gebhart/patrepeval huggingface dataset:
Biosynthesis and fate of compatible solutes in extremely halophilic phototrophic eubacteria (1990)

Most halophilic and halotolerant eubacteria are able to accumulate compatible solutes from their environment during salt stress. They are usually able to synthesize sugars and amino acids. These compatible solutes, however, are of less importance in extremely halophilic eubacteria, where usually glycinebetaine or ectoine is required. Extremely halophilic phototrophic sulfur bacteria of the genus Ectothiorhodospira are able to synthesize the three compatible solutes glycinebetaine, trehalose and ectoine. While glycinebetaine is the major compatible solute under all conditions the percentage of trehalose and ectoine varies depending on the availability of nitrogen sources. Using acetate plus bicarbonate as simultaneous substrates the three compatible solutes were analysed by 13C-NMR spectroscopy. The label found indicated the following biosynthesis pathways: glycine, derived from glyoxylate out of the Kornberg cycle, undergoes a three-fold methylation with S-adenosylmethionine as methyl donor. The latter is derived from the tetrahydrofolate pathway. Several enzymes of this pathway have been found and are under investigation. The labelling of trehalose indicates that the Calvin cycle is blocked in the presence of acetate. The two glucose moieties of trehalose are linked by trehalose-6-phosphate synthase. The enzyme was characterized. Ectoine is synthesized from aspartate via aspartophosphate, aspartate semialdehyde and α, β-diaminobutyrate. Dilution stress leads to rapid excretion of betaine and ectoine, followed by immediate uptake to balance overshoot excretion. Trehalose is not excreted under dilution stress but is degraded by trehalase and subsequently metabolized.
Electric field gradients in nonmagnetic dilute alloys of aluminum and copper (1984)

The electric field gradient (EFG) and the asymmetry parameter ($\ensuremath{\eta}$) are investigated at the first-, second, third-, and fourth-nearest-neighbor (NN) sites for nonmagnetic dilute alloys of Al and Cu. The impurity effective valency is calculated according to the Friedel criterion of bound states. The impurity-induced electronic charge density is calculated self-consistently in the Hohenberg-Kohn-Sham density-functional formalism and is used to evaluate the valence-effect contribution to the EFG. The size-effect contribution to the EFG is estimated in the elastic continuum model. Reliable values of the core-enhancement and Sternheimer antishielding factors are used. No size-strength parameter is introduced to explain the EFG's at the 2NN, 3NN, and 4NN sites. However, the EFG's at the 1NN site are explained with the help of a size-strength parameter ${C}^{\ensuremath{'}}$ which accounts for the deficiency of the elastic continuum model. The calculated values of EFG and are $\ensuremath{\eta}$ found to be in reasonable agreement with the experimental values for most of the alloys. In Al alloys the size-effect EFG is found to be dominant at the 1NN site and the valence-effect EFG is found to be dominant at the 2NN, 3NN, and 4NN sites. In Cu alloys the size-effect EFG is dominant at all the NN sites.
Breaking the equilibrium at the interface: microwave-assisted reactive distillation (MARD) (2019)

In microwave-assisted reactive distillation, the selective heating of the water content at the liquid–vapour interface intensifies the evaporation of water molecules.
Predictive value of in-vitro testing anti-cancer therapy sensitivity on 3D micro-tumors (tumoroids) from patients with metastatic colorectal cancer: A feasibility study (2018)

