gebhart/patrepeval huggingface dataset:
Quencher diffusion in chemically amplified poly(4-hydroxystyrene-co-t-butyl methacrylate) resist (2015)

Understanding of resist fundamentals is important for the efficient development of resist materials. In this study, we investigated the quencher diffusion in a chemically amplified resist consisting of poly(4-hydroxystyrene-co-t-butyl methacrylate), triphenylsulfonium nonafluorobutanesulfonate (an acid generator), and tri-n-octylamine (a quencher). The dose-pitch matrices of line width and line edge roughness were analyzed on the basis of the sensitization and reaction mechanisms of chemically amplified extreme ultraviolet resists. The ratio of the diffusion constant of tri-n-octylamine to that of nonafluorobutanesulfonic acid was estimated to be 1.2 ± 0.7.
Comparison of several techniques for the detection of apoptotic astrocytes in vitro (2001)

Implication of apoptosis in numerous physiological and pathological processes has resulted in the development of numerous methods to detect apoptosis, but none of them is adapted to all cell types. In this study, we induced apoptosis on murine immortalized astrocytes with urine from multiple sclerosis (MS) patients. Among techniques allowing the detection of apoptotic cells, only a few are adapted to adherent cells such as astrocytes. We compared several techniques (propidium iodide labelling and flow cytometry analysis, TUNEL and annexin V labelling in immunofluorescence, DNA ladder, ELISA tests to detect nucleosomes) in order to choose the method best adapted to our adherent cellular model and to discuss their practicability for the detection of apoptosis on adherent cells. For technical course, propidium iodide labelling followed by flow cytometry analysis as a quantitative technique, and TUNEL in IF (easier and quicker than propidium iodide) as a semiquantitative test were both retained as best adapted to our case. Moreover, in our model, we have observed that phosphatydilserine externalization and DNA fragmentation were concomittant after induction of apoptosis. Techniques studied in this article would allow an enlarged study of the apoptotic mechanism in several pathologies by culture of adherent cells sensitive to apoptosis in vitro.
Tumor hypoxia: an important regulator of tumor progression or a potential modulator of tumor immunogenicity? (2021)

Hypoxia in the tumor microenvironment has been shown to be a strong indicator of tumor aggressiveness, metastases, and promotes cancer progression.1 Several studies have indicated that tumor hypoxi...
The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up (2020)

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.
Crystalline fiber Ho3+:YAG laser resonantly pumped by high-spectral-brightness laser diodes (2012)

Recent advances of high power and narrow bandwidth laser diodes emitting at 1.9 &#956;m open the path to direct diode pumping of Ho<sup>3+</sup>:YAG lasers. The usual method to pump such laser is to use thulium fiber laser which has an excellent beam quality with high power and narrow bandwidth emission. The draw back of this system is the low efficiency of this fiber laser and the increased overall complexity. In this paper we present first results of resonantly diode pumping of a Ho<sup>3+</sup>:YAG laser with fiberlike geometry. The fiber coupled diode modules used for pumping in this work (BrightLock<sup>TM</sup>Ultra-500) produce each 25 W at 1.91 &#956;m with 3 nm linewidth. The fiber has a core diameter of 600 &#956;m with 0.22 numerical aperture. The Ho<sup>3+</sup>:YAG crystal has a diameter of 1.2 mm, a length of 60 mm, a doping concentration of 0.75 at.% and is symmetrically pumped by two diode modules from both ends. Total internal reflection on the polished rod barrel allows a high pump intensity along the rod length. The Ho<sup>3+</sup>:YAG laser cavity is composed of a high reflective flat mirror and a concave output coupler with a radius of curvature of 500 mm. With an output coupler of 50 % we measured a threshold of 11 W. The maximum output power was 11.87 W with a wavelength of 2.09 &#956;m. The incident power to output power slope efficiency was 0.38 at currently 4 % of internal losses.
Ligand Binding Properties of Myoglobin Reconstituted with Iron Porphycene:  Unusual O2 Binding Selectivity against CO Binding1 (2004)

