gebhart/patrepeval huggingface dataset:
Effect of Photoperiod on the Levels of Endogenous Gibberellins in Spinach as Measured by Combined Gas Chromatography-selected Ion Current Monitoring (1980)

The changes in the levels of five endogenous gibberellins (GAs) in spinach in relation to photoperiodic treatment have been examined by combined gas chromatography-selected ion current monitoring. Long-day treatment caused a 5-fold decline in the level of GA(19) while the levels of GA(20) and GA(29) increased dramatically during the same period. In absolute terms, the level of GA(20) increased from 0.8 microgram per 100 grams dry weight in short days to 5.5 micrograms per 100 grams dry weight after 14 long days. The levels of GA(17) and GA(44) did not change significantly with long-day treatment. These results are consistent with the hypothesis that GA(19) is converted to GA(20) and that this conversion is under photoperiodic control. Since stem growth in spinach is correlated with an increase in the level of GA(20), one major aspect of photoperiodic control of stem growth might be the availability of GA(20) through regulation of the conversion of GA(19) to GA(20).
A Cascaded H-Bridge Multilevel Inverter with SOC Battery Balancing (2017)

In this paper, we present a single phase 5 levels H-Bridge multilevel inverter (CHMLI) with battery balancing technique. Each single full bridge is directly connected to a battery inside the power bank. The different combinations and batteries wiring sets offer the possibility to control the batteries discharge. The cascaded H-Bridge multilevel inverter is first described and the discharge is studied in normal conditions under different stress scenarios. State of charge (SOC) balancing technique is then achieved using an equalization algorithm controlling the different switching combination inside the power bank. Results of the simulation model with and without the SOC balancing is presented using Matlab.
Environments and tools for parallel scientific computing (1993)

Part 1: Communications and Computations Libraries for Multicomputers. The Design of Scalable Software Libraries for Distributed Memory Concurrent Computers (J. Choi, J.J. Dongarra, D.W. Walker). Level 3 BLAS for Distributed Memory Concurrent Computers (J. Choi, J.J. Dongarra, D.W. Walker). Two Dimensional Basic Linear Algebra Communication Subprograms (J.J. Dongarra, R. van de Geiin, C. Whaley). Implementation of Linear Algebra and Communications Libraries on the T.node Reconfigurable Machine (C. Bonello, F. Desprez). Part 2: Post-Mortem Visualization of Parallel Programs. Process and Processor Interaction: Architecture Independent Visualisation Schema (E. Zabala, R. Taylor). Program Visualization by Integration of Advanced Compiler Technology with Configurable Views (D. Kimelman, G. Sang'udi). Distributed Monitoring for Scalable Massively Parallel Machines (S. Poinson, B. Tourancheau, X. Vigouroux). Standardization of Event Traces Considered Harmful or Is An Implementation of Object-Independent Event Trace Monitoring and Analysis Systems Possible? (B. Mohr). Programming Tools for Massively Parallel Supercomputers (T. Bemmerl). Part 3: Tools for Parallel Program Development. PVM and HENCE: Tools for Heterogeneous Network Computing (A. Beguelin et al.). ParaRex: A Programming Environment Integrating Execution Replay and Visualization (E. Leu, A. Schiper). Visage - Visualization of Attribute Graphs: A Foundation for a Parallel Programming Environment (A. Rudich, D. Zemik, G. Zodik). A Programming Environment Dedicated to a Model of Explicit Parallelism (M. Alabau et al.). ALPES: A Tool for the Performance Evaluation of Parallel Programs (J.P. Kitajima, C. Tron, B. Plateau). Part 4: Methodologies for Parallel Program Development. Libraries and Tools for Object Parallel Programming (D. Gannon). Stream-Based Interface in C++ for Programming Heterogeneous Systems (R. Pozo). Building Blocks for Iterative Solution of Linear Systems (R. Barrett et al.). Allocating Communication Channels to Parallel Tasks (D. Barthou, F. Gasperoni, U. Schwiegelshohn). Part 5: Automatic Parallelization. Compiling Sequential Programs for Distributed Memory Parallel Computers with Pandore II (F. Andre, O. Cheron, J.-L. Pazat). Loop Nest Scheduling and Transformations (A. Darte, T. Risset, Y. Robert). Interprocedural Analyses for Programming Environments (F. Irigoin). Array Redistributions on Boolean Cubes (M. Loi).
Functional Identification of the Central Projections of Afferent Renal Nerves (1987)

