gebhart/patrepeval huggingface dataset:
Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome (2021)

Paenibacillus species are Gram-positive bacteria that have been isolated from a diverse array of plant species and soils, with some species exhibiting plant growth-promoting (PGP) activities. Here we report two strains (S02 and S25) of a novel Paenibacillus sp. that were isolated from perennial ryegrass (Lolium perenne) seeds. Comparative genomics analyses showed this novel species was closely related to P. polymyxa. Genomic analyses revealed that strains S02 and S25 possess PGP genes associated with biological nitrogen fixation, phosphate solubilisation and assimilation, as well as auxin production and transportation. Moreover, secondary metabolite gene cluster analyses identified 13 clusters that are shared by both strains and three clusters unique to S25. In vitro assays demonstrated strong bioprotection activity against phytopathogens (Colletotrichum graminicola and Fusarium verticillioides), particularly for strain S02. A transcriptomics analysis evaluating nitrogen fixation activity showed both strains carry an expressed nif operon, but strain S02 was more active than strain S25 in nitrogen-free media. Another transcriptomics analysis evaluating the interaction of strains with F. verticillioides showed strain S02 had increased expression of core genes of secondary metabolite clusters (fusaricidin, paenilan, tridecaptin and polymyxin) when F. verticillioides was present and absent, compared to S25. Such bioactivities make strain S02 a promising candidate to be developed as a combined biofertiliser/bioprotectant.
Regional Entrainment of Atrial Fibrillation in Man (1996)

Regional entrainment of chronic atrial fibrillation is feasible in humans.
Diazatruxenes from the Condensation Reaction of Indoles with Ninhydrin (2016)

The reaction of indoles with ninhydrin has been reported to provide only 1:1 condensation products (cf. A or 8 ) that show good antioxidant and anti‐inflammatory activity. In the present work, our synthetic challenge for the synthesis of innovative, highly substituted tetra‐indole indanes of type 1 via a 4:1 condensation reaction in acetic acid gave two unexpected new products, the diazatruxene derivatives 3 and 4 . The novel structures have been characterized by their analytical and spectral data including 1D‐ and 2D‐NMR. With 5‐chloroindole, only the known 1:1 reaction.
A Model Based Approach for Efficient Segmentation of Knee Cartilage From MR Image Data (2001)

Abstract A novel algorithm was developed to facilitate segmentation of the articular cartilage of the knee from magnetic resonance (MR) image data. The new approach uses a model of the bone and cartilage elements of the knee as a template. The operator initializes the template by aligning certain bony anatomic landmarks. The inner cartilage surface (ICS) is determined through a standard seed growing segmentation approach; the bone elements of the template are then fit to the ICS through an elastic registration technique. The deformation fields thus obtained are subsequently applied to the appropriate cartilage templates. The deformed templates and ICS normals, in conjunction with a gaussian probability distribution function and the subject image data, are used to produce the final estimate of the cartilage surfaces.
Collision Avoidance for Dynamic Obstacles with Uncertain Predictions using Model Predictive Control (2022)

We propose a Model Predictive Control (MPC) for collision avoidance between an autonomous agent and dynamic obstacles with uncertain predictions. The collision avoidance constraints are imposed by enforcing positive distance between convex sets representing the agent and the obstacles, and tractably reformulating them using Lagrange duality. This approach allows for smooth collision avoidance constraints even for polytopes, which otherwise require mixed-integer or non-smooth constraints. We consider three widely used descriptions of the uncertain obstacle position: 1) Arbitrary distribution with polytopic support, 2) Gaussian distributions and 3) Arbitrary distribution with first two moments known. For each case we obtain deterministic reformulations of the collision avoidance constraints. The proposed MPC formulation optimizes over feedback policies to reduce conservatism in satisfying the collision avoidance constraints. The proposed approach is validated using simulations of traffic intersections in CARLA.
Dendritic Cells in Innate Immune Responses Against HIV (2002)

