gebhart/patrepeval huggingface dataset:
Empirical Hydrogen Bonding Donor (HBD) Parameters of Organic Solvents Using Solvatochromic Probes – A Critical Evaluation (2023)

The solvatochromicity of established solvatochromic UV/Vis probes, which appear to be sensitive to the so-called hydrogen bond donor (HBD) property of the solvent, is analysed using the hydroxyl group density of alcoholic solvents D<sub>HBD</sub> as a physical parameter in comparison to the pKa, the chemical benchmark for acidity. Reichardt's dye B30, Kosowers Z-indicator 1-ethyl-4-(methoxycarbonyl) pyridinium iodide (K), Kamlet-Tafts α, Dragos S parameter, Catalans SA scale, the cis-dicyano-bis (1,10-phenanthroline) iron II complex (Schilt's Ferrocyphen dye, Fe) and Gutmann's acceptor number (AN) have been investigated. The observed dependencies of the empirical polarity parameters as a function of D<sub>HBD</sub> for several alcoholic solvent families requires a ompletely new physicochemical understanding of these established HBD parameters. Only the AN scale (or Fe) is able to bridge the gap between global polarity and acidity, provided the values are interpreted correctly and applied accordingly.
High-performance optical polymers for low-cost high-port-count planar wavelength-division-multiplexing devices (2002)

High-port-count WDM devices produced in glass optical fibers are difficult to fabricate, and as a result are quite expensive. Polymeric materials, on the other hand, offer the potential to create low-cost highly complex optical interconnection circuitry on a planar substrate. In addition, they provide the possibility for a much higher degree of ruggedness and hermeticity. We have developed in detail one technology for polymeric optical interconnection which addresses the needs of the telecom industry. Our polymeric waveguiding structures are very low loss (0.06 dB/cm at 1550 nm), temperature resistant (they can endure more than 65 years at 100/spl deg/C before a loss of 0.1 dB/cm is thermally induced), humidity resistant (no humidity effects on bare device after 600 hours at 85/spl deg/C 85% RH), and exhibit low dispersion and low birefringence.
Solution Synthesis of a New Thermoelectric Zn1+xSb Nanophase and Its Structure Determination Using Automated Electron Diffraction Tomography (2010)

Engineering materials with specific physical properties have recently focused on the effect of nanoscopic inhomogeneities at the 10 nm scale. Such features are expected to scatter medium- and long-wavelength phonons thereby lowering the thermal conductivity of the system. Low thermal conductivity is a prerequisite for effective thermoelectric materials, and the challenge is to limit the transport of heat by phonons, without simultaneously decreasing charge transport. A solution-phase technique was devised for synthesis of thermoelectric "Zn(4)Sb(3)" nanocrystals as a precursor for phase segregation into ZnSb and a new Zn-Sb intermetallic phase, Zn(1+delta)Sb, in a peritectoid reaction. Our approach uses activated metal nanoparticles as precursors for the synthesis of this intermetallic compound. The small particle size of the reactants ensures minimum diffusion paths, low activation barriers, and low reaction temperatures, thereby eliminating solid-solid diffusion as the rate-limiting step in conventional bulk-scale solid-state synthesis. Both phases were identified and structurally characterized by automated electron diffraction tomography combined with precession electron diffraction. An ab initio structure solution based on electron diffraction data revealed two different phases. The new pseudo-hexagonal phase, Zn(1+delta)Sb, was identified and classified within the structural diversity of the Zn-Sb phase diagram.
Erythropoietin Activates Raf1 by an Shc-Independent Pathway in CTLL-EPO-R Cells (1997)