Sperm whale myoglobin, an oxygen storage hemoprotein, was successfully reconstituted with the iron porphycene having two propionates, 2,7-diethyl-3,6,12,17-tetramethyl-13,16-bis(carboxyethyl)porphycenatoiron. The physicochemical properties and ligand bindings of the reconstituted myoglobin were investigated. The ferric reconstituted myoglobin shows the remarkable stability against acid denaturation and only a low-spin characteristic in its EPR spectrum. The Fe(III)/Fe(II) redox potential (-190 mV vs NHE) determined by the spectroelectrochemical measurements was much lower than that of the wild-type. These results can be attributed to the strong coordination of His93 to the porphycene iron, which is induced by the nature of the porphycene ring symmetry. The O2 affinity of the ferrous reconstituted myoglobin is 2600-fold higher than that of the wild-type, mainly due to the decrease in the O2 dissociation rate, whereas the CO affinity is not so significantly enhanced. As a result, the O2 affinity of the reconstituted myoglobin exceeds its CO affinity (M' = K(CO)/K(O2) < 1). The ligand binding studies on H64A mutants support the fact that the slow O2 dissociation of the reconstituted myoglobin is primarily caused by the stabilization of the Fe-O2 sigma-bonding. The IR spectra for the carbon monoxide (CO) complex of the reconstituted myoglobin suggest several structural and/or electrostatic conformations of the Fe-C-O bond, but this is not directly correlated with the CO dissociation rate. The high O2 affinity and the unique characteristics of the myoglobin with the iron porphycene indicate that reconstitution with a synthesized heme is a useful method not only to understand the physiological function of myoglobin but also to create a tailor-made function on the protein.
Another JA/COI1-independent role of OPDA detected in tomato embryo development (2012)

Jasmonates (JAs) are ubiquitously occurring signaling compounds in plants formed in response to biotic and abiotic stress as well as in development. (+)-7-iso-jasmonoyl isoleucine, the bioactive JA, is involved in most JA-dependent processes mediated by the F-box protein COI1 in a proteasome-dependent manner. However, there is an increasing number of examples, where the precursor of JA biosynthesis, cis-(+)-12-oxophytodienoic acid (OPDA) is active in a JA/COI1-independent manner. Here, we discuss those OPDA-dependent processes, thereby giving emphasis on tomato embryo development. Recent data on seed coat-generated OPDA and its role in embryo development is discussed based on biochemical and genetic evidences.
Broadband metamaterial-enabled hybrid-mode horn antennas (2010)

In this paper, we show a broadband metasurface satisfying the balanced hybrid condition and its use as a liner to implement hybrid-mode horns. The design approach combines a nature-inspired optimization technique and an efficient full-wave electromagnetic solver, making it possible to realize metamaterials or metasurfaces with customized dispersive properties. With regard to surface impedances, the metasurface is found to be equivalent to a homogeneous metamaterial slab backed by a PEC ground plane. Therefore, we will consider the results of a numerical study of a conical horn antenna with a homogeneous metamaterial liner. The far-field radiation patterns and aperture field distribution confirm hybrid-mode operation over a wide bandwidth, validating the metasurface design methodology.
Laboratorio Unico Metropolitano: innovazione e alta tecnologia per un nuovo paradigma di medicina di laboratorio (2021)

Il Laboratorio Unico Metropolitano (LUM) e un intervento di programmazione sanitaria nato sulla spinta delle indicazioni della Regione Emilia- Romagna e volto a ridefinire le capacita produttive attraverso la riduzione delle duplicazioni. Il LUM e un esempio di integrazione in rete tra le strutture e soprattutto tra i professionisti che si occupano di salute. E il primo caso in Italia di cessione del ramo d'azienda tra Aziende Pubbliche: Azienda Ospedaliero-Universitaria Sant'Orsola-Malpighi (AOU), AUSL Imola, Istituto Ortopedico Rizzoli (IOR) hanno "ceduto" le risorse umane e tecnologiche, nonche i contratti di qualsiasi natura relativi alle attivita di diagnostica di laboratorio di patologia clinica, all'AUSL Bologna, individuata quale Azienda Capofila del progetto, presso la quale e localizzata la struttura del Laboratorio Unico.
Reflection properties of scintillator-septum candidates for a pixelated MeV detector (2014)

In order to predict and improve the performance of pixelated detectors, it is important to understand the optical properties of the basic unit of the scintillating structure in the detector. To measure one of the essential optical properties, reflectance, we have used a device composed of a laser and photodiode array. We have also developed an analytical model of the optical phenomena based on Snell's law and the Fresnel equations to simply analyze measured results and reflectance parameters at the interface. The computed and experimentally measured results typically have good agreement, validating the analytical model and measurements. The optical parameters are used as inputs to GEANT4 [1]. The simulations are then leveraged to optimize an imager design before a prototype is built. The optical reflectance was measured by using relatively inexpensive samples. A sample has scintillator, glue, and septum (reflector) layers, and each sample has a different scintillator surface (polished/rough) and/or reflector [ESR film/aluminum-sputtered (coated) ESR film] condition. A high-refractive-index hemisphere was attached on the top surface of a sample to increase the maximum incidence angle at the scintillator-glue interface from 27&deg; to 52&deg;. The sample including ESR film demonstrated average reflectance approximately 1.3 times higher than that from the sample with aluminum-sputtered ESR film as a reflector, and the polished surface condition showed higher reflectance than the rough-cut surface condition.
Distance estimation from received signal strength under log-normal shadowing: Bias and variance (2008)