Dendritic cells (DCs) were recently found to be innate immunity effectors against tumoral cells and viruses. (i) In response to most viruses, including HIV, plasmacytoid DCs are responsible for most of the type I IFN secretion, which is strongly anti-viral and induces TH1 type responses. Myeloid DCs secrete IL-12, which is also important for TH1-type and cytotoxic responses. In HIV patient blood, both DC population numbers decrease as early as the primary stage. Plasmacytoid DC numbers correlate with type I IFN secretion, which is a prognosis predictor, particularly under treatment. IL-12 secretion is also defective. Immunotherapies to replace the defective cytokines or to restore a potentially defective DC-T lymphocyte feed-back might help patients restore their immune responses under antiviral therapy. (ii) After measles and other viral infections, or incubation with dsRNA, DCs become cytotoxic and consequently exhibit natural killer function, through upregulation of type I IFN secretion which enhances TRAIL expression. In HIV infection, this mechanism was not demonstrated yet, but it might a) be responsible for the massive apoptosis of uninfected lymphocytes, and b) increase specific immunity through cross-presentation of antigens from infected cells killed by DCs. (iii) DCs direct expansion and effector functions of NK cells in the absence of adaptive-type cytokines and modulate NKT cell IFN-gamma production. Reciprocally, NK activation triggers DC maturation. HIV-1 Tat inhibits NK cell cytotoxicity directly and probably through inhibition of IL-12 secretion by DC. Therefore, understanding the functions of DCs in innate immune responses and in pathogenesis will help obtain better HIV replication control.
Aqueous Extract ofPaeonia lactifloraand Paeoniflorin as Aggregation Reducers Targeting Chaperones in Cell Models of Spinocerebellar Ataxia 3 (2013)

Spinocerebellar ataxia (SCA) types 1, 2, 3, 6, 7, and 17 as well as Huntington's disease are a group of neurodegenerative disorders caused by expanded CAG repeats encoding a long polyglutamine (polyQ) tract in the respective proteins. Evidence has shown that the accumulation of intranuclear and cytoplasmic misfolded polyQ proteins leads to apoptosis and cell death. Thus suppression of aggregate formation is expected to inhibit a wide range of downstream pathogenic events in polyQ diseases. In this study, we established a high-throughput aggregation screening system using 293 ATXN3/Q75-GFP cells and applied this system to test the aqueous extract of Paeonia lactiflora (P. lactiflora) and its constituents. We found that the aggregation can be significantly prohibited by P. lactiflora and its active compound paeoniflorin. Meanwhile, P. lactiflora and paeoniflorin upregulated HSF1 and HSP70 chaperones in the same cell models. Both of them further reduced the aggregation in neuronal differentiated SH-SY5Y ATXN3/Q75-GFP cells. Our results demonstrate how P. lactiflora and paeoniflorin are likely to work on polyQ-aggregation reduction and provide insight into the possible working mechanism of P. lactiflora in SCA3. We anticipate our paper to be a starting point for screening more potential herbs for the treatment of SCA3 and other polyQ diseases.
Synthesis of Alkyne-Functionalized Helical Polycarbodiimides and their Ligation to Small Molecules using ‘Click’ and Sonogashira Reactions (2011)

New terminal alkyne side chain functionalized polycarbodiimides, have been synthesized and “alkyne” ligation tools—“click” (copper-catalyzed Huisgen 1,3-dipolar cycloaddition reaction) and Sonogashira couplings—were utilized to create functional polymers in one step postpolymerization modifications. Polycarbodiimides are interesting synthetic, helical, nanodimensional scaffolds that are capable of presenting a variety of functional groups in highly regular periodic fashion. Herein, we report the synthesis of the first alkyne substituted polycarbodiimides, Poly-1, Poly-2, and Poly-3 and the quantitative coupling of functional azides to the alkyne repeat units of these polymers, as evidenced by IR and 1H NMR and 13C NMR spectra. We are able to couple benzyl azide, carboxylic acid azide, and N-Boc amine azide by “click” and N-Boc-l-phenylalanine by Sonogashira reactions to the alkyne side chain of Poly 1 to provide Poly-1a, -1b, -1c and -1phe, respectively. Poly-1b and Poly-1c provide peptide-coupling sites and are precursors for synthetic helical polymer-peptide conjugates. This was demonstrated by coupling l-alanine methylester to Poly-1b with excellent conversion. Aliphatic-terminal alkyne functionalized polymer, Poly-2 with the flexible methylene linker to the backbone provides more degrees of steric freedom for the incorporated groups, fixes the groups closer to the chiral, helical backbone, and reduces the hydrophobic nature of the polymer. However, Poly-3 offers all of these advantages and with two clickable handles per repeat unit doubles the functional sites along the polymer backbone.
Supplementary Text from Growth of Triple-Negative Breast Cancer Cells Relies upon Coordinate Autocrine Expression of the Proinflammatory Cytokines IL-6 and IL-8 (2023)

