gebhart/patrepeval huggingface dataset:
Strong limits on the 20- m emission from the high-redshift galaxy IRAS 10214 + 4724 (1993)

We report new observations at 20 µm of the high-redshift galaxy IRAS 10214 + 4724 which, if the previous identification is correct, is the most luminous object known. In 6.6 h of integration time using the Infrared Telescope Facility bolometer, we determined the flux density to be 12 ± 18 mJy. Combination of this measurement with a published one made with the same instrument results in a 3 σ upper limit of 23 mJy at 20.0 µm. This strong limit is markedly inconsistent with that expected for this galaxy using published starburst models which fit well the infrared spectral energy distribution at other wavelengths. However, we show that the spectral energy distribution incorporating our result is similar to those of some galaxies that are experiencing intense starbursts, and so our new results provide a basis for modification of the models.
Surface Salt Bridges, Double-Mutant Cycles, and Protein Stability:  an Experimental and Computational Analysis of the Interaction of the Asp 23 Side Chain with the N-Terminus of the N-Terminal Domain of the Ribosomal Protein L9 (2003)

Experimental and theoretical double-mutant cycles have been used to investigate a salt bridge in the N-terminal domain of the protein L9. Aspartic acid 23 is the only acidic residue involved in a well-defined pairwise interaction, namely, a partially solvent-exposed salt bridge with the protonated N-terminus of the protein. Mutations were studied in which Asp 23 was substituted by alanine, asparagine, and nitrile alanine. Interactions with the N-terminus were probed by comparisons between proteins with a protonated and acetylated N-terminus. The mutants were all folded, and the structures were unchanged from wild type as judged by CD and 2-D NMR. The coupling free energy between the N-terminus and the side chain of Asp 23 measured through double-mutant cycle analysis was favorable and ranged from -0.7 to -1.7 kcal mol(-)(1), depending upon the set of mutants used. This relatively large coupling free energy for a surface salt bridge likely arises from geometric factors that reduce the entropy loss associated with salt-bridge formation and from structural relaxation in the mutants. Coupling free energies computed with continuum electrostatic calculations agreed well with the experimental values when full account was taken of all potential interactions, particularly those involving Asp 23 and the acetylated N-terminus as well as interactions with solvent. The measured and calculated coupling free energy decreased only slightly when the salt concentration was increased from 100 to 750 mM NaCl. The calculations suggest that the coupling free energy between D23 and the N-terminus measured through the experimental double-mutant cycle analysis is significantly smaller than the actual interaction free energy between the groups in the wild-type structure because of the inapplicability of assumptions frequently used to interpret double-mutant cycles.
Benefits and challenges of design process that employs a multi-objective optimization approach for industrial applications (2015)

In this paper, total performance of two 20 kVA UPS realizations based on different design processes are compared in terms of losses and volumes. One of the design process employs a multi-objective optimization approach and Pareto analysis for selecting optimal design parameters. The other design process employs traditional industrial design approach. Employing the multi-objective optimization approach and Pareto analysis in the design process enables comparison and selection of suitable combinations of power semiconductor device for achieving minimum semiconductor losses. Thus, not only lower semiconductor losses but also lower heat sink volumes are achieved. In addition, it also enables selection of suitable magnetic material and design parameters, switching frequencies and relative current ripple, for reducing losses and volumes of inductors. As a result, the total volume of realized system based on the optimized design is 47% less than the other realization. On the other hand, costs are considered as one of the most important performance index in the industrial application. Challenges for including systematic costs analysis into the design process are also discussed.
B cells imprint adoptively transferred CD8 + T cells with enhanced tumor immunity (2022)

Our results demonstrate a novel way to use TLR agonists to improve immunotherapy and reveal a vital role for B cells in the generation of potent CD8<sup>+</sup> T cell-based therapies. Our findings have immediate implications in the clinical treatment of advanced solid tumors.
5G Backhaul Challenges and Emerging Research Directions: A Survey (2016)

