gebhart/patrepeval huggingface dataset:
SPAD chlorophyll levels in canola genotypes under field conditions. (2015)

&lt;p&gt;&lt;b&gt;A&lt;/b&gt;. Decrease in chlorophyll level in transgenic (6.6.38, 6.6.40 and 7.1.38), null control (6.2 and 7.6) and WT during ripening period; onset of flowering (150 DAP) till near to maturity (178 DAP). &lt;b&gt;B&lt;/b&gt;. Chlorophyll level in genotypes at 178 days after sowing. Data is mean ± SD. Bars with different letters indicate significant difference at P&lt;0.05. NC, null control; T, transgenic, WT, wild type.&lt;/p&gt;
Supplementary Figure 1 from Oncolytic Vaccinia Virus Disrupts Tumor-Associated Vasculature in Humans (2023)

&lt;p&gt;Supplementary Figure 1 PDF file - 74K, VEGF- and FGF-2 stimulate vaccinia replication&lt;/p&gt;
Abstract 3156: Meta-analysis of lung cancer single-cell RNA data reveals novel gene modules associated with lineage, stage, and genetic alterations (2023)

Abstract Objective: Combinations of somatic alterations, epigenetic changes, and interactions with cells in the tumor microenvironment can induce gene expression changes in cancer cells. Single-cell RNA-seq can provide valuable insights into the heterogeneity of cancer cells within and across tumor samples. We performed a meta-analysis of single-cell RNA-seq (scRNA-seq) datasets containing primary tumor samples from patients with non-small-cell-lung cancer (NSCLC) to characterize modules of co-expressed genes and determine associations with histological, genetic, and immune features. Methods: scRNA-seq data of 116,260 cells from 127 NSCLC samples including lung adenocarcinomas (LUADs) and lung squamous cell carcinomas (LUSCs) were collected and merged from 12 datasets. Cancer cells were identified by inferring copy number variations (CNVs). Celda was used to identify 163 gene co-expression modules across cancer cells. MAST was used to assess association of each module with histology, stage, and study. CaDrA was used to identify combinations of genomic features associated with gene modules projected into TCGA bulk RNA-seq. Result: Broad biological category of modules included those related to lineage, cell cycle and proliferation, extracellular matrix production (ECM), epithelial-to-mesenchymal transition (EMT), antigen presentation, xenobiotic metabolism, stress response, chemokine signaling, interferon signaling, housekeeping, and other general cellular processes. The modules most strongly associated with study-specific effects were enriched in housekeeping and ribosomal genes. Several ECM and cell-cycling modules were induced in advanced LUADs while MHC class II modules were reduced in late stage disease. Several modules containing different surfactant proteins or secretoglobins were identified and displayed heterogeneity within and across early-stage LUADs. Three modules in LUSCs were enriched for detoxification enzymes and associated with somatic mutations in different members of the Nrf2 pathway. A module of genes involved in keratinization displayed intra- and inter-tumoral heterogeneity across LUSCs and was associated with neutrophil infiltration scores in samples from TCGA. Conclusion: We employed a novel meta-analysis approach to study gene co-expression patterns that are active in lung cancer cells profiled with single-cell RNA-seq. Characterization of these modules revealed the biological processes and cancer hallmarks active within and across lung tumors. Citation Format: Rui Hong, Sarah Mazzilli, Stefano Monti, Avrum Spira, Joshua D. Campbell. Meta-analysis of lung cancer single-cell RNA data reveals novel gene modules associated with lineage, stage, and genetic alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3156.
Dictionary learning-based reverberation removal enables depth-resolved photoacoustic microscopy of cortical microvasculature in the mouse brain (2018)

Photoacoustic microscopy (PAM) capitalizes on the optical absorption of blood hemoglobin to enable label-free high-contrast imaging of the cerebral microvasculature in vivo. Although time-resolved ultrasonic detection equips PAM with depth-sectioning capability, most of the data at depths are often obscured by acoustic reverberant artifacts from superficial cortical layers and thus unusable. In this paper, we present a first-of-a-kind dictionary learning algorithm to remove the reverberant signal while preserving underlying microvascular anatomy. This algorithm was validated in vitro, using dyed beads embedded in an optically transparent polydimethylsiloxane phantom. Subsequently, we demonstrated in the live mouse brain that the algorithm can suppress reverberant artifacts by 21.0 ± 5.4 dB, enabling depth-resolved PAM up to 500 µm from the brain surface.
Auger recombination in long-wave infrared InAs/InAsSb type-II superlattices (2015)

