gebhart/patrepeval huggingface dataset:
Ferrocene and Inconel assisted growth of dense carbon nanotube forests on copper foils (2011)

Aligned growth of carbon nanotubes on copper substrates has been achieved using a nickel-based catalyst, Inconel, which is first deposited on the copper foil substrate before the growth of nanotubes via thermal chemical vapor deposition (CVD). An additional catalyst, iron, is supplied by mixing ferrocene with the carbon feedstock, xylene, during the CVD growth. For specific ranges of the film thickness, 10–12 nm, and under certain growth conditions, dense, aligned growth of carbon nanotubes is observed. This technique represents a relatively simple process for direct growth of carbon nanotubes on copper substrates without the need for additional barrier layers and plasma-enhanced CVD techniques. Scanning electron microscopy was used to qualitatively evaluate the density of the nanotubes and the tendency to align in a direction perpendicular to the substrates. Transmission electron microscopy and Raman spectroscopy were used to examine the structure and quality of the nanotubes, as well as the composition of the catalyst particles.
Activation-Free Sulfonyl Fluoride Probes for Fragment Screening (2023)

SuFEx chemistry is based on the unique reactivity of the sulfonyl fluoride group with a range of nucleophiles. Accordingly, sulfonyl fluorides label multiple nucleophilic amino acid residues, making these reagents popular in both chemical biology and medicinal chemistry applications. The reactivity of sulfonyl fluorides nominates this warhead chemotype as a candidate for an external, activation-free general labelling tag. Here, we report the synthesis and characterization of a small sulfonyl fluoride library that yielded the 3-carboxybenzenesulfonyl fluoride warhead for tagging tractable targets at nucleophilic residues. Based on these results, we propose that coupling diverse fragments to this warhead would result in a library of sulfonyl fluoride bits (SuFBits), available for screening against protein targets. SuFBits will label the target if it binds to the core fragment, which facilitates the identification of weak fragments by mass spectrometry.
Proteomic and biological profiling of extracellular vesicles from Alzheimer's disease human brain tissues (2020)

In addition to Aβ and tau, ANXA5, VGF, GPM6A, and ACTZ are new signature proteins in AD EVs.
Work function of small radius carbon nanotubes and their bundles (2007)

Carbon nanotube work functions can deviate from that of graphene due to geometric and structural factors. The authors have systematically investigated the work functions of various forms of small radius carbon nanotubes and their derivatives by density functional calculations. They considered and compared the work functions of tubes and tube bundles in order to understand the effects of chirality, tube length, and capping condition. Systematic trends are unraveled and discussed.
Fast Dissolving Curcumin Cocrystals (2011)

Curcumin is the principal curcuminoid of the popular Indian spice turmeric. Despite the diverse pharmacological activities of this bioactive phenol, its application as a drug is severely limited by poor aqueous solubility. We report novel cocrystals of curcumin (1) with resorcinol and pyrogallol obtained by liquid-assisted grinding. Curcumin–resorcinol (1a) (1:1) and curcumin–pyrogallol (1b) (1:1) were characterized by X-ray diffraction, thermal analysis, FT-IR, FT-Raman, and solid-state 13C NMR spectroscopy. The 1:1 cocrystal stoichiometry is sustained by O–H···O hydrogen bonds between the phenolic OH groups of the coformers to the carbonyl group of curcumin. The melting point of the cocrystals is in between that of curcumin and the coformer and the lower melting cocrystal 1b is more soluble than higher melting 1a. The dissolution rates of curcumin–resorcinol (1a) and curcumin–pyrogallol (1b) in 40% EtOH–water are ∼5 and ∼12 times faster than that for curcumin.
Mable: A Technique for Efficient Machine Simulation (1994)

We present a framework for an efficient instruction-level machine simulator which can be used with existing software tools to develop and analyze programs for a proposed processor architecture. The simulator exploits similarities between the instruction sets of the emulated machine and the host machine to provide fast simulation. Furthermore, existing program development tools on the host machine such as debuggers and profilers can be used without modification on the emulated program running under the simulator. The simulator can therefore be used to debug and tune application code for the new processor without building a whole new set of program development tools. The technique has applicability to a diverse set of simulation problems. We show how the framework has been used to build simulators for a shared-memory multiprocessor, a superscalar processor with support for speculative execution, and a dual-issue embedded processor.
From Caging to Grasping (2011)

