gebhart/patrepeval huggingface dataset:
Mycobacterium avium Subspecies paratuberculosis Recombinant Proteins Modulate Antimycobacterial Functions of Bovine Macrophages (2015)

It has been shown that Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) activates the Mitogen Activated Protein Kinase (MAPK) p38 pathway, yet it is unclear which components of M. paratuberculosis are involved in the process. Therefore, a set of 42 M. paratuberculosis recombinant proteins expressed from coding sequences annotated as lipoproteins were screened for their ability to induce IL-10 expression, an indicator of MAPKp38 activation, in bovine monocyte-derived macrophages. A recombinant lipoprotein, designated as MAP3837c, was among a group of 6 proteins that strongly induced IL-10 gene transcription in bovine macrophages, averaging a 3.1-fold increase compared to non-stimulated macrophages. However, a parallel increase in expression of IL-12 and TNF-α was only observed in macrophages exposed to a subset of these 6 proteins. Selected recombinant proteins were further analyzed for their ability to enhance survival of M. avium within bovine macrophages as measured by recovered viable bacteria and nitrite production. All 6 IL-10 inducing MAP recombinant proteins along with M. paratuberculosis cells significantly enhanced phosphorylation of MAPK-p38 in bovine macrophages. Although these proteins are likely not post translationally lipidated in E. coli and thus is a limitation in this study, these results form the foundation of how the protein component of the lipoprotein interacts with the immune system. Collectively, these data reveal M. paratuberculosis proteins that might play a role in MAPK-p38 pathway activation and hence in survival of this organism within bovine macrophages.
MRI-Safe Robot for Endorectal Prostate Biopsy (2013)

This paper reports the development of an MRI-Safe robot for direct (interventional) MRI-guided endorectal prostate biopsy. The robot is constructed of nonmagnetic and electrically nonconductive materials, and is electricity free, using pneumatic actuation and optical sensors. Targeting biopsy lesions of MRI abnormality presents substantial clinical potential for the management of prostate cancer. The paper describes MRI-Safe requirements, presents the kinematic architecture, design and construction of the robot, and a comprehensive set of preclinical tests for MRI compatibility and needle targeting accuracy. The robot has a compact and simple 3 degree-of-freedom (DoF) structure, two for orienting a needle-guide and one to preset the depth of needle insertion. The actual insertion is performed manually through the guide and up to the preset depth. To reduce the complexity and size of the robot next to the patient, the depth setting DoF is remote. Experimental results show that the robot is safe to use in any MRI environment (MRI-Safe). Comprehensive MRI tests show that the presence and motion of the robot in the MRI scanner cause virtually no image deterioration or signal to noise ratio (SNR) change. Robot's accuracy in bench test, CT-guided in-vitro, MRI-guided in-vitro and animal tests are 0.37mm, 1.10mm, 2.09mm, and 2.58mm respectively. These values are acceptable for clinical use.
Culture Differences in Advance Care Planning and Implications for Social Work Practice (2021)

Abstract Advance care planning (ACP) is the process of making plans and decisions regarding end-of-life care (EOLC) in advance while one has the physical and cognitive capacity to do so. However, even if health practitioners recognize the importance of ACP, they may be constrained by social and cultural factors in engaging their clients in ACP. This study examined cultural differences in ACP and various strategies that social workers use to initiate conversations on ACP in a range of settings. Using the case study method, we conducted in-depth interviews with 7 social workers who work in South Korea, 2 Korean-American social workers working in the Korean-American communities in the US, and 3 American social workers serving diverse populations in the US. Their practice sites include: university hospitals, day care centers, a community senior center, a nursing home, and a hospice agency. Social workers in both countries emphasized the need to build rapport with their clients early on and to empower them to take the lead in their ACP while they were still healthy. In Korean and Korean-American communities, social workers recognized their clients’ reluctance to speak about EOLC and highlighted the importance of communicating with their family due to their clients’ preference for family-centered decision-making. When doing this, a step-by-step approach in giving relevant information was recommended. We identified relationship-building, empowerment, and culturally sensitive approaches as common strategies in initiating discussions on ACP in both countries.
Intracameral bevacizumab effectively reduces aqueous vascular endothelial growth factor concentrations in neovascular glaucoma (2008)