The Auger lifetime is a critical intrinsic parameter for infrared photodetectors as it determines the longest potential minority carrier lifetime and consequently the fundamental limitations to their performance. Here, Auger recombination is characterized in a long-wave infrared InAs/InAsSb type-II superlattice. Auger coefficients as small as 7.1×10−26 cm6/s are experimentally measured using carrier lifetime data at temperatures in the range of 20 K–80 K. The data are compared to Auger-1 coefficients predicted using a 14-band K·p electronic structure model and to coefficients calculated for HgCdTe of the same bandgap. The experimental superlattice Auger coefficients are found to be an order-of-magnitude smaller than HgCdTe.
MASH Test 3-11 on the Texas T101 Bridge Rail (2011)

Cyclic peptoids are macrocyclic oligomers of N-substituted glycines with specific folding abilities and excellent metal binding properties. In this work, we show how strategic positioning of chiral (<i>S</i>)- and (<i>R</i>)-(1-carboxyethyl)glycine units influences the conformational stability of water-soluble macrocyclic peptoids as sodium complexes. The reported results are based on nuclear magnetic resonance spectroscopy, extensive computational studies, and X-ray diffraction analysis using single crystals grown from aqueous solutions. The studies include <sup>1</sup>H relaxometric investigations of hexameric cyclic peptoids in the presence of the Gd<sup>3+</sup> ion to assess their thermodynamic stabilities and relaxivities.
Precision medicine in pediatric oncology: Lessons learned and next steps (2016)

The maturation of genomic technologies has enabled new discoveries in disease pathogenesis as well as new approaches to patient care. In pediatric oncology, patients may now receive individualized genomic analysis to identify molecular aberrations of relevance for diagnosis and/or treatment. In this context, several recent clinical studies have begun to explore the feasibility and utility of genomics-driven precision medicine. Here, we review the major developments in this field, discuss current limitations, and explore aspects of the clinical implementation of precision medicine, which lack consensus. Lastly, we discuss ongoing scientific efforts in this arena, which may yield future clinical applications.
Metabolomics-Driven Identification of the Rate-Limiting Steps in 1-Propanol Production (2022)

The concerted effort for bioproduction of higher alcohols and other commodity chemicals has yielded a consortium of metabolic engineering techniques to identify targets to enhance performance of engineered microbial strains. Here, we demonstrate the use of metabolomics as a tool to systematically identify targets for improved production phenotypes in <i>Escherichia coli</i>. Gas chromatography/mass spectrometry (GC/MS) and ion-pair LC-MS/MS were performed to investigate metabolic perturbations in various 1-propanol producing strains. Two initial strains were compared that differ in the expression of the citramalate and threonine pathways, which hold a synergistic relationship to maximize production yields. While this results in increased productivity, no change in titer was observed when the threonine pathway was overexpressed beyond native levels. Metabolomics revealed accumulation of upstream byproducts, norvaline and 2-aminobutyrate, both of which are derived from 2-ketobutyrate (2KB). Eliminating the competing pathway by gene knockouts or improving flux through overexpression of glycolysis gene effectively increased the intracellular 2KB pool. However, the increase in 2KB intracellular concentration yielded decreased production titers, indicating toxicity caused by 2KB and an insufficient turnover rate of 2KB to 1-propanol. Optimization of alcohol dehydrogenase YqhD activity using an ribosome binding site (RBS) library improved 1-propanol titer (g/L) and yield (g/g of glucose) by 38 and 29% in 72 h compared to the base strain, respectively. This study demonstrates the use of metabolomics as a powerful tool to aid systematic strain improvement for metabolically engineered organisms.
Detection and Discrimination of Formaldehyde with CuO/SnO2 dual layers MOS Gas Sensors Operated with a Pulsed Temperature Modulation (2020)

International audience
Enzyme-mediated depletion of serum l -Met abrogates prostate cancer growth via multiple mechanisms without evidence of systemic toxicity (2020)