Background: The treatment of cancer may be improved by testing the chemo sensitivity of cancer cells obtained from the patient’s tumor. 3D culture represents a promising method for modeling of patient tumors in vitro. The purpose of this study was to test the feasibility of a clinical trial offering patients with metastatic colorectal cancer treatment based on in-vitro testing anti-cancer therapy sensitivity. Methods: Main inclusion criteria were stage IV colorectal cancer, PS 0-1, previous exposure to 5FU, oxaliplatin, irinotecan, bevacizumab and, if RAS/RAF wild-type, an EGFR inhibitor. Fresh cancer tissues from metastases were cultivated as tumoroids. The culturing protocol which was originally developed for resected tissue was optimized for the smaller tissue amounts received from needle biopsies. Ten patients were to be included and at least five of them to have clinically applicable results in order for the procedure to be feasible. Results: Ten patients were included from September to December 2017 in one institution. Biopsies were from liver (6), peritoneum (2), retroperitoneum (1) and lung (1). Rebiopsies were allowed and a total of 19 biopsy sessions were performed with ultrasound (14), CT (3) or sigmoidoscopy (2). In seven cases, the biopsy, tumorsphere formation and sensitivity testing was successful. Median time from biopsy to result was 34 days (range 19-50). A notable challenge was obtaining sufficient viable tumor tissue resulting in increased culture times or the need for re-biopsies. Conclusions: This is the first clinical study of its kind. The method of selecting last-line treatment of colorectal cancer based on fresh biopsies was feasible as results were obtained in seven out of ten cases. The trial is now extended to a phase II trial with PFS as the primary endpoint. Clinical trial identification: NCT03251612. Legal entity responsible for the study: Lars Henrik Jensen. Funding: 2cureX. Disclosure: L.H. Jensen: Travel grants: Roche, Amgen, Bayer. G. Hagel, H. Harling, O. Thastrup: 2cureX. All other authors have declared no conflicts of interest.
Global Optimality of Encoders and MSE Decoders for Communicating Unstable Markov Processes over Unstable Gaussian Recursive Models with Feedback: A Nonanticipative RDF Approach (2019)

Shannon's coding capacity of memoryless additive Gaussian noise (AGN) channels with noiseless feedback, is known to be achieved by the Elias [1] coding scheme of communicating the mean square-error (MSE) of a Gaussian RV X ~ N(0, σ'), from past channel outputs, and decoding it using a MSE decoder. Further, it is known that among all encoders, and decoders that minimize the MSE, then the Elias encoder and decoder are globally optimal. In this paper we derive analogous results, for communicating unstable Gaussian Markov processes over unstable multiple-input multiple-output (MIMO) Gaussian recursive models (GRM) with memory, often called infinite impulse response (IIR) models, subject to an average cost of quadratic form. However, unlike memoryless AGNs, certain conditions are required, for such generalizations. Further, to show global optimality, we need to invoke Gorbunov and Pinsker [2] nonanticipatory € entropy, instead of the classical rate distortion function of the source. Another important observation is that we need a two-parameter coding scheme, instead of the one-parameter coding scheme of memoryless AGN channels.
REVIEW OF RESPIRATOR PERFORMANCE TESTING IN THE WORKPLACE: ISSUES AND CONCERNS (1992)

Performance capability of respirators has traditionally been evaluated by testing components of the respirator (e.g., filter efficiency), facepiece fit, total inward leakage, or some other measure of performance evaluated under laboratory conditions. In recent years, increased emphasis has been placed on development of test methods suitable for evaluating respirator performance in the workplace. The goal of such testing is to evaluate the level of protection provided by respirators in the work environment. The AIHA Respiratory Protection Committee believes that workplace testing of respirators has the potential to be an excellent tool for increasing knowledge about the effectiveness of respiratory protection. However, a number of technical issues remain to be addressed before optimal test protocols and data analysis methods can be defined. The progress made to date in workplace testing will be reviewed, and broader discussion about key elements that must be considered when developing guidelines for testing respirators in the workplace will be initiated.
Josephson junctions loaded by transmission lines: A revisited problem (2011)

The problem of evaluating dissipative effects in Josephson junctions loaded by transmission lines is reexamined, for either the symmetric or the asymmetric case, with particular consideration of the time domain in which the interaction between junction and load system occurs.
Electron Spin Dynamics as a Controlling Factor for Spin-Selective Charge Recombination in Donor−Bridge−Acceptor Molecules (2010)

