gebhart/patrepeval huggingface dataset:
Carbonate Complexation of Mn<sup>2+</sup> in the Aqueous Phase:  Redox Behavior and Ligand Binding Modes by Electrochemistry and EPR Spectroscopy (2006)

The chemical speciation of Mn2+ within cells is critical for its transport, availability, and redox properties. Herein we investigate the redox behavior and complexation equilibria of Mn2+ in aqueous solutions of bicarbonate by voltammetry and electron paramagnetic resonance (EPR) spectroscopy and discuss the implications for the uptake of Mn2+ by mangano-cluster enzymes such as photosystem II (PSII). Both the electrochemical reduction of Mn2+ to Mn0 at an Hg electrode and EPR (in the absence of a polarizing electrode) revealed the formation of 1:1 and 1:2 Mn-(bi)carbonate complexes as a function of Mn2+ and bicarbonate concentrations. Pulsed EPR spectroscopy, including ENDOR, ESEEM, and 2D-HYSCORE, were used to probe the hyperfine couplings to 1H and 13C nuclei of the ligand(s) bound to Mn2+. For the 1:2 complex, the complete 13C hyperfine tensor for one of the (bi)carbonate ligands was determined and it was established that this ligand coordinates to Mn2+ in bidentate mode with a 13C-Mn distance of 2.85 +/- 0.1 angstroms. The second (bi)carbonate ligand in the 1:2 complex coordinates possibly in monodentate mode, which is structurally less defined, and its 13C signal is broad and unobservable. 1H ENDOR reveals that 1-2 water ligands are lost upon binding of one bicarbonate ion in the 1:1 complex while 3-4 water ligands are lost upon forming the 1:2 complex. Thus, we deduce that the dominant species above 0.1 M bicarbonate concentration is the 1:2 complex, [Mn(CO3)(HCO3)(OH2)3]-.
Modern Cardiac Valve Devices? Bioprostheses and Mechanical Prostheses: State of the Art (1993)

The choice of bioprostheses and mechanical prostheses as valvular substitutes for cardiac valve replacement surgery has existed for over 20 years. The extensive developments over the past three decades have been introduced to reduce or eliminate valve related complications, namely thromboembolism, anticoagulant related hemorrhage, and structural failure, as well as to optimize hemodynamic performance. The biological valvular prostheses, namely porcine aortic or bovine pericardium, have been developed with tissue preservation, together with stent designs, that contribute to preservation of anatomical characteristics and biomechanical properties of the leaflets. The mechanical prostheses have been developed to eliminate structural failure, to facilitate prevention of blood status and thrombus formation, to facilitate radiopacity for evaluation of prosthesis function, and to facilitate intraoperative leaflet positioning. The implantation of the various present generation bioprostheses and mechanical prostheses requires special considerations to avoid technical complications and support ventricular performance. The studies of biological and mechanical prostheses, both randomized and nonrandomized, as well as specific prosthesis assessments, have contributed to the establishment of indications for types of prostheses. Bioprostheses have a high risk of structural failure and reoperation, while mechanical prostheses have a high risk of thromboembolism and anticoagulant hemorrhage. Within the bioprostheses population, the risk factors for structural valve deterioration are younger age and mitral prosthesis. Older patients (> 65 years of age) have a greater risk of valve related complications with mechanical prostheses, while younger patients (< 40 years of age) are at greater risk with bioprostheses. Comparison of large bioprostheses and mechanical prostheses populations by age groups revealed that regardless of the differences in the freedom from structural valve deterioration, the freedom from treatment failure (valve related mortality and permanent impairment from thromboembolism, anticoagulant hemorrhage, and septal emboli from prosthetic valve endocarditis) is essentially the same for mechanical prostheses and bioprostheses at 10 years. The quality of life is superior with bioprostheses, while patient survival and total valve related morbidity/mortality are similar with both types of prostheses.
Physical properties of gasoline/methanol mixtures (1977)

