gebhart/patrepeval huggingface dataset:
Synthesis and thermal properties of a novel lactose-containing poly(N-isopropylacrylamide-co-acrylamidolactamine) hydrogel (1999)

An improved, simple, and efficient method for the synthesis of lactose-containing monomer acrylamidolactamine (LAM) has been reported. Free radical copolymerization of this monomer with N-isopropylacrylamide (NIPAM) in the presence of the crosslinking reagent N,N′-methylenebisacrylamide (BisA) (1.2 mol %) proceeded smoothly in an aqueous solution using potassium persulfate (KPS) and N,N,N′,N′-tetramethylethylenediamine (TMEDA) as the initiating system and gave transparent hydrogels. Reactivity ratios were estimated from copolymerization reactions carried out in solution without BisA crosslinker and at low conversion, by using both linearization and nonlinearization methods. They were found to be rLAM = 0.75 and rNIPAM = 1.22. The swelling behavior of the hydrogels was studied by immersion of the hydrogels in deionized water at different temperatures. Equilibrium water uptake was increased when the LAM content was higher than 47 mol %, and reached ≈ 44-fold with 100 mol % LAM at room temperature. Depending on the composition, the gels showed sharp swelling transitions with small changes in temperature. Differential scanning calorimetry (DSC) was used to characterize the swelling transition and the organization of water in the copolymer hydrogels. The amounts of freezable water in these hydrogels ranged from 81 to 89%, and was not correlated to the content of the sugar monomer. These gels have potential applications as biocompatible materials. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1393–1402, 1999
Glucose transport and hypoxia–reoxygenation injury in the perfused rat liver (1994)

During liver transplantation, oxidative stress occurs during hypoxia and reoxygenation of the donor organ. Chemical oxidative stress impairs cell membrane transport. Therefore, in this study the influence of hypoxia and reoxygenation on hepatocellular membrane transport was investigated. Specifically, glucose transport was studied in the perfused rat liver using the multiple indicator-dilution technique. First, it was observed that in normal rat livers, glucose transport was rapid but saturable (Km 48 +/- 10 mmol/L and Vmax 9.4 +/- 0.9 mumol/s per g of liver). To stimulate hypoxia and reoxygenation, livers were perfused for 30 min with nitrogen-saturated buffer and then with oxygen-saturated buffer for 20 min. The livers from fed rats were protected from hypoxia-reoxygenation injury whereas those from fasted rats were highly susceptible to injury as determined by lactate dehydrogenase release. After reoxygenation, the rate of glucose influx decreased significantly by approximately 50% in the fasted livers (P < 0.001) but was unaffected in the fed livers. This impairment of the hepatocellular transport of glucose, which could be secondary to oxidative injury to the hepatocyte membrane, has implications for the function of donor livers that have sustained hypoxia-reoxygenation ('preservation') injury during transplantation.
MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-widecis-regulatory module analysis (2016)

Myogenic regulatory factors of the MyoD family have the ability to reprogram differentiated cells toward a myogenic fate. In this study, we demonstrate that Six1 or Six4 are required for the reprogramming by MyoD of mouse embryonic fibroblasts (MEFs). Using microarray experiments, we found 761 genes under the control of both Six and MyoD. Using MyoD ChIPseq data and a genome-wide search for Six1/4 MEF3 binding sites, we found significant co-localization of binding sites for MyoD and Six proteins on over a thousand mouse genomic DNA regions. The combination of both datasets yielded 82 genes which are synergistically activated by Six and MyoD, with 96 associated MyoD+MEF3 putative cis-regulatory modules (CRMs). Fourteen out of 19 of the CRMs that we tested demonstrated in Luciferase assays a synergistic action also observed for their cognate gene. We searched putative binding sites on these CRMs using available databases and de novo search of conserved motifs and demonstrated that the Six/MyoD synergistic activation takes place in a feedforward way. It involves the recruitment of these two families of transcription factors to their targets, together with partner transcription factors, encoded by genes that are themselves activated by Six and MyoD, including Mef2, Pbx-Meis and EBF.
Large multiplication-bandwidth products in APDs with a thin InP multiplication layer (2005)

In this paper APD is fabricated with an 80 nm InP multiplication layer. The maximum bandwidth of 21 GHz, the multiplication-bandwidth product of 170 Hz and the intrinsic avalanche build up time of 0.4 ps (390 GHz) were obtained. The results shows that an APD for next generation 40 Gbit/s system can be achieved using a conventional InP multiplication layer.
Automated support for software development with frameworks (1995)

