreated cells and argues for a supercoiling activity in the cell.
Involvement Of Capsaicin-Sensitive Mechanism(S) In The Antiulcer Defence Of Intestinal Mucosa In Rats (1987)

Capsaicin desensitization increases degree and incidence of indomethacin-induced intestinal ulcers in rats, suggesting the existence of a capsaicin-sensitive mechanism(s) in the protection of the intestinal mucosa against indomethacin-induced ulceration. Sensory innervation thus may be involved in the pathogenesis of ulcers of the small bowel, as well as in gastric ulcers. Administration of exogenous CGRP and somatostatin, sensory neuropeptides which are depleted by capsaicin desensitization, does not afford protection toward the capsaicin-induced aggravation of intestinal ulcers. The protective effect of exogenous prostaglandins toward indomethacin-induced intestinal ulceration is not mediated by capsaicin-sensitive nerve fibers.
DNA‐ and Field‐Mediated Assembly of Magnetic Nanoparticles into High‐Aspect Ratio Crystals (2019)

Under an applied magnetic field, superparamagnetic Fe<sub>3</sub> O<sub>4</sub> nanoparticles with complementary DNA strands assemble into crystalline, pseudo-1D elongated superlattice structures. The assembly process is driven through a combination of DNA hybridization and particle dipolar coupling, a property dependent on particle composition, size, and interparticle distance. The DNA controls interparticle distance and crystal symmetry, while the magnetic field leads to anisotropic crystal growth. Increasing the dipole interaction between particles by increasing particle size or external field strength leads to a preference for a particular crystal morphology (e.g., rhombic dodecahedra, stacked clusters, and smooth rods). Molecular dynamics simulations show that an understanding of both DNA hybridization energetic and magnetic interactions is required to predict the resulting crystal morphology. Taken together, the data show that applied magnetic fields with magnetic nanoparticles can be deliberately used to access nanostructures beyond what is possible with DNA hybridization alone.
Structural, transport and microwave properties of 123/sapphire films: Thickness effect (1995)

The effect of thickness and growth conditions on the structure and microwave properties has been investigated for the 123/sapphire films. It has been shown that in the conditions of epitaxial growth the Al atoms do not diffuse from substrate into the film and the films with thickness up to 100 nm exhibit the excellent direct current (DC) properties. The increase of thickness of GdBaCuO films causes the formation of extended line-mesh defects and the increase of the surface resistance (R(sub S)). The low value of surface resistance R(sub S)(75 GHz, 77K) = 20 mOhm has been obtained for the two layer YBaCuO/CdBaCuO/sapphire films.
Sample Preparation and Data Collection for High-Speed Fixed-Target Serial Femtosecond Crystallography (2017)

We have developed a protocol for high-speed xed-target serial femtosecond crystallography \(SFX) at Xray free electron lasers \(XFELs). Using the Roadrunner goniometer for fast scanning of microcrystals loaded on a micro-patterned silicon chip, our method allows for usage of the full 120 Hz repetition rate of the Linear Coherent Light Source \(LCLS). By synchronizing the sample exchange to the arrival of the LCLS X-ray pulses our approach results in most e cient use of sample material and beamtime. The presented protocol describes the loading of microcrystals on micro-patterned silicon chips and subsequent data collection using the Roadrunner goniometer installed at an XFEL beamline. Data collection can be performed either at cryogenic or room temperature. We further describe the Roadrunner control and data acquisition software and data processing using cppxfel. Due to the small sample amounts required and the low background scattering levels achievable, the method is ideally suited for data collection of precious microcrystals from viruses or membrane proteins, where often only limited amounts are available.
Nitrogenated graphene and carbon nanomaterials by carbonization of polyfurfuryl alcohol in the presence of urea and dicyandiamide (2014)

Nitrogenated multilayer graphene is prepared from renewable feedstocks in a cost-efficient route to meet the emerging demand for graphene-based materials.
Bayesian mapping with probabilistic cubic splines (2010)

This proposal presents the integration of interpolating global cubic splines into a general function regression framework to approximate curved functions or more dimensional curves based on noisy observations. We rearrange the iterative process of spline parameter calculation and obtain a practical linear matrix formulation. Then we employ Bayesian techniques to estimate spline model parameters and to perform model selection. While the number of basis functions is equal to the number of spline supporting points, this regularizer is automatically adapted towards an optimal trade-off between model complexity and model predicting performance, when Bayesian model selection is performed. Finally, we apply the proposed method within a robotic mapping scenario and learn geometric shapes of roads from noisy GPS positions measurements.
Isonitriles et réactions multicomposants (2010)

Les isonitriles sont des isomères de nitriles possédant un carbone terminal divalent. Découverts il y a plus de 150 ans, ces composés ne sont réellement exploités que depuis quelques décennies. Leur stabilité, leur facilité d'accès et la variété de leurs réactivités chimiques uniques en font un outil incontournable pour la chimie moderne. En effet, utilisés lors de réactions multicomposants, ils permettent de réaliser des économies d'atomes et d'étapes. Ce principe de modération faisant justement partie des objectifs actuels de la chimie organique respectueuse de l'environnement (la chimie verte), les isonitriles s'avèrent particulièrement intéressants. Cet article présente les différentes méthodes de synthèse d'isonitriles, ainsi que leur réactivité générale. Les principales réactions multicomposants dans lesquelles ils interviennent sont également détaillées.
2D Spectrally Encoded Confocal Microscopy and its Application for Simultaneous Imaging and Laser Surgery with a Single Fiber Probe (2009)

