gebhart/patrepeval huggingface dataset:
Molecular and Functional Characteristics of Cloned Human Organic Cation Transporters (2005)

Within the last 5 years the organic cation transport field has moved from tissue and cellular levels to a molecular level of investigation. As we gain a better understanding of the genes and proteins responsible for the multiple mechanisms of organic cation transport, we can begin to apply this knowledge to pharmaceutical and drug discovery research. For example, in the future, we will know all of the transporters that are expressed in each tissue and have a substrate/inhibitor profile for each transporter. With this information, we could begin to predict, for example, organ-specific clearances or organ-specific distributions of drugs. Perhaps we will discover a brain-specific organic cation transporter which could serve as a drug target. It will be years and perhaps several more decades before all of these transporters are cloned and characterized. We have made a good start and there will be years of exciting work and discovery in the organic cation transport field in the future.
Data from The Role of Protein Binding in Induction of Apoptosis by Phenethyl Isothiocyanate and Sulforaphane in Human Non–Small Lung Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Induction of apoptosis underlies a mechanism for inhibiting tumorigenesis by phenethyl isothiocyanate (PEITC) and sulforaphane (SFN). However, the upstream events by which isothiocyanates (ITC) induce apoptosis have not been fully investigated. As electrophiles, ITCs could trigger apoptosis by binding to DNA or proteins or by inducing oxidative stress. To better understand the molecular mechanisms of apoptosis by ITCs, we examined, as a first step, the role of these events in human non–small lung cancer A549 cells. PEITC was a more potent inducer than SFN; it induced apoptosis at 20 μmol/L, whereas SFN induced at 40 μmol/L but not at 20 μmol/L. To study binding with cellular proteins and DNA, cells were treated with &lt;sup&gt;14&lt;/sup&gt;C-ITCs; the initial protein binding by PEITC was almost 3-fold than that of SFN. The binding by PEITC increased with time, whereas binding by SFN remained low. Therefore, 4 h after incubation proteins became the predominant targets for PEITC with a 6-fold binding than that of SFN. To characterize the chemical nature of binding by the ITCs, we used bovine serum albumin (BSA) as a surrogate protein. PEITC also modified BSA covalently to a greater extent than SFN occurring exclusively at cysteine residues. Surprisingly, neither PEITC nor SFN bound to DNA or RNA at detectable levels or caused significant DNA strand breakage. The levels of oxidative damage in cells, measured as reactive oxygen species, 8-oxo-deoxyguanosine, and protein carbonyls formation, were greater in cells treated with SFN than PEITC. Because PEITC is a stronger inducer of apoptosis than SFN, these results indicate that direct covalent binding to cellular proteins is an important early event in the induction of apoptosis by the ITCs. [Cancer Res 2007;67(13):6409–16]&lt;/p&gt;&lt;/div&gt;
P485 Development and implementation of a remote monitoring tool for real-world assessment of mild, moderate and severe infectious complications in Inflammatory Bowel Disease patients (2021)