Extensive studies in prostate cancer and other malignancies have revealed that l-methionine (l-Met) and its metabolites play a critical role in tumorigenesis. Preclinical and clinical studies have demonstrated that systemic restriction of serum l-Met, either via partial dietary restriction or with bacterial l-Met-degrading enzymes exerts potent antitumor effects. However, administration of bacterial l-Met-degrading enzymes has not proven practical for human therapy because of problems with immunogenicity. As the human genome does not encode l-Met-degrading enzymes, we engineered the human cystathionine-γ-lyase (hMGL-4.0) to catalyze the selective degradation of l-Met. At therapeutically relevant dosing, hMGL-4.0 reduces serum l-Met levels to >75% for >72 h and significantly inhibits the growth of multiple prostate cancer allografts/xenografts without weight loss or toxicity. We demonstrate that in vitro, hMGL-4.0 causes tumor cell death, associated with increased reactive oxygen species, S-adenosyl-methionine depletion, global hypomethylation, induction of autophagy, and robust poly(ADP-ribose) polymerase (PARP) cleavage indicative of DNA damage and apoptosis.
Diseased Science (2014)

We have recently observed a widespread affliction of scientists known as impact factor mania (1), also referred to as impactis (2), for which there appears to be no cure. This has led us to consider whether additional unrecognized medical conditions may be unique or overrepresented among scientists.
Table S1, Table S3, Figures S1-S8 from Characterization of the Selective Indoleamine 2,3-Dioxygenase-1 (IDO1) Catalytic Inhibitor EOS200271/PF-06840003 Supports IDO1 as a Critical Resistance Mechanism to PD-(L)1 Blockade Therapy (2023)

&lt;p&gt;Table S1 shows the plasma protein binding and blood to plasma ratio in mouse, rat, dog and human. Table S3 shows the plasma concentrations following a single oral dose of PF-06840003. Figure S1 shows that PF-06840003 does not impact cell viability. Figure S2 shows that PF-06840003 rescues T-cell proliferation in a co-culture assay. Figure S3 shows tumor growth inhibition of CT26 tumors at different dose levels. Figure S4 shows that IDO1 inhibitor mediated tumor growth inhibition depends on CD8+ T cells. Figure S5 shows a combination benefit with anti-PD-L1 treatment in CT26 tumors. Figure S6 shows IDO1i mediated tumor growth inhibition of MDA-MB-231 breast tumors in humanized mice. Figure S7 shows that PF-06840003 improves the TGI of avelumab in a humanized mouse breast tumor model. Figure S8 shows the fractions of CT26 tumor immune infiltrating cells.&lt;/p&gt;
Effect of experimental immunization of pigs with a suspension of Yersinia enterocolitica selected strains on changes in serum immunoglobulin G levels (2012)

The major reservoir of Yersinia enterocolitica and the main source of risk posed to human health are pigs. The objective of this study was to develop a method for pigs immunization with a suspension of immunogenic strains of Y. enterocolitica and to analyze the impact of this immunization on the course of immunological processes in animals, and thus to search for possibilities of preventing or reducing potentially negative effects of Y. enterocolitica experimental infections in pigs.
Vibrational and Electronic Spectroscopy of a Donor−Acceptor Substituted Distyrylbenzene and Its Covalent Dimers (2004)

Absorption spectra, resonance Raman spectra and depolarization ratios, fluorescence spectra and emission polarizations, and simulations of the resonance Raman excitation profiles and absorption spectra are reported for a donor−acceptor substituted distyrylbenzene (DADSB) and two covalent “dimers” formed by joining two DADSB chains at their center phenyl ring through a paracyclophane moiety. Semiempirical and density-functional theory calculations of the ground-state geometries and ZINDO calculations of the electronic excitations are also reported. Both the spectroscopic results and the electronic structure calculations agree that the electronic states of these “dimers” are not adequately described by excitonic coupling between the nominally degenerate electronic transitions localized on each DADSB moiety. The resonance Raman spectra of both dimers are essentially identical but show additional lines and intensity differences relative to the monomer. The excitation profiles of all three molecules exhibit interference effects between the Raman amplitudes for the first two strongly allowed electronic transitions. All three molecules exhibit Raman depolarization ratios of 1/3 throughout the lowest-energy absorption band, but the fluorescence of both dimers immobilized in polymer matrixes is considerably depolarized relative to that of the monomer. This suggests that the electronic excitation, initially delocalized over both conjugated chains of the dimers, may become localized on a single chain as geometric relaxation and solvent reorganization occur.
F4‐06‐03: INSIGHTS FROM NEUROPATHOLOGY AND MODULATION OF INNATE IMMUNITY AS A THERAPEUTIC APPROACH FOR ALZHEIMER'S DISEASE (2018)