We demonstrate an endoscope-compatible, mechanical-scan-free microscopy technique and its application as a highly flexible fiber probe which can simultaneously perform imaging and high precision in-situ laser microsurgery.
Dynamic Multi-Goal Motion Planning with Range Constraints for Autonomous Underwater Vehicles Following Surface Vehicles (2021)

Autonomous underwater vehicles (AUVs) are often required to reach multiple goal locations while staying within the communication range of a surface vehicle. The goals, which could be dispersed throughout the environment, are dynamically discovered by the surface vehicle as it moves along a predefined trajectory. As the goals are discovered, they are communicated to the AUV. This paper develops an efficient multi-layered planner that generates collision-free and dynamically-feasible trajectories that enable the AUV to reach as many goals as possible while always staying within the communication range of the surface vehicle. The planner relies on a roadmap to capture the connectivity of the environment in order to facilitate navigation. The high-level layer is based on discrete search to find paths over the roadmap that increase the sum of the rewards to the known goals while maintaining the range constraints. The low-level layer relies on sampling-based motion planning to expand a tree of feasible motions along paths computed by the discrete layer. These layers interact with each other to update the planned motions as new goals are dynamically discovered. Experiments using 3D environments, second-order AUV models, and an increasing number of goals, demonstrate the efficiency of the planner to solve dynamic multi-goal motion-planning problems with range constraints.
Identifying Topological Prototypes using Deep Point Cloud Autoencoder Networks (2019)

Data mining of engineering designs generated by topology optimization methods is a challenging task. A topology optimization method maximizes one or more performance objectives by redistributing the material in a design space for a given set of boundary conditions and constraints. The performance objective could be stiffness and the constraint could be the allowed mass fraction in the design space. If the constraints are not too restrictive or unknown at the initial stages of the design process, multiple feasible designs are possible and are generally generated to inspire new design ideas. Since a designer cannot manually review all the designs, one needs to select a few representative and interesting topologies based on performance or geometric features. In this paper, we propose a method to group designs with similar geometric features which are extracted from a point cloud representation of the geometry using a deep autoencoder network. The point cloud representation is generated by sampling points on the surface of geometry. The extracted features - called latent code - can be used to cluster topologies and identify prototypes in each cluster. The proposed method could be used on designs generated by topology optimization and other design generation methods. To evaluate the method, we use it on complex truss-like topology datasets with prespecified design types which have been recognized by the proposed method with high precision and recall. Also, the prototypes of the different categories are identified.
Supplemental Figure S1 from Guidance Molecule SEMA3A Restricts Tumor Growth by Differentially Regulating the Proliferation of Tumor-Associated Macrophages (2023)

&lt;p&gt;SEMA3A DOES NOT AFFECT TUMOR CELL METABOLISM.&lt;/p&gt;
mRNA expression levels of E2F transcription factors correlate with dihydrofolate reductase, reduced folate carrier, and thymidylate synthase mRNA expression in osteosarcoma. (2003)

Previous studies have shown that decreased expression of the reduced folate carrier (RFC) and increased expression of dihydrofolate reductase (DHFR) are associated with intrinsic and acquired methotrexate resistance, respectively, in osteosarcoma (OS). It has also been shown in colorectal cancer that E2F-1 expression correlates with thymidylate synthase (TS) and, to a lesser extent, DHFR expression. To begin to investigate the regulation of DHFR and RFC expression in OS samples, mRNA expression of E2F-1 and E2F-4 were measured in OS tumor samples and related to DHFR, RFC, and TS mRNA expression. Using fluorescent quantitative real-time PCR, 112 human OS patient samples were investigated for potential E2F-1/E2F-4:DHFR, E2F-1/E2F-4:RFC, and E2F-1/E2F-4:TS correlations. The expression ranges for each gene are as follows: DHFR, 0.02-33.13 (median = 0.20); RFC, 0.02-229.13 (median = 1.91); TS, 0.01-9.99 (median = 0.15); E2F-1, 0.05-69.07 (median = 0.52); and E2F-4, 0.24-52.35 (median = 1.45). Spearman correlation coefficients (r(s)) for E2F-1:DHFR, E2F-1:RFC, E2F-1:TS, E2F-4:DHFR, E2F-4:RFC, and E2F-4:TS were calculated to be 0.53, 0.63, 0.60, 0.41, 0.58, and 0.33, respectively (P < 0.001). On the basis of this data, moderate correlations exist between E2F-1/E2F-4 and DHFR, RFC, and TS. These results suggest E2F-1/E2F-4 may play a role in the regulation of RFC expression, which has not been reported previously. The E2F transcription factors are also related to DHFR and TS expression in OS samples, suggesting a possible involvement in methotrexate resistance. Although E2F mRNA levels correlate with DHFR, RFC, and TS mRNA expression, additional experiments are necessary to determine the direct effects of these transcription factors and identify other proteins that may influence this relationship.