gebhart/patrepeval huggingface dataset:
Quantitative phase-digital holographic microscopy: a new imaging modality to identify original cellular biomarkers of diseases (2016)

Quantitative phase microscopy (QPM) has recently emerged as a powerful label-free technique in the field of living cell imaging allowing to non-invasively measure with a nanometric axial sensitivity cell structure and dynamics. Since the phase retardation of a light wave when transmitted through the observed cells, namely the quantitative phase signal (QPS), is sensitive to both cellular thickness and intracellular refractive index related to the cellular content, its accurate analysis allows to derive various cell parameters and monitor specific cell processes, which are very likely to identify new cell biomarkers. Specifically, quantitative phase-digital holographic microscopy (QP-DHM), thanks to its numerical flexibility facilitating parallelization and automation processes, represents an appealing imaging modality to both identify original cellular biomarkers of diseases as well to explore the underlying pathophysiological processes.
Active multivariable optimal control of a planar magnetic levitator (2002)

We discuss multivariable optimal control of a six-degree-of-freedom magnetic levitator with large planar motion capability. A single moving part, namely the platen, generates all the motions required for focusing and alignment, and large planar motions (50/spl times/50 mm) for positioning for photolithography in semiconductor manufacturing. We derive a state-space dynamic model for the planar levitator, and implement a multivariable optimal controller for its lateral mode control. The magnetically levitated stage shows tens-of-nanometer positioning noise suitable for the next generation photolithography. We also demonstrate that it follows a 20-mm step motion command in only 120 ms. The position command is planned by adapting a time-optimal control result. Magnetic levitation is a promising technology for use in high-precision active motion control applications.
Suitability of Food Resources and Physicochemical Parameters in the Lower Trinity River, Texas for Paddlefish (1995)

ABSTRACT We examined the zooplankton community and physicochemical parameters of the lower Trinity River, Texas during March 1992-March 1993, and evaluated the suitability of each for survival of paddlefish Polyodon spathula. Samples were collected every 2–4 weeks from mid-river channel and backwater stations at each of four sites. Eight paddlefish stomachs were analyzed, and eighteen paddlefish were aged and their relative weight values were determined. Physicochemical parameters generally were suitable for paddlefish survival. Zooplankton densities were low (overall mean 30.1 organisms/L) but similar to other river systems supporting paddlefish. The zooplankton community was dominated by rotifers; cladocerans and copepods were not abundant. Paddlefish stomach analysis indicated rotifers were being consumed by paddlefish. Paddlefish growth appeared to be rapid despite seemingly low food densities.
Circumventing size-bandwidth limits in imaging with flat lenses (2021)

Recent theoretical work suggested upper bounds on the operating bandwidths of flat lenses. Here, we show how these bounds can be circumvented via a multi-level diffractive lens (MDL) of diameter = 100 mm, focal length = 200 mm, device thickness = 2.4μ m and operating bandwidth from ? = 400 nm to 800 nm. We further combine the MDL with a refractive lens to demonstrate a hybrid telescope. By appealing to coherence theory, we show that the upper bound on relative bandwidth is surprisingly independent of lens diameter or numerical aperture, but is only limited by the bandwidth of the image sensor. Since large-area achromatic flat lenses produce significant reductions in weight over their refractive counterparts, these calculations and experiments open up opportunities for very large scale diffractive and diffractive-refractive telescopes.
15.4: Cavity Effects Determining The Outcoupling Efficiency of Organic Light‐Emitting Devices (2003)

Abstract A classical electromagnetic approach using the radiative dipole model is applied to study the cavity effects on outcoupling efficiency for archetype top‐emitting organic light‐emitting devices. Predicted optical performances will be compared with the combinatorial experiments.
Rectangular Holes in Porphyrin Isomers Act As Mono- and Binucleating Ligands: Stereochemistry of Mono- and Diboron Porphycenes and Their Protonation Behaviors (2020)

