gebhart/patrepeval huggingface dataset:
Chitin Digestion and Assimilation by Seabirds (1992)

As a structural component of crustacean exoskeletons, chitin is the most important carbohydrate in the diets of many marine carnivores. To investigate the physiological and biochemical adaptations that may enable seabirds to break down this “prey defense,” we estimated chitin digestibilities for Sooty Albatrosses (Phoebetria fusca), White-chinned Petrels (Procellaria aequinoctialis), Rockhopper Penguins (Eudyptes chrysocome), Gentoo Pen­ guins (Pygoscelis papua), King Penguins (Aptenodytes patagonicus) and Leach's Storm-Petrels (Oceanodroma leucorhoa) fed Antarctic krill (Euphausia superba). These species retain a substantial proportion (46.5 ± SD of 13.1%, 39.1 ± 4.9%, 52.8 ± 37.6%, 45.3 ± 5.6%, 84.8 ± 11.7% and 35 ± 12.2%, respectively) of ingested chitin. We also obtained preliminary estimates of chitinolytic activity in the gastric mucosae of the above six species by incubating extracts of tissue samples with a chitin substrate and measuring the production of the end product of chitin hydrolysis, N-acetyl-D-glucosamine (NAG). Chitinolytic activity (up to 5,000 11-g NAG h- 1 g-1 expressed per gram tissue) was measured from proventricular tissue and within the activity range (1,350 to 61,650 11-g NAG h- 1 g- 1) reported for eight other avian species. In order to assess the energetic and nutritional benefits of chitinolytic activity in seabirds, we studied gastrointestinal absorption of the end products of chitinolysis in Leach's Storm­ Petrels. The overall absorption efficiency of NAG and its deacetylated precursor, glucosamine (Gln), in this species was 44.0 ± 3.0% and 11.0 ± 1.9%, respectively. These absorption effi­ ciencies were significantly less than for glucose, which was absorbed with an efficiency of 90.6 ± 2.5%. No absorption of NAG and Gln occurred in the proventriculus. Overall, we showed that seabirds have a capacity to assimilate a considerable portion of the carbon and nitrogen present as chitin in the exoskeleton of their prey, but we have not demonstrated that assimilation actually occurs. The potential costs and benefits of chitin hydrolysis, as well as the absorption of the breakdown products, need to be assessed.
Exoskeletal Force-Sensing End-Effectors With Embedded Optical Fiber-Bragg-Grating Sensors (2009)

Force sensing is an essential requirement for dexterous robot manipulation. We describe composite robot end-effectors that incorporate optical fibers for accurate force sensing and estimation of contact locations. The design is inspired by the sensors in arthropod exoskeletons that allow them to detect contacts and loads on their limbs. In this paper, we present a fabrication process that allows us to create hollow multimaterial structures with embedded fibers and the results of experiments to characterize the sensors and controlling contact forces in a system involving an industrial robot and a two-fingered dexterous hand. We also briefly describe the optical-interrogation method used to measure multiple sensors along a single fiber at kilohertz rates for closed-loop force control.
Low power realization of residue number system based FIR filters (2002)

In this paper, we present algorithmic and architectural transforms for low power realization of Residue Number System (RNS) based FIR filters. These transforms have been systematically derived so as to achieve power reduction by voltage scaling, switched capacitance reduction and reduction in signal activity. We show how some of the existing techniques can be suitably adopted to RNS based implementations and also propose new techniques that exploit the specific properties of RNS based computation. We present results to show the effectiveness of our techniques. The results for modulo-5 and modulo-7 indicate that using just two of these techniques (coefficient encoding and coefficient ordering), power reduction of up to 33% can be achieved.
Mathematical microscopy (2013)