The central integration of cardiovascular reflexes produced by activation of renal sensory mechanisms was examined by studying arterial pressure and regional blood flow responses to electrical stimulation of the renal afferent nerves. Spinal transection, rostral to the entry into the cord of renal afferent projections, abolished the cardiovascular response consisting of an a fall in arterial pressure, mesenteric vasoconstriction and vasodilation in the hindquarters. Several supraspinal structures at medullary, midbrain and forebrain levels were identified by lesion studies to be important for the reflex responses. Lesion of NTS abolished the hindquarter vasodilator response but left the mesenteric vasoconstrictor response intact. Lesions of the parabrachial complex produce similar effects whereas lesions in the periventricular preoptic region of hypothalamus abolished mesenteric vasoconstriction and left hindquarter vasodilation unaffected. These studies demonstrate that cardiovascular reflexes elicited by activation of renal sensory nerves require integrity of spinal pathways and are differentially integrated at several levels of the neuraxis.
Creating Interactive Virtual Acoustic Environments (1999)

The theory and techniques for virtual acoustic modeling and rendering are discussed. The creation of natural sounding audiovisual environments can be divided into three main tasks: sound source, room acoustics, and listener modeling. These topics are discussed in the context of both non-real-time and real-time virtual acoustic environments. Implementation strategies are considered, and a modular and expandable simulation software is described.
Vitreous Hemorrhage: An Experimental Study (1970)

Through photographic and isotopic analysis, this study of experimental intravitreous hemorrhages traces the fate of red blood cells after injection of whole blood and hemoglobin into rabbit vitreous. The vitreous is almost entirely translucent two months after hemoglobin injection, but 25% of ferric chloride Fe<sup>59</sup>remains within the eye. Comparing photographs of experimental intravitreous hemorrhages with spontaneous intravitreal hemorrhages in humans shows that the two types are similar.
Activation in Human MT/MST by Static Images with Implied Motion (2000)

A still photograph of an object in motion may convey dynamic information about the position of the object immediately before and after the photograph was taken (implied motion). Medial temporal/medial superior temporal cortex (MT/MST) is one of the main brain regions engaged in the perceptual analysis of visual motion. In two experiments we examined whether MT/MST is also involved in representing implied motion from static images. We found stronger functional magnetic resonance imaging (fMRI) activation within MT/MST during viewing of static photographs with implied motion compared to viewing of photographs without implied motion. These results suggest that brain regions involved in the visual analysis of motion are also engaged in processing implied dynamic information from static images.
Dihydronaphthalene‐Fused Boron–Dipyrromethene (BODIPY) Dyes: Insight into the Electronic and Conformational Tuning Modes of BODIPY Fluorophores (2010)

A new series of boron-dipyrromethene (BDP, BODIPY) dyes with dihydronaphthalene units fused to the beta-pyrrole positions (1a-d, 2) has been synthesised and spectroscopically investigated. All the dyes, except pH-responsive 1d in polar solvents, display intense emission between 550-700 nm. Compounds 1a and 1b with a hydrogen atom and a methyl group in the meso position of the BODIPY core show spectroscopic properties that are similar to those of rhodamine 101, thus rendering them potent alternatives to the positively charged rhodamine dyes as stains and labels for less polar environments or for the dyeing of latex beads. Compound 1d, which carries an electron-donating 4-(dimethylamino)phenyl group in the meso position, shows dual fluorescence in solvents more polar than dibutyl ether and can act as a pH-responsive "light-up" probe for acidic pH. Correlation of the pK(a) data of 1d and several other meso-(4-dimethylanilino)-substituted BODIPY derivatives allowed us to draw conclusions on the influence of steric crowding at the meso position on the acidity of the aniline nitrogen atom. Preparation and investigation of 2, which carries a nitrogen instead of a carbon as the meso-bridgehead atom, suggests that the rules of colour tuning of BODIPYs as established so far have to be reassessed; for all the reported couples of meso-C- and meso-N-substituted BODIPYs, the exchange leads to pronounced redshifts of the spectra and reduced fluorescence quantum yields. For 2, when compared with 1a, the opposite is found: negligible spectral shifts and enhanced fluorescence. Additional X-ray crystallographic analysis of 1a and quantum chemical modelling of the title and related compounds employing density functional theory granted further insight into the features of such sterically crowded chromophores.
A comparison of the molecular subtypes of triple-negative breast cancer among non-Asian and Taiwanese women (2017)

