gebhart/patrepeval huggingface dataset:
Effect of Synthetic Parameters on Defects, Structure, and Electrochemical Properties of Layered Oxide LiNi<sub>0.80</sub>Co<sub>0.15</sub>Al<sub>0.05</sub>O<sub>2</sub> (2018)

LiNi0.80Co0.15Al0.05O2, a cathode material of the high energy density layered oxide family, was synthesized at various time and temperature values to form single particles. The result of each synthesis condition was comprehensively characterized, demonstrating differing purity, morphology, and electrochemical properties, expanding the current knowledge of the LiNi0.80Co0.15Al0.05O2 system. 800°C was found to be the temperature in which particle growth was reliably observed. Particle size was shown to correlate with annealing time, concurrent to Li/Ni site mixing. Morphology was also dependent on annealing time. Shorter anneals yielded particles of platelet morphology, while longer anneals yielded more three-dimensional structures. Samples that had longer total annealing times resulted in higher specific capacity values.
Composition of High Molecular Weight Excretions-Secretions from Infective Larvae of Meloidogyne javanica. (1989)

Infective larvae (J2) of Meloidogyne javanica were incubated in distilled water for up to 14 days, and their high molecular weight (> 1,000 daltons) excretions-secretions (ES) were isolated and partially characterized. The ES consisted of a mixture of proteins, glycoproteins, and proteoglycans or polysaccharides as revealed by differential staining on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and compositional analysis. Carbohydrate, with approximately equal amounts of neutral monosaccharides and hexosamines, was the major constituent of the ES, with only low levels of protein detected. Acidic sugar residues, including sialic acids, were not detected.
Variable-Fidelity Aerodynamic Optimization for Turbulent Flows Using a Discrete Adjoint Formulation (2004)

An aerodynamic shape optimization methodology based on a discrete adjoint solver for Navier‐Stokes flows is described. The flow solver at the heart of this optimization process is a Reynolds-averaged Navier‐Stokes code for multiblock structured grids. It uses Osher’s approximate Riemann solver and the algebraic turbulence model of Baldwin‐Lomax. A corresponding discrete Navier‐Stokes adjoint solver is derived analytically. It has to calculate accurately the Jacobian, including the effect of the turbulence modeling. The shape deformations
Acute lymphoblastic leukemia with TEL-AML1 fusion has lower expression of genes involved in purine metabolism and lower de novo purine synthesis (2004)

Because de novo purine synthesis (DNPS) is a target of widely used antileukemic agents (eg, methotrexate, mercaptopurine), we determined the rate of DNPS and the expression of genes involved in purine metabolism in different subtypes of acute lymphoblastic leukemia (ALL). Among 113 children with newly diagnosed ALL, lymphoblasts with the TEL-AML1 translocation had significantly lower DNPS than all other genetic subtypes of B-lineage ALL or T-lineage ALL (352 +/- 57 versus 1001 +/- 31 or versus 1315 +/- 76 fmol/nmol/h, P <.0001). By assessing the expression of 82 genes involved in purine metabolism (KEGG pathway database) in ALL blasts from 38 patients with B-lineage ALL (14 with TEL-AML1, 24 without), we identified 16 genes that were differentially expressed in TEL-AML1-positive and TEL-AML1-negative ALL (P <.001, false discovery rate [FDR] = 5%). The pattern of expression of these 16 genes discriminated TEL-AML1-positive ALL with a true accuracy of 84% in an independent test set (n = 17, confidence interval 70% to 94%, P <.001). Western blots of selected genes documented corresponding levels of the proteins encoded. Differentially expressed genes included HPRT, IMPDH, PAICS, and GART, all of which were expressed at a significantly lower level in TEL-AML1 ALL. These findings have established that TEL-AML1 ALL has significantly lower de novo purine synthesis and differential expression of genes involved in purine metabolism.
Comparison of Inhibitory Effects of Prolinal-Containing Peptide Derivatives on Prolyl Endopeptidases from Bovine Brain and Flavobacterium1 (1985)

