gebhart/patrepeval huggingface dataset:
Thermal and electrical effects of staggered micropin-fin dimensions for cooling of 3D microsystems (2014)

Microfluidic cooling shows promise in cooling next generation 3D microsystems when integrated with through-silicon-vias. In this work, electrical and thermal effects of staggered micropin-fin heat sink dimensions are analyzed using deionized water. An experimental study of five different silicon micropin-fin arrays with a nominal height of 200 μm and diameters down to 30 μm was conducted at flow rates up to approximately 100mL/min and pressure drops up to approximately 200 kPa. The lowest convective thermal resistance achieved was 0.098 °C/W across a 1 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> die. These experimental results were then used to simulate temperature profiles of an interposer-cooled 3D stack.
Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells (2018)

Human immunodeficiency virus (HIV) infection is currently incurable, due to the persistence of latently infected cells. The 'shock and kill' approach to a cure proposes to eliminate this reservoir via transcriptional activation of latent proviruses, enabling direct or indirect killing of infected cells. Currently available latency-reversing agents (LRAs) have however proven ineffective. To understand why, we used a novel HIV reporter strain in primary CD4<sup>+</sup> T cells and determined which latently infected cells are reactivatable by current candidate LRAs. Remarkably, none of these agents reactivated more than 5% of cells carrying a latent provirus. Sequencing analysis of reactivatable vs. non-reactivatable populations revealed that the integration sites were distinguishable in terms of chromatin functional states. Our findings challenge the feasibility of 'shock and kill', and suggest the need to explore other strategies to control the latent HIV reservoir.
Ligands tune the local and global motions of neurotensin receptor 1 (NTS1): a DFT-guided solution NMR analysis (2022)

Summary Unlike many signaling proteins that function as binary switches between ‘on and off’ states, G protein-coupled receptors (GPCRs) exhibit basal activity that can be increased or decreased by numerous ligands. A given receptor can recognize multiple ligands, allosteric modulators, and transducers to create a complex free energy landscape. Many of the lowest energy states have been captured by static structural techniques while detailing the wells’ widths, metastable states, and the transition between them, is still in its infancy. Nuclear magnetic resonance (NMR) spectroscopy can monitor the structure and dynamics of GPCR ensembles across fifteen orders-of-magnitude, but technical challenges have limited its application to super-microsecond timescales. Focusing on a prototypical peptide-binding GPCR, the neurotensin receptor 1 (NTS 1 ), we employed NMR and density functional theory (DFT) to probe global sub-nanosecond motions. The near random coil chemical shifts of the apo receptor produced a poor correlation with theoretical predictions that may indicate a high degree of conformational averaging in solution, a crystallization artifact, or both. Whereas orthosteric agonists and antagonists both rigidified the receptor, but to varying degrees, which suggests conformational entropy differentially contributes to their respective pharmacology. The strong correlations of observed and theoretical chemical shifts lend confidence to interpreting spectra in terms of local structure, methyl dihedral angle geometry, and pico-second timescale transitions. Together, our results suggest a role for sub-nanosecond dynamics and conformational entropy in GPCR ligand discrimination.
Utilization of ICU Rehabilitation Services in Pediatric Patients With a Prolonged ICU Stay* (2021)

Institutional use of rehabilitative services for children with prolonged critical illness varies greatly in the United States. Further research is needed into the potential benefits for patients cared for at centers with high usage of rehabilitation services in the ICU during prolonged critical illness.
Immunocytochemistry of matrix proteins in calcified tissues: functional biochemistry on section (2009)