This paper digs into the relationship between grasps and cages of a rigid body, in particular into the use of cages as waypoints to grasp an object. We introduce the concept of pregrasping cages, caging configurations from which the object can be reached while maintaining the cage on it. In the well understood case of two-fingered manipulators, the squeezing/stretching caging characterization implies that all cages are indeed pregrasping cages and, as a consequence, are useful waypoints to grasp an object. We show in this paper that the same does not hold for more than two fingers. There are caging configurations from which a grasp of the object cannot be reached without breaking the cage on it. We explore the natural generalization of the squeezing/stretching characterization to the case of n fingers and exploit it to give sufficient conditions for a cage to be a pregrasping cage.
Total Syntheses of Amphidinolide T1, T3, T4, and T5. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
High Current Electron Beam Transport and Focusing at the Linear Induction Accelerator (2020)

The paper is devoted to the theoretical and experimental results of the transport investigation of high current electron beam (5 MeV, 2 kA, 160 ns) generated at the new linear induction accelerator (LIA) at BINP [1], as well as the beam focusing on the target [2].
Creation of Optical Nonlinearity in Organic Polymer-Dye Films by Asymmetric Charge Injection (1995)

Bulk second order optical nonlinearity in organic polymers containing hyperpolarizable dye molecules is normally created by electrostatic field poling at elevated temperature, where the electric field induces a polar alignment of the dyes. In contrast to this approach, we have used asymmetric injection of electric charge into the polymer to create bulk nonlinearity in the polymer [1]. We show that the charge injection mechanism is fundamentally different from dipole alignment of the dye, and has both similarities and differences to poling of glass.
Highly-reliable ultra-thin oxide formation using hydrogen-radical-balanced steam oxidation technology (1994)

A new oxide formation technology featuring oxidation in a strongly reductive ambient followed by an Ar gas annealing has been developed. We call this oxidation method H/sup */-H/sub 2/O oxidation. In this oxidation process, only the strong Si-O bond which is perfectly resistant even to the strongly reductive ambient survives and a high integrity oxide film can be grown. From the results of the breakdown tests by stepped voltage (E/sub BD/) and constant current stress (Q/sub BD/), the gate voltage shift (Vg shift) measurement under constant current stress, and the stress induced leakage current test, it has been revealed that the thin oxide film featuring high-integrity in breakdown and strong immunity from electrical stress is obtained by H/sup */-H/sub 2/O oxidation with post-oxidation-annealing in Ar ambient. This oxidation method is effective to form the thin oxide used under high electric field condition such as a tunnel oxide for flash memories.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Volatile fatty acid and aldehyde abundances evolve with behavior and habitat temperature inSceloporuslizards (2020)

Animal signals evolve by striking a balance between the need to convey information through particular habitats and the limitations of what types of signals can most easily be produced and perceived. Here, we present new results from field measures of undisturbed behavior and biochemical analyses of scent marks from 12 species of <i>Sceloporus</i> lizards to explore whether evolutionary changes in chemical composition are better predicted by measures of species behavior, particularly those associated with visual displays, chemoreception, and locomotion, or by measures of habitat climate (precipitation and temperature). We found that more active lizard species used fewer compounds in their volatile scent marks, perhaps conveying less specific information about individual and species identity. Scent marks from more active lizard species also had higher proportions of saturated fatty acids, and the evolution of these compounds has been tracking the phylogeny closely as we would expect for a metabolic byproduct. In contrast, the proportions of unsaturated fatty acids were better explained by evolutionary shifts in habitat temperature (and not precipitation), with species in warmer climates using almost no volatile unsaturated fatty acids. The proportion of aldehydes was explained by both behavior and environment, decreasing with behavioral activity and increasing with habitat temperature. Our results highlight the evolutionary flexibility of complex chemical signals, with different chemical compounds responding to different elements of the selective landscape over evolutionary time.
Supplementary Figures S1-S6 from Novel Anti-TM4SF1 Antibody–Drug Conjugates with Activity against Tumor Cells and Tumor Vasculature (2023)