Diverse pathways produce imbalances of amyloid beta (Aβ) clearance/production as a trigger for AD, with pathogenic forms of the tau protein being an “executioner”, giving rise to key disease symptoms. A critical aspect of these abnormalities is immune dysregulation. Neuropathological examination of AD and AD model tissue is essential in gaining a better understanding of the pathogenesis of AD and developing effective therapeutic interventions. To better understand the heterogeneity of AD pathogenesis we have developed a method that allows localized proteomics on individual cell populations isolated from formalin fixed paraffin embedded tissue sections using laser capture microdissection and LC-MS/MS. We have applied this powerful new technique to compare rapidly progressive AD (rpAD) versus sporadic slowly progressive AD (spAD). We performed the most comprehensive analysis of amyloid plaque associated proteins to date, identifying numerous novel amyloid associated proteins. Importantly, we have shown for the first time that not all amyloid plaques contain the same proteins, suggesting that there may be different subtypes of plaques, which in turn could help to clarify the heterogeneity in AD pathogenesis and better target therapeutic approaches. Given the diversity of the pathogenesis of AD we have developed a number of non-mutually exclusive therapeutic approaches including blocking the interaction between Aβ and apolipoprotein E, using peptoids; use of active and passive immunization that is directed against the shared pathological conformation of Aβ and tau oligomers concurrently, as well as the stimulation of innate immunity with TLR9 agonist CpG oligodeoxynucleotides. Our results show that these diverse, non-mutually exclusive approaches are efficacious in several different transgenic AD models as well as in a non-human primate model of AD, squirrel monkeys. Our localized proteomic strategy provides new insights into the heterogeneous underpinnings of AD neuropathology, allowing for the development of a number of non-mutually exclusive therapeutic approaches that address immune dysregulation in AD.
X-ray absorption spectroscopy to probe surface composition and surface deprotection in photoresist films. (2004)

Near-edge X-ray absorption fine structure spectroscopy (NEXAFS) is utilized to provide insight into surface chemical effects in model photoresist films. First, NEXAFS was used to examine the resist/air interface including surface segregation of a photoacid generator (PAG) and the extent of surface deprotection in the film. The concentration of PAG at the resist-air interface was higher than the bulk concentration, which led to a faster deprotection rate at that interface. Second, a NEXAFS depth profiling technique was utilized to probe for compositional gradients in model resist line edge regions. In the model line edge region, the surface composition profile for the developed line edge was dependent on the post exposure bake time.
Champs électromagnétiques exaltés à la surface de films métalliques semi-continus (2000)

La localisation des excitations optiques dans des films semi-metalliques aleatoires est observee, a l'aide d'un microscope optique en champ proche, dans des domaines sub-longueur d'onde. Cet effet est attribue a la localisation d'Anderson des modes plasmons de surface dans ces films. Les fluctuations geantes du champ local sont tres superieures au champ applique et sont concentrees spatialement dans des domaines dont la taille typique est celle des grains metalliques (-30 nm). Le spectre optique de champ proche (700 nm< λ < 800 nm), constitue de pics de resonance, est detecte et observe experimentalement. Il depend fortement de la zone du film etudiee.
Supramolecular Aggregation of Hexameric Water Clusters into a 2D Water Polymer Containing (H2O)18 Holes (2006)

We report herein a novel infinite two-dimensional water morphology, found in a metallo-organic host, made up of discrete cyclic water hexamers and which contains large circular holes defined by 18 molecules of water.
Vimentin: A Novel Chemopreventive Target for Breast Cancer Metastasis. (2009)