Experimental work was done to relate selected physical properties of gasoline/methanol solutions, containing contaminant levels of water, to compositional and physical properties of the blending gasoline. Water tolerance, octane number, vapor pressure, and distillation data are presented for eight gasolines and for their methanol solutions at methanol levels up to 20 wt-pct. The water tolerances of these fuels were strongly dependent upon temperature, methanol concentration, and gasoline composition. To cover a wider range of compositional effects, water tolerance measurements were made at selected methanol levels on a variety of individual hydrocarbons, refinery stocks, and gasolines selected for specific compositional characteristics. These selections provided a sufficient range of property variation for the data to permit useful water-tolerance/gasoline composition correlations. The results presented in this report supplement and expand published data on water tolerances of gasoline/methanol mixtures. It is shown that an estimate can be made of the water tolerance of a gasoline/methanol mixture when the composition of the gasoline is known in sufficient detail. Portions of the D-86 distillation curves of gasoline/methanol mixtures can be estimated from a knowledge of the base gasoline distillation curves. In the region of 5 to 20 pct methanol content, vapor pressures can be estimated from those of the gasolines. The blending octane numbers resulting from the study agree well with previously published values. The referenced material and their associated bibliographies are intended to serve as a source of information regarding previous work on methanol and methanol/gasoline solutions for use as automotive fuel.
The Transcriptome of the Baculovirus Autographa californica Multiple Nucleopolyhedrovirus in Trichoplusia ni Cells (2013)

Baculoviruses are important insect pathogens that have been developed as protein expression vectors in insect cells and as transduction vectors for mammalian cells. They have large double-stranded DNA genomes containing approximately 156 tightly spaced genes, and they present significant challenges for transcriptome analysis. In this study, we report the first comprehensive analysis of AcMNPV transcription over the course of infection in Trichoplusia ni cells, by a combination of strand-specific RNA sequencing (RNA-Seq) and deep sequencing of 5' capped transcription start sites and 3' polyadenylation sites. We identified four clusters of genes associated with distinctive patterns of mRNA accumulation through the AcMNPV infection cycle. A total of 218 transcription start sites (TSS) and 120 polyadenylation sites (PAS) were mapped. Only 29 TSS were associated with a canonical TATA box, and 14 initiated within or near the previously identified CAGT initiator motif. The majority of viral transcripts (126) initiated within the baculovirus late promoter motif (TAAG), and late transcripts initiated precisely at the second position of the motif. Analysis of 3' ends showed that 92 (77%) of the 3' PAS were located within 30 nucleotides (nt) downstream of a consensus termination signal (AAUAAA or AUUAAA). A conserved U-rich region was found approximately 2 to 10 nt downstream of the PAS for 58 transcripts. Twelve splicing events and an unexpectedly large number of antisense RNAs were identified, revealing new details of possible regulatory mechanisms controlling AcMNPV gene expression. Combined, these data provide an emerging global picture of the organization and regulation of AcMNPV transcription through the infection cycle.
Pedometer Measures of Free-Living Physical Activity: Comparison of 13 Models (2004)

The KZ, YX200, NL, and YX701 appear to be suitable for most research purposes. Given the potential for pedometers in physical activity research, it is necessary that there be consistency across studies in the measurement of "steps per day."
Advanced solder bumping technology through super solder (2002)

Furukawa Electric has developed method of eluding high-purity solder directly onto fine-pitch contacts through lattice substitution, called Super Solder (SS). The technology has already been adopted in precoating for boards mounting Pentium chips. SS supplies solder to fine-pitch electrode pads through a very simple process consisting of paste coat and heating, and is well suited to the needs of bump formation, especially on boards. This paper covers the configuration and characteristics of a production line providing fully-automatic bump formation with high yield, low labor requirements, and at a low capital investment.
Pulse of the city: Visualizing Urban Dynamics of Special Events (2010)

How does a city perform during a special event? How can we inform local authorities and urban dwellers of public happenings? Until today it has been difficult to monitor urban dynamics in real time. Traditional methods, like head counts, surveys, and aerial inspection, are costly and limited. In this paper we present our twofold approach to the processing and visualization of real time information gathered from the telecommunication infrastructures that percolate modern cities. This paper presents visualizations for a popular audience that examine the social psychogeography of the cityscape. Our work is a step towards understanding the functions of the city through digitally-enabled urban functions such as the pervasive telecommunications network. Based on an analysis of data from a telecom network, we illustrate how special events influence the
On Channel Reliability Measure Training for Multi-Camera Face Recognition (2007)