The inhibitory effects of proline-containing peptides and their derivatives on prolyl endopeptidases from Flavobacterium meningosepticum and bovine brain were compared. Replacement of the carboxyl terminal proline in N-blocked peptides with prolinal resulted in remarkable decreases in Ki values for both prolyl endopeptidases. Further reduction of the prolinal to prolinol led to a decrease in their inhibitory effects. Z-Pro-, Z-Val-, and Suc-Pro-prolinals were similarly inhibitory for both the enzymes with Ki values of nM order. However, the inhibitory effects of Z-Pyr-prolinal and Boc-Pro-prolinal on these enzymes were significantly distinguished: they strongly inhibited the mammalian prolyl endopeptidase with Ki values of nM order, while the Ki values of these compounds for the microbial enzyme were only of microM order. These results suggest that there are some structural differences in the S2 and S3 subsites between the two enzymes, though their substrate specificities are apparently indistinguishable.
Availability of irinotecan in a second-line setting confers survival benefit to patients with advanced gastric cancer refractory to fluoropyrimidine-based regimens (2011)

Optimal second-line chemotherapy may contribute to favorable survival in patients who receive first-line treatment for advanced gastric cancer. The aim of this retrospective study was to compare a second-line setting using irinotecan with paclitaxel in terms of survival benefit and safety. A total of 179 patients with recurrent or unresectable gastric cancer who had received prior chemotherapy with a fluoropyrimidine-based regimen were treated with irinotecan alone at 150 mg/m(2) on days 1 and 15 every 4 weeks (Cohort I) or weekly paclitaxel at 80 mg/m(2) on days 1, 8 and 15 every 4 weeks (Cohort P) between April, 2004 and March, 2009. Patient characteristics, overall response rate, disease control rate, progression-free survival, overall survival and safety were investigated. Of the 179 patients, 92 received irinotecan and 87 patients who were contraindicated for irinotecan received weekly paclitaxel. The overall response and disease control rates in Cohort I were 6.5 and 43.5%, respectively, as compared with 9.8 and 54.9%, respectively, in Cohort P. No variation was noted in median progression-free survival (Cohort I vs. P, 2.6 vs. 2.8 months; P=0.812), whereas median overall survival (Cohort I vs. P, 9.8 vs. 4.9 months; P<0.0001) differed significantly between the two cohorts. The most common grade 3/4 adverse events were neutropenia, leukopenia, anemia and anorexia, which were tolerable in each treatment cohort. Availability of irinotecan in a second-line setting confers a survival benefit to advanced gastric cancer patients in whom fluoropyrimidine-based first-line chemotherapy was unsuccessful.
Faculty Opinions recommendation of Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. (2001)

Osmolytes stabilize proteins to thermal and chemical denaturation. We have studied the effects of the osmolytes sarcosine, betaine, trimethylamine-N-oxide, and taurine on the structure and stability of the protein.peptide complex RNase S using x-ray crystallography and titration calorimetry, respectively. The largest degree of stabilization is achieved with 6 m sarcosine, which increases the denaturation temperatures of RNase S and S pro by 24.6 and 17.4 degrees C, respectively, at pH 5 and protects both proteins against tryptic cleavage. Four crystal structures of RNase S in the presence of different osmolytes do not offer any evidence for osmolyte binding to the folded state of the protein or any perturbation in the water structure surrounding the protein. The degree of stabilization in 6 m sarcosine increases with temperature, ranging from -0.52 kcal mol(-1) at 20 degrees C to -5.4 kcal mol(-1) at 60 degrees C. The data support the thesis that osmolytes that stabilize proteins, do so by perturbing unfolded states, which change conformation to a compact, folding competent state in the presence of osmolyte. The increased stabilization thus results from a decrease in conformational entropy of the unfolded state. PMID: 11373282
Stille Couplings Catalytic in Tin:  The “Sn−O” Approach (2001)

A one-pot tandem Pd-catalyzed hydrostannylation/Stille coupling protocol for the stereoselective generation of vinyltins and their subsequent union, employing only catalytic amounts of tin, is described. By recycling the organotin halide Stille byproduct back to organotin hydride, a hydrostannylation/cross-coupling sequence can be carried out with catalytic amounts of tin. Such a process is most effective with Me(3)SnCl serving as the tin source. This protocol allows a 94% reduction of the tin requirement, while maintaining good yields (up to 90%) for a variety of Stille products. Furthermore, since one cycle requires the tin to undergo at least four transformations, each moiety of trialkyltin is experiencing a minimum of 60 reactions over the course of the hydrostannylation/Stille sequence.
Fruiting and abscission patterns in cashew (1983)

