gebhart/patrepeval huggingface dataset:
The Association of Serologic Inflammatory Markers with Microscopic Colitis Disease Activity (2011)

Purpose: Microscopic colitis (MC) is a major cause of chronic diarrhea that requires colon biopsies for diagnosis. In addition, biopsies are often required when a patient with MC has recurrent symptoms, to confirm that recurrent disease is responsible, rather than an alternate diagnosis. Serologic markers of inflammation, such as erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) would be attractive biomarkers of disease activity if they correlated with other parameters of activity such as diarrhea or physician's and patient's global assessment of disease activity and severity. Therefore, our aim was to assess the correlation of ESR and CRP with these parameters. Methods: In patients with active MC, ESR and CRP were measured. Patients were also evaluated clinically and with a questionnaire that assessed clinical factors including number of bowel movements (BMs) per day as well as the patient's global assessment of disease activity. The clinical information (but not the patient's global assessment score) was reviewed by a single physician (DSP) and used to assign a physician's global assessment of disease activity. The correlations between these clinical factors and ESR and CRP (measured as continuous variables) were assessed using the Pearson correlation coefficient. Results: Seventy-three cases of MC were identified: 30 (41%) with lymphocytic colitis and 43 (59%) with collagenous colitis. The median age at diagnosis was 68 years (range, 26-85) and 73% were women. Among 63 patients with known ESR and 36 patients with known CRP, 10 (15%) and 8 (22%) had an elevated values, respectively. There was no correlation between ESR and number of BMs, patient global assessment and physician global assessment (p=0.93, p=0.96, p=0.16, respectively). After excluding one patient whose data was an outlier, there also was no correlation between CRP and number of BMs, patient general assessment and physician general assessment (p=0.90, p=0.44, p=0.41, respectively). Conclusion: ESR and CRP were not significantly correlated with disease activity in patients with MC as measured by the number of BMs per day, patient global assessment, or physician global assessment. These markers are therefore not useful in judging MC disease activity.
A strategy to accelerate protein production from a pool of clones in Chinese hamster ovary cells for toxicology studies (2017)

In the biopharmaceutical industry, a clonally derived cell line is typically used to generate material for investigational new drug (IND)-enabling toxicology studies. The same cell line is then used to generate material for clinical studies. If a pool of clones can be used to produce material for IND-enabling toxicology studies (Pool for Tox (PFT) strategy) during the time a lead clone is being selected for clinical material production, the toxicology studies can be accelerated significantly (approximately 4 months at Genentech), leading to a potential acceleration of 4 months for the IND submission. We explored the feasibility of the PFT strategy with three antibodies-mAb1, mAb2, and mAb3-at the 2 L scale. For each antibody, two lead cell lines were identified that generated material with similar product quality to the material generated from the associated pool. For two antibody molecules, mAb1 and mAb2, the material generated by the lead cell lines from 2 L bioreactors was tested in an accelerated stability study and was shown to have stability comparable to the material generated by the associated pool. Additionally, we used this approach for two antibody molecules, mAb4 and mAb5, at Tox and GMP production. The materials from the Tox batch at 400 L scale and three GMP batches at 2000 L scale have comparable product quality attributes for both molecules. Our results demonstrate the feasibility of using a pool of clonally derived cell lines to generate material of similar product quality and stability for use in IND-enabling toxicology studies as was derived from the final production clone, which enabled significant acceleration of timelines into clinical development. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1449-1455, 2017.
Localization, Secretion, and Action of Inhibin in Human Placenta (1987)

Inhibin is a gonadal glycoprotein hormone that regulates the production of follicle-stimulating hormone (FSH) by the anterior pituitary gland and exhibits intragonadal actions as well. The present study shows that inhibin-like immunoreactivity (inhibin-LI) is present in cells of the cytotrophoblast layer of human placenta at term and in primary cultures of human trophoblasts. Human chorionic gonadotropin (hCG) stimulated secretion of inhibin-LI from these cultured placental cells. This effect was mimicked by 8-bromo-cyclic adenosine monophosphate (8-bromo-cAMP), forskolin, and cholera toxin, suggesting that the mechanism of hCG induction of placental inhibin-LI secretion is cAMP-dependent. Incubation with an antiserum that binds the alpha-subunit of human inhibin increased the secretion of hCG and gonadotropin-releasing hormone-like immunoreactivity (GnRH-LI) from trophoblast cells in culture, suggesting a local tonic inhibitory action of endogenous inhibin on hCG and GnRH-LI release. The action of inhibin on hCG secretion may partially require the presence of placental GnRH, as suggested by evidence that a synthetic GnRH antagonist partially reverses the hCG increase induced by inhibin immunoneutralization. Results suggest paracrine roles for both inhibin and GnRH in the regulation of placental hCG production.
Chamber and target technology development for inertial fusion energy (1999)