Abstract Background Immunomodulators and biologicals are cornerstones in the current management of Inflammatory Bowel Disease (IBD), but are associated with increased risk of infections. Post-marketing surveillance studies are important to assess the risk for infectious side effects in real-world populations, yet mainly focus on severe infections. Data on mild and moderate infections in IBD patients are scarce, primarily since self-limiting infections and infections treated by the general practitioner are not systematically captured in surveillance registries. Mild and moderate infections take longer to clear in immunosuppressed patients, have a large impact on (work) disability and quality of life, and potentially precede severe infections. In the current study, we aimed to develop and implement a remote monitoring tool for real-world assessment of infections in IBD patients. Methods Through a structured iterative process with input from IBD specialists, nurse practitioners, and a comprehensive literature review, a 7-item Questionnaire comprising 15 different types of infections (covering e.g. upper/lower respiratory tract; urinary tract; eye; and skin infections) was developed to measure Patient-Reported Infections (PRIQ) with a recall period of 3 months. Infection severity was defined as either mild (self-limiting or requiring topical/local treatment), moderate (requiring oral antibiotic, antiviral or antifungal drugs) or severe (requiring hospitalization and/or IV treatment). To ascertain comprehensiveness and comprehensibility in the intended study population prior to implementation, in three rounds a total of 36 randomly selected IBD patients visiting the outpatient clinic were interviewed individually until saturation was reached. Results Overall, patient understanding of the PRIQ was good and cognitive interviews did not result in reduction of questionnaire-items. Analysis of feedback from interviews resulted in addition of definitions to certain response options (e.g. definition for antivirals) and minor linguistic adjustments to further improve patient understanding. A total of three patients (8.3%) raised concerns on the recall period of 3 months, which after expert consensus, did not result in alteration of the recall period. Next, the PRIQ was digitized and implemented in myIBDcoach, an established telemedicine platform for management of IBD. Conclusion We developed a remote monitoring tool (PRIQ) to assess patient-reported infections in IBD and ascertained patient understanding through cognitive interviewing. A prospective multicentre study using the myIBDcoach platform is ongoing to validate the PRIQ and subsequently report the risk of mild and moderate infections across different treatment regimens in IBD patients (NCT04151420).
A virtual node method for handling well bore boundary conditions in modeling multiphase flow in porous and fractured media (2000)

How to treat well boundary conditions is a difficult issue when formulating and coding a multiphase numerical reservoir simulator. The difficulty arises because the partial differential equation governing multiphase subsurface flow is of a mixed parabolic‐hyperbolic type. Maximum changes in primary variables and mass/heat fluxes occur at boundaries or well nodes. Consequently, these well nodes with small volume tend to be singular, leading to computational convergence problems. The conventional method of well treatment in geothermal or oil reservoir simulators is to use a sink/source term approach and to distribute flow rates by a potential or mobility allocation scheme for a multilayered well. However, this traditional method cannot handle a backflow problem, which may occur in a multilayered well in heterogeneous formations. This paper presents a “virtual node” method to handle a well bore either as a single node or several computational nodes screened and connected to many neighboring nodes for a multilayered well. The well bore can be vertical, inclined, or horizontal, and the well borehole node is treated in the same way as any other nonwell node for flow calculations. The solution at the well is then obtained by solving mass balance equations for the well node. It is shown that the new method provides a natural, physically consistent, and numerically efficient approach to handling well flow problems. Implementation of this new method for a three‐phase flow reservoir simulator is discussed, and three examples are provided.
Identification and characterization of a cardiac-specific transcriptional regulatory element in the slow/cardiac troponin C gene. (1992)

The slow/cardiac troponin C (cTnC) gene has been used as a model system for defining the molecular mechanisms that regulate cardiac and skeletal muscle-specific gene expression during mammalian development. cTnC is expressed continuously in both embryonic and adult cardiac myocytes but is expressed only transiently in embryonic fast skeletal myotubes. We have reported previously that cTnC gene expression in skeletal myotubes is controlled by a developmentally regulated, skeletal muscle-specific transcriptional enhancer located within the first intron of the gene (bp 997 to 1141). In this report, we show that cTnC gene expression in cardiac myocytes both in vitro and in vivo is regulated by a distinct and independent transcriptional promoter and enhancer located within the immediate 5' flanking region of the gene (bp -124 to +32). DNase I footprint and electrophoretic mobility shift assay analyses demonstrated that this cardiac-specific promoter/enhancer contains five nuclear protein binding sites (designated CEF1, CEF-2, and CPF1-3), four of which bind novel cardiac-specific nuclear protein complexes. Functional analysis of the cardiac-specific cTnC enhancer revealed that mutation of either the CEF-1 or CEF-2 nuclear protein binding site abolished the activity of the cTnC enhancer in cardiac myocytes. Taken together, these results define a novel mechanism for developmentally regulating a single gene in multiple muscle cell lineages. In addition, they identify previously undefined cardiac-specific transcriptional regulatory motifs and trans-acting factors. Finally, they demonstrate distinct transcriptional regulatory pathways in cardiac and skeletal muscle.
Aligned Functional Paste (2018)

