gebhart/patrepeval huggingface dataset:
Data from Predicting Tumor Killing and T-Cell Activation by T-Cell Bispecific Antibodies as a Function of Target Expression: Combining <i>In Vitro</i> Experiments with Systems Modeling (2023)

&lt;div&gt;Abstract&lt;p&gt;Targeted T-cell redirection is a promising field in cancer immunotherapy. T-cell bispecific antibodies (TCB) are novel antibody constructs capable of binding simultaneously to T cells and tumor cells, allowing cross-linking and the formation of immunologic synapses. This in turn results in T-cell activation, expansion, and tumor killing. TCB activity depends on system-related properties such as tumor target antigen expression as well as antibody properties such as binding affinities to target and T cells. Here, we developed a systems model integrating &lt;i&gt;in vitro&lt;/i&gt; data to elucidate further the mechanism of action and to quantify the cytotoxic effects as the relationship between targeted antigen expression and corresponding TCB activity. In the proposed model, we capture relevant processes, linking immune synapse formation to T-cell activation, expansion, and tumor killing for TCBs &lt;i&gt;in vitro&lt;/i&gt; to differentiate the effect between tumor cells expressing high or low levels of the tumor antigen. We used cibisatamab, a TCB binding to carcinoembryonic antigen (CEA), to target different tumor cell lines with high and low CEA expression &lt;i&gt;in vitro&lt;/i&gt;. We developed a model to capture and predict our observations, as a learn-and-confirm cycle. Although full tumor killing and substantial T-cell activation was observed in high expressing tumor cells, the model correctly predicted partial tumor killing and minimal T-cell activation in low expressing tumor cells when exposed to cibisatamab. Furthermore, the model successfully predicted cytotoxicity across a wide range of tumor cell lines, spanning from very low to high CEA expression.&lt;/p&gt;&lt;/div&gt;
Towards a low CO2 emission building material employing bacterial metabolism (1/2): The bacterial system and prototype production (2019)

The production of concrete for construction purposes is a major source of anthropogenic CO2 emissions. One promising avenue towards a more sustainable construction industry is to make use of naturally occurring mineral-microbe interactions, such as microbial-induced carbonate precipitation (MICP), to produce solid materials. In this paper, we present a new process where calcium carbonate in the form of powdered limestone is transformed to a binder material (termed BioZEment) through microbial dissolution and recrystallization. For the dissolution step, a suitable bacterial strain, closely related to Bacillus pumilus, was isolated from soil near a limestone quarry. We show that this strain produces organic acids from glucose, inducing the dissolution of calcium carbonate in an aqueous slurry of powdered limestone. In the second step, the dissolved limestone solution is used as the calcium source for MICP in sand packed syringe moulds. The amounts of acid produced and calcium carbonate dissolved are shown to depend on the amount of available oxygen as well as the degree of mixing. Precipitation is induced through the pH increase caused by the hydrolysis of urea, mediated by the enzyme urease, which is produced in situ by the bacterium Sporosarcina pasteurii DSM33. The degree of successful consolidation of sand by BioZEment was found to depend on both the amount of urea and the amount of glucose available in the dissolution reaction.
Design and Characterization of X-Ray Multilayer Analyzers for the 50–1000 eV Region (1990)

This report describes a synthesis of more than 10 years of this program's development and application of multilayer analyzers for absolute Bragg spectrometry in the low-energy x-ray region of 50–1000 eV. Multilayers, denned here as systems of periodic layered structures parallel to the analyzer surface, have been applied principally in the diagnostics and application of the new, intense sources of synchrotron and high-temperature plasma x radiation. Detailed absolute reflectivity characterizations are presented for selected examples of these multilayers which have been semiempirically determined for mica, potassium acid phthalate, and the fabricated Langmuir-Blodgett and sputtered multilayer analyzers with d-spacings in the 10–200 Å range. Design requirements for absolute spectrometry are established. Efficient analytical multilayer reflectivity models are derived and parameterized (based upon a modification of the Darwin-Prins model for the low-energy x-ray region), including, for the sputtered multilayers, parameters for defining interface structure. The dependence of the reflectivity characteristics, high-order Bragg diffraction suppression, and overall efficiency upon the model parameters is analyzed. A special spectrograph and procedure for the absolute measurement of the relevant reflectivity characteristics are described. Detailed measurements and semiempirical characterizations are presented. Programs for small laboratory computers have been developed that allow rapid and flexible spectral analysis, transforming measured spectra to absolute Spectra.
ECONOMIES OF SIZE OF A COORDINATED BIOREFINERY FEEDSTOCK HARVEST SYSTEM (2003)