Fusion chambers and high pulse-rate target systems for inertial fusion energy (IFE) must: regenerate chamber conditions suitable for target injection, laser propagation, and ignition at rates of 5 to 10 Hz; extract fusion energy at temperatures high enough for efficient conversion to electricity; breed tritium and fuel targets with minimum tritium inventory; manufacture targets at low cost; inject those targets with sufficient accuracy for high energy gain; assure adequate lifetime of the chamber and beam interface (final optics); minimize radioactive waste levels and annual volumes; and minimize radiation releases under normal operating and accident conditions. The primary goal of the US IFE program over the next four years (Phase I) is to develop the basis for a Proof-of-Performance-level driver and target chamber called the Integrated Research Experiment (IRE). The IRE will explore beam transport and focusing through prototypical chamber environment and will intercept surrogate targets at high pulse rep-rate. The IRE will not have enough driver energy to ignite targets, and it will be a non-nuclear facility. IRE options are being developed for both heavy ion and laser driven IFE. Fig. 1 shows that Phase I is prerequisite to an IRE, and the IRE plus NIF (Phase II) is prerequisite to a high-pulse rate. Engineering Test Facility and DEMO for IFE, leading to an attractive fusion power plant. This report deals with the Phase-I R&D needs for the chamber, driver/chamber interface (i.e., magnets for accelerators and optics for lasers), target fabrication, and target injection; it is meant to be part of a more comprehensive IFE development plan which will include driver technology and target design R&D. Because of limited R&D funds, especially in Phase I, it is not possible to address the critical issues for all possible chamber and target technology options for heavy ion or laser fusion. On the other hand, there is risk in addressing only one approach to each technology option. Therefore, in the following description of these specific feasibility issues, we try to strike a balance between narrowing the range of recommended R&D options to minimize cost, and keeping enough R&D options to minimize risk.
Homogeneous liquid crystal alignment on inorganic–organic hybrid silica thin films derived by the sol–gel method (2011)

We developed an inorganic–organic hybrid thin film via the sol–gel method for a new liquid crystal alignment layer and investigated the influence of an organic species on the alignment characteristics of the liquid crystals (LCs). A thin film of methyl-doped amorphous silicon oxide (a-SiOx:CH3) was fabricated from the hydrolysis and condensation reaction of the initial precursors of methyltriethoxysilane (MTES) and tetraethoxysilane (TEOS) at a proper ratio. A low-energy ion beam (IB) treatment gives rise to the homogeneous alignment of LC in an IB condition on a-SiOx:CH3 thin film; however, it is difficult to control the LC alignment on a-SiOx thin film derived only from TEOS as a precursor. The LC alignment depending on the chemical structure of the silica thin film was investigated and analyzed in terms of the sensitivity of the axis-selective destruction of the chemical bonding on the surface of the thin silica film.
The Human Telomeric Proteome During Telomere Replication (2020)

Summary Telomere shortening can cause detrimental diseases and contribute to aging. It occurs due to the end replication problem in cells lacking telomerase. Furthermore, recent studies revealed that telomere shortening can be attributed to difficulties of the semi-conservative DNA replication machinery to replicate through the bulk of telomeric DNA repeats. To investigate telomere replication in a comprehensive manner, we develop QTIP-iPOND, which enables purification of proteins that associate with telomeres specifically during replication. We identify in addition to the core replisome a large number of proteins that associate with telomere replication forks and validate their importance. We find that POT1 is depleted, whereas histone H1 is specifically enriched, at telomere replication forks. Our work reveals the dynamic changes of the telomeric proteome during replication, providing a valuable resource of telomere replication proteins. To our knowledge, this is the first study that examines the replisome at a specific region of the genome.
Offline Multiobjective Optimization for Fast Charging and Reduced Degradation in Lithium-Ion Battery Cells Using Electrochemical Dynamics (2020)