SUMMARY The variation in setting fruit and immature fruit abscission at successive nodes of an individual panicle, and in panicles at different directions of the canopy in an individual tree, were studied in cashew ( Anacardium occidentale L.). The numbers of perfect flowers and fruits set increased from the proximal to the distal end with the maximum yield at the fifth or sixth nodes in a panicle of 8–10 branches. The productivity of an entire inflorescence or a whole fruiting branch was related to its orientation with respect to the sun. The numbers of nodes and fruits set and the percentage of fruit retained were maximal in panicles located on the western and southern sides of the canopy. Tea mosquito damage was also less on these sides of the canopy but the physiological disorder of ‘apple’ cracking was higher here than on the eastern and northern sides. These variations are discussed in relation to the differences in the incident photosynthetically active radiation on these sides.
RNA Polymerase Activity Associated with Bacteriophage  6 Nucleocapsid (1979)

SUMMARY The Pseudomonas phaseolicola bacteriophage ϕ6 nucleocapsid incorporated ATP, UTP, CTP and GTP into ssRNA products which sedimented at the same rate as heat-denatured small and medium dsRNA components. Hybridization of the separated ssRNA products with denatured dsRNA revealed that the small ssRNA hybridized only to small dsRNA and the medium ssRNA to the medium dsRNA. Synthesis of the large ssRNA was not observed. The RNA polymerase reaction proceeded through a replicative intermediate-like RNA probably via a semiconservative mechanism.
Finite horizon model reduction and the appearance of dissipation in Hamiltonian systems (2004)

An apparent paradox in classical statistical physics is the mechanism by which conservative, time-reversible microscopic dynamics, can give rise to seemingly dissipative behavior. In this paper we use system theoretic tools to show that dissipation can arise as an artifact of incomplete observations over a finite horizon. In addition, this approach allows us to obtain finite-time, low order, approximations of systems with moderate size and to establish how the approach to the thermodynamic limit depends on the different physical parameters.
Modulation of CCAAT/Enhancer Binding Protein Homologous Protein (CHOP)-dependent DR5 Expression by Nelfinavir Sensitizes Glioblastoma Multiforme Cells to Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL) (2011)

Human glioblastoma multiforme cells demonstrate varying levels of sensitivity to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis. Endoplasmic reticulum (ER) stress has been shown to trigger cell death through apoptosis. We therefore pursued a strategy of integrating clinically relevant investigational agents that cooperate mechanistically through the regulation of ER stress and apoptosis pathways. Nelfinavir belongs to the protease inhibitor class of drugs currently used to treat patients with HIV and is in clinical trials as an anti-tumor agent. We found that Nelfinavir treatment led to ER stress-induced up-regulation of the DR5 receptor. This transactivation was mediated by the transcription factor CCAAT/enhancer binding protein homologous protein (CHOP). We also determined that ER stress-induced ATF4 up-regulation was responsible for modulation of CHOP. In contrast, DR4 receptor expression was unchanged by Nelfinavir treatment. Combining Nelfinavir with TRAIL led to a significantly enhanced level of apoptosis that was abrogated by siRNA silencing of DR5. We provide evidence that Nelfinavir-induced ER stress modulates DR5 expression in human glioblastoma multiforme cells and can enhance TRAIL efficacy. These studies provide a potential mechanistic rationale for the use of the Food and Drug Administration-approved agent Nelfinavir in combination with DR5 agonists to induce apoptosis in human malignancies.
Photo-patterning of non-fouling polymers and biomolecules on paper (2014)

Functional cellulose substrates with tetrazole moieties are generated to serve as universal platforms for the spatio-temporal immobilization of synthetic ultra-low fouling polymer brushes and protein species via a nitrile imine-mediated tetrazole-ene cycloaddition (NITEC)-based protocol. Poly(carboxybetaine acrylamide) brushes are grafted from initiators photo-patterned by NITEC utilizing single electron transfer living radical polymerization. Streptavidin is photo-immobilized with remarkable efficiency, opening the possibility to generate new materials for biomedical and biosensing applications.
Imaging properties of a defocusing gradient-index rod (1983)

In this paper we report studies on imaging through a defocusing gradient-index rod. We have obtained analytic expressions for the third-order aberration of this system and compared it with the total aberration obtained by numerical ray tracing. Our studies show that the rod length can be critically optimized for low aberrations depending on the numerical aperture requirement. Further, a value of the fourth-order grading parameter exists for which the aberration can be reduced to a minimum for fixed values of other parameters.
Electrolyte Effects on Chemical Stability of NaO2 in Na-O2 Batteries (2015)