The organic matrix of calcified tissues comprises collagenous and/or noncollagenous matrix proteins (NCPs). Identification and precise mapping of these matrix components is essential for determining their function, formulating coherent hypotheses on their mechanism(s) of action, and developing novel therapeutic approaches based on biologics. Fibrillar collagen can be readily identified by its conspicuous structure, however, NCPs, in general, do not individually exhibit characteristic structural features that permit to identify them and morphologically determine their localization. To address this limitation, we have used immunocytochemistry, a form of "biochemistry on section", to correlate composition with structure. For cytochemical characterizations, including immunolabeling, our laboratory has opted for colloidal gold labelings and pioneered their application to calcified tissues because they yield high spatial resolution and are quantitative. Over the years, this approach has been applied to identify and map various NCPs in bone and teeth and, in this review of our work, we will emphasize some selected studies that highlight it application to also achieve functional information.
Properties of a Chicken Lymphoblastoid Cell Line From Marek's Disease Tumor (1975)

Properties of a chicken lymphoblastoid cell line (MSB-1) from a Marek's disease tumor were studied. The cell line grew well at 41 degrees C in medium RPMI-1640 supplemented with 10% bovine fetal serum and had a doubling time of 8-12 hours. Cells grown in stationary suspension culture did not attach to the vessel and had the morphology of typical lymphoblasts. At 37 degrees C, the cell line grew initially but ceased to divide after several subcultures. In the subcultures maintained for 48-72 hours, 1-2% of the cells produced Marek's disease virus (MDV)-specific intracellular and mambrane antigens and contained herpesvirus particles when examined by the electron microscope. Cocultivation of these cells with duck or chicken embryo fibroblast cultures resulted in transfer of infection and production of microplaques typical of MDV. Peripheral nerve lesions and lymphoid tumors characteristic of Marek's disease were caused by inoculation of susceptible chicks with MSB-1 cells or duck cells infected with strain BC-1 of MDV recovered from the MSB-1 cell line. No specific tumors were produced at the site of inoculation, and infection was readily transmitted to cagemates. Tumors were also produced in the skeletal muscles and seemed to be largely virus induced. MSB-1 cell line was free of C-type virus particles.
Practical spontaneous metastasis model for in vivo therapeutic studies using a human melanoma. (1991)

In vivo studies aimed at therapy of spontaneous human tumor metastases have been hampered by the lack of practical experimental models. The LOX amelanotic melanoma model described here represents a transplantation model which rapidly and reproducibly results in spontaneous pulmonary metastasis following s.c. inoculation into athymic mice. Pulmonary lesions can be detected using a simple bioassay procedure which is useful for estimation of metastatic cell killing. Using this model we demonstrate that systemic therapy with cyclophosphamide or dacarbazine can produce metastatic cell killing consistent with complete eradication of established pulmonary metastases. This model may also prove useful for future experimental therapeutic studies aimed at prevention of metastases by manipulating tumor staging interval and treatment schedule.
Functional inactivation of the conserved Sem1p in yeast by intrabodies (2003)

Intrabody technology was applied to characterize the function and intracellular localization of a highly conserved Saccharomyces cerevisiae Sem1 protein. DSS1, the mammalian homologue of Sem1p, is functionally conserved between yeast and mammalian cells, and in mammalian cells physically interacts with the strong tumour supressor BRCA2. Yeast and the generated intrabodies are thus expected to offer a useful system for studies on Sem1p/DSS1 function. Sem1p-specific antibody isolated from a phage display library was expressed intracellularily and targeted to either the cytosol or the nucleus of yeast cells. Analysis of the applicability of different antibody fragments as intrabodies showed that the Fab intrabody was expressed most efficiently. Expression of nuclear-targeted anti-Sem1p Fab intrabodies inhibited the growth of the sigma1278b yeast strain in a manner similar to deletion of the SEM1 gene. This indicates that the Fab intrabodies interact in vivo with Sem1p and result in inactivation of Sem1p. Localization of the Fab intrabody with or without the nuclear localization signal to the nucleus in Sem1p-dependent manner suggests that Sem1p mediates the nuclear transport of the intrabody without any targeting signal. Our results suggest that Sem1p function in yeast cells is in part manifested in the nucleus.
Structural basis for angiopoietin-1–mediated signaling initiation (2013)