Vascular endothelial growth factor (VEGF) levels in both the aqueous and vitreous are elevated in ocular ischemia secondary to exudative age-related macular degeneration, diabetes mellitus, and other retinal vascular diseases.1,2 Retinal ischemia upregulates VEGF production resulting in neovascularization of the retina and the iris (NVI). VEGF is significantly elevated in neovascular glaucoma (NVG).3 In the following case series, we demonstrate elevated aqueous VEGF levels in two patients with NVI that significantly declined with concurrent resolution of NVI following off-label intracameral injections of bevacizumab.
Magnetic behavior of yttrium–iron–garnet nanoparticles dispersed in glass composites (2002)

By absorbing amorphous yttrium–iron–garnet (YIG) nanoparticles into nanosized pores of a controlled pore glass (CPG) followed by heat treatment, we synthesized YIG nanocrystal-dispersed glass composites. In a sample which was prepared with a 300 nm pore size CPG and heat treated at 800 °C for 2 h, almost all the amorphous YIG nanoparticles transformed to YIG nanocrystals. The mass fraction of YIG was estimated to be 4.7% from the measured saturation magnetization. In a sample which was prepared from a 49 nm pore size CPG with the same heat treatment, the amount of YIG was estimated to be only 0.54%. Magnetization measurements of different samples revealed that heat treatment at higher temperatures or for longer times resulted in reactions of the YIG particles with the SiO2 of the CPG, and the composites became paramagnetic. However, even in those samples, large initial magnetic susceptibilities were measured, implying the presence of a small amount of unreacted YIG nanocrystals.
Integrated Optics for Microwave and Millimeter Wave Detection and Signal Processing (1990)

Integrated optical electrooptic modulators can play a crucial role in the sensing, control and processing of microwave and millimeter wave signals of phased array antenna systems. Integrated optical single side band modulators with narrowband resonant microwave electrode structures can serve as ideal microwave/optical transducers for antenna elements. The single side band modulation scheme allows the encoding of the microwave frequency and phase information onto an optical carrier shifted by the microwave frequency. This allows the use of coherent optical techniques for beam steering and signal processing of microwave signals used in phased array antenna systems.
Software adaptation in quality sensitive applications to deal with hardware variability (2010)

In this work, we propose a method to reduce the impact of process variations by adapting the application's algorithm at the software layer. We introduce the concept of hardware signatures as the measured post manufacturing hardware characteristics that can be used to drive software adaptation across different die. Using H.264 encoding as an example, we demonstrate significant yield improvements (as much as 40% points at 0% over-design), a reduction in over-design (by as much as 10% points at 80% yield) as well as application quality improvements (about 2.6dB increase in average PSNR at 80% yield). Further, we investigate implications of limited information exchange (i.e. signature measurement granularity) on yield and quality. We show that our proposed technique for determining optimal signature measurement points results in an improvement in PSNR of about 1.3dB over naive sampling for the H.264 encoder. We conclude that hardware-signature based application adaptation is an easy and inexpensive (to implement), better informed (by actual application requirements) and e ffective way to manage yield-cost-quality tradeoffs in application-implementation design flows.
Analytical Construct Resins for Analysis of Solid-Phase Chemistry (2002)

Rapid and unambiguous analysis of reactions performed on resin supports can be achieved by using "analytical constructs". These resins allow the synthesis of materials using solid-phase methods in the usual manner, but they also contain functionality enabling cleavage of analytically enhanced derivatives of the resin-bound products. This is possible due to the use of two linkers bound in series to the polymer. Cleavage at the first linker yields the products attached to an analytical enhancer that facilitates detection. Orthogonal cleavage at the second linker yields the desired products in the usual manner.
Presence of NGAL/MMP-9 complexes in human abdominal aortic aneurysms (2007)