Rechargeable metal-air (oxygen) batteries are receiving intense interest as possible alternatives to lithium-ion batteries, because of their potential to provide higher gravimetric energies. 1 While much attention has been focused on aprotic Li-O 2 batteries, substantial challenges must be addressed before widespread commercialization is possible. Recently, a metal-air battery in which lithium has been replaced by sodium has received increasing attention. 2 Although Na-O 2 batteries present lower gravimetric energies on a cell basis (1605 or 1108 Wh/kg based on Na 2 O 2 or NaO 2 discharge products, respectively) 2 than Li-O 2 batteries (3505 Wh/kg Li2O2 ), 1 much lower charge overpotentials (~100 mV) than those in typical Li-O 2 batteries (~1000 mV) have been reported based on reversible sodium superoxide (NaO 2 ) formation . Unlike Li-O 2 batteries, for which Li 2 O 2 is the only discharge product, NaO 2 , sodium peroxide (Na 2 O 2 ) and sodium peroxide dihydrate (Na 2 O 2 · 2H 2 O), or a mixture, have been identified in Na-O 2 batteries in ether-based electrolytes using a range of carbon electrode types. Here we show NaO 2 as the only discharge product from Na-O 2 cells with carbon nanotubes in 1,2-dimethoxyethane from X-ray diffraction and Raman spectroscopy. Immediately after discharge, no Na 2 O 2 · 2H 2 O was found in the discharged electrode, even with H 2 O present in the electrolyte up to 6000 ppm. However, Na 2 O 2 · 2H 2 O was detected upon ageing the electrode in the electrolyte, and the amount of Na 2 O 2 · 2H 2 O was seen to increase with increasing rest time in the electrolyte. More importantly, the reversibility of the reaction is affected by the presence of Na 2 O 2 · 2H 2 O, where the cells charged immediately after discharge show a reversible reaction , and the cells charged after resting the electrode in the electrolyte for several hours showed poor reversibility. The rechargeable nature of a Na-O 2 cell is governed by the formation and oxidation of NaO 2 , making it vital to study the stability of the electrolyte in the presence of NaO 2 , and also to prevent the formation of irreversible side products. REFERENCES 1. D. G. Kwabi, N. Ortiz-Vitoriano, S. A. Freunberger, Y. Chen, N. Imanishi, P. G. Bruce, Y. Shao-Horn, MRS Bull. 39 , 443 (2014). 2. P. Hartmann, C. L. Bender, M. Vračar, A. K. Dürr, A. Garsuch, J. Janek, P. Adelhelm, Nat. Mater. 12 , 228 (2013).
Diagnosis of Bacterial Overgrowth after Culturing Proximal Small-Bowel Aspirate Obtained during Routine Upper Gastrointestinal Endoscopy (1992)

The purpose of this study was to evaluate the method of obtaining aspirated fluid for culture from the small intestine through a fiberoptic gastrointestinal endoscope for diagnosing small-bowel overgrowth. The study population consisted of 10 healthy volunteers and 26 patients with various gastrointestinal problems referred for routine endoscopic examination. The material to be cultured was obtained under direct visualization approximately 25 to 30 cm distal to the pylorus or from the afferent loop (in Billroth-II patients) with a sterilized sheathed wash pipe passed through the suction channel of the endoscope. Cultures were considered positive for bacterial overgrowth if total counts of organisms were 10(5)/ml or more. All healthy volunteers and 16 of 21 unoperated patients had sterile or insignificant growth, whereas all 5 patients who had Billroth-II operations had positive overgrowth. The endoscopic method for collection of proximal gastrointestinal fluid for culture is simple and can be performed during routine endoscopy.
Plasma homocysteine levels elevated and inversely related to insulin sensitivity in preeclampsia (1999)

Women with preeclampsia have high plasma homocysteine levels that are inversely related to insulin sensitivity.
A Cell Line Expressing Vesicular Stomatitis Virus Glycoprotein Fuses at Low <i>p</i> H (1984)