5G is the next cellular generation and is expected to quench the growing thirst for taxing data rates and to enable the Internet of Things. Focused research and standardization work have been addressing the corresponding challenges from the radio perspective while employing advanced features, such as network densification, massive multiple-input-multiple-output antennae, coordinated multi-point processing, inter-cell interference mitigation techniques, carrier aggregation, and new spectrum exploration. Nevertheless, a new bottleneck has emerged: the backhaul. The ultra-dense and heavy traffic cells should be connected to the core network through the backhaul, often with extreme requirements in terms of capacity, latency, availability, energy, and cost efficiency. This pioneering survey explains the 5G backhaul paradigm, presents a critical analysis of legacy, cutting-edge solutions, and new trends in backhauling, and proposes a novel consolidated 5G backhaul framework. A new joint radio access and backhaul perspective is proposed for the evaluation of backhaul technologies which reinforces the belief that no single solution can solve the holistic 5G backhaul problem. This paper also reveals hidden advantages and shortcomings of backhaul solutions, which are not evident when backhaul technologies are inspected as an independent part of the 5G network. This survey is key in identifying essential catalysts that are believed to jointly pave the way to solving the beyond-2020 backhauling challenge. Lessons learned, unsolved challenges, and a new consolidated 5G backhaul vision are thus presented.
Novel Approaches to the Synthesis and Analysis of Branched RNA (1995)

Abstract This report describes a novel solid-phase synthesis of bRNA. The deprotected branched oligoribonucleotides were analysed by capillary electrophoresis and conveniently characterized by subjecting them to the yeast lariat debranching enzyme.
Statistical estimation of parameters in a disease transmission model: analysis of a Cryptosporidium outbreak (2002)

Population dynamic models, commonly used tools in the study of epidemics and other complex population processes, are implicit non-linear mathematical equations. Inference based on such models can be difficult due to the problems associated with high dimensional parameters that may be non-identified and complex likelihood functions that are difficult to maximize. To address a problem of non-identifiability due to collinearity of parameter estimates in a mathematical model of the 1993 Milwaukee Cryptosporidium parvum outbreak, we examined the utility of a constrained profile likelihood approach. This method was used to study two parameters of interest from the mathematical model: (i). the rate of secondary transmission; (ii). the proportional increase in primary transmission due to water treatment failure. The estimated values of these parameters were shown to depend strongly on poorly understood aspects of Cryptosporidium epidemiology such as asymptomatic proportion and the population immune status. Our analysis demonstrated that the combination of a disease transmission model and a constrained profile likelihood procedure provides an effective approach for inference and estimation of important parameters regulating infectious disease outbreaks.
A Thermodynamic Frame for the Kinetics of Polymer Crystallization under Processing Conditions (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Relative Permeabilities at Near-miscible Conditions - Effects of Connate Water Saturation, Wettability, Hysteresis and Permeability (2011)

We present a series of two-phase (oil and gas) drainage and imbibition relative permeability (kr) curves at near-miscible (IFT=0.04 mN/m) conditions. An equilibrium mixture of methane/n-Butane at 38°C and 1840 psia was used as the oil and gas in the unsteady-state coreflood experiments which were carried out to obtain the kr curves. A high-permeability (1000 mD) and a lower permeability (65 mD) cores were used in the experiments and both water-wet and mixed-wet wettability conditions were examined. The results show that the present of immobile water saturation in water-wet cores could improve oil relative permeabilities and reduce gas relative permeabilities in both imbibition and drainage directions. The results show that despite a very low gas-oil IFT, there is still significant hysteresis between imbibition and drainage cycles for both the oil and gas relative permeabilities in the 65md core. The results help us better understand the impacts of some of the important parameters of multiphase flow through porous media on kr curves and their hysteresis especially in low IFT gas-oil systems and mixed-wet rocks. Obtaining accurate kr and kr hysteresis is extremely important for predicting the performance of gas injection in oil reservoirs.
Pleiotrophin as a Growth Factor and Therapeutic Target in Breast Cancer (1997)