In source localization one estimates the location of a source using a variety of relative position information. Many algorithms use certain powers of distances to effect localization. In practice, such distances are not directly available but must be deduced from information such as received signal strength (RSS) or time difference of arrival. This paper considers bias and variance issues in estimating powers of distances from RSS affected by log-normal shadowing. We show that the underlying estimation problem is inefficient and that the maximum likelihood estimate yields a bias and error variance that both increase exponentially with the noise power. By considering the class of twice differentiable estimators, we show that there is a unique unbiased estimator in this class, but that its error variance also grows exponentially with the noise power. Finally, we propose an estimate the bias and error variance of which are both bounded in the noise power.
XXIV World Allergy Congress 2015 (2016)

Purpose: Pirfenidone has been shown to have anti-fibrotic and antiinflammatory effects in the lungs. The purpose of this study was to evaluate the inhibitory effects of pirfenidone on transforming growth factor (TGF)-1-induced myofibroblast differentiation and extracellular matrix accumulation. We also determined the molecular mechanisms of pirfenidone in nasal polyp-derived fibroblasts (NPDFs). Methods: NPDFs were isolated from nasal polyps from eight patients who had chronic rhinosinusitis with nasal polyp. Pirfenidone was used to treat TGF-1-induced NPDFs. Cytotoxicity was evaluated using a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl-tetrazolium bromide assay. Fibroblast migration was evaluated with scratch assays. Expression levels of -smooth muscle actin (SMA), fibronectin, and phosphorylated Smad2/3 were determined by western blot and/or reverse transcription-polymerase chain reaction and immunofluorescent staining. Total collagen production was analyzed with the Sircol collagen assay and contractile activity was measured by a collagen gel contraction assay. Results: Pirfenidone (0 -2 mg/ml) has no significant cytotoxic effects in TGF-1-induced NPDFs. Migration of NPDFs was significantly inhibited by pirfenidone treatment. The expression levels of -SMA and fibronectin were significantly reduced in pirfenidonetreated NPDFs. Collagen contraction and production were also significantly decreased by pirfenidone treatment. Finally, pirfenidone significantly inhibited phosphorylation of Smad2/3 pathway in TGF-1-induced NPDFs. Conclusions: Pirfenidone has an inhibitory effect on TGF-1-induced migration, myofibroblast differentiation (-SMA), extracellular matrix accumulation, and collagen contraction by blocking the phosphorylation of Smad2/3 pathways in NPDFs. Thus, pirfenidone may inhibit TGF-1-induced extracellular matrix by regulating Smad2/3.
Design and Electrochemical Characterization of Spiral Electrochemical Notification Coupled Electrode (SENCE) Platform for Biosensing Application (2020)

C-reactive protein (CRP) is considered to be an important biomarker associated with many diseases. During any physiological inflammation, the level of CRP reaches its peak at 48 h, whereas its half-life is around 19 h. Hence, the detection of low-level CRP is an important task for the prognostic management of diseases like cancer, stress, metabolic disorders, cardiovascular diseases, and so on. There are various techniques available in the market to detect low-level CRP like ELISA, Western blot, etc. An electrochemical biosensor is one of the important miniaturized platforms which provides sensitivity along with ease of operation. The most important element of an electrochemical biosensor platform is the electrode which, upon functionalization with a probe, captures the selective antibody-antigen interaction and produces a digital signal in the form of potential/current. Optimization of the electrode design can increase the sensitivity of the sensor by 5-10-fold. Herein, we come up with a new sensor design called the spiral electrochemical notification coupled electrode (SENCE) where the working electrode (WE) is concentric in nature, which shows better response than the market-available standard screen-printed electrode. The sensor is thoroughly characterized using a standard Ferro/Ferri couple. The sensing performance of the fabricated platform is also characterized by the detection of standard H<sub>2</sub>O<sub>2</sub> using a diffusion-driven technique, and a low detection limit of 15 µM was achieved. Furthermore, we utilized the platform to detect a low level (100 ng/mL) of CRP in synthetic sweat. The manuscript provides emphasis on the design of a sensor that can offer good sensitivity in electrochemical biosensing applications.
P049: Reduced features of T-cell activation before and during anti-PD-1 treatment in classical Hodgkin lymphoma (2022)