&lt;p&gt;Supplementary Text - PDF file 109K, Supplementary Figure Legends&lt;/p&gt;
Supplementary Figure S3 from Preclinical Antitumor Efficacy of BAY 1129980—a Novel Auristatin-Based Anti-C4.4A (LYPD3) Antibody–Drug Conjugate for the Treatment of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Internalization of C4.4A-Ab.&lt;/p&gt;
The Mastomys Gastric Carcinoid: Aspects of Enterochromaff in-Like Cell Function (1994)

The mastomys rodent exhibits a genetic propensity to develop gastric carcinoid tumors. Utilizing acid inhibitory pharmacotherapy (histamine-2 receptor antagonists and proton pump inhibitors), we have demonstrated transformation from normal to neoplastic enterochromaffin-like (ECL) cells in a well-defined fashion over a period of 4 months. In addition, we have demonstrated inhibition of tumor growth with either somatostatin or histamine-1 receptor antagonists (terfenadine and cyproheptadine). In order to define the regulation of growth and secretion of transformed ECL cells, we developed an isolated pure ECL cell system. ECL cells secrete histamine in response to gastrinergic (gastrin), muscarinic (carbachol), and beta-adrenergic (isoproterenol) stimulation. Both cAMP and intracellular calcium-dependent mechanisms are involved in the process of histamine secretion.
Re-evaluation of physicochemical and NMR data of triol ginsenosides Re, Rf, Rg2, and 20-gluco-Rf from Panax ginseng roots (2014)

Ginseng roots were extracted with aqueous methanol, and extracts were suspended in water and extracted successively with ethyl acetate and n-butanol. Column chromatography using the n-butanol fraction yielded four purified triol ginseng saponins: the ginsenosides Re, Rf, Rg2, and 20-gluco-Rf. The physicochemical, spectroscopic, and chromatographic characteristics of the ginsenosides were measured and compared with reports from the literature. For spectroscopic analysis, two-dimensional nuclear magnetic resonance (NMR) methods such as (1)H-(1)H correlation spectroscopy, nuclear Overhauser effect spectroscopy, heteronuclear single quantum correlation, and heteronuclear multiple bond connectivity were employed to identify exact peak assignments. Some peak assignments for previously published (1)H- and (13)C-NMR spectra were found to be inaccurate. This study reports the complete NMR assignment of 20-gluco-Rf for the first time.
Forced arm use is superior to voluntary training for motor recovery and brain plasticity after cortical ischemia in rats (2014)

We show that physical training after photothrombotic stroke significantly and permanently improves functional recovery after stroke, and that forced arm training is clearly superior to voluntary running training. The behavioral outcomes seen correlate with patterns and extent of gene expression changes in all brain areas examined. We propose that physical training induces a fundamental change in plasticity-relevant gene expression in several brain regions that enables recovery processes. These results contribute to the debate on optimal rehabilitation strategies, and provide a valuable source of molecular entry points for future pharmacological enhancement of recovery.
Decreased Gray Matter Concentration in the Lateral Geniculate Nuclei in Human Amblyopes (2010)

These findings add further weight to the role of the LGN in the cortical deficits exhibited in human strabismic amblyopes.
γ9δ2 T-Cell Expansion and Phenotypic Profile Are Reflected in the CDR3δ Repertoire of Healthy Adults (2022)

γ9δ2T cells fill a distinct niche in human immunity due to the unique physiology of the phosphoantigen-reactive γ9δ2TCR. Here, we highlight reproducible TCRδ complementarity-determining region 3 (CDR3δ) repertoire patterns associated with γ9δ2T cell proliferation and phenotype, thus providing evidence for the role of the CDR3δ in modulating <i>in vivo</i> T-cell responses. Features that determine γ9δ2TCR binding affinity and reactivity to the phosphoantigen-induced ligand <i>in vitro</i> appear to similarly underpin <i>in vivo</i> clonotypic expansion and differentiation. Likewise, we identify a CDR3δ bias in the γ9δ2T cell natural killer receptor (NKR) landscape. While expression of the inhibitory receptor CD94/NKG2A is skewed toward cells bearing putative high-affinity TCRs, the activating receptor NKG2D is expressed independently of the phosphoantigen-sensing determinants, suggesting a higher net NKR activating signal in T cells with TCRs of low affinity. This study establishes consistent repertoire-phenotype associations and justifies stratification for the T-cell phenotype in future research on γ9δ2TCR repertoire dynamics.
Pulmonary Complication of Heroin Intoxication (1972)