The objective of this research is to determine the cost to harvest lignocellulosic biomass, such as crop residue and perennial grasses, for use as biorefinery feedstock, and to determine the potential economies of size that might result from a coordinated structure. The estimates show that substantial size economies are possible.
Role of Natural Autoantibodies and Natural IgM Anti-Leucocyte Autoantibodies in Health and Disease (2016)

We review how polyreactive natural IgM autoantibodies (IgM-NAA) protect the host from invading micro-organisms and host neo-antigens that are constantly being produced by oxidation mechanisms and cell apoptosis. Second, we discuss how IgM-NAA and IgM anti-leukocyte antibodies (IgM-ALA) inhibits autoimmune inflammation by anti-idiotypic mechanisms, enhancing removal of apoptotic cells, masking neo-antigens, and regulating the function of dendritic cells (DC) and effector cells. Third, we review how natural IgM prevents autoimmune disorders arising from pathogenic IgG autoantibodies, triggered by genetic mechanisms (e.g., SLE) or micro-organisms, as well as by autoreactive B and T cells that have escaped tolerance mechanisms. Studies in IgM knockout mice have clearly demonstrated that regulatory B and T cells require IgM to effectively regulate inflammation mediated by innate, adaptive, and autoimmune mechanisms. It is, therefore, not surprising why the host positively selects such autoreactive B1 cells that generate IgM-NAA, which are also evolutionarily conserved. Fourth, we show that IgM-ALA levels and their repertoire can vary in normal humans and disease states and this variation may partly explain the observed differences in the inflammatory response after infection, ischemic injury, or after a transplant. We also show how protective IgM-NAA can be rendered pathogenic under non-physiological conditions. We also review IgG-NAA that are more abundant than IgM-NAA in plasma. However, we need to understand if the (Fab)(2) region of IgG-NAA has physiological relevance in non-disease states, as in plasma, their functional activity is blocked by IgM-NAA having anti-idiotypic activity. Some IgG-NAA are produced by B2 cells that have escaped tolerance mechanisms and we show how such pathogenic IgG-NAA are regulated to prevent autoimmune disease. The Fc region of IgG-NAA can influence inflammation and B cell function in vivo by binding to activating and inhibitory FcγR. IgM-NAA has therapeutic potential. Polyclonal IgM infusions can be used to abrogate on-going inflammation. Additionally, inflammation arising after ischemic kidney injury, e.g., during high-risk elective cardiac surgery or after allograft transplantation, can be prevented by pre-emptively infusing polyclonal IgM or DC pretreated ex vivo with IgM or by increasing in vivo IgM with a vaccine approach. Cell therapy is appealing as less IgM will be required.
Geomagnetic Disturbances and Ventricular Arrhythmia in Patients with Implantable Cardioverter Defibrillators from a US-Based Hospital (2022)