The first boron complexes of porphycenes, structural isomers of porphyrin, are reported. They are synthesized in good yields by reacting the free-base porphycene ligands with BF<sub>3</sub>·Et<sub>2</sub>O through a microwave-assisted method. Depending on the substituent group of porphycenes, two different coordination structures, mono- and diboron porphycenes, are obtained simultaneously. The single crystal structures and DFT calculations suggest that the boron atom of the monoboron porphycene is favorably coordinated on the dipyrroethene site, and the regioisomer of diboron porphycene is of <i>cisoid</i> stereochemistry, which is more stable than <i>transoid</i>. We also investigate the protonation behavior of boron porphycene complexes. Diboron porphycene does not undergo protonation, whereas monoboron porphycene undergoes protonation at the nonboron coordinating pyrroline site, resulting in a red shift in both absorption and emission spectra. Protonation and deprotonation of monoboron porphycene can be reversibly triggered using acids and bases.
Influence of Electrostatics on Small Molecule Flux through a Protein Nanoreactor (2015)

Nature uses protein compartmentalization to great effect for control over enzymatic pathways, and the strategy has great promise for synthetic biology. In particular, encapsulation in nanometer-sized containers to create nanoreactors has the potential to elicit interesting, unexplored effects resulting from deviations from well-understood bulk processes. Self-assembled protein shells for encapsulation are especially desirable for their uniform structures and ease of perturbation through genetic mutation. Here, we use the MS2 capsid, a well-defined porous 27 nm protein shell, as an enzymatic nanoreactor to explore pore-structure effects on substrate and product flux during the catalyzed reaction. Our results suggest that the shell can influence the enzymatic reaction based on charge repulsion between small molecules and point mutations around the pore structure. These findings also lend support to the hypothesis that protein compartments modulate the transport of small molecules and thus influence metabolic reactions and catalysis in vitro.
Combining system scenarios and configurable memories to tolerate unpredictability (2008)

Process variability and the dynamism of new applications increase the uncertainty of embedded systems and force designers to use pessimistic assumptions, which have a tremendous impact on both the performance and energy consumption of their memory organizations. In this article we introduce an experimental framework which tries to mitigate the effects of both sources of unpredictability. At compile time, an extensive profiling helps us to detect system scenarios and bounds application dynamism. At the organization level, we incorporate a heterogeneous memory architecture composed by several configurable memories. A calibration process and a runtime control system adapt the platform to the current application needs. Our approach manages to reduce significantly the energy overhead associated to both variability and application dynamism (up to 60%, according to our simulations) without compromising the timing constraints existing in our target domain of dynamic periodic multimedia applications.
Acquired Cystic Disease of the Kidney: A Management Dilemma (1992)

No AccessJournal of UrologyReview Article1 Apr 1992Acquired Cystic Disease of the Kidney: A Management Dilemma Paramjit S. Chandhoke, Ralph J. Torrence, Ralph V. Clayman, and Marcos Rothstein Paramjit S. ChandhokeParamjit S. Chandhoke Dornier/American Foundation for Urologie Disease scholar More articles by this author , Ralph J. TorrenceRalph J. Torrence More articles by this author , Ralph V. ClaymanRalph V. Clayman More articles by this author , and Marcos RothsteinMarcos Rothstein More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)37436-0AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1992 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited byFarivar-Mohseni H, Perlmutter A, Wilson S, Shingleton W, Bigler S and Fowler J (2018) Renal Cell Carcinoma and End Stage Renal DiseaseJournal of Urology, VOL. 175, NO. 6, (2018-2021), Online publication date: 1-Jun-2006.WOLF J (2018) EVALUATION AND MANAGEMENT OF SOLID AND CYSTIC RENAL MASSESJournal of Urology, VOL. 159, NO. 4, (1120-1133), Online publication date: 1-Apr-1998.Doublet J, Peraldi M, Gattegno B, Thibault P and Sraer J (2018) Renal Cell Carcinoma of Native Kidneys: Prospective Study of 129 Renal Transplant PatientsJournal of Urology, VOL. 158, NO. 1, (42-44), Online publication date: 1-Jul-1997.Jefferson R, Burns J and Rosenthal J (2018) Urological Evaluation of Adult Renal Transplant RecipientsJournal of Urology, VOL. 153, NO. 3, (615-618), Online publication date: 1-Mar-1995.Levine L and Gburek B (2018) Acquired Cystic Disease and Renal Adenocarcinoma Following Renal TransplantationJournal of Urology, VOL. 151, NO. 1, (129-132), Online publication date: 1-Jan-1994. Volume 147Issue 4April 1992Page: 969-974 Advertisement Copyright & Permissions© 1992 by The American Urological Association Education and Research, Inc.Keywordskidney failure, chronickidney diseaseskidney, cystichemodialysiskidney neoplasmsMetricsAuthor Information Paramjit S. Chandhoke Dornier/American Foundation for Urologie Disease scholar More articles by this author Ralph J. Torrence More articles by this author Ralph V. Clayman More articles by this author Marcos Rothstein More articles by this author Expand All Advertisement PDF downloadLoading ...
Polyester/Poly(meth)acrylate Block Copolymers by Combined Polycondensation/ATRP: Characterization and Properties (2011)