Angiogenesis is a complex cellular process involving multiple regulatory growth factors and growth factor receptors. Among them, the ligands for the endothelial-specific tunica intima endothelial receptor tyrosine kinase 2 (Tie2) receptor kinase, angiopoietin-1 (Ang1) and Ang2, play essential roles in balancing vessel stability and regression during both developmental and tumor-induced angiogenesis. Despite possessing a high degree of sequence identity, Ang1 and Ang2 have distinct functional roles and cell-signaling characteristics. Here, we present the crystal structures of Ang1 both unbound and in complex with the Tie2 ectodomain. Comparison of the Ang1-containing structures with their Ang2-containing counterparts provide insight into the mechanism of receptor activation and reveal molecular surfaces important for interactions with Tie2 coreceptors and associated signaling proteins. Using structure-based mutagenesis, we identify a loop within the angiopoietin P domain, adjacent to the receptor-binding interface, which confers the specific agonist/antagonist properties of the molecule. We demonstrate using cell-based assays that an Ang2 chimera containing the Ang1 loop sequence behaves functionally similarly to Ang1 as a constitutive Tie2 agonist, able to efficiently dissociate the inhibitory Tie1/Tie2 complex and elicit Tie2 clustering and downstream signaling.
A highly efficient (>6%) Cd₁₋ₓMnₓSe quantum dot sensitized solar cell (2014)

Quantum dot sensitized solar cells (QDSCs) have attracted considerable attention recently and become promising candidates for realizing a cost-effective solar cell. The design and synthesis of quantum dots (QDs) for achieving high photoelectric performance is an urgent need imposed on scientists. Here, we have succeeded in designing a QDSC with a high efficiency η of 6.33% based on Cd₀.₈Mn₀.₂Se quantum dots by facile chemical bath deposition (CBD). The effects of Mn²⁺ ions on the physical, chemical, and photovoltaic properties of the QDSCs are investigated. The Mn²⁺ ions doped into QDs can increase the light harvesting to produce more excitons. In addition, the Mn²⁺ dopant also raises the conduction band of CdSe, accelerates the electron injection kinetics and reduces the charge recombination, improving the charge transfer and collection. The increase of the efficiencies of light-harvesting, charge-transfer and charge-collection results in the improvement of the quantum efficiency of the solar cells. The power conversion efficiency of the solar cell is increased to 6.33% (Vₒc = 0.58 V, Jₛc = 19.15 mA cm⁻², and FF = 0.57).
Framework of joint auction and mixed graph for Licensed Shared Access systems (2015)

Licensed Shared Access offers an opportunity to further increase data rates in 5G networks. Considering that different commercial operators have no knowledge of each other, their base stations should be coordinated by a management entity to enable them to access the licensed shared spectrum without interference. An auction mechanism is often used as an efficient tool for resource allocation where rivalry is high. In this paper, we propose an on-line auction framework using a mixed graph due to the spatial reusability of spectrum. This proposed scheme allows each base station to make a concession by asking for a second shrinking interference-free area if its initial area overlaps some other base stations. We use a mixed graph to model the interference between them, because a mixed graph can quantify the interference much closer to the practical cases than an undirected graph does. We also propose to take the bid comparison into account when grouping the independent nodes in the interference graph. These two feathers together make the spectrum spatial efficiency improved, which leads to a higher revenue and a better buyer satisfaction.
Spectral Signature Multiplexing in Multispectral Camera Communication (2022)