Background and Aim: Episodes of ventricular arrhythmias (VA) have been associated with environmental exposures such as air pollution. Solar driven geomagnetic disturbances may alter autonomic nervous system activity, modify systemic oxidative stress, or induce changes in aerosols. However, few studies have investigated if there is an association between VA and geomagnetic disturbances (GMD). The aim of this study was to assess whether GMD is associated with the initiation of VA in patients with implantable cardioverter defibrillators (ICDs). Methods: This study examined the association between GMD driven by solar activity on VA, defined as sustained and non-sustained ventricular fibrillation or ventricular tachycardia, in patients with ICDs using a time-stratified case-crossover analysis between September 2006 and March 2010 from Tufts Medical Center’s Cardiac Arrythmia Center in Boston, MA. Patients were identified from a single Massachusetts-based Medical Center and VAs were identified from retrieved ICD records as part of routine care. We considered several pollutants such as PM2.5, black carbon (BC), O3, NO2 and ultrafine particles (PN) in our analyses using time lags prior to the event. Daily GMD information was appended for the week previous to each event and matched control day. Results: During the study period, 91 patients had a total of 1,050 VA. During periods of increased GMD, patients with low ejection fraction and a history of a MI or coronary intervention had increased odds of VA , with patients who had a coronary bypass graph being the highest (OR: 1.63, 95% CI 1.05, 2.52 ). Conclusions: Among patients with ICDs, exposure to GMD was associated with higher odds of VA in those with pre-existing heart disease and/or a history of coronary interventions. GMD driven by solar activity has the potential to affect heart health in patients with cardiac comorbidities. Keywords: Solar activity, geomagnetic disturbances, implantable cardioverter defibrillator, ventricular arrhythmia
The Use of Quantitative Real Time Polymerase Chain Reaction to Quantify Some Rumen Bacterial Strains in anIn VitroRumen System (2013)

The aim of this work was to quantify four rumen bacterial strains (Butyrivibrio fibrisolvens, Ruminococcus albus, Streptococcus bovis, Megasphaera elsdenii) in an in vitro batch rumen fermentative system by quantitative real time polymerase chain reaction (qPCR). The experiment was a 2×2 factorial arrangement with two types of liquid rumen, collected from dairy cows (DC) and fattening bulls (FB) and two types of fermentation substrate (forage: concentrate ratios, 75:25 and 25:75) and was replicated in two fermentation runs. Fermentation fluids from FB compared to those from DC had lower pH, higher total VFA concentrations (averages of 0 and 24 h samplings, 6.70 vs 7.04 and 72.6 vs 42.7 mmol/l P<0.001) and contained less acetic (P=0.014) and more propionic (P<0.01) and butyric (P=0.029) acids. The two types of substrates incubated produced very small differences in the end fermentation products.B. fibrosolvens concentrations were higher (P<0.001) in the DC fermentation fluids compared to that from bulls (averages of 0 and 24 h sampling times, 3.47 vs 1.38 x109 copies /mL), while M. elsdenii was detected only in FB fermentation fluids. R. albus and S. bovis concentrations were not different between the two types of rumen liquid. With the only exception for B. fibrosolvens, bacteria strains considered in this study increased their concentrations in the fermentation fluid during the 24 h of in vitro incubation.
Mechanisms in the chlorinolysis of sulfinyl chlorides (1984)

The successful synthesis and chlorinolysis of α-mercaptodimefhyl sulfone have provided additional support for our contention that Pummerer rearrangements may occur during the chlorinolyses of α-sulfonyl sulfinyl chlorides. Further exploration of chlorinolyses of α-sulfonyl systems has uncovered the first observations of CS bond cleavage during the chlorinolyses of (i) a sulfinyl chloride and (ii) a sulfinate ester.
Metrological Aspects of Activity Measurements in Mixed Electrolytes by Ion‐Selective Electrodes (2007)

Abstract Based on the model equation for the measurand analyte activity, all significant sources of uncertainty are identified, their magnitude estimated from published and experimental data and finally combined to give the uncertainty in the reported value of the analyte activity. It is found that the combined uncertainty is dominated by the uncertainties in the diffusion potential E J and the time‐dependent response behavior κ of the sensor. Using Henderson's approach E J is calculated not to vary more than 150 μV for physiological analytes in contact with a 3 M KCl reference solution. The stability of the reference electrode as well as the flow characteristics in the vicinity of the sensing element greatly influence the response time of the sensor. By minimizing the mentioned contributions of E J and κ in the uncertainty budget, combined uncertainties for activity values in the range of 2% are feasible for univalent ions.
Storage, surgery, outcome, and complications of corneal and conjunctival grafts (1993)