Abstract Polyester/poly(meth)acrylate block copolymers are synthesized using a combination of polycondensation and ATRP. All block copolymers are characterized by means of NMR and GPC. Agreement between theoretical molecular weights of the polymers with observed GPC values suggests controlled polymerization. In the case of unsaturated‐polyester‐based block copolymers the main chain double bond in the polyester backbone remains almost unaffected during ATRP. The unsaturated block copolymers are crosslinkable and can form networks upon photoirradiation in the presence of a suitable photoinitiator. These copolymers might be interesting candidates for coatings with better overall properties than those based on neat polyesters. magnified image
The complication probability factor: a method for selection of radiation treatment plans (1978)

The problem of selecting the best radiation treatment plan from several that may offer subtle differences has been considered. A method is introduced in which the concept of a complication probability factor (CPF) can be used to quantify the relative merits of such treatment plans. The CPF is a variant of integral dose and consists of a weighted volume of irradiated normal tissue which may relate to radiation-related complications. Treatment plans for irradiation of a pelvic tumour volume using parallel opposed, 360 deg rotational and four-field techniques with X-ray beams of 4, 8, 22, and 45 MV have been analyzed to demonstrate the utility of the method. This analysis suggests that complex radiation delivery techniques may offer a substantial improvement in dose distribution characteristics, while higher beam energies are relatively less advantageous.
Directly modulated AM-VSB lightwave video transmission system using dispersion-compensating fiber and three cascaded EDFAs, providing 50-dB power budget over 38 km of standard single-mode fiber (1996)

Summary form only given. In this paper we show that with a directly modulated transmitter in a CATV transport and distribution system with cascaded Er-doped fiber amplifiers (EDFAs) similar power budgets and transmission distances can be achieved as in an externally modulated system, without electronic predistortion, by using dispersion compensating fiber (DCF) and carefully designed EDFAs with low gain-slope.
Pattern shift error induced by coating and developing (1996)

Improvement of pattern placement accuracy is an important factor for the development of the electron beam (EB) lithography system for the next-generation photomask. It has been qualitatively pointed out that pattern shift error is induced by surface distortion of photomask. In this paper, we quantified pattern shift error induced by mask process and have identified aeolotropic magnification error and negligible orthogonality error. These results obtained by experiment and simulation indicate that attention must be paid to pattern shift error induced by mask process in fabrication of the next-generation photomask. Thus, a more rigid and stiffer photomask will be required to reduce pattern shift error induced by coating and developing.
Spectroscopic ellipsometry as a sensitive monitor of materials contamination (1995)

Spectroscopic ellipsometry is demonstrated to be extremely sensitive to contamination layers in the thickness range from 0.1 nm to 10 microns. In the present experiments we deposit either a thin lubricating oil (WD-40) or mineral oil continuously onto Ir, Cu, Al, Au, and V substrates from a bubbler, and monitor its thickness growth from sub-nanometer to tens of nanometers as a function of time. Re-evaporation of contaminant oils is also monitored in real-time by ellipsometry.
A phase I study of MORab-009, a monoclonal antibody against mesothelin, in mesothelioma, pancreatic and ovarian cancer (2008)