This paper proposes a new interaction method called aligned functional paste. The method allows users to select handwritten keywords, to apply some mapping function to the keywords and to align results of the mapping function in a few steps.
STRANDS: Interactive Simulation of Thin Solids using Cosserat Models (2002)

Strandsare thin elastic solids that are visually well approximated as smooth curves, and yet possess essential physical behaviors characteristic of solid objects such as twisting. Common examples in computer graphics include: sutures, catheters, and tendons in surgical simulation; hairs, ropes, and vegetation in animation. Physical models based on spring meshes or 3D finite elements for such thin solids are either inaccurate or inefficient for interactive simulation. In this paper we show that models based on the Cosserat theory of elastic rods are very well suited for interactive simulation of these objects. The physical model reduces to a system of spatial ordinary differential equations that can be solved efficiently for typical boundary conditions. The model handles the important geometric non-linearity due to large changes in shape. We introduce Cosserat-type physical models, describe efficient numerical methods for interactive simulation of these models, and implementation results.
Self-Induced Harmonic Generation in a Storage-Ring Free-Electron Laser (2008)

Coherent radiation from a relativistic electron beam is a valuable way to overcome the present limitations of conventional lasers and synchrotron radiation light sources. The typical scheme has electrons, directly from a linac, in a single-pass interaction with a laser pulse in the presence of a static undulator magnetic field. We demonstrate that a storage-ring free-electron laser can also achieve harmonic generation (down to 36.5 nm), presenting both experimental and theoretical results, and offer a reliable interpretation of the peculiar underlying physical processes involved.
Actions of General Anesthetic on Voltage-Gated Ion Channels (2003)

Neuronal signaling depends on rapid changes in electrical fields across cell membranes mediated by ion channels. Three important properties of these transmembrane proteins facilitate the rapid changes in membrane potential: passive conduction of ions, ion selectivity, and open and closing (gating) in response to electrical, mechanical, or chemical signals.
The Effect of Electric Current on the Healing time of Crural Fractures (1972)

(1972). The Effect of Electric Current on the Healing time of Crural Fractures. Acta Orthopaedica Scandinavica: Vol. 43, No. 5, pp. 421-437.
Kinetic Study of Silicon Nitride Growth from Dichlorosilane and Ammonia (1996)

The model of silicon nitride film deposition in a batch furnace from dichlorosilane ( SiH 2 Cl 2 ; DCS) and ammonia ( NH 3 ) is presented. The gas-phase and surface reaction rates of DCS are estimated from thickness profiles along the gas stream direction, and surface reaction and DCS decomposition are found to be of Langmuir and Lindemann types, respectively. It means that at a normal deposition temperature ( ∼1000 K), some DCS molecules adsorb directly on the Si surface while others decompose into a more reactive intermediate, SiCl 2 . At higher temperatures, the reverse reaction of DCS decomposition and the subsequent reaction of SiCl 2 with NH 3 may play significant roles. Using the present reaction rates, we estimate the film thickness profiles across a 12-inch wafer.
PARP Inhibitors and Prostate Cancer: To Infinity and BeyondBRCA (2020)

The U.S. Food and Drug Administration recently approved two poly-adenosine diphosphate-ribose polymerase (PARP) inhibitors, olaparib and rucaparib, for treatment of biomarker-positive metastatic castrate resistant prostate cancer. The benefits of PARP inhibition have been well characterized in patients who have BRCA1 and BRCA2 mutations in several forms of cancer. BRCA1 and BRCA2 occupy key roles in DNA damage repair, which is comprised of several different pathways with numerous participants. Patients with mutations in other key genes within the DNA damage repair pathway may also respond to treatment with PARP inhibitors, and identification of these alterations could significantly increase the percentage of patients that may benefit from PARP inhibition. This review focuses on the potential for synthetically lethal interactions between PARP inhibitors and non-BRCA DNA damage repair genes. IMPLICATIONS FOR PRACTICE: The treatment potential of PARP inhibition has been well characterized in patients with BRCA1 and BRCA2 mutations, but there is compelling evidence for expanding the use of PARP inhibitors to mutations of other non-BRCA DNA damage repair (DDR) genes. This could increase the percentage of patients that may benefit from treatment with PARP inhibitors alone or in combination with other therapies. Understanding the significance of PARP inhibitor-sensitizing alterations in other common non-BRCA DDR genes will help guide clinical decisions to provide targeted treatment options to a wider population of patients.
Unsteady Plasma Actuators for Separation Control of Low-Pressure Turbine Blades (2006)