Under goal 1 of this award we studied the mechanisms of regulation of the pleiotrophin (PTN) gene. We discovered a germ line retroviral insertion that contributes to the transcriptional regulation of this gene. Phylogenetic analysis showed that the retroviral insertion happened approximately 25 million years ago and affects tissue-specific expression of the gene. The same retroviral element was found inserted into the human BRCA-1 gene locus suggesting some overlapping regulation mechanisms between the two genes. Under goal 2 the effects of PTN expression were studied and found to contribute to tumorigenicity of non-expressing cells. Under goal 3 we analyzed the functional domains of the PTN protein and studied its signal transduction. We showed that MAP kinase / PI 3-kinase pathways are used for mitogenesis and identified candidate receptor proteins. Most recently, we identified a PTN receptor candidate and now report data on the effects of targeting and depletion of this receptor from human breast cancer cells that express PTN as well as from cells that respond to PTN. We found that the tumor cells utilize the PTN / PTN-receptor interaction in an autocrine manner. Furthermore, we show that depletion of the receptor mRNA also abolishes the ability of PTN to stimulate growth of receptor positive cells. Under goal 4 we studied the effects of the repression of PTN production on the tumorigenic phenotype and showed that PTN expression is rate-limiting for tumor growth, invasion, angiogenesis and metastasis.
ChemInform Abstract: Synthesis and Chemistry of a Dinuclear Iridium Bis‐μ‐oxo Complex: Observation of Oxygen Transfer and Phosphorus‐Carbon Bond Cleavage. (1989)

Abstract The title bis‐μ‐oxo complex (II) rapidly transfers oxygen to CO, isocyanates and phosphines under conversion to the products (III), (VI) and (VIII), respectively.
Direct synthesis and chemical vapor deposition of 2D carbide and nitride MXenes (2022)

Two-dimensional (2D) transition metal carbides and nitrides (MXenes) are a large family of materials actively studied for various applications, especially in the field of energy storage. To date, MXenes are commonly synthesized by etching the layered ternary compounds, MAX phases. Here we demonstrate a direct synthetic route for scalable and atom-economic synthesis of MXenes, including phases that have not been synthesized from MAX phases, by the reactions of metals and metal halides with graphite, methane or nitrogen. These directly synthesized MXenes showed excellent energy storage capacity for Li-ion intercalation. The direct synthesis enables chemical vapor deposition (CVD) growth of MXene carpets and complex spherulite-like morphologies. The latter form in a process resembling the evolution of cellular membranes during endocytosis.
Separation system with a sheath-flow supported electrochemical detector (2023)

An electrochemical detector including side channels associated with a separation channel of a sample component separation apparatus is provided. The side channels of the detector, in one configuration, provide a sheath-flow for an analyte exiting the separation channel which directs the analyte to the electrically developed electrochemical detector.
ChemInform Abstract: Cobalt‐Mediated (2 + 2 + 2)Cycloadditions of Alkynes to the Pyrrole 2,3‐Double Bond: A Novel Construction of Fused Dihydroindoles. (1987)

Abstract The N‐alkynyl or alkynoyl pyrroles (IIIa) ‐ (IIIc) undergo cyclization with the acetylenes (IV) or (IX) in the presence of the coppercarbonyl cyclopentadienyl complex (V), yielding the fused indoles (VI) and (VII) or (X) and (XI).
Voltage polarity effects in GST-based phase change memory: Physical origins and implications (2010)

We show that bias polarity can greatly accelerate device failure in GST- based (GeSbTe) PCM devices, and trace this effect to elemental segregation, initially driven by bias across the melt but then enhanced during the crystallization process. Implications include device, pulse, and materials design for high endurance.
Effect of nitrogen doping into SiO2 studied by photoemission spectroscopy (2003)

Photoemission spectroscopy using synchrotron radiation has been performed on ultrathin Si oxynitride films on Si(001) to investigate a change of the energy-band structure by nitrogen doping. The valence-band spectra obtained by subtracting the contribution of the Si substrate clearly show the difference in nitrogen doping and two valence-band maxima, assigned as SiO2 and Si3N4, are deduced. The chemical analysis in N 1s spectra suggests a possibility that two phases, SiO2 and Si3N4, are separated in the SiOxNy films, since the sample with high nitrogen concentration (1.7×1022 cm−3) shows a valence-band maximum similar to Si3N4. A change of the valence-band maximum by nitrogen doping can be explained by an increase of the Si3N4 domain size in the SiOxNy film.
Host‐bacteria interactions in the intestine: homeostasis to chronic inflammation (2009)