Abstract Background: Cancer metastasis is the major cause of death in nearly all tumor types; however, most treatments target the primary tumor and not the highly invasive metastatic cells. We propose to prevent cancer metastasis by precisely targeting the cancer invasion machinery. To do this we disrupt a novel target-the vimentin cytoskeleton. Vimentin is overexpressed in nearly all invasive solid tumors and is critical for cell migration. Here we show that Withania sominifera root extracts (WRE) and one of its primary constituent, Withaferin A (WFA), targets vimentin to inhibit cancer cell motility and migration while having negligible effects on viability. WFA is a steroidal natural product with 4-rings (A-D) connected to a lactone ring. We test the hypothesis that WFA is an anti-invasive compound that disrupts vimentin function with limited toxicity.Material and Methods: We employ cutting-edge live cell confocal imaging studies in combination with traditional molecular biology techniques to dissect the precise mechanism of how WRE or WFA inhibits cancer cell migration and invasion. We have employed a wounding model and Matrigel invasion assay to determine the anti-migratory and anti-invasive properties of WRE and WFA using MDAMB-231 cells. We have used GFP-vimentin to visualize the changes in vimentin dynamics. Effect of WRE and WFA on cell cycle was analyzed by Flow cytometry.Results: Our results show WFA has weak anti-proliferative activity at low concentrations but potently inhibits breast cancer migration and invasion in a dose-dependent manner. High resolution confocal images reveal that in WFA-treated cells, vimentin fails to invade the lamellipodia resulting in decreased cell migration. This is supported by live cell confocal imaging showing that at high doses WFA treatment depolymerizes GFP: vimentin. Furthermore, treatment with WFA results in aberrant vimentin phosphorylation, likely resulting in a net depolymerized phenotype. In order to determine if the vimentin-binding A ring of WFA is critical for its anti-invasive efficacy, we synthesized and tested A-ring modified analogs of WFA. All three analogs showed severely reduced potency in inhibiting cancer cell migration and invasion, suggesting that the A ring is critical for its anti-invasive activity.Discussion: The present study shows that WRE or WFA inhibits breast cancer cell migration at nanomolar concentrations by disrupting vimentin at concentrations that have minimal effect on proliferation. We believe its strong anti-migratory activity make this an appropriate compound as an anti-metastatic chemopreventative. Ultimately, we envision WFA can be used as a vimentin-targeting chemopreventative in high-risk metastatic patients and has the potential to be used with traditional cytotoxics. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5063.
In vivo wireless channel modeling (2016)

In this chapter, the state of the art of in vivo wireless channel characterization has been presented. Various studies described in the literature are dedicated to the in vivo communication channel, and they consider different parameters in studying various anatomical regions. Furthermore, the location-dependent characteristics of in vivo wireless communication at 915 MHz are analyzed in detail via numerical and experimental investigations. A complete model for the in vivo channel is not available and remains an open research problem. However, considering the expected future growth of implanted technologies and their potential use for the detection and diagnosis of various health-related issues in the human body, the channel modeling studies should be further extended to develop better and more efficient communications systems for future in vivo systems.
A Simple LC–MS Method for the Quantitation of Alkaloids in Endophyte-Infected Perennial Ryegrass (2019)

The rapid identification and quantitation of alkaloids produced by <i>Epichloë</i> endophyte-infected pasture grass is important for the agricultural industry. Beneficial alkaloids, such as peramine, provide the grass with enhanced insect protection. Conversely, ergovaline and lolitrem B can negatively impact livestock. Currently, a single validated method to measure these combined alkaloids in planta does not exist. Here, a simple two-step extraction method was developed for <i>Epichloë</i>-infected perennial ryegrass (<i>Lolium perenne</i> L.). Peramine, ergovaline and lolitrem B were quantified using liquid chromatography-mass spectrometry (LC-MS). Alkaloid linearity, limit of detection (LOD), limit of quantitation (LOQ), accuracy, precision, selectivity, recovery, matrix effect and robustness were all established. The validated method was applied to eight different ryegrass-endophyte symbiota. Robustness was established by comparing quantitation results across two additional instruments; a triple quadruple mass spectrometer (QQQ MS) and by fluorescence detection (FLD). Quantitation results were similar across all three instruments, indicating good reproducibility. LOQ values ranged from 0.8 ng/mL to 6 ng/mL, approximately one hundred times lower than those established by previous work using FLD (for ergovaline and lolitrem B), and LC-MS (for peramine). This work provides the first highly sensitive quantitative LC-MS method for the accurate and reproducible quantitation of important endophyte-derived alkaloids.