Figure 1: Unbiased Clonality by primary and follow-up biopsies of different cohorts. Stars denote a statistically significant difference in Unbiased Clonalities of two cohorts (Welch’s Two Sample t-test, ** p < 0.01, *** p<0.001) Hodgkin- and Reed-Sternberg cells (HRSC) proliferate in a presumably highly immunogenic tumor microenvironment (TME) containing abundant CD4+ and CD8+ T-cells. Even though anti-PD-1 directed treatment is clinically well established, the mechanism of action in classical Hodgkin lymphoma (cHL) is still incompletely understood. To elucidate features of a T-cell mediated immune response in cHL, we studied HRSC immunogenicity defined by human leukocyte antigen (HLA) expression, associated T-cell expansion, and TME composition. We analyzed T-cell Receptor (TCR) repertoires, bulk gene expression levels and whole-slide images of treatment-naïve cHL patients before (n=90) and on anti-PD-1 therapy (n=4) in the NIVAHL phase II trial (Bröckelmann et al. JAMA Oncol 2020). In independent cohorts of breast cancer (n=6), benign lymph nodes (n=8) and cHL treated with chemotherapy (n=18), a biopsy both at primary diagnosis and relapse was available. To describe the proliferative activity of T-cells in the TME, we used three measures: debiased Simpson’s clonality (Unbiased Clonality; UC), Percentage of Singletons (PoS), and clonal expansion. We identified significantly lower UC and higher PoS in pre-treatment cHL compared to breast cancer specimens. Moreover, cHL showed less expansion of TCR clones in follow-up biopsies than breast cancer. A pair-wise comparison of pre- and on-anti-PD-1 treatment cHL specimens did not show a significant difference in UC or PoS. However, an analysis of primary versus relapse (after chemotherapy) biopsies of cHL showed a trend to increased UC in relapse specimens. Next, we analyzed bulk gene expression and TCR repertoires with respect to HLA I and II status on HRSC. HLA status was not associated with UC or PoS. However, we observed a significant enrichment of CD8+ T-cells and up-regulation of cytotoxicity genes in the bulk TME of HLA I+ HRSC. This trend seems to persist for both CD8+ T-cells close and more distant to HRSC (see Müller-Meinhard et al., ISHL12 submission). In summary, we did not observe features of a T-cell activation (UC, PoS, clonal expansion) in cHL pre- and on-anti-PD-1 treatment biopsies. Our findings suggest a cHL TME that contains a polyclonal mass of T-cells not activated early during anti-PD-1 treatment. However, our analyses cannot exclude an increased clonality in cHL at later timepoints or in relapse biopsies after conventional chemotherapy.
Two-wave-plate compensator method for single-point retardation measurements (2004)

The two-wave-plate compensator (TWC) technique is introduced for single-point retardation measurements. The TWC method uses a known wave plate together with a wave plate of unknown retardation and produces a linearly polarized output that allows a null of intensity to be detected. The TWC method is compared both theoretically and experimentally with the existing Brace-Köhler and Sénarmont methods. The resolution of the TWC is shown to be 0.02 nm. TWC enables the measurement of a sample retardation with as little as 0.13% error and thus is more accurate than either the Brace-Kohler or the Sénarmont method.
Molecular analysis of the human immunoglobulin V lambda II gene family. (1994)

The 8.12 idiotype characterizes a subpopulation of anti-DNA antibodies in patients with systemic lupus erythematosus (SLE). The idiotype is present on lambda light chains and has previously been shown to be exclusively encoded by V lambda II light chains. RFLP analysis of the V lambda II gene family has shown the family to consist of 10 to 15 members. Thus far, the sequences of seven V lambda II germline genes are reported in the literature with one of these a pseudogene. To identify the V lambda II genes that encode 8.12 positive antibodies and to further characterize the V lambda II family, germline V lambda II clones were derived from a patient with SLE. Two libraries were constructed: a genomic DNA library and a library of PCR-derived V lambda II gene products obtained using a conserved V lambda II leader region primer and a primer for the nonamer region 3' of the coding sequence. We now describe seven new germline genes, two of which are pseudogenes. Comparison of V lambda II germline genes to sequences of 8.12 positive light chains produced by EBV-transformed B cell lines show that all 8.12 positive light chains are encoded by a limited number of highly homologous members of the V lambda II family. 8.12 negative V lambda II encoded light chains also derive from a limited number of V lambda II genes, suggesting that only a subset of the apparently available V lambda II genes are commonly expressed.
The effect of corneal edema on visual function. (1977)

Corneal edema was produced by atmospheric-induced anoxia and the visual effect was assesed by conventional acuity tests and compared with contrast sensitivity measurements. For the degree of edema which this technique produced, contrast sensitivity was depressed for only high spatial frequencies and could be considered in terms of equivalent defocus. This was not the case ofr a greater degree of edema which was simulated by a diffuser with a particle size that mimics the diffraction effects from an edematous cornea. Equivalent blur was not applicable, since low spatial frequencies were also affected and the letter and contrast sensitivity tests gave radically different results. In the light of these findings, the validity of the present letter acuity evaluation of visual function for patients in which intraocular scattering is involved is questioned.