This document presents some of the results of an industrial research project on automation of software development. The project's objective is to improve productivity and quality of software development. We see software development based on frameworks and libraries of prefabricated components as a step in this direction. An adequate development style consists of two complementary activities: the creation of frameworks and new components for functionality not available and the composition and configuration of existing components.
Relative Positional Encoding for Transformers with Linear Complexity (2021)

Recent advances in Transformer models allow for unprecedented sequence lengths, due to linear space and time complexity. In the meantime, relative positional encoding (RPE) was proposed as beneficial for classical Transformers and consists in exploiting lags instead of absolute positions for inference. Still, RPE is not available for the recent linear-variants of the Transformer, because it requires the explicit computation of the attention matrix, which is precisely what is avoided by such methods. In this paper, we bridge this gap and present Stochastic Positional Encoding as a way to generate PE that can be used as a replacement to the classical additive (sinusoidal) PE and provably behaves like RPE. The main theoretical contribution is to make a connection between positional encoding and cross-covariance structures of correlated Gaussian processes. We illustrate the performance of our approach on the Long-Range Arena benchmark and on music generation.
Nichtinvasive Carotisdiagnostik mit MRA und 16-MSCT (2004)

Ziele: Überprüfung der Messergebnisse von MRA und MSCT bei Carotisstenosen. Methode: Bei 50 Patienten mit Verdacht auf eine hochgradige Carotisstenose wurde eine MRA (Magnetom Symphony) und CTA (Somatom Sensation 16) durchgeführt. Zur MRA wurde eine 3D-TOF -Sequenz (TR=34ms, TE=6.95ms, a=25°, Voxelgröße=0.8×0.4×0.8mm3, Messzeit=4:02min) im Bereich der Carotisbifurkation durchgeführt. Die CE-MRA (TR=3.89ms, TE=1.54ms, a=35°, 20ml Gd-DTPA, Voxelgröße=1.2×0.6×0.8mm3, Messzeit=0:21min) und die CTA (SC=16×0.75mm, pitch=1.5, 120kV, 120effmAs, 60ml KM, Voxelgröße=0.2×0.2×0.5mm3, Messzeit=0:09min) wurden vom Aortenbogen bis einschließlich des Circulus Willisii gemessen. Für beide Modalitäten wurde die Kreislaufzeit per Test-Bolus bestimmt. Zur Auswertung wurden MIP und interaktive MPR verwendet um das Gefäßlumen zu messen, zur Stenoseklassifizierung wurden die NASCET-Kriterien angewendet. Es werden die Interobserver-Variabilitäten sowie der Einfluss unterschiedlicher Messmethoden angegeben. Ergebnis: Die durchschnittliche Untersuchungszeit (incl. Nachverarbeitung) für die MRA und CTA betrug 20–30 Minuten. Die kurze Untersuchungszeit verhinderte venöse Überlagerungen in beiden Modalitäten. Die Auswertung der Daten zeigte die gute Übereinstimmung der Stenosegrade mit CTA und 3D-TOF bei höchstgradigen Stenosen, während mit der CE-MRA eine Tendenz zur Überschätzung bestand. Die MPR-Auswertung der MRA-Daten zeigen vergleichbare Ergebnisse zur MIP-Auswertung. Schlussfolgerung: Die 16-MSCT und die hochaufgelöste MRA (CE-MRA + 3D-TOF) stellen in Bezug auf die Genauigkeit zur präoperativen, nicht-invasiven Abklärung von Carotisstenosen gleichberechtigte Alternativen dar.
Biogas infrastructures from farm to regional scale, prospects of biogas transport grids (2016)