Corneal transplantation is still limited by a shortage of donor material, but the type of storage medium used once a cornea has been acquired is probably irrelevant to graft outcome. Vancomycin HCl shows promise as a supplement to gentamicin sulfate in storage media. New methods of HLA typing using donor ocular tissue have largely helped to overcome the problems associated with typing of cadaveric blood, but the value of HLA typing in improving corneal graft survival is now in doubt. Alternative regimens of immunosuppression are being tested in animal models, but there is still no consensus on the best ways to use existing agents such as corticosteroids. Rejection remains the most common cause of unsuccessful corneal grafting in large cohorts, but glaucoma and astigmatism also limit postoperative graft function. Limbal stem cell grafts are promising for the management of many ocular surface diseases and conjunctival limbal autografts for pterygia may be the most successful surgical method for preventing recurrence.
Deep-AIR: A Hybrid CNN-LSTM Framework for Air Quality Modeling in\n Metropolitan Cities (2021)

Air pollution has long been a serious environmental health challenge,\nespecially in metropolitan cities, where air pollutant concentrations are\nexacerbated by the street canyon effect and high building density. Whilst\naccurately monitoring and forecasting air pollution are highly crucial,\nexisting data-driven models fail to fully address the complex interaction\nbetween air pollution and urban dynamics. Our Deep-AIR, a novel hybrid deep\nlearning framework that combines a convolutional neural network with a long\nshort-term memory network, aims to address this gap to provide fine-grained\ncity-wide air pollution estimation and station-wide forecast. Our proposed\nframework creates 1x1 convolution layers to strengthen the learning of\ncross-feature spatial interaction between air pollution and important urban\ndynamic features, particularly road density, building density/height, and\nstreet canyon effect. Using Hong Kong and Beijing as case studies, Deep-AIR\nachieves a higher accuracy than our baseline models. Our model attains an\naccuracy of 67.6%, 77.2%, and 66.1% in fine-grained hourly estimation, 1-hr,\nand 24-hr air pollution forecast for Hong Kong, and an accuracy of 65.0%,\n75.3%, and 63.5% for Beijing. Our saliency analysis has revealed that for Hong\nKong, street canyon and road density are the best estimators for NO2, while\nmeteorology is the best estimator for PM2.5.\n
Signaling Mechanisms and Pharmacological Modulators Governing Diverse Aquaporin Functions in Human Health and Disease (2022)

The aquaporins (AQPs) are a family of small integral membrane proteins that facilitate the bidirectional transport of water across biological membranes in response to osmotic pressure gradients as well as enable the transmembrane diffusion of small neutral solutes (such as urea, glycerol, and hydrogen peroxide) and ions. AQPs are expressed throughout the human body. Here, we review their key roles in fluid homeostasis, glandular secretions, signal transduction and sensation, barrier function, immunity and inflammation, cell migration, and angiogenesis. Evidence from a wide variety of studies now supports a view of the functions of AQPs being much more complex than simply mediating the passive flow of water across biological membranes. The discovery and development of small-molecule AQP inhibitors for research use and therapeutic development will lead to new insights into the basic biology of and novel treatments for the wide range of AQP-associated disorders.
Efficient Multiple UAV Deployment for Maximizing Connections with Non-Uniformly Distributed Users (2021)

This paper considers the problem of determining the optimal flying locations for multiple UAV base stations to maximize the number of connected users. We consider the case of non-uniformly distributed users. We propose an adhoc approach to find optimal 3D UAV placement using a gravity inspired clustering algorithm and a two-tier connectivity model. We compare our proposed approach with existing approaches and show that our proposed approach has significantly higher expected number of connected UEs than existing approaches.
Resonance vector mode locking (2015)

A mode locked fibre laser as a source of ultra-stable pulse train has revolutionised a wide range of fundamental and applied research areas by offering high peak powers, high repetition rates, femtosecond range pulse widths and a narrow linewidth. However, further progress in linewidth narrowing seems to be limited by the complexity of the carrier-envelope phase control. Here for the first time we demonstrate experimentally and theoretically a new mechanism of resonance vector self-mode locking where tuning in-cavity birefringence leads to excitation of the longitudinal modes sidebands accompanied by the resonance phase locking of sidebands with the adjacent longitudinal modes. An additional resonance with acoustic phonons provides the repetition rate tunability and linewidth narrowing down to Hz range that drastically reduces the complexity of the carrier-envelope phase control and so will open the way to advance lasers in the context of applications in metrology, spectroscopy, microwave photonics, astronomy, and telecommunications.
[Studies on absorption mechanism of loganin in intestines of rats]. (2008)