The rapid charging of lithium ion battery cells while minimizing degradation is a key challenge in battery management. Offline optimal control frameworks employing physics-based models provide a first-principles approach to this problem that provides critical insights and benchmarks for real-time oriented online optimization algorithms. In this letter, we approach the optimal control problem of minimizing both charging time and degradation of a NMC battery using the single shooting optimization framework, employing a coupled electrochemical-thermal-aging model. The aging mechanism used captures growth of the SEI layer, solvent diffusion. The effectiveness of the single shooting method using a piecewise polynomial control and the low sensitivity of the method to chosen numerical parameters in the multi-objective problem is illustrated. The tradeoff between charging time and degradation is investigated numerically.
Abschlussbericht zum Verbundprojekt 'Entwicklung und Einsatz von Katalysatoren zur Oxidation von niedermolekularen Kohlenhydraten' : Förderkennzeichen: 22018203/22008004 ; Laufzeit des Vorhabens: 01.10.2004-29.02.2008 (2008)

Die Ergebnisse des Vorhabens eröffnen einen sehr aussichtsreichen Weg zur kostengünstigen Herstellung von Zuckersauren, die vielfaltige Einsatzmöglichkeiten z B als biologisch abbaubare Komplexierungsmittel haben. Damit kann eine potentiell verbesserte Wettbewerbsfähigkeit gegenüber petrochemisch-basierten Konkurrenzprodukten erreicht werden, die zu einer Stärkung der Position des nachwachsenden Rohstoffs „Zucker" gegenüber Erdöl führen. Durch die weitgehende CO2-Neutralität nachwachsender Rohstoffe sowie die biologische Abbaubarkeit der Produkte wird ein Beitrag zum Umweltschutz und zur Losung bereits bestehender ökologischer Probleme erbracht. In dem Projekt wurden gegenüber dem Stand des Wissens vor Projektbeginn in den folgenden Bereichen wesentliche Fortschritte erzielt - Entwicklung von Goldträgerkatalysatoren, die mit sehr hoher Aktivität, bisher nicht gekannter Langzeitstabilität und praktisch 100 %iger Selektivität Aldosen zu den entsprechenden Aldonsäure (z B. Glucose zu Gluconsäure) oxidieren - Widerlegung der gängigen Meinung, dass mittels der incipient wetness-Methode keine kleinen Goldpartikel gebildet und somit aktive Goldkatalysatoren hergestellt werden können - Erfolgreiches Scale-up der Katalysatorpräparation bis in den Maßstab von mehreren hundert Gramm - Umfassende kinetische Charakterisierung von Katalysator und Reaktion, Ableitung neuer mechanistischer Details zur Oxidationsreaktion der Glucose - Umfassende reaktionstechnische Charakterisierung des Reaktionssystems, Ableitung technisch vorteilhafter Reaktionsbedingungen - Entwicklung eines kontinuierlichen Ruhrkesselreaktorsystems fur pulverförmige Katalysatoren - Ableitung aussichtsreicher Ansatzpunkte zur selektiven Oxidation der primären Alkoholfunktion an der C6-Position von Kohlenhydraten zu den entsprechenden Uronsäuren Im Bereich der Kohlenhydratoxidation konnte gezeigt werden, dass die entwickelten Goldkatalysatoren ein immenses Potentialfür eine technische Nutzung zur Herstellung von Zuckersäuren wie Gluconsäure oder Lactobionsäure aufweisen.
Ultrahigh Performance Close-Focusing Large-Ratio Zoom Lens for the Visible Waveband (1994)

The specification, design and fabrication of a close focusing, large ratio, visible zoom lens which rivals the performance of fixed focal length lenses is described.
Data from Anti-spike T-cell and Antibody Responses to SARS-CoV-2 mRNA Vaccines in Patients with Hematologic Malignancies (2023)