The volume of biogas produced in agricultural areas is expected to increase in coming years. An increasing number of local and regional initiatives show a growing interest in decentralized energy production, wherein biogas can play a role. Biogas transport from production sites to user, i.e. a CHP, boiler or an upgrading installation, induces a scale advantage and an efficiency increase. Therefore the exploration of the costs and energy use of biogas transport using a dedicated infrastructure is needed. A model was developed to describe a regional biogas grid that is used to collect biogas from several digesters and deliver it to a central point. The model minimizes transport costs per volumetric unit of biogas in a region. Results are presented for different digester scales, different sizes of the biomass source area and two types of grid lay-out: a star lay-out and a fishbone lay-out. The model shows that transport costs in a fishbone lay-out are less than 10 €ct m−3 for a digester scale of 100 m3 h−1; for the star lay-out costs can go up to 45 €ct m−3. For 1800 m3 h−1 digesters, these values are 4.0 €ct m−3 and 6.1 €ct m−3, respectively. The results indicate that cooperation between biogas producers in collecting biogas by means of a fishbone lay-out reduces the biogas transport costs relative to using a star lay-out. Merging smaller digesters into a smaller number of larger ones reduces the costs of biogas transport for the same biomass source area.
Immune-instructive copolymer scaffolds using plant-derived nanoparticles to promote bone regeneration (2022)

We have shown that PLCA scaffolds functionalized with plant-derived RG-I with a relatively higher amount of galactose play a role in the modulation of inflammatory responses both in vitro and in vivo subcutaneously and promote the initiation of bone formation in a critical-sized bone defect of an aged rodent. Our study addresses the increasing demand in bone tissue engineering for immunomodulatory 3D scaffolds that promote osteogenesis and modulate immune responses.
The coexistence of an equal amount of Alzheimer's amyloid‐β 40 and 42 forms structurally stable and toxic oligomers through a distinct pathway (2014)

Fibrillar amyloid-β (Aβ) is the major constituent of senile plaques in the brain of patients with Alzheimer's disease (AD). Aβ is a short peptide generated from amyloid precursor protein with two main isoforms, Aβ40 and Aβ42, with the latter having two additional hydrophobic residues at the C-terminus. The two isoforms have distinct characteristics, in which Aβ42 plays a more pathogenic role. Some early-onset familial AD cases possess an elevated Aβ42/Aβ40 level, and biochemical studies show the two species interact with each other. Therefore, understanding structural conversion in the aggregation of mixed Aβ isoforms is essential for elucidating AD pathogenesis. Here, we systematically examined the differences between Aβ42, Aβ40 and various Aβ42/Aβ40 mixtures by monitoring the fibrillization kinetics, epitope changes, assembly, morphology and induced cytotoxicity. We found that the minor Aβ species in different mixing ratios modulated the major aggregation pathway. Size exclusion chromatography, circular dichroism spectroscopy and photo-crosslinking assay showed that soluble Aβ42 oligomers were stabilized after Aβ40 addition, and the equimolar Aβ42/Aβ40 mixture rapidly formed spherical oligomers. These oligomers were the most toxic among those examined as evidenced by neurite degeneration and neuronal toxicity. However, the oligomers were not responsible for intracellular calcium elevation. Overall, our results demonstrated that differently mixed Aβ species repartitioned oligomer intermediates on the major aggregation pathway. Furthermore, the equimolar mixture rapidly formed structurally stable and the most toxic oligomers. These results provided information on the potential pathological mechanisms underlying the elevated Aβ42/Aβ40 ratio in familial AD patients and in the local environment of sporadic AD brains.
Generation of DPSK Signals Using a Directly Modulated Passive Feedback Laser (2012)

The generation of DPSK signals is demonstrated using a directly modulated passive feedback laser at 10.709, 14 and 16 Gb/s. The quality of the DPSK signals was assessed using both noncoherent detection (10.709 Gb/s) and coherent detection with digital signal processing involving a look-up table pattern-dependent distortion compensation scheme.
A human-robot collaborative Traveling Salesman Problem: Robotic site inspection with human assistance (2016)

In this paper, we consider a collaborative human-robot Traveling Salesman Problem (TSP), where a robot is tasked with site inspection and target classification, under a limited motion energy budget and with a limited access to a human operator. More specifically, a robotic field operation is considered where a robot has to co-optimize seeking human assistance (via asking questions) and selective TSP tour design (for a closer inspection) based on an initial remote sensing. The robot has a limited budget for both communication with the human operator and site inspection motion consumption. By utilizing our past work on the target classification performance of humans and robots, we show how the collaborative human-robot TSP can be solved under limited resources. We further theoretically characterize the average correct classification probability as a function of the given number of questions to the human operator and the given motion energy budget. Extensive simulation results confirm our theoretical derivations.
Comparing the Performance of L*A*B* and HSV Color Spaces with Respect to Color Image Segmentation (2015)