Stimulation of the erythropoietin receptor (EPO-R) or the interleukin-2 receptor (IL-2-R) by their respective ligands has been reported to activate tyrosine phosphorylation of the cytoplasmic protein, Shc. We have recently characterized a cell line, CTLL-EPO-R, that contains functional cell-surface receptors for both EPO and IL-2. Although stimulation with IL-2 or IL-15 resulted in the rapid, dose-dependent tyrosine phosphorylation of Shc, stimulation with EPO failed to activate Shc. EPO, IL-2, and IL-15 activated the tyrosine phosphorylation of the adaptor protein, Shp2, and the association of Shp2/Grb2/cytokine receptor complexes. In addition, EPO, IL-2, and IL-15 activated Raf1 and ERK2, demonstrating that the Raf1/MEK/MAP kinase pathway was activated. These results indicate that multiple biochemical pathways are capable of conferring a mitogenic signal in CTLL-EPO-R. EPO can activate the Raf1/MEK/MAP kinase pathway via Shc-dependent or Shc-independent pathways, and Shc activation is not required for EPO-dependent cell growth in CTLL-EPO-R.
E-beam lithography experimental results and simulation for the 45-nm node (2004)

E-Beam Lithography is still the driving technology for semiconductor manufacturing of critical levels at the 45nm node. Mask costs, yields and representation of the mask on wafer are important factors to consider. Mask-less E-beam lithography is being considered, but major manufacturing is still done by scanner technology. Therefore the same emphasis on modeling applied in the 1990's on the wafer is now being applied to mask technologies to drive down costs, improve yields and to develop viable mask to wafer transfer patterns. Yield is ultimately connected to process latitude, which is limited by a variety of electron-material interaction issues. As in the optical world, the question is how to maximize the process window considering all the systematic and statistical error sources. Simulation can be used to find out the magnitude of yield limiting effects, and to evaluate the contributing error sources such as PEC file contributions. Film stacks are now becoming an important contributor to statistical error due to technologies such as tri-tone attenuated masks that place a thin layer of chrome over MoSi. In this paper we will compare the SELID E-beam simulation to cross-sections of line-space and contact patterns. Demonstrations of simulation to real data and the use of simulation to further evaluate process window to enhance the learning mode during development cycles will be presented.
High Electron Mobility in [1]Benzothieno[3,2-b][1]benzothiophene-Based Field-Effect Transistors: Toward n-Type BTBTs (2019)

The first example of an n-type [1]benzothieno[3,2-b][1]benzothiophene (BTBT)-based semiconductor, D(PhFCO)-BTBT, has been realized via a two-step transition-metal-free process without using chromatographic purification. Physicochemical and optoelectronic characterizations of the new semiconductor were performed in detail, and the crystal structure was accessed. The new molecule exhibits a large optical band gap (∼2.9 eV) and highly stabilized (ΔELUMO = 1.54 eV)/π-delocalized lowest unoccupied molecular orbital (LUMO) mainly comprising the BTBT π-core and in-plane carbonyl units. The effect of out-of-plane twisted (64°) pentafluorophenyl groups on LUMO stabilization is found to be minimal. Polycrystalline D(PhFCO)-BTBT thin films prepared by physical vapor deposition exhibited large grains (∼2–5 μm sizes) and “layer-by-layer” stacked edge-on oriented molecules with an in-plane herringbone packing (intermolecular distances ∼3.25–3.46 Å) to favor two-dimensional (2D) source-to-drain (S → D) charge transport. The corresponding TC/BG-OFET devices demonstrated high electron mobilities of up to ∼0.6 cm2/V·s and Ion/Ioff ratios over 107−108. These results demonstrate that the large band gap BTBT π-core is a promising candidate for high-mobility n-type organic semiconductors and, combination of very large intrinsic charge transport capabilities and optical transparency, may open a new perspective for next-generation unconventional (opto)electronics.
The Suitability of polyethylene terephthalate copolyester for radiation sterilized dry small volume parenterals (1993)

Small volume parenterals (SVP) are typically terminally sterilized through autoclaving. This technique works when the containers are filled with a liquid. However, in the case of sterile powders, autoclaving is not a viable method nor is dry heat since most products can not withstand 2 50C for a half hour. Thus gamma irradiation may be an acceptable method to terminally sterilize this class of product. One of the drawbacks of gamma irradiation is that it will discolor glass which is currently the package material of choice due to superior barrier properties and relative inertness. This paper explores the possibility of packaging one product in a manner to accept gamma irradiation sterilization. In doing so, the various reguirements of SVP's are reviewed. The package used was a polyethylene terephthalate copolyester (PETG) vial that could withstand the required level of radiation without any discernible effects. The product was tested to determine what level of radiation it could withstand. Finally, product was irradiated and placed on stability to determine whether this package and process are suitable. The PETG vial was found to inadequately protect this product from moisture.
The Dendrimer Effect in Homogeneous Catalysis (2006)