Photoinitiated charge separation and thermal charge recombination (CR) in a covalent donor−bridge−acceptor (D-B-A) system consisting of a perylene-3,4:9,10-bis(dicarboximide) (PDI) acceptor, 2,7-oligofluorene bridge (FLn), and phenothiazine donor (PTZ) (PTZ−FLn−PDI) have been shown to transition from superexchange to charge hopping mechanisms as the D−A distance increases. In work presented here, the spin-selective multiple CR pathways in PTZ−FLn−PDI are studied by a detailed analysis of the magnetic field effect (MFE) on the radical ion pair (RP) lifetime and triplet yield. A kinetic analysis of the MFE gives the spin-selective CR rates and the RP singlet−triplet (S-T) relaxation rates for n = 2−4. When n = 2 and 3, where the S-T splitting (2J) of the RP is large, slow S-T relaxation results in a kinetic bottleneck slowing the observed total CR rate at zero magnetic field. These results show that spin state mixing is an important controlling factor for CR reaction rates in these systems. The CR rate constant for the triplet RP (kCRT) obtained by MFE analysis is about 10 times faster than the corresponding rate for the singlet RP (kCRS) when n = 2−4, indicating that kCRT occurs near the maximum of the Marcus rate vs free energy dependence, whereas kCRS is deep in the inverted region. The distance dependence of both kCRS and kCRT is explained by the crossover from superexchange (n = 1 and 2) to distant independent thermal hopping (n = 3 and 4). A possible mechanism of the S-T relaxation is proposed based on S-T dephasing, which may be induced by fluctuations of 2J resulting from bridge torsional dynamics.
A tool to evaluate the liquid‐crystal‐aligning properties of rubbed polymer orientation layers for LCDs (1994)

Abstract— The influence of various rubbing parameters on the optical phase retardation and pretilt‐angle‐inducing properties of rubbed polymer orientation layers has been investigated. A direct correlation has been found between the rubbing‐induced optical phase retardation of the polymer layer and the resulting pretilt angle induced by the rubbed polymer orientation layer in the liquid‐crystal layer. The observed correlation is independent of the rubbing conditions used to obtain the rubbing‐induced optical phase retardation. Hence, optical phase retardation can be used as a tool to evaluate the liquid‐crystal‐aligning properties of a rubbed polymer layer, without having to process the rubbed layer into a cell filled with liquid crystal. The possibility of using optical phase retardation as an in‐line control parameter of the rubbing process in an actual LCD production facility is considered.
COMPARISON BETWEEN CRP SERUM VALUES AND HEMATOLOGICAL PARAMETERS FOR DIAGNOSIS AND THERAPEUTIC SURVEILLANCE OF NEONATAL INFECTION (1984)

COMPARISON BETWEEN CRP SERUM VALUES AND HEMATOLOGICAL PARAMETERS FOR DIAGNOSIS AND THERAPEUTIC SURVEILLANCE OF NEONATAL INFECTION was published in Volume 2 Proceedings of the Second Symposium Lyon, France, June 27–30, 1983 on page 485.
Monte Carlo calculations of coupled boson-fermion systems. I (1981)

We present a formalism for carrying out Monte Carlo calculations of field theories with both boson and fermion degrees of freedom. The basic approach is to integrate out the fermion degrees of freedom and obtain an effective action for the boson fields to which standard Monte Carlo techniques can be applied. We study the structure of the effective action for a wide class of theories. We develop a procedure for making rapid calculations of the variation in the effective action due to local changes in the boson fields, which is essential for practical numerical calculations.
Supplementary Methods from SHP2 Inhibition Sensitizes Diverse Oncogene-Addicted Solid Tumors to Re-treatment with Targeted Therapy (2023)

&lt;p&gt;Supplementary Data Title Page, Methods, References&lt;/p&gt;
PLA2-Triggered Activation of Cyclosporine-Phospholipid Prodrug as a Drug Targeting Approach in Inflammatory Bowel Disease Therapy (2022)