Important improvements and breakthroughs in microscopy acquisition methods can be achieved by incorporating innovative signal/image processing ingredients directly into the acquisition and/or reconstruction protocols, and by developing the new paradigm of mathematical microscopy. First, we will present some recent developments of smart acquisition methods in digital holography imaging whereby it is possible with compressed sensing-based computational tools to recover a high quality image from very fewer samples than the full acquisition and to design smart dynamic imaging protocols. Then, we will present a new framework for Structured Illumination Microscopy (SIM) which is based on a Bayesian inverse problem formulation approach that enables the computation of one high-resolution image from a reduced number of low-resolution images and has no specific constraints on the modulation pattern. We will demonstrate the efficiency of this approach through numerical evaluations on simulated data and examples on real microscopy data.
Abstract 2984: Building an in vitro blood brain barrier model to test the influence of tight junction gene alleles on disruption by focused ultrasound to treat brain tumors (2021)

Abstract Treating primary or metastatic tumors in the brain (glioblastomas, melanoma, lung cancer, breast cancer) proves challenging by virtue of the protective function of the blood brain barrier (BBB). Recently, it has been shown that low intensity focused ultrasonic (LIFU) waves stably cavitate infused microbubbles which then mechanically disrupt the tight junctions of the BBB. This leads to temporary, recoverable opening of the BBB, and passage of otherwise disqualified cancer-therapeutic drugs at precise locations targeted by the focused ultrasound. To date, potential genetic influences on the durability and vulnerability of tight junctions to LIFU have not been elucidated, nor have the determinants of tight junction repair post LIFU been thoroughly investigated. We report the development of an ultrasound transparent organ-on-chip model to test LIFU with microbubble infusion treatment on a cell-engineered BBB. The BBB is developed using brain-specific endothelial cells derived from genomically characterized immortalized pluripotent stem cells (iPSC). Furthermore, to test genetic variation effects we propose that alleles coding for the proteins involved in tight junction assembly contribute to LIFU disruption variability. Developing preclinical models of the BBB to accommodate cell sources with tight junction genes of different allele makeup will shed light on how individuals will respond to different ultrasound frequencies. The in vitro BBB device is composed of two orthogonally stacked fluidic channels formed by top and bottom polydimethylsiloxane (PDMS) membranes and a middle polyester membrane with 3 µm pores. An ultrasound system is constructed with a waveform generator, amplifier, and 1MHz ultrasound transducer. A 0.5 MHz receiving transducer and a digital storage oscilloscope are used for stable cavitation monitoring. Nanobubbles (FUS Instruments) transduce the LIFU into a mechanical vibration force to disrupt the BBB. To deliver the ultrasonic waves, the device is submerged in degassed DI water in a custom tank. Fluid flow was achieved, and subharmonic ultrasound signal is observed using the digital oscilloscope with Fast Fourier Transform (FFT). Preliminary results convey stable cavitation with LIFU and the formation of tight junctions in a brain microvascular endothelial cell monolayer in the device, eventually leading to a versatile platform to evaluate genetic-based vulnerability of the BBB. Citation Format: Jayashree Iyer, Adam Akkad, Nanyun Tang, Michael E. Berens, Frederic Zenhausern, Jian Gu. Building an in vitro blood brain barrier model to test the influence of tight junction gene alleles on disruption by focused ultrasound to treat brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2984.
Synthesis and Characterization of Fibre Reinforced Silica Aerogel Blankets for Thermal Protection (2016)

Using tetraethoxysilane (TEOS) as the source of silica, fibre reinforced silica aerogels were synthesized via fast ambient pressure drying using methanol (MeOH), trimethylchlorosilane (TMCS), ammonium fluoride (NH 4 F), and hexane. The molar ratio of TEOS/MeOH/(COOH) 2 /NH 4 F was kept constant at 1 : 38 : 3.73 × 10 −5 : 0.023 and the gel was allowed to form inside the highly porous meta-aramid fibrous batting. The wet gel surface was chemically modified (silylation process) using various concentrations of TMCS in hexane in the range of 1 to 20% by volume. The fibre reinforced silica aerogel blanket was obtained subsequently through atmospheric pressure drying. The aerogel blanket samples were characterized by density, thermal conductivity, hydrophobicity (contact angle), and Scanning Electron Microscopy. The radiant heat resistance of the aerogel blankets was examined and compared with nonaerogel blankets. It has been observed that, compared to the ordinary nonaerogel blankets, the aerogel blankets showed a 58% increase in the estimated burn injury time and thus ensure a much better protection from heat and fire hazards. The effect of varying the concentration of TMCS on the estimated protection time has been examined. The improved thermal stability and the superior thermal insulation of the flexible aerogel blankets lead to applications being used for occupations that involve exposure to hazards of thermal radiation.
The Yersiniabactin Biosynthetic Gene Cluster of Yersinia enterocolitica : Organization and Siderophore-Dependent Regulation (1998)