&lt;p&gt;Supplementary Figures S1-S6. Supplementary Figure S1. Liquid chromatography electrospray ionization tandem mass spectrometry analysis; Supplementary Figure S2. TM4SF1 expression in human breast and colon cancers; Supplementary Figure S3A. Clearance of anti-TM4SF1 antibody from HUVEC surface; Supplementary Figure S3B. Uptake of anti-TM4SF1 antibody in HUVEC; Supplementary Figure S4A. NSCLC killing by anti-TM4SF1 ADC; Supplementary Figure S4B. Tumor cell killing by anti-TM4SF1 ADC; Supplementary Figure S5. Expression level of TM4SF1 and other endothelial cell markers in tumor xenografts; Supplementary Figure S6. Clearance of anti-TM4SF1 ADCs; tolerance in mice.&lt;/p&gt;
Sensitive and stable pre-calibrated solid-phase extraction columns for environmental and forensic quantification using isotope dilution mass spectrometry (2015)

A technique has been developed to pre-calibrate solid-phase extraction columns for quantification using isotope dilution mass spectrometry.
Identification and Odor Generation Pattern of Odor-Causing Compounds in Digested Biosolids During Long-Term Storage (2011)

Identification and Odor Generation Pattern of Odor-Causing Compounds in Digested Biosolids During Long-Term StorageThe main objective of this research was to identify the compounds responsible for persistent odors in biosolids during long-term storage using olfactometry measurements and to determine their generation pattern with regard to time of appearance and decline using gas chromatography-mass spectrometry (GC-MS). Headspace analysis was used to quantify shortterm odor-causing organic sulfur compounds and...Author(s)Ritika KackerJohn T. NovakMatthew J. HigginsSourceProceedings of the Water Environment FederationSubjectSession 99: Biosolids StabilizationDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2011ISSN1938-6478SICI1938-6478(20110101)2011:9L.6409;1-DOI10.2175/193864711802766731Volume / Issue2011 / 9Content sourceWEFTECFirst / last page(s)6409 - 6429Copyright2011Word count167Subject keywordsBiosolidsOdorsbutyric acidp-cresolindoleskatoleanaerobic digestiondewatering
ChemInform Abstract: PHOTOCHEMISCHE UMWANDLUNGEN 50. MITT. BINORBORNADIENYLIDEN, BIQUADRICYCLANYLIDEN (1974)

Abstract Biquadricyclanyliden (V) wird aus Quadricyclanon (I) nach der Thiadiazolidinmethode synthetisiert.
The potential use of selective 5-HT2Cagonists in treating obesity (2006)

Activation of central 5-HT2C receptors as a strategy for appetite suppression and weight control is supported by animal pharmacology and human clinical studies. Considerable evidence comes from the weight-loss effects of fenfluramine, a non-selective 5-HT2C agonist. Advances in molecular pharmacology have led to an understanding of the effects of 5-HT2C receptor activation on food intake and satiety, in addition to providing insight into the causes of cardiac valvular insufficiency and pulmonary hypertension associated with the use of fenfluramine. However, clinically validated animal models of drug-induced disease and knowledge of the molecular mechanisms of these safety issues is lacking. For this reason, the development of selective 5-HT2C agonists for the treatment of obesity has remained a challenge.
The Farnesyltransferase Inhibitor FTI-277 Suppresses the 24-kDa FGF2-Induced Radioresistance in HeLa Cells Expressing Wild-Type RAS (1999)

In this paper, we describe the effect of the inhibitor of farnesyltransferase (FTI-277) on radioresistance induced by the 24-kDa isoform of FGF2 in human cells expressing wild-type RAS. Treatment with FTI-277 (20 microM) for 48 h prior to irradiation led to a significant decrease in survival of radioresistant cells expressing the 24-kDa isoform (HeLa 3A) but had no effect on the survival of control cells (HeLa PINA). The radiosensitizing effect of FTI-277 is accompanied by a stimulation of postmitotic cell death in HeLa 3A cells and by a reduction in G(2)/M-phase arrest in both cell types. These results clearly demonstrate that at least one farnesylated protein is involved in the regulation of the radioresistance induced by the 24-kDa isoform of FGF2. Furthermore, the radiation-induced G(2)/M-phase arrest is also under the control of farnesylated protein. This work also demonstrates that FTase inhibitors may be effective radiosensitizers of certain human tumors with wild-type RAS.
Zernike expansions for non-Kolmogorov turbulence (1996)