Oral medication with activity specifically at the inflamed sites throughout the gastrointestinal tract and limited systemic exposure would be a major advance in our therapeutic approach to inflammatory bowel disease (IBD). For this purpose, we have designed a prodrug by linking active drug moiety to phospholipid (PL), the substrate of phospholipase A2 (PLA2). PLA2 expression and activity is significantly elevated in the inflamed intestinal tissues of IBD patients. Since PLA2 enzyme specifically hydrolyses the sn-2 bond within PLs, in our PL-based prodrug approach, the sn-2 positioned FA is replaced with cyclosporine, so that PLA2 may be exploited as the prodrug-activating enzyme, releasing the free drug from the PL-complex. Owing to the enzyme overexpression, this may effectively target free cyclosporine to the sites of inflammation. Four PL-cyclosporine prodrugs were synthesized, differing by their linker length between the PL and the drug moiety. To study the prodrug activation, a novel enzymatically enriched model was developed, the colonic brush border membrane vesicles (cBBMVs); in this model, tissue vesicles were produced from colitis-induced (vs. healthy) rat colons. PLA2 overexpression (3.4-fold) was demonstrated in diseased vs. healthy cBBMVs. Indeed, while healthy cBBMVs induced only marginal activation, substantial prodrug activation was evident by colitis-derived cBBMVs. Together with the PLA2 overexpression, these data validate our drug targeting strategy. In the diseased cBBMVs, quick and complete activation of the entire dose was obtained for the 12-carbon linker prodrug, while slow and marginal activation was obtained for the 6/8-carbon linkers. The potential to target the actual sites of inflammation and treat any localizations throughout the GIT, together with the extended therapeutic index, makes this orally delivered prodrug approach an exciting new therapeutic strategy for IBD treatment.
SU‐E‐I‐47: Comparison of Risks for Two Medical Imaging Procedures (2012)

Relative risks can quantify risks comparisons between imaging procedures.
Combined Benefit of Prediction and Treatment: A Criterion for Evaluating Clinical Prediction Models (2014)

Clinical treatment decisions rely on prognostic evaluation of a patient's future health outcomes. Thus, predictive models under different treatment options are key factors for making good decisions. While many criteria exist for judging the statistical quality of a prediction model, few are available to measure its clinical utility. As a consequence, we may find that the addition of a clinical covariate or biomarker improves the statistical quality of the model, but has little effect on its clinical usefulness. We focus on the setting where a treatment decision may reduce a patient's risk of a poor outcome, but also comes at a cost; this may be monetary, inconvenience, or the potential side effects. This setting is exemplified by cancer chemoprevention, or the use of statins to reduce the risk of cardiovascular disease. We propose a novel approach to assessing a prediction model using a formal decision analytic framework. We combine the predictive model's ability to discriminate good from poor outcome with the net benefit afforded by treatment. In this framework, reduced risk is balanced against the cost of treatment. The relative cost-benefit of treatment provides a useful index to assist patient decisions. This index also identifies the relevant clinical risk regions where predictive improvement is needed. Our approach is illustrated using data from a colorectal adenoma chemoprevention trial.
Compilation of Diversity Factors and Schedules for Energy and Cooling Load Calculations, ASHRAE Research Project 1093, Preliminary Report, Literature Review and Database Search (1999)

In this report we describe the related literature for the ASHRAE 1093-RP project. To&#13;\naccomplish this we have divided the previous works into three categories: (1) existing literature&#13;\non diversity factor and load shape calculations, (2) literature that reports on existing databases of&#13;\nmonitored data in the U.S. and Europe, and (3) relevant studies about classifications of&#13;\ncommercial buildings. In the literature on diversity factors and load shapes, we covered papers&#13;\nreporting the existence of databases of monitored end-uses in commercial building, methods&#13;\nused in developing the daytypes and load shapes, and what classification schemes were used in&#13;\nthe commercial building sector. We report the names of the scholars and energy analysts whom&#13;\nwe contacted in the U.S. and Europe, that provided detailed information (in a tabulated format)&#13;\non existing databases on monitored end-uses in commercial buildings in the U.S. Finally, we&#13;\nsummarize the classification schemes of the commercial building sector that are reported in&#13;\nnational standards and codes.
Highly Conserved Residues in the Helical Domain of Dengue Virus Type 1 Precursor Membrane Protein Are Involved in Assembly, Precursor Membrane (prM) Protein Cleavage, and Entry (2014)