Optical camera communication (OCC) is a technology foreseen to have a fundamental role in future communication applications due to the ubiquity of the cameras embedded in most consumer electronic devices and their increasing capabilities (high resolution, scanning frequency, etcetera). However, high-spectral-resolution cameras, such as multispectral cameras, present particular characteristics that can be exploited to provide new features to OCC links. Furthermore, as LED spectral responses are different when their temperature changes, more than one communication channel can be achieved using the same LED device if the camera can capture those modifications and distinguish the different LED spectral signatures due to the temperature variation. This novel approach is followed in this research, including some equalization techniques applied to the channel matrix to improve the extraction of the transmitted signal in the receiver reducing the inter-channel interference (ICI). This work shows that up to two distinct channels can be obtained with the same LED at different temperatures, getting a bit error rate (BER) below the forward error correction (FEC) limit.
Cluster-based concept invention for statistical relational learning (2004)

We use clustering to derive new relations which augment database schema used in automatic generation of predictive features in statistical relational learning. Entities derived from clusters increase the expressivity of feature spaces by creating new first-class concepts which contribute to the creation of new features. For example, in CiteSeer, papers can be clustered based on words or citations giving "topics", and authors can be clustered based on documents they co-author giving "communities". Such cluster-derived concepts become part of more complex feature expressions. Out of the large number of generated features, those which improve predictive accuracy are kept in the model, as decided by statistical feature selection criteria. We present results demonstrating improved accuracy on two tasks, venue prediction and link prediction, using CiteSeer data.
Principles in quality assurance. Part 1. Sink or swim (2002)

Abstract The regulated pharmaceutical industry is an ocean of complexity and detail through which Quality Assurance (QA) professionals must steer the best course, playing a crucial role in the profitability of the industry and the well‐being of patients. How best to keep the 'good ship' QA stable and effective while being battered by the numerous changing priorities, last‐minute demands, or unforeseen events, is a challenge to us all, and the subject of this paper. The ideas presented here are simple, perhaps simplistic, and stem from the idea that, in order to be effective in this complex environment, we have to find some fundamental unifying concepts that can be applied consistently to our work. Semantics aside, we will consider these unifying concepts to be 'principles' and this paper will describe their definition and application within a bioanalytical Contract Research Organization (CRO). Copyright © 2002 John Wiley &amp; Sons, Ltd.
Microscopic analysis of document handling while reading paper documents to improve digital reading device (2014)

We conducted microscopic analysis on several frequently observed types of work-related reading to find ways to support each type of reading. We obtained empirical data from video recording, concurrent verbal reporting, and retrospective reporting by 18 participants in 10 target types of reading that use paper. Using these data, first, we categorized the ways people interact with paper documents when reading in detail. We analyzed which types of behaviors were frequently observed in each type of reading based on these categories. We will discuss what kind of support is required for each type of reading by specifying what types of behaviors were frequently observed for certain types of reading.
Human Lyme Arthritis and the Immunoglobulin G Antibody Response to the 37-Kilodalton Arthritis-Related Protein of <i>Borrelia burgdorferi</i> (2005)

In Borrelia burgdorferi-infected C3H-scid mice, antiserum to a differentially expressed, 37-kDa spirochetal outer-surface protein, termed arthritis-related protein (Arp), has been shown to prevent or reduce the severity of arthritis. In this study, we determined the immunoglobulin G (IgG) antibody responses to this spirochetal protein in single serum samples from 124 antibiotic-treated human patients with early or late manifestations of Lyme disease and in serial serum samples from 20 historic, untreated patients who were followed longitudinally from early infection through the period of arthritis. These 20 patients were representative of the spectrum of the severity and duration of Lyme arthritis. Among the 124 antibiotic-treated patients, 53% with culture-proven erythema migrans (EM) had IgG responses to recombinant glutathione S-transferase (GST)-Arp, as did 59% of the patients with facial palsy and 68% of those with Lyme arthritis. In addition, 75 to 80% of the 20 past, untreated patients had reactivity with this protein when EM was present, during initial episodes of joint pain, or during the maximal period of arthritis. There was no association at any of these three time points between GST-Arp antibody levels and the severity of the maximal attack of arthritis or the total duration of arthritis. Thus, after the first several weeks of infection, 60 to 80% of patients had IgG antibody responses to GST-Arp, but this response did not correlate with the severity or duration of Lyme arthritis.
Breakthroughs in Photonics 2014: Optical Physical-Layer Network Coding, Recent Developments, and Challenges (2015)