&lt;div&gt;Abstract&lt;p&gt;The anti-spike T-cell and antibody responses to SARS-CoV-2 mRNA vaccines in patients with B-cell malignancies were examined in a real-world setting. A next-generation sequencing (NGS)–based molecular assay was used to assess SARS-CoV-2–specific T-cell responses. After the second dose, 58% (166/284) of seropositive and 45% (99/221) of seronegative patients display anti-spike T cells. The percentage of patients who displayed T-cell response was higher among patients receiving mRNA-1273 vaccines compared with those receiving BNT162b2 vaccines. After the third vaccination, 40% (137/342) of patients seroconverted, although only 22% displayed sufficient antibody levels associated with the production of neutralizing antibodies. 97% (717/738) of patients who were seropositive before the third dose had markedly elevated anti-spike antibody levels. Anti-spike antibody levels, but not T-cell responses, were depressed by B cell–directed therapies. Vaccinated patients with B-cell malignancies with a poor response to SARS-CoV-2 vaccines may remain vulnerable to COVID-19 infections.&lt;/p&gt;Significance:&lt;p&gt;This study represents the first investigation of SARS-CoV-2–specific immune responses to vaccination in a patient registry using an NGS-based method for T-cell receptor repertoire–based analysis combined with anti-spike antibody assessments. Vaccinated patients with B cell–derived hematologic malignancies are likely at higher risk of infection or severe COVID-19.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/bloodcancerdiscov/article/doi/10.1158/2643-3230.BCD-3-6-ITI" target="_blank"&gt;This article is highlighted in the In This Issue feature, p. 476&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Photoinduced electron-transfer processes of carbon nanohorns with covalently linked pyrene chromophores: charge-separation and electron-migration systems (2007)

Carbon nanohorns (CNHs) have been covalently functionalized with pyrene chromophores forming dispersible nanohybrids in CH2Cl2. Their photo-physical properties have been investigated by complementary steady-state and time-resolved absorption and fluorescence spectroscopies as well as electrochemistry. Upon photo-excitation of CNH–pyrene nanohybrids, in the presence of hexyl-viologen dication (HV2+) and a hole trap, the HV˙+ was accumulated in the polar organic solvent. This observation suggests that photoinduced charge-separation takes place, producing CNH˙−–pyrene˙+, which was further confirmed by observing pyrene˙+ in the nanosecond time-scale transient absorption spectra. From CNH˙−, an electron is migrated to HV2+ and a hole shifts from pyrene˙+ to the hole trap, which suppresses the back electron transfer resulting in the persistence of HV˙+.
Assessment of magnetization transfer effects in myocardial tissue using balanced steady‐state free precession (bSSFP) cine MRI (2009)

Magnetization transfer imaging (MTI) by means of MRI exploits the mobility of water molecules in tissue and offers an alternative contrast mechanism beyond the more commonly used mechanisms based on relaxation times. A cardiac MTI method was implemented on a commercially available 1.5 T MR imager. It is based on the acquisition of two sets of cardiac-triggered cine balanced steady-state free precession (bSSFP) images with different levels of RF power deposition. Reduction of RF power was achieved by lengthening the RF excitation pulses of a cine bSSFP sequence from 0.24 ms to 1.7 ms, while keeping the flip angle constant. Normal volunteers and patients with acute myocardial infarcts were imaged in short and long axis views. Normal myocardium showed an MT ratio (MTR) of 33.0 +/- 3.3%. In acute myocardial infarct, MTR was reduced to 24.5 +/- 9.2% (P < 0.04), most likely caused by an increase in water content due to edema. The method thus allows detection of acute myocardial infarct without the administration of contrast agents.
Supplementary Figure 3 from Nitric Oxide Boosts Chemoimmunotherapy via Inhibition of Acid Sphingomyelinase in a Mouse Model of Melanoma (2023)

Supplementary Figure 3 from Nitric Oxide Boosts Chemoimmunotherapy via Inhibition of Acid Sphingomyelinase in a Mouse Model of Melanoma
Single freeform surface imaging design with unconstrained object to image mapping (2014)