Color image segmentation is a very emerging topic for image processing research. Since it has the ability to present the result in a way that is much more close to the human yes perceive, so todays more research is going on this area. Choosing a proper color space is a very important issue for color image segmentation process. Generally LAB and HSV are the two frequently chosen color spaces. In this paper a comparative analysis is performed between these two color spaces with respect to color image segmentation. For measuring their performance, we consider the parameters: mse and psnr . It is found that HSV color space is performing better than LAB.
Medium-chain fatty acids suppress lipotoxicity-induced hepatic fibrosis via the immunomodulating receptor GPR84 (2022)

Medium-chain triglycerides (MCTs), which consist of medium-chain fatty acids (MCFAs), are unique forms of dietary fat with various health benefits. G protein-coupled 84 (GPR84) acts as a receptor for MCFAs (especially C10:0 and C12:0); however, GPR84 is still considered an orphan receptor, and the nutritional signaling of endogenous and dietary MCFAs via GPR84 remains unclear. Here, we showed that endogenous MCFA-mediated GPR84 signaling protected hepatic functions from diet-induced lipotoxicity. Under high-fat diet (HFD) conditions, GPR84-deficient mice exhibited nonalcoholic steatohepatitis (NASH) and the progression of hepatic fibrosis but not steatosis. With markedly increased hepatic MCFA levels under HFD, GPR84 suppressed lipotoxicity-induced macrophage overactivation. Thus, GPR84 is an immunomodulating receptor that suppresses excessive dietary fat intake-induced toxicity by sensing increases in MCFAs. Additionally, administering MCTs, MCFAs (C10:0 or C12:0, but not C8:0), or GPR84 agonists effectively improved NASH in mouse models. Therefore, exogenous GPR84 stimulation is a potential strategy for treating NASH.
CD5L is a pleiotropic player in liver fibrosis controlling damage, fibrosis and immune cell content (2019)

Our study identifies CD5L as a key pleiotropic inhibitor of chronic liver injury. FUND: Fundació Marató TV3, AGAUR and the ISCIII-EDRF.
Dentin bonding: effect of tubule orientation on hybrid‐layer formation (1997)

In an attempt to compare the morphology of the resin-dentin interface in areas where the dentinal tubules run perpendicularly or at an angle to the cavity surface with that of areas where they run parallel to it, we studied a dentin adhesive system using transmission electron microscopy and fluorescence confocal laser scanning microscopy. The design of the study included the simulation of the normal hydrostatic pressure within the pulp and the dentinal tubules. Following acid etching of the dentinal surface with maleic acid/HEMA, the smear layer was removed, and a superficial zone was demineralized in such a way that the exposed collagenous dentin matrix retained its integrity. Confocal laser scanning microscopal investigations using primer labeled with rhodamine B showed that the penetration of the primer occurred not only vertically via surface porosities, but mainly laterally, via the dentinal tubules. The adhesive resin labeled with fluorescein completely infiltrated the demineralized layer, thereby forming a hybrid layer. The orientation of the dentinal tubules had a profound effect on the formation of the hybrid layer. In areas with perpendicular tubule orientation, the layer was 3.2 +/- 0.8 microns thick, showing solid 27.2 +/- 0.8 microns long resin tags in the dentinal tubules, and a network of tiny tags in their side-branches. In areas with parallel tubule orientation the layer was significantly thinner (1.3 +/- 0.6 microns) and resin tags were absent.
A Novel Particle Filter Based SLAM Algorithm for Lunar Navigation and Exploration (2019)

This paper presents a simultaneous localization and mapping (SLAM) system for lunar exploration. The proposed SLAM algorithm presents a significantly lower computational complexity compared to the state-of-the-art solutions, due the use of a Rao-Blackwellised particle filter with adaptive and compound resampling. The proposed SLAM sensor system consists of one light detecting and ranging sensor (LIDAR) and one IMU, to minimize illumination-dependent errors; as the lunar environment, and in particular the target exploration region around the Marius Hills hole, presents very variable illumination conditions. The system was tested via simulation, using existing environmental data from the mare tranquillitatis pit crater.
3D object modeling with a voxelset carving approach (2005)