It has been suggested that the intraluminal thrombus of abdominal aortic aneurysms (AAAs) predisposes for AAA enlargement and rupture. The growth of the AAA is dependent on proteolytic degradation of elastin. Here, we analysed whether the neutrophil gelatinase-associated lipocalin (NGAL) is expressed within the thrombus and the aneurysm wall. NGAL can bind to metalloproteinase-9 (MMP-9) and inhibit its degradation, thereby preserving enzymatic activity. Biopsies were obtained from thrombus-free and thrombus-covered aneurysm wall and the intraluminal thrombus from patients undergoing elective surgery for AAA. Immunohistochemistry and real-time PCR were used to study NGAL and MMP-9 expression. Immunoprecipitation, gel zymography, Western blot and ELISA were used to detect and quantify NGAL/MMP-9 complexes. NGAL was detected in the thrombus, the interface between the thrombus and the underlying wall and in the wall itself. Double staining showed that neutrophils are the major source of NGAL expression. Immunoprecipitation of MMP-9 with antibody against NGAL showed that complexes of NGAL and active MMP-9 were present in thrombus, the interface fluid and the aneurysm wall. Western blot analyses using non-reducing conditions and gel zymography demonstrated that high-molecular-weight complexes of NGAL/MMP-9 were present within the different regions. The concentration of the NGAL/MMP-9 complex was highest in the luminal part of the thrombus. In conclusion, NGAL in complex with activated MMP-9 is present in AAA wall and thrombus. Neutrophil-derived NGAL could enhance the proteolytic activity associated with AAA, but the importance of this mechanism for aneurysm growth remains to be shown.
Development of a device for the incorporation of multiple scanivalves into a computer-controlled data system. (1979)

A controller (designated HG-78K) was built to permit manual and computer-directed acquisition of pneumatic data from multiple Scanivalves. The controller incorporated a low cost digital electronic circuit which was designed as a peripheral device on the Hewlett-Packard Interface Bus (HP-IB) to enable computer interrogation of port addresses of multiple Scanivalves. Computer programs were written in BASIC and FORTRAN languages and operation of the system was verified using HP-9830A and HP-21MX computers. (Author)
Algorithmic Computability of the Signal Bandwidth (2021)

The bandwidth of a bandlimited signal is an important number that is relevant in many applications and concepts. For example, according to the Shannon sampling theorem, the bandwidth determines the minimum sampling rate that is required for a perfect reconstruction. In this paper we consider bandlimited signals with finite energy and bandlimited signals that are absolutely integrable and analyze whether the bandwidth of these signals can be determined algorithmically. We employ the concept of Turing computability, a theoretical model that describes the fundamental limits of what can be solved algorithmically on a digital hardware, and ask if, for a given computable bandlimited signal, it is possible to compute its bandwidth on a Turing machine. We show that this is not possible in general, because there exist computable bandlimited signals for which the bandwidth is a non-computable real number. Even the weaker question if the bandwidth of a given signal is smaller than a predefined value cannot be always answered algorithmically. Further, we prove that in the case where the bandwidth in not computable, it is even impossible to algorithmically determine a sequence of upper bounds that converges to the actual bandwidth of the signal. As a positive result, we show that the set of signals whose bandwidth is larger than some given value is semi-decidable.
Early australian clinical studies with pegylated recombinant human megakaryocyte growth and development factor (1998)

Pegylated recombinant human megakaryocyte growth and development factor (PEG-rHuMGDF, an Mpl ligand) is a truncated form of native thrombopoietin currently undergoing clinical development. A series of studies in Australia have examined the safety and biological activities of PEG-rHuMGDF. Administration of PEG-rHuMGDF causes a dose-dependent increase in platelet count but has no effect on white cell count or hematocrit. These platelets are morphologically and functionally normal. When administered following moderately myelosuppressive chemotherapy, PEG-rHuMGDF significantly enhances platelet recovery, although scheduling in relation to chemotherapy may be important in optimizing the full effects. PEG-rHuMGDF mobilizes progenitor cells of multiple hematopoietic lineages, and alters the kinetics of peripheral blood progenitor cell mobilization after chemotherapy and filgrastim. PEG-rHuMGDF is well tolerated and does not cause toxicity similar to that observed with other thrombopoietic cytokines. Numerous studies are underway to help determine the precise role of PEG-rHuMGDF in clinical practice.
Post-traitement des émissions polluantes des moteurs thermiques à combustion interne - Moteurs à allumage commandé (2011)