The ability to synthesize and uptake the Yersinia siderophore yersiniabactin is a hallmark of the highly pathogenic, mouse-lethal species Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica 1B. We have identified four genes, irp1, irp3, irp4, and irp5, on a 13-kb chromosomal DNA fragment of Y. enterocolitica 08, WA-314. These genes constitute the yersiniabactin biosynthetic gene cluster together with the previously defined irp2. The irp1 gene consists of 9,486 bp capable of encoding a 3,161-amino-acid high-molecular-weight protein 1 (HMWP1) polypeptide with a predicted mass of 384.6 kDa. The first 3,000 bp of irp1 show similarity to the corresponding regions of the polyketide synthase genes of Bacillus subtilis and Streptomyces antibioticus. The remaining part of irp1 is most similar to irp2, encoding HMWP2, which might be the reason for immunological cross-reactivity of the two polypeptides. Irp4 was found to have 41.7% similarity to thioesterase-like protein of the anguibactin biosynthetic genes of Vibrio anguillarum. Irp5 shows 41% similarity to EntE, the 2,3-dihydroxybenzoic acid-activating enzyme utilized in enterobactin synthesis of Escherichia coli. Irp4 and Irp5 are nearly identical to YbtT and YbtE, recently identified in Y. pestis. irp3 has no similarity to any known gene. Inactivation of either irp1 or irp2 abrogates yersiniabactin synthesis. Mutations in irp1 or fyuA (encoding yersiniabactin/pesticin receptor) result in downregulation of irp2 that can be upregulated by the addition of yersiniabactin. A FyuA-green fluorescent protein translational fusion was downregulated in an irp1 mutant. Upregulation was achieved by addition of yersiniabactin but not desferal, pesticin, or pyochelin, which indicates high specificity of the FyuA receptor and autoregulation of genes involved in synthesis and uptake of yersiniabactin.
INSIGHTS INTO THE APPLICATION OF PRESSURE PULSING FOR THE COLD RECOVERY OF HEAVY OIL (2022)

Current thermal oil-recovery techniques are invasive and suffer from many operational limitations. Thus, the quest for non-invasive techniques for the recovery of heavy oil has garnered recently immense research interest. The objective of this study is to evaluate the effect of pulsing pressure on the cold recovery of heavy oil by water flooding glass micromodels. The experimental setup consisted of a micromodel, a digital camera, a source of illumination, a syringe pump, and a pressure pulsing generator. The micromodel inlet pressure was recorded using a high-precision transducer. The oil saturation history in the micromodel was video recorded. The recorded video was cut into images which were digitized to calculate the oil recovery factor. Impact of two permeability values (1776 mD, and 18 mD), three pulsed pressures (low, medium, and high), and two crude viscosities (232 cp and 641 cp) on the oil recovery factor and the breakthrough time were assessed. The adequate pulsing pressure required for heavy-oil displacement using cold water injection appeared to depend on the viscosity of the crude. A 232-cp crude required at least low pulsing pressure (0.73 psi) to obtain an oil recovery higher than that obtained from the constant rate injection displacement (injection without pulsing). On the other hand, a 641-cp crude required at least medium pulsing pressure (1.29 psi) to obtain an oil recovery higher than that of the constant rate injection displacement. For both crude viscosities, the larger the pulsing pressure was, the faster the breakthrough time became, and the greater the oil recovery-factor was. Water flooding, conducted at a sufficiently high pulsed pressure,
Application of Molecular Dynamics Simulation To Predict the Compatability between Water-Insoluble Drugs and Self-Associating Poly(ethylene oxide)-b-poly(ε-caprolactone) Block Copolymers (2008)