We investigate the expression of non-Kolmogorov turbulence in terms of Zernike polynomials. Increasing the power-law exponent of the three-dimensional phase power spectrum from 2 to 4 results in a higher proportion of wave-front energy being contained in the tilt components. Closed-form expressions are given for the variances of the Zernike coefficients in this range. For exponents greater than 4 a von Kármán spectrum is used to compute the variances numerically as a function of exponent for different outer-scale lengths. We find in this range that the Zernike-coefficient variances depend more strongly on outer scale than on exponent and that longer outer-scale lengths lead to more energy in the tilt terms. The scaling of Zernike-coefficient variances with pupil diameter is an explicit function of the exponent.
Transcriptional Responses of Beauveria bassiana Blastospores Cultured Under Varying Glucose Concentrations (2021)

Culturing the entomopathogenic fungus, <i>Beauveria bassiana</i>, under high glucose concentrations coupled with high aeration results in a fungal developmental shift from hyphal growth to mostly blastospores (yeast-like cells). The underlying molecular mechanisms involved in this shift remain elusive. A systematic transcriptome analysis of the differential gene expression was preformed to uncover the fungal transcriptomic response to osmotic and oxidative stresses associated with the resulting high blastospore yield. Differential gene expression was compared under moderate (10% w/v) and high (20% w/v) glucose concentrations daily for three days. The RNAseq-based transcriptomic results depicted a higher proportion of downregulated genes when the fungus was grown under 20% glucose than 10%. Additional experiments explored a broader glucose range (4, 8, 12, 16, 20% w/v) with phenotype assessment and qRT-PCR transcript abundance measurements of selected genes. Antioxidant, calcium transport, conidiation, and osmosensor-related genes were highly upregulated in higher glucose titers (16-20%) compared to growth in lower glucose (4-6%) concentrations. The class 1 hydrophobin gene (<i>Hyd1</i>) was highly expressed throughout the culturing. <i>Hyd1</i> is known to be involved in spore coat rodlet layer assembly, and indicates that blastospores or another cell type containing hydrophobin 1 is expressed in the haemocoel during the infection process. Furthermore, we found implications of the HOG signaling pathway with upregulation of homologous genes <i>Ssk2</i> and <i>Hog1</i> for all fermentation time points under hyperosmotic medium (20% glucose). These findings expand our knowledge of the molecular mechanisms behind blastospore development and may help facilitate large-scale industrial production of <i>B. bassiana</i> blastospores for pest control applications.
ChemInform Abstract: STUDIES ON THE SYNTHESES OF HETEROCYCLIC COMPOUNDS. 776. CYCLIZATION OF N‐SUBSTITUTED MANDELOHYDRAZIDE WITH FORMALDEHYDE (1979)

Abstract Die Mandelsäurehydrazide (I) kondensieren mit Paraformaldehyd (II) zu den Hexahydrotetrazinen (III), deren Umsetzung mit Acetanhydrid (IV) den Diester (V) liefert, der auch durch Rea tion des Hexahydrotetrazins (VI) mit dem Säurechlorid (VII) zugänglich ist; (V) kan auch aus (I) über den Amidester (IX) sowie (VIII) mit Paraformaldehyd (II) dargestellt werden.
ARN helicasas en dos procesos de desarrollo: variación antigénica y enquistamiento de giardia lamblia (2012)