Dans le domaine des transports et plus precisement celui de l’automobile, l'energie mecanique reste essentiellement produite par des moteurs a combustion interne. Ces dernieres annees, la technologie des processus de combustion a grandement evolue, les specifications des carburants egalement. Pour autant, outre le dioxyde de carbone, l’eau, l’azote et l’oxygene, un grand nombre de polluants reglementes sont encore retrouves a l’echappement des vehicules. La reconnaissance des effets nocifs sur la sante des emissions gazeuses et particulaires a conduit a une reglementation au niveau mondial, et a l’utilisation de dispositifs de post-traitement, comme les catalyseurs et les filtres. Dans l’objectif de reduction des molecules polluantes au sein des mecanismes catalytiques, le role de la chimie apparait fondamental. Dans le cas des moteurs a allumage commande, les gaz residuels renferment autant d'especes oxydantes que d'especes reductrices. Le post-traitement se fait alors, avec un tres bon rendement, sur un catalyseur dit trois-voies.
Synthesis and characterizations of (Mg, Co, Ni, Cu, Zn)O high-entropy oxides (2021)

Abstract High-temperature structural ceramic materials require stability in terms of thermal and mechanical properties. High entropy oxides (HEOs) are among the emerging novel family of advanced ceramic materials with peculiar functional properties. However, their thermal stabilities and mechanical properties are not well investigated. In this work, HEO systems were synthesized from binary oxides of MgO, CoO, NiO, CuO, and ZnO using solid-state reaction method at high temperature, after obtaining the individual oxides through co-precipitation methods. The phase purity of as-synthesized and sintered samples was characterized using X-ray powder diffraction, while the microstructural investigation was performed using Scanning electron microscopy. Mechanical property of the sintered samples at different sintering times and temperatures was investigated and the sample sintered at a sintering temperature of 1200 °C for 15 h sintering time showed a maximum Vickers hardness of about 16 GPa. This result is comparable with some of the hard ceramic materials, and therefore the materials could be a potential candidate for structural applications.
Faculty Opinions recommendation of On the role of electrostatic interactions in the design of protein-protein interfaces. (2002)

Here, the methods of continuum electrostatics are used to investigate the contribution of electrostatic interactions to the binding of four protein-protein complexes; barnase-barstar, human growth hormone and its receptor, subtype N9 influenza virus neuraminidase and the NC41 antibody, the Ras binding domain (RBD) of kinase cRaf and a Ras homologue Rap1A. In two of the four complexes electrostatics are found to strongly oppose binding (hormone-receptor and neuraminidase-antibody complexes), in one case the net effect is close to zero (barnase-barstar) and in one case electrostatics provides a significant driving force favoring binding (RBD-Rap1A). In order to help understand the wide range of electrostatic contributions that were calculated, the electrostatic free energy was partitioned into contributions of individual charged and polar residues, salt bridges and networks involving salt bridges and hydrogen bonds. Although there is no one structural feature that accounts for the differences between the four interfaces, the extent to which the desolvation of buried charges is compensated by the formation of hydrogen bonds and ion pairs appears to be an important factor. Structural features that are correlated with contribution of an individual residue to stability are also discussed. These include partial burial of a charged group in the free monomer, the formation of networks involving charged and polar amino acids, and the formation of partially exposed ion-pairs. The total electrostatic contribution to binding is found to be inversely correlated with buried total and non-polar surface area. This suggests that different interfaces can be designed to exploit electrostatic and hydrophobic forces in very different ways.Copyright 2002 Elsevier Science Ltd. PMID: 12054776 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: GM-30518
Variations in the Quantum Efficiency of Multiple Exciton Generation for a Series of Chemically Treated PbSe Nanocrystal Films (2009)