In the present work, molecular dynamics (MD) simulation was applied to study the solubility of two water-insoluble drugs, fenofibrate and nimodipine, in a series of micelle-forming PEO-b-PCL block copolymers with combinations of blocks having different molecular weights. The solubility predictions based on the MD results were then compared with those obtained from solubility experiments and by the commonly used group contribution method (GCM). The results showed that Flory-Huggins interaction parameters computed by the MD simulations are consistent with the solubility data of the drug/PEO-b-PCL systems, whereas those calculated by the GCM significantly deviate from the experimental observation. We have also accounted for the possibility of drug solubilization in the PEO block of PEO-b-PCL.
Voxel Models as Input for Heat Transfer Simulations Based on X-ray Microtomography Images of Random Fiber Reinforced Composites (2018)

This paper proposes a method for the creation of a three-dimensional finite element model representing fiber reinforced insulation materials for the simulation software Siemens NX. VoxTex software, a tool for quantification of µCT images of fibrous materials, is used for the transformation of microtomography images of random fiber reinforced composites into finite element models. The paper describes the numerical tools used for the image quantification and the conversion and illustrates them on several thermal simulations of fiber reinforced insulation blankets filled with low thermal conductive fillers. The experimental measurements validate the prediction of the thermal conductivity.
Data from ESM1 as a Marker of Macrotrabecular-Massive Hepatocellular Carcinoma (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Macrotrabecular-massive hepatocellular carcinoma (MTM-HCC) is a novel morphological subtype of HCC associated with early relapse after resection or percutaneous ablation, independently of classical clinical and radiological prognostic factors. The aim of the present study was to identify immunohistochemical markers of MTM-HCC, to ease its diagnosis and implementation into clinical practice.&lt;/p&gt;Experimental Design:&lt;p&gt;To identify potential biomarkers of MTM-HCC, we first analyzed gene expression profiling data from The Cancer Genome Atlas study and further selected two candidate biomarkers. Performance of both biomarkers for diagnosis of MTM-HCC was further tested by immunohistochemistry in two independent series of 67 and 132 HCC biopsy samples.&lt;/p&gt;Results:&lt;p&gt;Analysis of RNA sequencing data showed that MTM-HCC was characterized by a high expression of neoangiogenesis-related genes. Two candidate biomarkers, Endothelial-Specific Molecule 1 (ESM1) and Carbonic Anhydrase IX (CAIX), were selected. In the discovery series, sensitivity and specificity of ESM1 expression by stromal endothelial cells for the detection of MTM-HCC were 97% (28/29), and 92% (35/38), respectively. Sensitivity and specificity of CAIX were 48% (14/29) and 89% (34/38). In the validation set, sensitivity and specificity of ESM1 for the identification of MTM-HCC were 93% (14/15) and 91% (107/117), respectively. Interobserver agreement for ESM1 assessment was good in both series (Cohen Kappa 0.77 and 0.76).&lt;/p&gt;Conclusions:&lt;p&gt;Using a molecular-driven selection of biomarkers, we identified ESM1 as a reliable microenvironment immunohistochemical marker of MTM-HCC. The results represent a step toward the implementation of HCC morpho-molecular subtyping into clinical practice.&lt;/p&gt;&lt;/div&gt;
S100B and S100A6 Differentially Modulate Cell Survival by Interacting with Distinct RAGE (Receptor for Advanced Glycation End Products) Immunoglobulin Domains (2007)

S100 proteins are EF-hand calcium-binding proteins with various intracellular functions including cell proliferation, differentiation, migration, and apoptosis. Some S100 proteins are also secreted and exert extracellular paracrine and autocrine functions. Experimental results suggest that the receptor for advanced glycation end products (RAGE) plays important roles in mediating S100 protein-induced cellular signaling. Here we compared the interaction of two S100 proteins, S100B and S100A6, with RAGE by in vitro assay and in culture of human SH-SY5Y neuroblastoma cells. Our in vitro binding data showed that S100B and S100A6, although structurally very similar, interact with different RAGE extracellular domains. Our cell assay data demonstrated that S100B and S100A6 differentially modulate cell survival. At micromolar concentration, S100B increased cellular proliferation, whereas at the same concentration, S100A6 triggered apoptosis. Although both S100 proteins induced the formation of reactive oxygen species, S100B recruited phosphatidylinositol 3-kinase/AKT and NF-kappaB, whereas S100A6 activated JNK. More importantly, we showed that S100B and S100A6 modulate cell survival in a RAGE-dependent manner; S100B specifically interacted with the RAGE V and C(1) domains and S100A6 specifically interacted with the C(1) and C(2) RAGE domains. Altogether these results highlight the complexity of S100/RAGE cellular signaling.
3D object recognition from range images using local feature histograms (2005)