The absorption of loganin in intestine of rat is a first-order kinetics, the absorption mechanism is probably the passive diffusion. It has specific absorption locus and access to locating administration, meanwhile it's the P-gp substrate, and could increase its fraction of bioavailability by corporation with P-gp inhibitor.
Glucokinase as Glucose Sensor and Metabolic Signal Generator in Pancreatic β-Cells and Hepatocytes (1990)

This article reviews evidence for a pivotal role of glucokinase as glucose sensor of the pancreatic beta-cells. Glucokinase explains the capacity, hexose specificity, affinities, sigmoidicity, and anomeric preference of pancreatic islet glycolysis, and because stimulation of glucose metabolism is a prerequisite of glucose stimulation of insulin release, glucokinase also explains many characteristics of this beta-cell function. Glucokinase of the beta-cell is induced or activated by glucose in contrast to liver glucokinase, which is regulated by insulin. Tissue-specific regulation corresponds with observations that liver and pancreatic beta-cell glucokinase are structurally distinct. Glucokinase could play a glucose-sensor role in hepatocytes as well, and certain forms of diabetes mellitus might be due to glucokinase deficiencies in pancreatic beta-cells, hepatocytes, or both.
3D microenvironment attenuates simulated microgravity-mediated changes in T cell transcriptome (2022)

Abstract Human space travel and exploration are of interest to both the industrial and scientific community. However, there are many adverse effects of spaceflight on human physiology. In particular, there is a lack of understanding to the extent by which microgravity affects the immune system. T cells, key players of the adaptive immune system and long term immunity, are present not only in blood circulation, but also reside within tissue. As of yet, studies investigating the effects of microgravity on T cells are limited to peripheral blood or traditional 2D cell culture that recapitulates circulating blood. To better mimic interstitial tissue, 3D cell culture has been well established for physiologically and pathologically relevant models. In this work, we utilize 2D and 3D cell culture to gain an understanding of how simulated microgravity affects both circulating and tissue resident T cells. T cells were studied in both resting and activated stages. We found that 3D cell culture attenuates the effects of simulated microgravity on the T cells transcriptome and nuclear irregularities compared to 2D cell culture. Interestingly, simulated microgravity appears to have less effect on activated T cells compared to those in the resting stage. Overall, our work provides novel insights into the effects of simulated microgravity on circulating and tissue resident T cells which could provide benefits for the health of space travelers.
Development of a New Rapid Identification Method for <i>Bifidobacterium globosum</i> and <i>B. pseudolongum</i>Using Published Genome Data (2023)

Bifidobacterium globosum is expected to be applied to foods as a probiotic, and a method to rapidly distinguish it from the related Bifidobacterium pseudolongum is necessary for product development and quality control. In this study, we evaluated existing methods of bacterial species classification for B. globosum/pseudolongum with the published whole-genomes. The results showed that the Polymerase Chain Reaction (PCR) - Restriction Fragment Length Polymorphism (RFLP) method by the restriction enzyme HaeIII for hsp60 genes and the sequence analysis of hsp60 and rpoB gene sequences could not accurately distinguish B. globosum/pseudolongum, and both species could be accurately distinguished by the sequence analysis of clpC gene sequences. The clpC gene sequence similarity was at least 97.9% in the same species and no more than 95.4% in different species. Therefore, we developed a novel method of RFLP by restriction enzyme BspT104I on PCR products of clpC genes to identify B. globosum/pseudolongum. This method was considered to be faster and more accurate than previously proposed methods for identification of B. globosum/pseudolongum. Thus, the method presented in this study enables efficient species classification and it is very useful in utilization of B. globosum/pseudolongum for foods.