An acute episode of heroin intoxication in a patient was complicated by aspiration of the gastric content and subsequent development of diffuse bronchiectasis. This clinical observation and certain experimental data in the literature suggest to us an etiologic role for aspiration in the development of necrotizing bronchitis and bronchiectasis and, perhaps, heroin pulmonary edema.
Recovery of microindents in a nickel–titanium shape-memory alloy: A “self-healing” effect (2002)

The thermally induced recovery of microscopic deformation in a nickel–titanium shape-memory alloy was examined. Surface deformation was simulated by indenting the alloy in the martensite phase at room temperature using both spherical and pyramidal indenters. We show that deformation in spherical microindents can be almost completely reversed by moderate heating. Partial recovery was observed for pyramidal impressions formed by a Vickers indenter and the recovery ratio was independent of the indentation depth. The observations were rationalized using the concept of representative strain and maximum stress under the spherical and pyramidal indenters.
Identification of Human GnIH Homologs, RFRP-1 and RFRP-3, and the Cognate Receptor, GPR147 in the Human Hypothalamic Pituitary Axis (2009)

The existence of a hypothalamic gonadotropin-inhibiting system has been elusive. A neuropeptide named gonadotropin-inhibitory hormone (GnIH, SIKPSAYLPLRF-NH(2)) which directly inhibits gonadotropin synthesis and release from the pituitary was recently identified in quail hypothalamus. Here we identify GnIH homologs in the human hypothalamus and characterize their distribution and biological activity. GnIH homologs were isolated from the human hypothalamus by immunoaffinity purification, and then identified as MPHSFANLPLRF-NH(2) (human RFRP-1) and VPNLPQRF-NH(2) (human RFRP-3) by mass spectrometry. Immunocytochemistry revealed GnIH-immunoreactive neuronal cell bodies in the dorsomedial region of the hypothalamus with axonal projections to GnRH neurons in the preoptic area as well as to the median eminence. RT-PCR and subsequent DNA sequencing of the PCR products identified human GnIH receptor (GPR147) mRNA expression in the hypothalamus as well as in the pituitary. In situ hybridization further identified the expression of GPR147 mRNA in luteinizing hormone producing cells (gonadotropes). Human RFRP-3 has recently been shown to be a potent inhibitor of gonadotropin secretion in cultured sheep pituitary cells by inhibiting Ca(2+) mobilization. It also directly modulates GnRH neuron firing. The identification of two forms of GnIH (RFRP-1 and RFRP-3) in the human hypothalamus which targets human GnRH neurons and gonadotropes and potently inhibit gonadotropin in sheep models provides a new paradigm for the regulation of hypothalamic-pituitary-gonadal axis in man and a novel means for manipulating reproductive functions.
Long-term Survival After Surgical Treatment of Renal Cell Carcinoma Metastasis Within the Pancreas. (2016)

The results of our analysis demonstrate promising long-term results with regard to disease-free and overall survival after surgical therapy for pancreatic metastases of renal cell carcinoma.
Toward acellular xenogeneic heart valve prostheses: Histological and biomechanical characterization of decellularized and enzymatically deglycosylated porcine pulmonary heart valve matrices (2020)

Abstract The use of decellularized xenogeneic heart valves might offer a solution to overcome the issue of human valve shortage. The aim of this study was to revise decellularization protocols in combination with enzymatic deglycosylation, in order to reduce the immunogenicity of porcine pulmonary heart valves, in means of cells, carbohydrates, and, primarily, Galα1‐3Gal (α‐Gal) epitope removal. In particular, the valves were decellularized with sodium dodecylsulfate/sodium deoxycholate (SDS/SD), Triton X‐100 + SDS (Tx + SDS), or Trypsin + Triton X‐100 (Tryp + Tx) followed by enzymatic digestion with PNGaseF, Endoglycosidase H, or O‐glycosidase combined with Neuraminidase. Results showed that decellularization alone reduced carbohydrate structures only to a limited extent, and it did not result in an α‐Gal free scaffold. Nevertheless, decellularization with Tryp + Tx represented the most effective decellularization protocol in means of carbohydrates reduction. Overall, carbohydrates and α‐Gal removal could strongly be improved by applying PNGaseF, in particular in combination with Tryp + Tx treatment, contrary to Endoglycosidase H and O‐glycosidase treatments. Furthermore, decellularization with PNGaseF did not affect biomechanical stability, in comparison with decellularization alone, as shown by burst pressure and uniaxial tensile tests. In conclusion, valves decellularized with Tryp + Tx and PNGaseF resulted in prostheses with potentially reduced immunogenicity and maintained mechanical stability.
Cholesterol-Rich Microdomains as Docking Platforms for Respiratory Syncytial Virus in Normal Human Bronchial Epithelial Cells (2011)