Our data suggested that there exist different presentations between non-Asian and Taiwanese TNBC subtypes, which provides important information when selection of therapeutic targets or designs for clinical trials for TNBC patients.
Differentiation stage alters matrix control of stem cells (2007)

Cues from the material to which a cell is adherent (e.g., adhesion ligand presentation, substrate elastic modulus) clearly influence the phenotype of differentiated cells. However, it is currently unclear if stem cells respond similarly to these cues. This study examined how the overall density and nanoscale organization of a model cell adhesion ligand (arginine-glycine-aspartic acid [RGD] containing peptide) presented from hydrogels of varying stiffness regulated the proliferation of a clonally derived stem cell line (D1 cells) and preosteoblasts (MC3T3-E1). While the growth rate of MC3T3-E1 preosteoblasts was responsive to nanoscale RGD ligand organization and substrate stiffness, the D1 stem cells were less sensitive to these cues in their uncommitted state. However, once the D1 cells were differentiated towards the osteoblast lineage, they became more responsive to these signals. These results demonstrate that the cell response to material cues is dependent on the stage of cell commitment or differentiation, and these findings will likely impact the design of biomaterials for tissue regeneration.
BIBF 1120: Triple Angiokinase Inhibitor with Sustained Receptor Blockade and Good Antitumor Efficacy (2008)

Inhibition of tumor angiogenesis through blockade of the vascular endothelial growth factor (VEGF) signaling pathway is a novel treatment modality in oncology. Preclinical findings suggest that long-term clinical outcomes may improve with blockade of additional proangiogenic receptor tyrosine kinases: platelet-derived growth factor receptors (PDGFR) and fibroblast growth factor receptors (FGFR). BIBF 1120 is an indolinone derivative potently blocking VEGF receptor (VEGFR), PDGFR and FGFR kinase activity in enzymatic assays (IC(50), 20-100 nmol/L). BIBF 1120 inhibits mitogen-activated protein kinase and Akt signaling pathways in three cell types contributing to angiogenesis, endothelial cells, pericytes, and smooth muscle cells, resulting in inhibition of cell proliferation (EC(50), 10-80 nmol/L) and apoptosis. In all tumor models tested thus far, including human tumor xenografts growing in nude mice and a syngeneic rat tumor model, BIBF 1120 is highly active at well-tolerated doses (25-100 mg/kg daily p.o.), as measured by magnetic resonance imaging of tumor perfusion after 3 days, reducing vessel density and vessel integrity after 5 days, and inducing profound growth inhibition. A distinct pharmacodynamic feature of BIBF 1120 in cell culture is sustained pathway inhibition (up to 32 hours after 1-hour treatment), suggesting slow receptor off-kinetics. Although BIBF 1120 is rapidly metabolized in vivo by methylester cleavage, resulting in a short mean residence time, once daily oral dosing is fully efficacious in xenograft models. These distinctive pharmacokinetic and pharmacodynamic properties may help explain clinical observations with BIBF 1120, currently entering phase III clinical development.
Differential effect of agonistic anti-CD40 on human mature and immature dendritic cells: the Janus face of anti-CD40 (2005)

Agonistic monoclonal antibodies to CD40 (CD40 mAbs) have a puzzling dual therapeutic effect in experimental animal models. CD40 mAbs induce tumor regression by potentiating antitumoral T-cell responses, yet they also have immunosuppressive activity in chronic autoimmune inflammatory processes. CD40 mAbs are thought to act on antigen presentation by dendritic cells (DCs) to T cells. DCs can be distinguished as either immature or mature by their phenotype and their ability to generate an effective T-cell response. Here we found that, on human cells, although anti-CD40 led immature DCs to mature and became immunogenic, it also reduced the capacity of lipopolysaccharide (LPS) and tumor necrosis factor alpha (TNF-alpha)-matured DCs to generate a specific CD4 T-cell response. This inhibitory effect was related to rapid and selective apoptosis of mature DCs. Anti-CD40-mediated apoptosis was due to an indirect mechanism involving cooperation with the death domain-associated receptor Fas, leading to activation of Fas-associated death domain protein (FADD) and caspase-8. On human cells, CD40 activation by such agonists could, therefore, trigger immune responses to antigens presented by immature DCs, which are otherwise nonimmunogenic, by inducing maturation. On the other hand, anti-CD40 mAbs, by rapidly inducing apoptosis, may reduce the capacity of inflammatory signal-matured immunogenic DCs to generate an effective T-cell response. These results call for caution in CD40 mAb-based immunotherapy strategies.
N‐halosuccinimide‐mercaptoethanol cohalogenation of olefinic fatty methyl esters: Synthesis of β‐halo thioethoxylates (2006)