We study multiple exciton generation (MEG) in two series of chemically treated PbSe nanocrystal (NC) films. We find that the average number of excitons produced per absorbed photon varies between 1.0 and 2.4 (+/-0.2) at a photon energy of approximately 4E(g) for films consisting of 3.7 nm NCs and between 1.1 and 1.6 (+/-0.1) at hnu approximately 5E(g) for films consisting of 7.4 nm NCs. The variations in MEG depend upon the chemical treatment used to electronically couple the NCs in each film. The single and multiexciton lifetimes also change with the chemical treatment: biexciton lifetimes increase with stronger inter-NC electronic coupling and exciton delocalization, while single exciton lifetimes decrease after most treatments relative to the same NCs in solution. Single exciton lifetimes are particularly affected by surface treatments that dope the films n-type, which we tentatively attribute to an Auger recombination process between a single exciton and an electron produced by ionization of the dopant donor. These results imply that a better understanding of the effects of surface chemistry on film doping, NC carrier dynamics, and inter-NC interactions is necessary to build solar energy conversion devices that can harvest the multiple carriers produced by MEG. Our results show that the MEG efficiency is very sensitive to the condition of the NC surface and suggest that the wide range of MEG efficiencies reported in the recent literature may be a result of uncontrolled differences in NC surface chemistry.
Effect of oxidized fats on the nutritive value of proteins. VII. Influence of amino acid supplementation to egg albumin reacted with oxidized lipids on liver lipids of rats. (1976)

Fatty infiltration in the liver of rats fed a low egg albumin diet was apparently disappeared by substituting the protein source for the albumin reacted with oxidized lipids (the mixture of egg albumin-ethyl linoleate (2:1, w/w) was kept at RH 80.4% and at 50°C for 7 days and defatted). The present study deals with the mechanism causing such a phenomenon. The decrease in the content of liver triglyceride (TG) due to feeding the reacted albumin was essentially disturbed by supplementing amino acids for lost ones accompanied by lipid oxidation. Feeding the amino acid mixture simulating the reacted albumin showed the same response to the reacted protein. Supplementation of basic amino acids damaged to the amino acid mixture simulating the reacted albumin increased the content of liver TG, while that of sulfur amino acids inclined to decrease liver TG. These results indicate that the disappearance of fatty liver in rats fed the reacted albumin is almost entirely, but not exclusively, ascribed to the change in the amino acid pattern, particulary to the loss of the basic amino acids. However, since the plasma lipid levels did not respond similarly, participation of other factor (s) could not be excluded.
Localized Quantum Chemistry on Quantum Computers (2021)

Quantum chemistry calculations of large, strongly correlated systems are typically limited by the computation cost that scales exponentially with the size of the system. Quantum algorithms, designed specifically for quantum computers, can alleviate this, but the resources required are still too large for today’s quantum devices. Here we present a quantum algorithm that combines a localization of multireference wave functions of chemical systems with quantum phase estimation (QPE) and variational unitary coupled cluster singles and doubles (UCCSD) to compute their ground state energy. Our algorithm, termed “local active space unitary coupled cluster” (LAS-UCC), scales linearly with system size for certain geometries, providing a polynomial reduction in the total number of gates compared with QPE, while providing accuracy above that of the variational quantum eigensolver using the UCCSD ansatz and also above that of the classical local active space self-consistent field. The accuracy of LAS-UCC is demonstrated by dissociating (H2)2 into two H2 molecules and by breaking the two double bonds in trans-butadiene and resources estimates are provided for linear chains of up to 20 H2 molecules.
Modeling the LPS-induced effects on transcription factor activation and gene expression in murine macrophages (2015)

Macrophages within the liver are of particular importance for a functional defense against bacterial infection. They exhibit a complex response to lipopolysaccharide and secrete a variety of pro-inflammatory cytokines and chemokines that both coordinate the immune response and regulate activity of the macrophages, themselves. In this context, the dynamic of pathway activation and gene expression is important for a better understanding of the role of activated macrophages in healthy and diseased states. Therefore, we present a representative model of LPS-induced macrophage activation that covers the principle regulatory motifs. Based on that, we propose a simplified model with a reduced number of states and parameters that allows estimation of transcription factor activity from gene expression data and can be easily extended to describe the full spectrum of gene regulation in LPS-activated macrophages.