This is a continuation of our work on the use of single dielectric barrier plasma actuators for controlling flow separation on turbine blades in the low-pressure turbine stage at low Reynolds numbers typical of high-altitude cruise. This used a linear cascade of Pratt & Whitney PakB shaped blades to provide generic low-pressure turbine conditions. The flow over one of the blades was documented through surface pressure, laser-Doppler velocimetry, and hot-wire measurements. These were used to define the location and size of the separated flow region on the suction side of the blade. Both steady and unsteady plasma actuators were implemented and found to be effective in separation control. For the unsteady actuators, there was an optimum excitation frequency to reattach the flow that corresponded to a Strouhal number, based on the length of the separated zone and the local freestream velocity, equal to unity. The unsteady actuator was more effective than the steady actuator in reattaching the flow while also requiring less power. It was suggested by the experimental results that the mechanism for the steady actuators was turbulence tripping, whereas the mechanism for the unsteady actuators was to generate a train of spanwise structures that promoted mixing.
THE EFFECT OF IMPLANT STEM LENGTH ON BONE STRAINS IN THE DISTAL ULNA (2009)

Stress shielding (i.e. reduction in bone strains) in the distal ulna is commonly noted following ulnar head replacement arthroplasty. Optimal design parameters for distal ulnar implants, including the length of the stem, are currently unknown. The purpose of this study was to investigate the effect of stem length on bone strains along the length of the ulna. Strain gauges were applied to each of eight cadaveric ulnae to measure bending loads at six locations along each ulna’s length (approximately 1.5, 2.5, 4.0, 6.0, 8.0, and 13.0cm from the ulnar head). The proximal portion of each bone was secured in a custom-designed jig. A materials testing machine applied loads (5–30N) to the ulnar head while native strains were recorded. The ulnar head was removed and the loading procedure repeated for cemented stainless steel stems 3 and 7cm in length, according to a previously reported technique (Austman et al, CORS 2006). Other stem lengths between 3 and 7cm were tested in 0.5cm intervals with a 20N load applied only. Data were analyzed using a two-way repeated measures ANOVA (a=0.05). In general, distal bone strains increased as stem length decreased (e.g. average microstrains at the second distal-most gauges: 138±13 (7cm), 147±15 (6cm), 159±21 (5cm), 186±40 (4cm), 235±43 (3cm)). The native strains were different from all stem lengths for the four distal-most gauges (p No stem length tested matched the native strains at all gauge locations. The 3cm stem results were closer to the native strains than the 7cm stem for all loads at gauges overtop of the stem. Overall, the 3cm stem produced the highest strains, and thus would likely result in less distal ulnar bone resorption after implantation. These results suggest that shorter (approximately 3cm) stems should be considered for distal ulnar implants to potentially reduce stress shielding, although this must be balanced by adequate stem length for fixation.
Crystallization properties and their drift dependence in phase-change memory studied with a micro-thermal stage (2011)

The crystallization properties of phase-change memory (PCM) cells are studied at microsecond time scales using a novel micro-thermal stage. The time for recrystallization due to thermal disturbances is measured for varying amorphous volume fractions and annealing temperatures. PCM cells of intermediate resistances programmed with three different programming schemes are investigated and compared. For multi-bit programming, controlling the pulse-tail duration may be preferable as it has better retention characteristics than pulse-amplitude modulation or current-filament control. The effect of incomplete crystalline filaments on crystallization speed is experimentally investigated in this work, and the Arrhenius parameters are extracted from our crystallization time measurements to support a proposed unified mechanism for crystallization and drift. We have also found that recrystallization can be suppressed by more than 20% when there is a second of delay time between thermal disturbances.
Proteome and biological functions of inner and outer perivitelline layers in the chicken egg (2022)