Abstract The immobilization of catalytic groups onto a dendritic support either at the core or at the periphery gives rise to unique properties that affect rates of reaction, substrate activation or selectivity, etc. When advantageous, these properties can be classified as a positive dendrimer effect. Positive dendrimer effects can arise from site isolation, transition state stabilization and/or dielectric effects in the case of core‐modified dendrimers, while peripherally modified dendrimers usually benefit from steric crowding or cooperativity for catalytic residues confined to the surface of the polymer. In this review, the appearance of positive dendrimer effects from the literature will be highlighted as well as prospects for future work in the field.
Collaborative Human-AI (CHAI): Evidence-Based Interpretable Melanoma\n Classification in Dermoscopic Images (2018)

Automated dermoscopic image analysis has witnessed rapid growth in diagnostic\nperformance. Yet adoption faces resistance, in part, because no evidence is\nprovided to support decisions. In this work, an approach for evidence-based\nclassification is presented. A feature embedding is learned with CNNs,\ntriplet-loss, and global average pooling, and used to classify via kNN search.\nEvidence is provided as both the discovered neighbors, as well as localized\nimage regions most relevant to measuring distance between query and neighbors.\nTo ensure that results are relevant in terms of both label accuracy and human\nvisual similarity for any skill level, a novel hierarchical triplet logic is\nimplemented to jointly learn an embedding according to disease labels and\nnon-expert similarity. Results are improved over baselines trained on disease\nlabels alone, as well as standard multiclass loss. Quantitative relevance of\nresults, according to non-expert similarity, as well as localized image\nregions, are also significantly improved.\n
Evaluation of Molecular Modeling of Agonist Binding in Light of the Crystallographic Structure of an Agonist-Bound A2AAdenosine Receptor (2011)

Molecular modeling of agonist binding to the human A(2A) adenosine receptor (AR) was assessed and extended in light of crystallographic structures. Heterocyclic adenine nitrogens of cocrystallized agonist overlaid corresponding positions of the heterocyclic base of a bound triazolotriazine antagonist, and ribose moiety was coordinated in a hydrophilic region, as previously predicted based on modeling using the inactive receptor. Automatic agonist docking of 20 known potent nucleoside agonists to agonist-bound A(2A)AR crystallographic structures predicted new stabilizing protein interactions to provide a structural basis for previous empirical structure activity relationships consistent with previous mutagenesis results. We predicted binding of novel C2 terminal amino acid conjugates of A(2A)AR agonist CGS21680 and used these models to interpret effects on binding affinity of newly synthesized agonists. d-Amino acid conjugates were generally more potent than l-stereoisomers and free terminal carboxylates more potent than corresponding methyl esters. Amino acid moieties were coordinated close to extracellular loops 2 and 3. Thus, molecular modeling is useful in probing ligand recognition and rational design of GPCR-targeting compounds with specific pharmacological profiles.
A Study of Interference Distributions in Millimeter Wave Cellular\n Networks (2019)

We study the distribution of the interference power in a millimeter wave\n(mmWave) cellular network. Such interference is random and highly dependent on\nthe employed transmission technique, as well as the varying channel conditions\nand the varying association between users and base stations. Traditional\nnetworks at lower frequencies usually employ omnidirectional transmission which\ncreates an (almost) equal amount of interference in any direction. MmWave\nnetworks, however, must employ directional beamforming transmission in order to\ncompensate for the high path loss in mmWave frequency bands. These directional\ntransmissions drastically change the network interference structure. We examine\nthe interference power distributions in an mmWave network employing beamforming\ntransmission under different user association schemes, and contrast with those\nunder omnidirectional transmission. Numerical results using an analytical\nmmWave channel model and a measurement-based channel generator, NYUSIM, show\nthat beamforming not only reduces the amount of strong interference and hence\nsignificantly enhances network throughput, but also user association can\nconsiderably alter network interference and throughput structures.\n
ChemInform Abstract: Design of Modified Amine Transfer Reagents Allows the Synthesis of α‐Chiral Secondary Amines via CuH‐Catalyzed Hydroamination. (2015)