An imaging design approach which is free of third-order astigmatism for one freeform optical surface and the image is presented in this paper. A set of differential equations is derived from generalized ray tracing. The solution of the above derived equations provides the anastigmatic freeform optical surface, the image surface and the object to image mapping. The obtained design can be used as a good starting point for optimization. As an example, a reflective freeform surface is designed for a single reflective Head Mounted Display (HMD). This example has a 3 mm pupil, 15mm eye clearance, 24-degree diagonal full field of view, and the final design yields an average MTF of 62.6% across 17 field points.
Optical bistable devices based on guided-mode resonance in slab waveguide gratings (2009)

We investigate properties of nonlinear resonant gratings with emphasis on optical bistability. Slab waveguide gratings with various quality factors are designed and their characteristics analyzed with a finite-difference time-domain method. Considerable field enhancements are observed in the gratings and the performance compares favorably with metallic bistable devices. Bistability based on coupled gratings is also treated. Mechanically controllable switching intensity realized by varying a gap distance between two gratings is demonstrated. Resonant nonlinear elements in this work may find applications in all-optical information processing and optical switching, and our investigation on the dependence of the normalized switching intensity and the response time on quality factor will provide a general guide line for grating-based bistable device design.
Adaptive Deconvolution Using a SAW Storage Correlator (1981)

A new analog adaptive filter for deconvolving distorted signals is described in this paper. The filter uses a storage correlator which implements a clipped version of the least mean squared (LMS) algorithm and uses a special iterative technique to achieve fast convergence. The new filter has a potential bandwidth of 100 MHz and would eventually handle pulsed signals of 10-µs width. For signals with time-bandwidth products of less than 100, the adaptation time is less than 1 ms, which allows operation in real time for most applications, including resolution of radar signals in a cluttered environment, removal of echoes from television signals, deconvolution of distorted signals in nondestructive evaluation, and also in telephony. The filter is particularly suited for radar and communications, as it processes signals directly in the VHF range. Two experiments related to ghost suppression of a pulse and to the field of NDE are described in this paper. The results are in good agreement with computer simulations and show a ghost suppression of 15 dB for the first example and a sidelobe suppression of 8 dB for a transducer signal. The adaptation time is less than 450 µs.
Onset of Convection in a Horizontal Layer of Cold Water (1983)

Parabolic, cubic, and higher order expressions have been used in previous investigations to relate temperature to density in the vicinity of the density extremum. Another equation of state, based on the careful measurement of the density variations of both pure and saline water, has been used here to determine the onset of convection in a horizontally confined layer of water near its density extremum. The simplicity of this equation gives rise to a minimum number of problem particular parameters, and relatively easily allows for the inclusion of both pressure and salinity level effects (neglecting saline diffusion). The boundaries are considered to be rigid-rigid and of infinite thermal capacity. Present numerical results are compared with those previously calculated using other density relationships, including that embodied in the linear Oberbeck-Boussinesq approximation. Density extremum effects are seen to be stabilizing, with critical Rayleigh numbers calculated to be about 10 percent below those obtained using a parabolic density-temperature relationship and quite close to those found using a fifth-order polynomial. There is an associated increase in calculated wave number with the inclusion of density extremum effects.
Meshless Electrophysiological Modeling of Cardiac Resynchronization Therapy—Benchmark Analysis with Finite-Element Methods in Experimental Data (2022)

Computational models of cardiac electrophysiology are promising tools for reducing the rates of non-response patients suitable for cardiac resynchronization therapy (CRT) by optimizing electrode placement. The majority of computational models in the literature are mesh-based, primarily using the finite element method (FEM). The generation of patient-specific cardiac meshes has traditionally been a tedious task requiring manual intervention and hindering the modeling of a large number of cases. Meshless models can be a valid alternative due to their mesh quality independence. The organization of challenges such as the CRT-EPiggy19, providing unique experimental data as open access, enables benchmarking analysis of different cardiac computational modeling solutions with quantitative metrics. We present a benchmark analysis of a meshless-based method with finite-element methods for the prediction of cardiac electrical patterns in CRT, based on a subset of the CRT-EPiggy19 dataset. A data assimilation strategy was designed to personalize the most relevant parameters of the electrophysiological simulations and identify the optimal CRT lead configuration. The simulation results obtained with the meshless model were equivalent to FEM, with the most relevant aspect for accurate CRT predictions being the parameter personalization strategy (e.g., regional conduction velocity distribution, including the Purkinje system and CRT lead distribution).