In the past decade it has become clear that the gut constitutes an important frontier of the body, which not only regulates the selective entry of nutrients while keeping vigilant against pathogens but also is largely responsible for shaping the immune response to educate the organism to recognize self from non-self. The very notion of self has undergone a dramatic change, with the acknowledgment that our 'selves' include a plethora of microbial species that actively participate in our body's homeostasis. The immune system continuously adapts to the microbiota in a cyclic, dynamic cross talk where intestinal epithelial cells play an important role in instructing noninflammatory responses for a steady-state control of bacterial growth, or triggering inflammatory mechanisms that can clear the gut from harmful invaders. The system is complex and robust in the sense that many players with partially overlapping roles act to keep the integrity of the intestinal mucosal barrier. Failure of these mechanisms involves genetic and environmental triggers and leads to inflammatory bowel disease. In this review, we seek to collect the state-of-the-art knowledge about how host and microbiota interact to promote gut homeostasis and provide evidences of malfunctioning of the described mechanisms in human inflammatory bowel disease.
Equilibrium configurations of large nanostructures using the embedded saturated-fragments stochastic density functional theory (2017)

An ab initio Langevin dynamics approach is developed based on stochastic density functional theory (sDFT) within a new embedded saturated fragment formalism, applicable to covalently bonded systems. The forces on the nuclei generated by sDFT contain a random component natural to Langevin dynamics, and its standard deviation is used to estimate the friction term on each atom by satisfying the fluctuation-dissipation relation. The overall approach scales linearly with the system size even if the density matrix is not local and is thus applicable to ordered as well as disordered extended systems. We implement the approach for a series of silicon nanocrystals (NCs) of varying size with a diameter of up to 3 nm corresponding to N<sub>e</sub> = 3000 electrons and generate a set of configurations that are distributed canonically at a fixed temperature, ranging from cryogenic to room temperature. We also analyze the structure properties of the NCs and discuss the reconstruction of the surface geometry.
Rules of comparison: a brief historical perspective (2022)

Department of Emergency Medicine, Wayne State University, Detroit, Michigan, USA Received 8 July 2022 Accepted 13 July 2022 Correspondence to Jeffrey A. Kline, MD, Department of Emergency Medicine, Wayne State University, 4201 St. Antoine, 3R-DRH, Detroit, MI, 48201, USA, Tel: +1 317 670 0541; e-mail: [email protected]
The canonical coordinates method for pattern deformation: theoretical and computational considerations (1992)

A method for the analysis of deformed patterns is presented and analyzed. The image is transformed into a new set of coordinates in which the deformation has a particular simple form. A number of deformations are considered. The practical implementation of the method is discussed. Similar aspects of biological vision are also considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Phonon-Assisted Exciton Transfer into Silicon Using Nanoemitters: The Role of Phonons and Temperature Effects in Förster Resonance Energy Transfer (2013)

We study phonon-assisted Förster resonance energy transfer (FRET) into an indirect band-gap semiconductor using nanoemitters. The unusual temperature dependence of this energy transfer, which is measured using the donor nanoemitters of quantum dot (QD) layers integrated on the acceptor monocrystalline bulk silicon as a model system, is predicted by a phonon-assisted exciton transfer model proposed here. The model includes the phonon-mediated optical properties of silicon, while considering the contribution from the multimonolayer-equivalent QD film to the nonradiative energy transfer, which is derived with a d(-3) distance dependence. The FRET efficiencies are experimentally observed to decrease at cryogenic temperatures, which are well explained by the model considering the phonon depopulation in the indirect band-gap acceptor together with the changes in the quantum yield of the donor. These understandings will be crucial for designing FRET-enabled sensitization of silicon based high-efficiency excitonic systems using nanoemitters.
Platform development for expression and purification of stable isotope labeled monoclonal antibodies inEscherichia coli (2018)