Single-camera face recognition has severe limitations when the subject is not cooperative, or there are pose changes and different illumination conditions. Face recognition using multiple synchronized cameras is proposed to overcome the limitations. We introduce a reliability measure trained from examples to evaluate the inherent quality of channel recognition. The recognition from the channel predicted to be the most reliable is selected as the final recognition results. In this paper, we enhance Adaboost to improve the component based face detector running in each channel as well as the channel reliability measure training. Effective features are designed to train the channel reliability measure using data from both face detection and recognition. The recognition rate is far better than that of either single channel, and consistently better than common classifier fusion rules
X-parameter measurement challenges for unmatched device characterization (2010)

X-parameter technology provides simulation-based design of non-linear circuits with inherent accuracy that is attributed to measurement-based model extraction. Recent advancements have combined Non-linear Vector Network Analyzer measurements with impedance tuners to compliment the equivalent accuracy of load-pull measurements with the analytic convenience of equation-based large-signal models. This paper investigates the challenges incurred when modeling high-power transistors under variable complex impedance matching conditions. It also compares the predicted performance of the X-parameter model against an independent large-signal model provided by the manufacturer for a 10W transistor. The results show a good correlation between the two models when compared under load-pull impedance modulation.
Handling data skew in parallel hash join computation using two-phase scheduling (2002)

A large number of parallel join algorithms has been proposed to maintain load-balancing in the presence of data skew. However, one important type of data skew-join product skew (JPS)-has been little studied. In this paper, a dynamic parallel join algorithm, which employs a two-phase scheduling procedure, is designed to handle the JPS problem. Two sets of scheduling heuristics are studied against various parameters. It is shown that many of the existing algorithms can be regarded as a special case of our algorithm, whose cost is based on the nature of data skew. While it can cope with JPS which other algorithms cannot approach, it can be as efficient as most existing algorithms when JPS does not exist.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Correction: Alternative mRNA Splicing from the Glial Fibrillary Acidic Protein (GFAP) Gene Generates Isoforms with Distinct Subcellular mRNA Localization Patterns in Astrocytes (2013)

The intermediate filament network of astrocytes includes Glial fibrillary acidic protein (Gfap) as a major component. Gfap mRNA is alternatively spliced resulting in generation of different protein isoforms where Gfapa is the most predominant isoform. The Gfapd isoform is expressed in proliferating neurogenic astrocytes of the developing human brain and in the adult human and mouse brain. Here we provide a characterization of mouse Gfapd mRNA and Gfapd protein. RT-qPCR analysis showed that Gfapd mRNA and Gfapa mRNA expression is coordinately increased in the post-natal period. Immunohistochemical staining of developing mouse brain samples showed that Gfapd is expressed in the sub-ventricular zones in accordance with the described localization in the developing and adult human brain. Immunofluorescence analysis verified incorporation of Gfapd into the Gfap intermediate filament network and overlap in Gfapd and Gfapa subcellular localization. Subcellular mRNA localization studies identified different localization patterns of Gfapd and Gfapa mRNA in mouse primary astrocytes. A larger fraction of Gfapa mRNA showed mRNA localization to astrocyte protrusions compared to Gfapd mRNA. The differential mRNA localization patterns were dependent on the different 39-exon sequences included in Gfapd and Gfapa mRNA. The presented results show that alternative Gfap mRNA splicing results in isoform-specific mRNA localization patterns with resulting different local mRNA concentration ratios which have potential to participate in subcellular region-specific intermediate filament dynamics during brain development, maintenance and in disease.
The Mechanism and Significance of Deletion of Parasite-specific CD4<b><sup>+</sup></b>T Cells in Malaria Infection (2002)