Network coding is a revolutionary technique that can enhance network throughput and protection. This paper introduces optical physical-layer network coding (OPNC) and the recent development of OPNC, with focused discussion on “common-channel” OPNC that can efficiently utilize network resources. It also describes the challenges ahead of OPNC, including incorporating more than two signals for OPNC; circumventing the higher signal processing complexity when higher order modulations are adopted; and exploiting OPNC in more sophisticated multichannel systems.
Specification of flame arresting devices for manifolded low pressure storage tanks (1991)

Abstract The current regulations and accepted recommended practices relating to the use of mechanical flame arresting devices on low pressure, flammable liquid storage tanks will be reviewed. The applicability of these recommendations to typical manifolded tank and closed piping vapor recovery systems, as opposed to the more common “stand alone”, venting to atmosphere storage tanks, will be examined with particular emphasis on the widely varying service conditions that mechanical flame arresting devices may encounter. The limitations placed on the use of commercially available Factory Mutual Approved and Underwriters Laboratories Listed flame arresters will be explained.
Role of endothelial CXCR4 in the development of aortic valve stenosis (2022)

The data collected throughout this study suggest the deletion of CXCR4 in endothelial cells is linked to the development of aortic valve stenosis and left ventricular hypertrophy. The statistically significant parameters measured indicate that endothelial cell CXCR4 plays an important role in aortic valve development and function. We have compiled compelling evidence that EC CXCR4 KO mice can be used as a novel model for AVS.
High‐Capacity NiO–(Mesocarbon Microbeads) Conversion Anode for Lithium‐Ion Battery (2015)

Abstract A conversion‐type, NiO–MCMB (mesocarbon microbeads) composite anode prepared by high‐energy ball milling is here characterized and tested in lithium half and full cells. An optimized and submicrometric morphology allows the NiO–MCMB electrode to achieve high cell performance and excellent rate capability, that is, delivering specific capacities of 515 and 450 mAh g −1 when cycled at current densities as high as 545 and 1090 mA g −1 , respectively. The NiO–MCMB composite anode is studied in a full lithium‐ion battery using a high‐voltage LiNi 0.5 Mn 1.5 O 4 electrode that is considered a suitable cathode in combination with conversion‐type electrodes. The battery delivers a specific capacity of 90 mAh g −1 with high coulombic efficiency and an average working voltage of 4.1 V. The electrochemical results suggest the viability of the alternative cell configuration here adopted for the development of low‐cost, high‐energy‐density lithium‐ion batteries.
ChemInform Abstract: Advances in Radical‐Trapping Antioxidant Chemistry in the 21St Century: A Kinetics and Mechanisms Perspective (2014)

Abstract Review: 165 refs.
A Quantitative Structure−Property Relationship Study of Lithium Cation Basicities (2004)

A quantitative structure−property relationship (QSPR) study of the gas-phase lithium cation basicity of a diverse set of 205 compounds provided a general six-parameter QSPR model (R2 = 0.801; R2cv = 0.785; F = 133.11; s2 = 8.78) using the CODESSA PRO program. Theoretical molecular descriptors, such as the minimum net atomic charge, highest occupied molecular orbital energy, total point-charge component of the molecular dipole, etc., logically explain the reaction equilibrium and electrostatic interaction between a lithium cation and a base.
Recording of the optical identification marks on CD (2006)

In present report the methods of the identification marks creation on the surface which are intended for the determination of licensability of CD production are considered. The main attention is devoted to the methods of the identification marks recording on master disks during the process of CD fabrication.
Orthogonal translation enables heterologous ribosome engineering in E. coli (2021)

The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.