3578 Background: MORAb-009 is a monoclonal antibody that targets mesothelin, a cell surface adhesion protein over-expressed in pancreatic cancer, mesothelioma and other malignancies, with minimal expression in normal human tissue. In vitro MORAb-009 inhibits tumor cell adhesion and mediates tumor cell killing. We initiated this phase I study to determine the safety of MORAb-009 administered weekly. Methods: Cohorts of 3 subjects received MORAb-009 intravenously on days 1, 8, 15 and 22 at doses of 12.5, 25, 50 100, 200 and 400 mg/m2. Disease evaluation with CT occurred on day 35. Serum drug levels were measured throughout the study. Subjects with stable disease or better by RECIST could receive additional cycles. Results: Enrollment is complete. 24 subjects were enrolled: advanced mesothelioma (13), pancreatic cancer (7), and ovarian cancer (4). Adverse events thought to be possibly, probably or definitely related to MORAb-009 included 2 allergic reactions, 4 acute infusion reactions (all grade 1 or 2), a thromboembolic event (grade 4), mild transient thrombocytopenia (grade 1) and dysgeusia (grade 1). At the 400 mg/m2 dose, 2 SAEs were observed: grade 4 elevation of liver enzymes and grade 3 serum sickness. These episodes were thought to have been related to the subjects’ conditions, but were conservatively called DLTs and thus the MTD was determined to be 200 mg/m2. Six subjects had stable disease and received additional cycles of therapy. One subject with previously progressive metastatic pancreatic cancer received 5 additional cycles of MORAb-009 and demonstrated stable disease for over 6 months. Another subject with pancreatic cancer, 2 with mesothelioma and 2 with ovarian cancer each received 1 additional cycle, a third subject with ovarian cancer received a partial additional cycle. Conclusions: MORAb-009 is well tolerated and the MTD when administered weekly is 200 mg/m2. Six subjects demonstrated stable disease warranting additional therapy. Given the favorable safety profile and possibility of clinical benefit, a phase II study of the efficacy of MORAb- 009 with gemcitabine in unresectable pancreatic cancer is underway. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Morphotek Morphotek Morphotek
Effect of Potassium-Channel Opener Therapy on Reperfused Infarction in Hypertrophied Hearts: Demonstration of Preconditioning by Using Functional and Contrast-Enhanced Magnetic Resonance Imaging (2004)

Effects of therapy with the potassium-channel opener and vasodilator nicorandil were studied in reperfused infarction of hypertrophied hearts by using magnetic resonance imaging (MRI), hemodynamic measurements, and histochemical staining. Aortic banding was performed on 22 Sprague-Dawley rats to induce left ventricular (LV) hypertrophy; 11 were the controls. Eight weeks later, the left coronary artery was occluded for 25 minutes in all 33 animals, followed by 3 hours of reperfusion. During occlusion, 11 rats with LV hypertrophy received nicorandil (0.1 mg/kg bolus and 1.5 mg/kg/h for 3 hours). The new necrosis-specific contrast agent Gadophrin-3 was administered to all animals to delineate infarction on multislice T1-weighted spin-echo MRI. Nicorandil increased ischemic tolerance of LV hypertrophy as shown by the reduction of infarction size from 19.3% +/- 1.3% to 10.0% +/- 2.5% LV (P = .005). Infarction size in treated animals was identical to control (9.3% +/- 1.6%). Close correlation was found between MRI and postmortem findings. Functional MRI revealed an improvement in ejection fraction in nicorandil-treated hearts (48.5% +/- 3.4% vs 38.1% +/- 3.2%, P = .04). LV end-diastolic volume and pressure, aortic pressure, and peripheral vascular resistance were highest in untreated hypertrophied hearts. Brief ischemia caused severe injury in hypertrophied hearts. Infusing nicorandil increased the tolerance of hypertrophied hearts to ischemia. MRI is a suitable technique for the evaluation of new therapies in LV hypertrophy.
High Mechanical Bandwidth Polysilicon Micromirrors for Large Area / High Deflection Angle Micromirror Arrays (2007)

We demonstrate a new design for micromirror arrays that allow for high tilt angles (0.75deg) of mirror elements in arbitrary directions, large actuated areas (0.64 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), and high actuation bandwidth (measured resonant frequencies range from 100 to 450 kHz). This is achieved by subdividing each actuated mirror into several small submirrors that are addressed simultaneously, so that they behave as one large composite mirror. Submirrors increase the resonance frequency, surface area, and tilt angle of each composite mirror, at the expense of a slight reduction in fill factor. Different designs for the individual micromirrors were fabricated from polysilicon using standard surface micromachining technology (MUMPs) and characterized; a 5 x 5 array of composite mirrors was also fabricated and tested.
Insulin-Mimicking Anti-Idiotypic Antibodies in Development of Spontaneous Autoimmune Diabetes in BB/E Rats (1990)