It is thought that both helper and effector functions of CD4(+) T cells contribute to protective immunity to blood stage malaria infection. However, malaria infection does not induce long-term immunity and its mechanisms are not defined. In this study, we show that protective parasite-specific CD4(+) T cells were depleted after infection with both lethal and nonlethal species of rodent PLASMODIUM: It is further shown that the depletion is confined to parasite-specific T cells because (a) ovalbumin (OVA)-specific CD4(+) T cells are not depleted after either malaria infection or direct OVA antigen challenge, and (b) the depletion of parasite-specific T cells during infection does not kill bystander OVA-specific T cells. A significant consequence of the depletion of malaria parasite-specific CD4(+) T cells is impaired immunity, demonstrated in mice that were less able to control parasitemia after depletion of transferred parasite-specific T cells. Using tumor necrosis factor (TNF)-RI knockout- and Fas-deficient mice, we demonstrate that the depletion of parasite-specific CD4(+) T cells is not via TNF or Fas pathways. However, in vivo administration of anti-interferon (IFN)-gamma antibody blocks depletion, suggesting that IFN-gamma is involved in the process. Taken together, these data suggest that long-term immunity to malaria infection may be affected by an IFN-gamma-mediated depletion of parasite-specific CD4(+) T cells during infection. This study provides further insight into the nature of immunity to malaria and may have a significant impact on approaches taken to develop a malaria vaccine.
Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations (2021)

The novel coronavirus disease, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), rapidly spreading around the world, poses a major threat to the global public health. Herein, we demonstrated the binding mechanism of PF-07321332, α-ketoamide, lopinavir, and ritonavir to the coronavirus 3-chymotrypsin-like-protease (3CL<sup>pro</sup>) by means of docking and molecular dynamic (MD) simulations. The analysis of MD trajectories of 3CL<sup>pro</sup> with PF-07321332, α-ketoamide, lopinavir, and ritonavir revealed that 3CL<sup>pro</sup>-PF-07321332 and 3CL<sup>pro</sup>-α-ketoamide complexes remained stable compared with 3CL<sup>pro</sup>-ritonavir and 3CL<sup>pro</sup>-lopinavir. Investigating the dynamic behavior of ligand-protein interaction, ligands PF-07321332 and α-ketoamide showed stronger bonding via making interactions with catalytic dyad residues His41-Cys145 of 3CL<sup>pro</sup>. Lopinavir and ritonavir were unable to disrupt the catalytic dyad, as illustrated by increased bond length during the MD simulation. To decipher the ligand binding mode and affinity, ligand interactions with SARS-CoV-2 proteases and binding energy were calculated. The binding energy of the bespoke antiviral PF-07321332 clinical candidate was two times higher than that of α-ketoamide and three times than that of lopinavir and ritonavir. Our study elucidated in detail the binding mechanism of the potent PF-07321332 to 3CL<sup>pro</sup> along with the low potency of lopinavir and ritonavir due to weak binding affinity demonstrated by the binding energy data. This study will be helpful for the development and optimization of more specific compounds to combat coronavirus disease.
Immunoglobulin E antibodies to pollens augmented in dogs by virus vaccines (1983)

An inbred "atopic dog colony" was established to study the effect of viruses on immunoregulation of immunoglobulin (Ig) E antibodies. Dogs were selected for high skin reactivity to grass and weed pollens. Their offspring were inoculated with pollen extracts in alum immediately after routine vaccinations (attenuated live-virus vaccines for canine distemper and infectious canine hepatitis, and a killed bacterin for Leptospira). Heat labile antipollen IgE antibodies were measured by passive cutaneous anaphylaxis. Pups vaccinated for canine distemper before being given pollen extracts had many more IgE antibodies than did their control littermates who were not vaccinated until after the last pollen extract injection. This may be a natural example of the "allergic break-through phenomenon."
Rearrangement of λ Light Chain Genes in Mature B Cells In Vitro and In Vivo. Function of Reexpressed Recombination-activating Gene (<i>RAG</i>) Products (1998)