The widespread use of monoclonal antibodies (mAbs) as a platform for therapeutic drug development in the pharmaceutical industry has led to an increased interest in robust experimental approaches for assessment of mAb structure, stability and dynamics. The ability to enrich proteins with stable isotopes is a prerequisite for the in-depth application of many structural and biophysical methods, including nuclear magnetic resonance (NMR), small angle neutron scattering, neutron reflectometry, and quantitative mass spectrometry. While mAbs can typically be produced with very high yields using mammalian cell expression, stable isotope labeling using cell culture is expensive and often impractical. The most common and cost-efficient approach to label proteins is to express proteins in Escherichia coli grown in minimal media; however, such methods for mAbs have not been reported to date. Here we present, for the first time, the expression and purification of a stable isotope labeled mAb from a genetically engineered E. coli strain capable of forming disulfide bonds in its cytoplasm. It is shown using two-dimensional NMR spectral fingerprinting that the unlabeled mAb and the mAb singly or triply labeled with <sup>13</sup>C, <sup>15</sup>N, <sup>2</sup>H are well folded, with only minor structural differences relative to the mammalian cell-produced mAb that are attributed to the lack of glycosylation in the Fc domain. This advancement of an E. coli-based mAb expression platform will facilitate the production of mAbs for in-depth structural characterization, including the high resolution investigation of mechanisms of action.
Large-scale 3D Point Cloud Classification Based On Feature Description Matrix By CNN (2018)

Large-scale 3D Point cloud classification is a basic topic for various applications. Traditional geometries features are usually independent of each other and difficult to adapt to a fixed classification model. With the rise of the neural network, deep learning is considered in 3D point cloud application. 3D points are difficult to feed the neural network directly based on deep learning, as they cannot be arranged in a fixed order as image pixels. In this paper, we combine traditional feature-based methods with the Convolutional neural network(CNN) to finish the classification task. The core idea is to construct a feasible structure called Feature Description Matrix(FDM) which encapsulates the local feature of the point to feed CNN for training and testing. By extracting geometry features and designed Feature Description Vectors(FDV) for FDM, a simple mechanism for point cloud classification is given, and experiments validate the effectiveness of our method, with higher classification accuracy compared to state-of-art works.
SCDT-06. QUANTIFIABLE LEVELS OF THE TRANSGENE, CYTOSINE DEAMINASE, IN TUMOR SAMPLES FOLLOWING INTRAVENOUS DELIVERY OF TOCA 511 IN PATIENTS WITH RECURRENT HIGH GRADE GLIOMA (2017)

Toca 511 (vocimagene amiretroprepvec) is an investigational, conditionally lytic, retroviral replicating vector that encodes an optimized yeast cytosine deaminase (CD) gene. The CD gene converts the prodrug, Toca FC (investigational, extended-release 5-fluorocytosine), into the chemotherapeutic, 5-FU in infected tumors. In a Phase 1 study (NCT01985256), Toca 511 was injected intravenously for 1, 3, or 5 days to patients with recurrent high grade glioma. Tumors were subsequently resected, and Toca 511 was injected into the resection cavity walls. At the time of resection, tissue from various regions of the tumor was collected and processed for quantitative PCR analysis of CD RNA and DNA. Tissue from corresponding locations was fixed for assessment of CD protein expression by immunohistochemistry (IHC). Expression of CD protein was quantified based on immunofluorescence signal and was shown to co-localize in cells with detectable levels of gag, a viral structural protein. CD protein expression by IHC was assessed in tissue from locations that corresponded with samples positive for CD by PCR and ranged from 1.16% to 10.4% area of the field. These data show that intravenous delivery of Toca 511 results in appreciable deposition of vector in the tumor. Further, we have observed an inverse correlation between T cell infiltrate in the tumor microenvironment and clinical benefit in a complementary Phase I study in which Toca 511 was solely delivered into the resection cavity. Therefore, the nature of the study design described herein, which uses IV delivery of Toca 511, provides a unique opportunity to assess the spatial relationship between CD protein expression and histological features of the tumor. Immunohistochemical assessment to determine spatial correlates between CD protein and T cells, T regulatory cells, and immunosuppressive myeloid cells will be presented. Updated clinical response data will also be presented.