BB/E rats spontaneously develop a form of autoimmune diabetes resembling insulin-dependent diabetes mellitus (IDDM) in humans. IDDM results from central destruction of the insulin-producing beta-cells of the pancreatic islets. Herein, we report that the outbreak of IDDM in BB/E rats is preceded by the spontaneous development of an anti-idiotypic antibody to a particular antibody to insulin made by the rats. This anti-idiotype, designated anti-DM-id, behaves as an antibody to the insulin-hormone receptor. Thus, a spontaneous anti-idiotypic antibody network whose products can affect the peripheral utilization of insulin seems to accompany the central destruction of beta-cells in developing IDDM.
Comparative analysis of an experimental subcellular protein localization assay and in silico prediction methods (2009)

The subcellular localization of a protein can provide important information about its function within the cell. As eukaryotic cells and particularly mammalian cells are characterized by a high degree of compartmentalization, most protein activities can be assigned to particular cellular compartments. The categorization of proteins by their subcellular localization is therefore one of the essential goals of the functional annotation of the human genome. We previously performed a subcellular localization screen of 52 proteins encoded on human chromosome 21. In the current study, we compared the experimental localization data to the in silico results generated by nine leading software packages with different prediction resolutions. The comparison revealed striking differences between the programs in the accuracy of their subcellular protein localization predictions. Our results strongly suggest that the recently developed predictors utilizing multiple prediction methods tend to provide significantly better performance over purely sequence-based or homology-based predictions.
Age-dependent shift in macrophage polarisation causes inflammation-mediated degeneration of enteric nervous system (2017)

A shift by macrophages towards a proinflammatory phenotype with ageing causes inflammation-mediated degeneration of the ENS.
The Feasibility of Interference Alignment for MIMO Interfering Broadcast—Multiple-Access Channels (2017)

The feasibility conditions of interference alignment (IA) are analyzed for interfering broadcast-multiple-access channels in which one cell operates as downlink but the other cell operates as uplink. Under a general multiple-input and multiple-output antenna configuration, a necessary condition and a sufficient condition for one-shot linear IA are established, i.e., linear IA without symbol or time extension. In various example networks of interest, the optimal sum degrees of freedom (DoFs) are characterized by the derived necessary condition and sufficient condition. For symmetric DoF within each cell, a sufficient condition is established in a more compact expression, which yields the necessary and sufficient condition for a class of symmetric DoFs. An iterative construction of transmit and receive beamforming vectors is further proposed, which provides a specific beamforming design satisfying one-shot IA. Simulation results demonstrate that the proposed IA not only achieves larger DoF, but also significantly improves the sum rate over the single-cell operation in the practical signal-to-noise ratio regime.
Listeria monocytogenes: Overview and Targeting Advances (2016)

Listeria monocytogenes is a serious foodborne zoonotic pathogen capable of causing gastroenteritis and severe systemic infections such as septicemia, meningitis or abortion in the infected individuals what is called listeriosis. The bacterium is reported as the third leading cause of death among the foodborne pathogens preceded by nontyphoidal Salmonella spp. and Toxoplasma gondii. The power to tolerate a wide range of temperatures is considered the most prominent trait distinguishing it from the other foodborne pathogens. Within the infected host, the bacteria harbor inside macrophages and jump from cell to another without leaving the safeguarding milieu of the host's cells utilizing a set of genes including hly (listeriolysin O), plcA (phosphatidylinositol-specific phospholipase c), plcB (phosphatidylcholine-phospholipase C) and actA (actin-assembly inducing protein). In addition to the health concerns associated with antibiotics, treatment failure likely occurs among listeriosis-infected persons especially with the inability of most antibiotics to access intracellular replicative niches and achieve the optimum therapeutic concentrations within the infected cells. Recently, one novel choice, peptide nucleic acid (PNA), has been emerged to target this bacterium as a model of targeting intracellular pathogens with anti-sense agents. PNA is a one of the DNA analogues which works via specific inhibition of bacterial gene expression.