V(D)J (V, variable; D, diversity; J, joining) combination of immunoglobulin (Ig) genes established in premature B cells has been thought to be conserved throughout differentiation at mature stages. However, germinal center (GC) B cells have been shown to reexpress recombination-activating gene (RAG)-1 and RAG-2 proteins in immunized mice. Here, we present several lines of evidence indicating that RAG proteins thus induced are functional as the V(D)J recombinase. DNA excision product reflecting Vlambda1 to Jlambda1 rearrangement was generated in parallel with the expression of RAG genes in mature mouse B cells that were activated in vitro with LPS and IL-4. Similar lambda chain gene rearrangement was observed in the draining lymph node of immunized mice. Further, B cells that underwent lambda gene rearrangement were shown by in situ PCR to be localized within GCs. Thus, secondary rearrangement of Ig genes (receptor editing) can occur in mature B cells.
High blood levels of soluble OX40 (CD134), an immune costimulatory molecule, indicate reduced survival in patients with advanced colorectal cancer (2019)

The interaction between tumor necrosis factor receptor superfamily, member 4 (OX40) on T cells and the OX40 ligand (OX40L) on antigen‑presenting cells (APCs) is a pivotal step for T‑cell activation and the promotion of antitumor immunity. However, it is hypothesized that soluble OX40 (sOX40) in blood suppresses T‑cell activation by blocking the OX40/OX40L interaction. In the present study, the association between blood sOX40 levels and the clinical characteristics of advanced colorectal cancer (CRC) patients was investigated. Blood was collected from 22 patients with advanced CRC. Blood sOX40 levels were determined by enzyme‑linked immunosorbent assay (ELISA). Messenger RNA (mRNA) expression encoding OX40 or cytokines was analyzed by quantitative RT‑PCR. Blood sOX40 levels were positively correlated with the blood levels of carbohydrate antigen (CA) 19‑9, carcinoembryonic antigen (CEA), C‑reactive protein (CRP) and soluble programmed cell death ligand‑1 (PD‑L1) in patients but negatively correlated with the blood levels of albumin. Blood sOX40 levels were not correlated with the mRNA expression of interferon (IFN)‑gamma, interleukin (IL)‑6, IL‑10 and IL‑4 in the peripheral blood mononuclear cells (PBMCs) of the patients and were not correlated with the frequency of programmed cell death‑1 (PD‑1) expressing CD4+, CD8+ and CD56+ cells. Notably, according to both univariate and multivariate analyses, high blood sOX40 levels were significantly correlated with a reduced survival time in patients. Although activated Jurkat cells (a human T cell line) exhibited an upregulation of sOX40 production and OX40 mRNA expression, the OX40 mRNA expression of the PBMCs of patients was not correlated with blood sOX40 levels. High blood levels of sOX40 were correlated with a reduced survival time in patients with advanced CRC, possibly associated with the suppression of antitumor immunity by sOX40.
Monofunctional Group-Modified Gold Nanoparticles from Solid Phase Synthesis Approach:  Solid Support and Experimental Condition Effect (2004)

We herein report a systematic study of solid-phase place exchange reactions for the synthesis of gold nanoparticles with a single surface functional group. This approach is based on a “catch and release” mechanism to control the number of functional groups attached to the nanoparticle surface. Bifunctional thiol ligands with a carboxylic end group were first immobilized on a solid polymer support in a controlled density. The density was low enough that neighboring thiol ligands were far apart from each other. When the modified polymer support was incubated in a butanethiol-protected nanoparticle solution, a one-to-one place exchange reaction took place between the polymer-bound thiol ligands and the nanoparticles. After cleaving off from the solid support, nanoparticles with a single carboxylic group were obtained as the major product. By varying the solid supports and reaction conditions, we succeeded to obtain monofunctional gold nanoparticles with enhanced yield and high purity.
Introduction (2019)

This introduction addresses the book’s main arguments and themes and provides historical background on the history of the Strait of Gibraltar as a political boundary. It also outlines the book’s sources and methodology and lays out the chapter-by-chapter narrative arc. The Strait of Gibraltar first became a political border in the sixteenth century, with several smaller borders proliferating on its shores as multiple empires carved out coastal exclaves and spheres of influence. These borders form the crucial starting point for understanding the region’s political geography. Borders are the key sites of negotiation between sovereign power and human mobility. They possess material, legal, political, and metaphorical meaning, all of which are central to the ongoing process of mediating relationships among the empires, ethno-religious groups, and trade networks operating in the region.