The envelope and precursor membrane (prM) proteins of dengue virus (DENV) are present on the surface of immature virions. During maturation, prM protein is cleaved by furin protease into pr peptide and membrane (M) protein. Although previous studies mainly focusing on the pr region have identified several residues important for DENV replication, the functional role of M protein, particularly the α-helical domain (MH), which is predicted to undergo a large conformational change during maturation, remains largely unknown. In this study, we investigated the role of nine highly conserved MH domain residues in the replication cycle of DENV by site-directed mutagenesis in a DENV1 prME expression construct and found that alanine substitutions introduced to four highly conserved residues at the C terminus and one at the N terminus of the MH domain greatly affect the production of both virus-like particles and replicon particles. Eight of the nine alanine mutants affected the entry of replicon particles, which correlated with the impairment in prM cleavage. Moreover, seven mutants were found to have reduced prM-E interaction at low pH, which may inhibit the formation of smooth immature particles and exposure of prM cleavage site during maturation, thus contributing to inefficient prM cleavage. Taken together, these results are the first report showing that highly conserved MH domain residues, located at 20-38 amino acids downstream from the prM cleavage site, can modulate the prM cleavage, maturation of particles, and virus entry. The highly conserved nature of these residues suggests potential targets of antiviral strategy.
Metal‐Free Catalysis in Ring‐Opening Polymerization (2009)

This chapter contains sections titled: Introduction Nucleophilic ROP Metal-Free Ionic ROP Summary and Prospects References
Complexation trends and binding constants between dextrin oligomers and small molecules as measured through affinity capillary electrophoresis (2003)

Quantitative aspects of a previously reported pre-equilibration affinity/capillary electrophoretic methodology (Hong, M., et al., Anal. Chem. 1998, 70, 3590-3597) were studied using fluorescently labeled oligosaccharides and analgesic drugs. Frontal analysis capillary electrophoresis (FA-CE) was investigated for these interaction systems. In order to fulfill certain FA requirements, the analysis conditions of the sugar-drug combinations had to be adjusted individually. Only after the establishment of these conditions, acceptable binding data (association constants) could be obtained. The constants are in the range of weak hydrogen bonding and are comparable to the constants that were independently obtained through 1H nuclear magnetic resonance (NMR) spectroscopy.
Calculating incoherent diffraction MTF (2008)

The incoherent diffraction MTF plays an increasingly important role in the range performance of imaging systems as the wavelength increases and the optical aperture decreases. Accordingly, all NVESD imager models have equations that describe the incoherent diffraction MTF of a circular entrance pupil. NVThermIP, a program which models thermal imager range performance, has built in equations which analytically model the incoherent diffraction MTF of a circular entrance pupil and has a capability to input a table that describes the MTF of other apertures. These can be calculated using CODE V, which can numerically calculate the incoherent diffraction MTF in the vertical or horizontal direction for an arbitrary aperture. However, we are not aware of any program that takes as input a description of the entrance pupil and analytically outputs equations that describe the incoherent diffraction MTF. This work explores the effectiveness of Mathematica to analytically and numerically calculate the incoherent diffraction MTF for an arbitrary aperture. In this work, Mathematica is used to analytically and numerically calculate the incoherent diffraction MTF for a variety of apertures and the results are compared with CODE V calculations.
Trajectory Tracking Controller for Vision-Based Probe and Drogue Autonomous Aerial Refueling (2006)

This paper addresses autonomous aerial refueling between an unmanned tanker aircraft and an unmanned receiver aircraft using the probe-and-drogue method. An important consideration is the ability to achieve successful docking in the presence of exogenous inputs such as atmospheric turbulence. Practical probe and drogue autonomous aerial refueling requires a reliable sensor capable of providing accurate relative position measurements of su‐cient bandwidth, integrated with a robust relative navigation and control algorithm. This paper develops a Reference Observer Based Tracking Controller that does not require a model of the drogue or presumed knowledge of its position, and integrates it with an existing vision based relative navigation sensor. A trajectory generation module is used to translate the relative drogue position measured by the sensor into a smooth reference trajectory, and an output injection observer is used to estimate the states to be tracked by the receiver aircraft. Accurate tracking is provided by a state feedback controller with good disturbance rejection properties. A frequency domain stability analysis for the combined reference observer and controller shows that the system is robust to sensor noise, atmospheric turbulence, and high frequency unmodeled dynamics. Feasibility and performance of the total system is demonstrated by simulated docking maneuvers of an unmanned receiver aircraft docking with the non-stationary drogue of an unmanned tanker, in the presence of atmospheric turbulence. Performance characteristics of the vision based relative navigation sensor are also investigated, and the total system is compared to an earlier version. Results presented in the paper indicate that the integrated sensor and controller enable precise aerial refueling, including consideration of realistic measurements errors, plant modeling errors, and disturbances.