Abstract Olefinic fatty methyl esters, undec‐10‐enoate ( 1 ), octadec‐ Z ‐9‐enoate ( 2 ), methyl‐12 hydroxy octadec‐ Z ‐9‐enoate ( 3 ), on reaction with N‐halosuccinimides ( 4,5 ), that is, N ‐bromosuccinimide ( 4 ) or N ‐chlorosuccinimide ( 5 ) and 2‐mercaptoethanol ( 6 ) in benzene, gave β‐bromo‐ or β‐chlorothioethoxylates ( 8–13 ). β‐Halothioethoxylates so formed were acetylated with acetyl chloride in CH 2 Cl 2 to form the respective acetylated products ( 20–25 ).
Neutrophil Adhesion Molecule Surface Expression and Responsiveness in Cystic Fibrosis (1998)

The neutrophil-dominated inflammation of the lung in cystic fibrosis (CF) has traditionally been seen as a physiological response to continuous opportunistic infection. Recent studies suggest, however, that regulation of the inflammatory response itself may be altered in CF. Neutrophil migration from the bloodstream involves alterations in surface expression of the adhesion molecules L-selectin and Mac-1 (CD11b/CD18). The aim of this study was to assess neutrophil adhesion molecule expression and responsiveness in CF. Neutrophils from chronic (n = 16) and acutely infected (n = 13) CF patients and 15 normal control subjects were directly assessed by Fluorescence-activated cell sorter (FACS) analysis for surface expression of L-selectin and CD11b before and after stimulation with interleukin 8 (IL-8) or f-Met-Leu-Phe (fMLP). Neutrophils from stable (n = 5) and acutely infected (n = 5) non-CF bronchiectasis patients were also assessed. Surface upregulation of CD11b was similar in all groups. Basal levels of L-selectin were also comparable among all groups, however, when stimulated, neutrophils from both stable and acutely infected CF patients shed significantly less L-selectin than those from control subjects (p < 0.05 and p < 0.01, respectively). This decreased responsiveness was not observed in either stable or acutely infected non-CF bronchiectasis patients. These results add to the accumulating evidence suggestive of a defective inflammatory response in CF.
Upper and Lower Probabilities Induced by a Multivalued Mapping (1967)

A multivalued mapping from a space $X$ to a space $S$ carries a probability measure defined over subsets of $X$ into a system of upper and lower probabilities over subsets of $S$. Some basic properties of such systems are explored in Sections 1 and 2. Other approaches to upper and lower probabilities are possible and some of these are related to the present approach in Section 3. A distinctive feature of the present approach is a rule for conditioning, or more generally, a rule for combining sources of information, as discussed in Sections 4 and 5. Finally, the context in statistical inference from which the present theory arose is sketched briefly in Section 6.
Targeting oncogenic Ras signaling in hematologic malignancies (2012)

Ras proteins are critical nodes in cellular signaling that integrate inputs from activated cell surface receptors and other stimuli to modulate cell fate through a complex network of effector pathways. Oncogenic RAS mutations are found in ∼25% of human cancers and are highly prevalent in hematopoietic malignancies. Because of their structural and biochemical properties, oncogenic Ras proteins are exceedingly difficult targets for rational drug discovery, and no mechanism-based therapies exist for cancers with RAS mutations. This article reviews the properties of normal and oncogenic Ras proteins, the prevalence and likely pathogenic role of NRAS, KRAS, and NF1 mutations in hematopoietic malignancies, relevant animal models of these cancers, and implications for drug discovery. Because hematologic malignancies are experimentally tractable, they are especially valuable platforms for addressing the fundamental question of how to reverse the adverse biochemical output of oncogenic Ras in cancer.
Energetics of plasmid-mediated arsenate resistance in Escherichia coli. (1982)