International audience
Class II Major Histocompatibility Complex on Melanocytes of Vogt-Koyanagi-Harada Disease (1991)

The eyes obtained from two Japanese autopsy cases of patients with Vogt-Koyanagi-Harada disease were immunohistochemically examined. Both patients, a 63-year-old woman and a 68-year-old man, were clinically and histologically diagnosed as having Vogt-Koyanagi-Harada disease. Immunohistochemically, the choroidal infiltrate was composed predominantly of T lymphocytes with a larger proportion of helper/inducer T cells than suppressor/cytotoxic T cells and it also included activated lymphocytes expressing CD26 and CD25 antigens. Class II major histocompatibility complex was expressed in the choroidal melanocytes as well as in the endothelium of the choriocapillaris. Depositions of complement, however, were focally noticed in the choroid. Our results indicate that the cell-mediated immune process plays an important role in the development and progression of Vogt-Koyanagi-Harada disease, while choroidal melanocytes appear to play a pathogenic role in this disease.
Homogeneous Substrate‐Labeled Fluorescent Immunoassay for Carbamazepine (1982)

Carbamazepine is an anticonvulsant drug useful in the management of epilepsy. Because of the narrow therapeutic range, serum carbamazepine monitoring is useful for ensuring adequate drug therapy without toxicity. We report the development of a homogeneous substrate-labeled fluorescent immunoassay for carbamazepine in human serum. A carbamazepine fluorogenic reagent (FR) has been synthesized. Upon hydrolysis by beta-galactosidase, the nonfluorescent FR produces a fluorescent product. This enzymic hydrolysis sin inhibited when the FR binds with antibody against carbamazepine. The inhibition is relieved when carbamazepine competes with FR for available antibody binding sites. Thus, increasing levels of carbamazepine result in increasing levels of fluorescence that can be conveniently monitored with any conventional fluorometer. For low, medium, and high control sera (4, 12, and 16 micrograms carbamazepine/ml), the within-run coefficient of variation for the assay is 5.5%, 1.6%, and 2.9%, respectively, while the respective between-run coefficients of variation are 3.5%, 1.9%, and 2.3%. Fifty-three clinical serum samples were assayed by the SLFIA, gas chromatography (GC), high pressure liquid chromatography (HPLC), and an enzyme immunoassay method. The SLFIA method compares favorably with the HPLC technique (r - 0.97, slope = 1.10, y-intercept = 1.21), the enzyme immunoassay (r = 0.98, slope = 1.07, y-intercept = 0.82), and the GC method (r = 0.95, slope = 1.01, y-intercept = -0.03).
High Strength Concrete from Low Water Demand Cement (1999)

Cementitious materials, chemical additives and optimization of granulometry have been the traditional components in commercial mixes of High Strength Concrete (HSC) which have reached commercial strengths of 124 MPa (18,000 psi) in 56 days. A new generation of cements named Low Water Demand Cements (LWDCs) have reached strengths of up to 152 MPa (22,000 psi) at 28 days and are being tested by a joint industry group in Chicago to verify strength, behavior and durability aspects.
Supplementary Tables 1 from A Multiparameter Molecular Classifier to Predict Response to Neoadjuvant Lapatinib plus Trastuzumab without Chemotherapy in HER2<sup>+</sup> Breast Cancer (2023)

&lt;p&gt;Supplementary Tables&lt;/p&gt;
Mitotane levels predict the outcome of patients with adrenocortical carcinoma treated adjuvantly following radical resection (2013)

Mitotane concentrations ≥ 14 mg/l predict response to adjuvant treatment being associated with a prolonged RFS. A monitored adjuvant mitotane treatment may benefit patients after radical removal of ACC.
Lacrimal gland pleomorphic adenoma and malignant epithelial tumours: clinical and imaging differences (2018)

Our study adds important information regarding differentiating clinical and radiological features between malignant and benign epithelial lacrimal gland tumours that would aid in their management.