The paper explores a view-based approach to recognize free-form objects in range images. We are using a set of local features that are easy to calculate and robust to partial occlusions. By combining those features in a multidimensional histogram, we can obtain highly discriminant classifiers without the need for segmentation. Recognition is performed using either histogram matching or a probabilistic recognition algorithm. We compare the performance of both methods in the presence of occlusions and test the system on a database of almost 2000 full-sphere views of 30 free-form objects. The system achieves a recognition accuracy above 93% on ideal images, and of 89% with 20% occlusion.
Grating-coupler-based optical proximity coupling for scalable computing systems (2011)

Silicon photonics is envisioned as a promising solution to address the interconnect bottleneck in large-scale multi-processor computing systems, owing to advantageous attributes such as wide bandwidth, high density, and low latency. To leverage these advantages, optical proximity coupler is one of the critical enablers. Chip-to-chip, layer-to-layer optical proximity couplers with low loss, large bandwidth, small footprint and integration compatibility are highly desirable. In this paper, we demonstrate chip-to-chip optical proximity coupling using grating couplers. We report the experimental results using grating couplers fabricated in a photonically-enabled commercial 130nm SOI CMOS process.
Binary metal sulfides and polypyrrole on vertically aligned carbon nanotube arrays/carbon fiber paper as high-performance electrodes (2015)

Rationally designed and coaxially grown Ni–Co–S and polypyrrole on vertically aligned carbon nanotube (VA-CNT) arrays/3D carbon fiber paper (CFP) are presented as novel freestanding electrodes for energy storage devices.
Multiple footprint stereo algorithms for 3D display content generation (2007)

This research focuses on the conversion of stereoscopic video material into an image + depth format which is suitable for rendering on the multiview auto-stereoscopic displays of Philips. The recent interest shown in the movie industry for 3D significantly increased the availability of stereo material. In this context the conversion from stereo to the input formats of 3D displays becomes an important task. In this paper we present a stereo algorithm that uses multiple footprints generating several depth candidates for each image pixel. We characterize the various matching windows and we devise a robust strategy for extracting high quality estimates from the resulting depth candidates. The proposed algorithm is based on a surface filtering method that employs simultaneously the available depth estimates in a small local neighborhood while ensuring correct depth discontinuities by the inclusion of image constraints. The resulting highquality image-aligned depth maps proved an excellent match with our 3D displays.
Quantitative Analysis of Hydrogen in Amorphous Films of Hydrogenated Carbon Nitride (2001)

The amorphous phase of hydrogenated carbon nitride, a -CN x :H (0 ≦ x ≦1), films may have clusters consisting of a mixture of sp 2 - and sp 3 -hybridized materials with cluster sizes of 0.2–2 nm. The hydrogen termination limits the size of the carbon and carbon nitride clusters. It also influences the mechanical properties of the sample. In this experiment, the relationship between the hydrogen content and the mechanical properties of carbon and related materials was investigated using elastic recoil detection analysis (ERDA), nanoindentation techniques and Raman spectroscopy. The samples were classified into three categories of hardness: mechanically soft a -CN x :H (hardness: 1–8 GPa), mechanically hard a -CN x :H (8–30 GPa) and hard hydrogenated amorphous carbon ( a -C:H) (more than 30 GPa). The hydrogen contents of the sample were 10–50 at.%, 5–40 at.%, and less than 3 at.% for soft a -CN x :H, hard a -CN x :H and hard a -C:H, respectively.