Plasmid R773, which codes for resistances to arsenate, arsenite, and antimony, was introduced into Escherichia coli strain AN120, a mutant deficient in the H+-translocating ATPase of oxidative phosphorylation. Cultures depleted of endogenous energy reserves were loaded with 74AsO3-4, and arsenate efflux was measured after dilution into medium containing various energy sources and inhibitors. Rapid extrusion of arsenate occurred when glucose was added. Arsenate was extruded both against and down a concentration gradient. In this strain glucose allows formation of both ATP via substrate-level phosphorylation and an electrochemical proton gradient (or protonmotive force) via oxidation of the products of glycolysis. When oxidation was inhibited by cyanide, glucose metabolism still produced arsenate efflux. Energy sources such as succinate, which supplies a protonmotive force but not ATP, did not result in efflux. Measurement of intracellular ATP concentration under each set of conditions demonstrated a direct correlation between the rate of efflux and ATP levels. Osmotically shocked cells lost the ability to extrude arsenate; however, no arsenate-binding activity was detected in osmotic shock fluid from induced cells. These results suggest that the arsenate efflux system is coupled to cellular ATP rather than an electrochemical proton gradient, possibly by an arsenate-translocating ATPase.
Efficient transcription, not translation, is dependent on adenovirus tripartite leader sequences at late times of infection (1988)

To determine whether the tripartite leader is required for efficient translation in adenovirus-infected cells at late times of infection, we constructed recombinant adenoviruses containing the influenza virus nucleocapsid protein (NP) gene expressed under the control of the adenovirus major late promoter (MLP). We chose the NP gene because previous results showed that the influenza virus NP mRNA was an extremely effective initiator of translation in cells which were superinfected with influenza virus at late times of adenovirus infection (M. G. Katze, B. M. Detjen, B. Safer, and R. M. Krug, Mol. Cell. Biol. 6:1741-1750, 1986). The NP gene in the adenovirus recombinants was inserted downstream of an MLP that replaced part of the early (E1A) region. The resulting NP mRNAs either lacked any tripartite leader sequences or contained at their 5' ends various portions of the tripartite leader: 33, 172, or all 200 nucleotides of the leader. The relative amounts of the NP protein synthesized by the recombinants were directly proportional to the amounts of the NP mRNA made, indicating that the presence of 5' tripartite leader sequences did not enhance the translation of NP mRNA. In addition, the sizes of the polysomes containing NP mRNA were not increased by the presence of tripartite leader sequences, indicating that the initiation of translation was not enhanced by these sequences. On the other hand, the presence of tripartite leader sequences immediately downstream of the MLP did enhance the transcription of the inserted NP gene, as shown by Northern (RNA) analysis of in vivo NP mRNA levels and by in vitro runoff assays with isolated nuclei. Our results indicate that more than 33 nucleotides of the first leader segment of the tripartite leader are required for optimal transcription from the MLP.
Combined optical imaging and mammography of the healthy breast: Optical contrast derived from breast structure and compression (2009)

In this paper, we report new progress in developing the instrument and software platform of a combined X-ray mammography/diffuse optical breast imaging system. Particularly, we focus on system validation using a series of balloon phantom experiments and the optical image analysis of 49 healthy patients. Using the finite-element method for forward modeling and a regularized Gauss-Newton method for parameter reconstruction, we recovered the inclusions inside the phantom and the hemoglobin images of the human breasts. An enhanced coupling coefficient estimation scheme was also incorporated to improve the accuracy and robustness of the reconstructions. The recovered average total hemoglobin concentration (HbT) and oxygen saturation (SO2) from 68 breast measurements are 16.2 microm and 71%, respectively, where the HbT presents a linear trend with breast density. The low HbT value compared to literature is likely due to the associated mammographic compression. From the spatially co-registered optical/X-ray images, we can identify the chest-wall muscle, fatty tissue, and fibroglandular regions with an average HbT of 20.1+/-6.1 microm for fibroglandular tissue, 15.4+/-5.0 microm for adipose, and 22.2+/-7.3 microm for muscle tissue. The differences between fibroglandular tissue and the corresponding adipose tissue are significant (p < 0.0001). At the same time, we recognize that the optical images are influenced, to a certain extent, by mammographical compression. The optical images from a subset of patients show composite features from both tissue structure and pressure distribution. We present mechanical simulations which further confirm this hypothesis.