Respiratory syncytial virus (RSV) is one of the major causes of respiratory infections in children, and it is the main pathogen causing bronchiolitis in infants. The binding and entry mechanism by which RSV infects respiratory epithelial cells has not yet been determined. In this study, the earliest stages of RSV infection in normal human bronchial epithelial cells were probed by tracking virions with fluorescent lipophilic dyes in their membranes. Virions colocalized with cholesterol-containing plasma membrane microdomains, identified by their ability to bind cholera toxin subunit B. Consistent with an important role for cholesterol in RSV infection, cholesterol depletion profoundly inhibited RSV infection, while cholesterol repletion reversed this inhibition. Merger of the outer leaflets of the viral envelope and the cell membrane appeared to be triggered at these sites. Using small-molecule inhibitors, RSV infection was found to be sensitive to Pak1 inhibition, suggesting the requirement of a subsequent step of cytoskeletal reorganization that could involve plasma membrane rearrangements or endocytosis. It appears that RSV entry depends on its ability to dock to cholesterol-rich microdomains (lipid rafts) in the plasma membrane where hemifusion events begin, assisted by a Pak1-dependent process.
Inertial Manipulation and Transfer of Microparticles Across Laminar Fluid Streams (2012)

A general strategy for controlling particle movement across streams would enable new capabilities in single-cell analysis, solid-phase reaction control, and biophysics research. Transferring cells across streams is difficult to achieve in a well-controlled manner, since it requires precise control of fluid flow along with external force fields or precisely manufactured mechanical structures. Herein a strategy is introduced for particle transfer based on passive inertial lift forces and shifts in the distribution of these forces for channels with shifting aspect ratios. Uniquely, use of the dominant wall-effect lift parallel to the particle rotation direction is explored and utilized to achieve controllable cross-stream motion. In this way, particles are positioned to migrate across laminar streams and enter a new solution without significant disturbance of the interface at rates exceeding 1000 particles per second and sub-millisecond transfer times. The capabilities of rapid inertial solution exchange (RInSE) for preparation of hematological samples and other cellular assays are demonstrated. Lastly, improvements to inline flow cytometry after RInSE of excess fluorescent dye and focusing for downstream analysis are characterized. The described approach is simply applied to manipulating cells and particles and quickly exposing them to or removing them from a reacting solution, with broader applications in control and analysis of low affinity interactions on cells or particles.
Rational Manual and Automated Scoring Thresholds for the Immunohistochemical Detection of TP53 Missense Mutations in Human Breast Carcinomas (2015)

Missense mutations in TP53 are common in human breast cancer, have been associated with worse prognosis, and may predict therapy effect. TP53 missense mutations are associated with aberrant accumulation of p53 protein in tumor cell nuclei. Previous studies have used relatively arbitrary cutoffs to characterize breast tumors as positive for p53 staining by immunohistochemical assays. This study aimed to objectively determine optimal thresholds for p53 positivity by manual and automated scoring methods using whole tissue sections from the Carolina Breast Cancer Study. p53-immunostained slides were available for 564 breast tumors previously assayed for TP53 mutations. Average nuclear p53 staining intensity was manually scored as negative, borderline, weak, moderate, or strong and percentage of positive tumor cells was estimated. Automated p53 signal intensity was measured using the Aperio nuclear v9 algorithm combined with the Genie histology pattern recognition tool and tuned to achieve optimal nuclear segmentation. Receiver operating characteristic curve analysis was performed to determine optimal cutoffs for average staining intensity and percent cells positive to distinguish between tumors with and without a missense mutation. Receiver operating characteristic curve analysis demonstrated a threshold of moderate average nuclear staining intensity as a good surrogate for TP53 missense mutations in both manual (area under the curve=0.87) and automated (area under the curve=0.84) scoring systems. Both manual and automated immunohistochemical scoring methods predicted missense mutations in breast carcinomas with high accuracy. Validation of the automated intensity scoring threshold suggests a role for such algorithms in detecting TP53 missense mutations in high throughput studies.