In the past few years several systems for object reconstruction based on the analysis of 2D images have been proposed. In order for such systems to be of practical use, the 3D data extraction process is expected to be fast and reliable. In this paper we propose a general approach for the reconstruction of complete 3D objects based on a mesh fusion algorithm. Every surface patch is obtained as a depth map using an algorithm based on graph cuts theory. Each depth map is then triangulated before using it in a fusion algorithm based on a voxel-set carving approach. The result of the process is a closed mesh representing the object surface with sub-voxel resolution.
Supplementary Methods from Therapeutic Targeting of Nemo-like Kinase in Primary and Acquired Endocrine-resistant Breast Cancer (2023)

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Optimal Inversion of the Anscombe Transformation in Low-Count Poisson Image Denoising (2010)

The removal of Poisson noise is often performed through the following three-step procedure. First, the noise variance is stabilized by applying the Anscombe root transformation to the data, producing a signal in which the noise can be treated as additive Gaussian with unitary variance. Second, the noise is removed using a conventional denoising algorithm for additive white Gaussian noise. Third, an inverse transformation is applied to the denoised signal, obtaining the estimate of the signal of interest. The choice of the proper inverse transformation is crucial in order to minimize the bias error which arises when the nonlinear forward transformation is applied. We introduce optimal inverses for the Anscombe transformation, in particular the exact unbiased inverse, a maximum likelihood (ML) inverse, and a more sophisticated minimum mean square error (MMSE) inverse. We then present an experimental analysis using a few state-of-the-art denoising algorithms and show that the estimation can be consistently improved by applying the exact unbiased inverse, particularly at the low-count regime. This results in a very efficient filtering solution that is competitive with some of the best existing methods for Poisson image denoising.
Addition of metabolomics to the omics spectrum for cancer biomarker development– demonstration with the KrasG12D mouse model for pancreatic carcinoma (2014)

Advancements in 'omics' technologies offer opportunities to complement current approaches in cancer diagnosis and assessment of response to therapy. While the relatively mature fields of transcriptomics and proteomics have demonstrated their utility in cancer diagnosis and prognosis, they typically rely on complicated and demanding methodologies requiring isolation of intact ribonucleic acid or protein and then analyses. Metabolomics is an emerging field with great potential for cancer screening and early diagnosis. Here metabolites, defined as small molecules typically less than 1 kDa, are assessed with modern analytical approaches that can detect thousands of different molecules, and identify informative subsets of manageable size for use in simpler cost-effective instrumentation in the field. Cancer cells show substantial perturbations in metabolism such as glycolysis, Warburg effect, and many laboratories are now assessing its utility in oncology.

In the case of pancreatic duct adenocarcinoma (PDAC), this tumor type is the fourth leading cancer worldwide with less than 6% 5-year survival rate. PDAC is associated with poor prognosis based on the late stage diagnosis of the disease, hence being referred to as the “silent killer”. Current diagnostic tests lack the sensitivity and specificity to identify markers of early staging, and efforts have been carried out at Georgetown University to identify metabolomic biomarkers in patient PDAC tissue which then can be assessed in biofluids such as urine and serum. To assess the feasibility of biomarker development in PDAC, we have also taken a mouse models approach using the p48-Cre/LSL-KrasG12D mouse model. This model shows malignant progression to PDAC analogous to the human disease stages via early and late pancreatic intra-epithelial neoplasia (PanIN) lesions. Serum was collected from mice with early PanIN lesions (at 3-5 months) and with late PanIN or invasive PDAC lesions (13-16 months), as determined by histopathology. Metabolomics analysis of the serum samples was conducted through Ultra Performance Liquid Chromatography coupled to Time-of-flight Mass Spectrometry (QTOF). Multivariate data analysis revealed distinct metabolic profiles between the pancreatic cancer progression stages. One of the metabolites was validated through tandem mass spectrometry and showed increased circulating levels in mice with late PanIN and PDAC. Immunohistochemical analysis of pancreatic tissue showed increased levels of the enzyme, which produces this metabolite, at the late stages of pancreatic cancer, correlating with circulating metabolite levels. The use of this approach in developing diagnostic strategies with metabolomics in the detection of at-risk subjects will be discussed as a complement to genomics approaches.
Isotropic Design of Spherical Parallel Manipulators (1994)

Abstract Manipulator designs with isotropic architectures have a number of advantages, including good servo accuracy and low sensitivity to measuring and manufacturing errors. The isotropic design continua of two classes of spherical 3-dof parallel manipulators are found. These continua describe the complete set of isotropic design possibilities for the respective manipulator types.