A stable cell line expressing a complementary DNA clone encoding the vesicular stomatitis virus glycoprotein fused and formed polykaryons at pH 5.5. The formation of polykaryons was dependent on the presence of glycoprotein anchored at the cell surface and could be prevented by incubation of cells with a monoclonal antibody to the glycoprotein. Fusion occurred at a pH 0.5 unit lower than that observed for cells infected with vesicular stomatitis virus.
Addressing the Stability Gap in Photoelectrochemistry: Molybdenum Disulfide Protective Catalysts for Tandem III–V Unassisted Solar Water Splitting (2020)

While photoelectrochemical (PEC) solar-to-hydrogen efficiencies have greatly improved over the past few decades, advances in PEC durability have lagged behind. Corrosion of semiconductor photoabsorbers in the aqueous conditions needed for water splitting is a major challenge that limits device stability. In addition, a precious-metal catalyst is often required to efficiently promote water splitting. Herein, we demonstrate unassisted water splitting using a nonprecious metal molybdenum disulfide nanomaterial catalytic protection layer paired with a GaInAsP/GaAs tandem device. This device was able to achieve stable unassisted water splitting for nearly 12 h, while a sibling sample with a PtRu catalyst was only stable for 2 h, highlighting the advantage of the nonprecious metal catalyst. In situ optical imaging illustrates the progression of macroscopic degradation that causes device failure. In addition, this work compares unassisted water splitting devices across the field in terms of the efficiency and stability, illustrating the need for improved stability.
Two-Step Energy Transfer in Solution (1964)

In the presence of terbium ions, a transfer of energy is observed from 4,4′-dimethoxybenzophenone (DMB) to europium ions. This transfer does not take place in the absence of terbium and it is concluded that the terbium ion serves as an intermediate in the energy transfer. Fluorescence and excitation spectra, fluorescence lifetimes, and time-resolved excitation spectra are presented to substantiate the proposed nonradiative two-step energy transfer.
Foreword (1993)

Undoubtedly, the discovery of the structure of the double helix in 1953 by James Watson and Francis Crick will be recorded as the foremost discovery in biology in this century. In just 40 years, the science of DNA has progressed to the stage where much is known about how genetic information is copied, transcribed, and organized. Moreover, gene therapy is now a reality, and a project to determine the complete sequence of the genomes of a number of organisms is well under way. It thus seemed natural to hold the 1993 Cold Spring Harbor Symposium, our 58th, on the topic of DNA. However, there were many celebratory meetings around the globe in honor of the 40 years of DNA, and we felt it was more appropriate to use the occasion to celebrate another significant milestone: Jim Watson's 25th year as Director of the Cold Spring Harbor Laboratory.
Cyclic Straining of Cell-Seeded Synthetic Ligament Scaffolds: Development of Apparatus and Methodology (2007)

Cyclic tensile strains acting along a ligament implant are known to stimulate cells that colonize it to proliferate and to synthesize an extracellular matrix (ECM), which will then remodel and form a new ligament structure. However, this process of tissue induction is poorly understood. As a first step toward elucidating this process, we aimed to investigate the effect of cyclic tensile strain on the proliferation of, and possible ECM synthesis by, cells colonizing ligament scaffolds. Because there was no commercially available apparatus to undertake such investigation the objectives of this study were to develop an apparatus for the application of cyclic tensile strains on cell-seeded synthetic ligament scaffolds and to develop and validate (through preliminary data obtained using the apparatus) methodology for studying the effect of cyclic strain on cell proliferation. We designed a multi-station test apparatus that operated inside an incubator. It allowed the application of tensile cyclic strains of between 0.5% and 5% at a frequency of 1 Hz on cell-seeded polyester ligament scaffolds immersed in culture medium. Test stations with windows in their bases could be easily de-coupled from the apparatus. This allowed monitoring of cell proliferation and morphology, with inverted light microscopy, through the transparent glass bases of the culture wells. Preliminary experiments lasting for 1 day or 9 weeks examined the effect of selected aspects of the cyclic strain on proliferation of cells seeded onto ligament scaffolds. Tests lasting for 1 day showed that the application of cyclic tensile strain of 5% for 4 h increased cell proliferation 24% above that observed in unstrained controls (p < .05). Scanning electron microscopy data from tests lasting for 9 weeks demonstrated further the dependency of cell proliferation and possible ECM synthesis on the magnitude of the strain. The larger the amplitude, the greater was the coverage of the scaffold with cells and ECM. Transmission electron microscopy of the ECM observed at 9 weeks showed evidence of collagen fibrils aligned in the direction of load in strained scaffolds, whereas the tissue on the control scaffolds was random.