Abstract The described method for the synthesis of chiral secondary amines uses a modified monoalkylamine transfer reagent, which limits side and competitive reactions of previously reported methods.
Supplementary Figures from A Synthetic DNA, Multi-Neoantigen Vaccine Drives Predominately MHC Class I CD8<sup>+</sup> T-cell Responses, Impacting Tumor Challenge (2023)

&lt;p&gt;Supplementary Figures S1-8&lt;/p&gt;
Cellular Response of Polyvalent Oligonucleotide—Gold Nanoparticle Conjugates* (2020)

Nanoparticles are finding utility in myriad biotechnological applications, including gene regulation, intracellular imaging, and medical diagnostics. One nanomaterial that is particularly promising for therapeutic and diagnostic applications is the polyvalent oligonucleotide-gold nanoparticle. The surface chemistry on the nanoparticle can greatly affect the rate of cellular uptake for the nanoconjugates. The changes associated with the citrate-stabilized nanoparticles are likely due to the citrate molecule’s weak association with the gold nanoparticle core. The number of nanoparticles in each sample was calculated based on the concentration of gold found in the sample. The changes associated with the citrate-stabilized nanoparticles are likely due to the citrate molecule’s weak association with the gold nanoparticle core. Indeed, in cell culture medium, the citrate-stabilized nanoparticles quickly aggregate, indicated by a red shift in their plasmon resonance and a concomitant color change from red to purple, and settle to the bottom of the culture flask over time.
Comprehensive anti-derivatives and parametric continuity (2018)

We present a poster and software demonstration regarding the calculation of indefinite integrals, or anti-derivatives, when parameters are present.
An Ada-compatible distributed database management system (1987)

Adaplex is an integrated language for programming database applications. It results from the embedding of the database sublanguage Daplex in the general-purpose programming language Ada [1]. This paper describes the design of DDM, a general-purpose distributed database management system implemented in Ada that supports the use of Adaplex as interface language. There are two novel aspects in the design of this system. First, this is the first full-scale distributed database system to support a semantically rich, functional data model. DDM goes beyond systems like Distributed INGRES and R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">*</sup> (which are based on the relational technology) in providing advanced data modeling capabilities and ease of use. Second, this is the first full-function distributed DBMS designed to be compatible with the Ada programming environment. The coupling between Ada and Daplex has been achieved at the expression level which is much tighter than the statement level integration attained in previous systems. This tight coupling poses new implementation problems but also creates new opportunities for optimization. The current paper highlights the Adaplex language and discusses innovative aspects in DDM's design that are intended to meet the dual objectives of good performance and high data availability.
A Glass Hook Allows Fishing of Hexa‐peri‐hexabenzocoronene Graphitic Nanotubes: Fabrication of a Macroscopic Fiber with Anisotropic Electrical Conduction (2006)

Fishing of graphitic nanotubes with a macroscopic glass hook: A ∼30 mm long fiber (see figure and cover) is readily processed from a suspension of self-assembled nanotubes with one-handed helical chirality, formed from the (R)- or (S)-enantiomer of chiral amphiphile 2. The majority of the nanotubes in the fiber are unidirectionally oriented along the fiber axis. Upon doping with I2, the fiber displays an anisotropic electrical conduction along the fiber axis more than an order of magnitude greater than that across the fiber axis.
Simultaneous Separation of Negatively and Positively Charged Species in Dynamic Field Gradient Focusing Using a Dual Polarity Electric Field (2009)

Dynamic field gradient focusing (DFGF) utilizes an electric field gradient established by a computer-controlled electrode array to separate and concentrate charged analytes at unique axial positions. Traditionally, DFGF has been restricted to the analysis of negatively charged species due to limitations in the software of our voltage controller. This paper introduces a new voltage controller capable of operating under normal polarity (positive potentials applied to the electrode array) and reversed polarity (negative potentials applied to the electrode array) for the separation of negatively and positively charged analytes, respectively. The experiments conducted under normal polarity and reversed polarity illustrate the utility of the new controller to perform reproducible DFGF separations (elution times showing less than 1% run-to-run variation) over a wide pH range (3.08 to 8.5) regardless of the protein charge. A dual polarity experiment is then shown in which the separation channel has been divided into normal polarity and reversed polarity regions. This simultaneous separation of negatively charged R-phycoerythrin (R-PE) and positively charged cytochrome c (CYTC) within the same DFGF apparatus is shown.
Model-Independent Extraction of Adhesion Energy from Indentation Experiments (2008)