Además de su importancia médica y veterinaria al ser una de las mayores causas de enfermedad intestinal con origen en el consumo de agua, Giardia es un excelente modelo para estudiar la evolución de importantes procesos celulares, ya que es una de las células eucariotas más primitivas que se conocen. Giardia utiliza dos mecanismos de adaptación a los cambios ambientales que confronta durante su ciclo de vida, ya sea para sobrevivir dentro del intestino del huésped como es la variación de sus antígenos de superficie, o fuera del mismo como es la diferenciación a quiste o enquistamiento. El Objetivo General de nuestro proyecto de investigación es el de comprender los mecanismos de adaptación y diferenciación celular en Giardia lamblia y utilizar esos conocimientos para el desarrollo de metodologías que permitan evitar la enfermedad y/o la transmisión del parásito así como también para definir nuevas técnicas diagnósticas. Las ARN Helicasas están presentes en muchas Archaea, casi todas las Eubacterias y todos los organismos eucariotas, y son necesarias o están involucradas en muchos procesos diferentes del metabolismo del ARN. En células eucariotas se las ha asociado desde la transcripción hasta la degradación del ARN, incluyendo pre-ARNm splicing, exportación del ARNm, biogénesis del ribosoma, iniciación de la traducción y expresión génica en organelas. Resultados previos indican que el mecanismo por el cual Giardia regula la expresión de sus proteínas variables de superficie es a nivel post-transcripcional, utilizando un mecanismo similar a ARN de interferencia. La presencia de los complejos de doble hebra de ARN promueve la acción de ARN Helicasas y ARNasas III que cortan el dsRNA en fragmentos cortos de 21-23 nt. Sin dudas ésta es la primera evidencia de un mecanismo de este tipo que participa fisiológicamente en la regulación génica diferencial. Por otro lado, se ha descripto la interacción de helicasas con deacetilasas de histonas (HDAC), las cuales según estudios realizados en nuestro laboratorio estarían involucradas en la regulación epigenética de la variación antigénica y el enquistamiento. Se busca por lo tanto comprender la participación de ARN Helicasas en ambos procesos de adaptación del parásito, evaluando el grado e importancia de las mismas. En particular se focalizará en la localización subcelular, la interacción con otros componentes de la maquinaria regulatoria y determinación de los dominios involucrados, como también la relación entre sus niveles de expresión y los diferentes fenotipos asociados a estos procesos de adaptación del parásito.
A Method for 3D Printing and Rapid Prototyping of Fieldable Untethered Soft Robots (2022)

Because they are made of elastically deformable and compliant materials, soft robots can passively change shape and conform to their environment, providing potential advantages over traditional robotics approaches. However, existing manufacturing workflows are often labor intensive and limited in their ability to create highly integrated three-dimensional (3D) heterogeneous material systems. In this study, we address this with a streamlined workflow to produce field-deployable soft robots based on 3D printing with digital light processing (DLP) of silicone-like soft materials. DLP-based 3D printing is used to create soft actuators (2.2 g) capable of exerting up to 0.5 Newtons of force that are integrated into a bioinspired untethered soft robot. The robot walks underwater at speeds comparable with its biological analog, the brittle star. Using a model-free planning algorithm and feedback, the robot follows remote commands to move to desired positions. Moreover, we show that the robot is able to perform untethered locomotion outside of a laboratory and in a natural aquatic environment. Our results represent progress in soft robot manufacturing autonomy for a 3D printed untethered soft robot.
Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia (2012)

A circuit level understanding of immune cells and hematological cancers has been severely impeded by a lack of techniques that enable intracellular perturbation without significantly altering cell viability and function. Here, we demonstrate that vertical silicon nanowires (NWs) enable gene-specific manipulation of diverse murine and human immune cells with negligible toxicity. To illustrate the power of the technique, we then apply NW-mediated gene silencing to investigate the role of the Wnt signaling pathway in chronic lymphocytic leukemia (CLL). Remarkably, CLL-B cells from different patients exhibit tremendous heterogeneity in their response to the knockdown of a single gene, LEF1. This functional heterogeneity defines three distinct patient groups not discernible by conventional CLL cytogenetic markers and provides a prognostic indicator for patients' time to first therapy. Analyses of gene expression signatures associated with these functional patient subgroups reveal unique insights into the underlying molecular basis for disease heterogeneity. Overall, our findings suggest a functional classification that can potentially guide the selection of patient-specific therapies in CLL and highlight the opportunities for nanotechnology to drive biological inquiry.
Compact Bragg gratings for long-range surface plasmon polaritons (2006)

By introducing periodic thickness modulation of thin metal stripes embedded in a dielectric, compact and efficient Bragg gratings for long-range surface plasmon polaritons (LR-SPPs) operating around 1550 nm are realized. Reflection and transmission spectra of the gratings having different lengths (from 20 to 160 /spl mu/m), heights (tens of nanometers), and widths of the metal ridges forming the grating were measured, and the reflectivity of up to 60% and bandwidths ranging from 5 to 40 nm are demonstrated. By using a simple lossless-uniform-grating description, the effective refractive-index modulation in LR-SPP gratings is estimated to be of the order of 10/sup -2/, and two different approaches for these calculations are compared. The LR-SPP loss incurred in the investigated gratings is also discussed.