We present a model-independent method for extraction of adhesion energy from indentation experiments in which force, deflection, and contact area are measured. It is based on calculating the difference between external work supplied and stored strain energy, the deficit, which is assigned as work expended in opening (or closing) an interface. The critical step in the method is determination of the elastic indentation response without adhesion, using measured compliance. We show that this model-independent method accurately reproduces results obtained using the Johnson-Kendall-Roberts theory when it is applicable, and is particularly useful when an analytical contact mechanics solution is unavailable.
A 50-GBaud QPSK Optical Receiver With a Phase/Frequency Detector for Energy-Efficient Intra-Data Center Interconnects (2022)

This paper describes the energy-efficient realization of a QPSK optical receiver (CoRX) for short-reach intra-datacenter interconnects based on analog coherent detection. The CoRX comprises inphase and quadrature channels for each polarization and a high-speed phase-frequency detector (PFD) that provides feedback to stabilize an optical local oscillator (LO) and maintain coherence with the received optical signal. Each receive (RX) channel consists of a transimpedance amplifier (TIA) based on a Cherry-Hooper emitter follower (CHEF). The electronic RX is implemented in a 130-nm SiGe HBT technology ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$f_{T} = 300$ </tex-math></inline-formula> GHz), consumes 534 mW of DC power for a total electrical RX energy efficiency of 5.34 pJ/bit, and occupies 2.8 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$mm^{2}$ </tex-math></inline-formula> . Electrical characterization of the CoRX on an FR-4 PCB assembly demonstrates operation up to 60 GBaud with a bit error rate (BER) of less than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−12</sup> . A co-packaged optical/electrical CoRX assembly with a silicon photonic receiver is characterized using a commercial-off-the-shelf quadrature phase-shift keying (QPSK) transmitter for constellations up to 50 GBaud (100 Gbps) at BER below KP4-FEC ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2.2\times 10^{-4}$ </tex-math></inline-formula> ).
Frame-shifted APOBEC3A encodes two alternative proapoptotic proteins that target the mitochondrial network (2021)

The human APOBEC3A (A3A) cytidine deaminase is a powerful DNA mutator enzyme recognized as a major source of somatic mutations in tumor cell genomes. However, there is a discrepancy between APOBEC3A mRNA levels after interferon stimulation in myeloid cells and A3A detection at the protein level. To understand this difference, we investigated the expression of two novel alternative "A3Alt" proteins encoded in the +1-shifted reading frame of the APOBEC3A gene. A3Alt-L and its shorter isoform A3Alt-S appear to be transmembrane proteins targeted to the mitochondrial compartment that induce membrane depolarization and apoptosis. Thus, the APOBEC3A gene represents a new example wherein a single gene encodes two proapoptotic proteins, A3A cytidine deaminases that target the genome and A3Alt proteins that target mitochondria.
Rapid selection of escape mutants by the first CD8 T cell responses in acute HIV-1 infection (2008)

The recent failure of a vaccine that primes T cell responses to control primary HIV-1 infection has raised doubts about the role of CD8+ T cells in early HIV-1 infection. We studied four patients who were identified shortly after HIV-1 infection and before seroconversion. In each patient there was very rapid selection of multiple HIV-1 escape mutants in the transmitted virus by CD8 T cells, including examples of complete fixation of non-synonymous substitutions within 2 weeks. Sequencing by single genome amplification suggested that the high rate of virus replication in acute infection gave a selective advantage to virus molecules that contained simultaneous and gained sequential T cell escape mutations. These observations show that whilst early HIV-1 specific CD8 T cells can act against virus, rapid escape means that these T cell responses are unlikely to benefit the patient and may in part explain why current HIV-1 T cell vaccines may not be protective.