gebhart/patrepeval huggingface dataset:
ACES characterization of surface micromachined microfluidic devices (2000)

Recent breakthroughs in surface micromachining led to development of the first generation surface micromachined microfluidic devices. The simplest microfluidic device is a microfluidic channel (microchannel). A typical surface micromachined microchannel is about 2 pm deep, its width and depth depend on the specific application, while its top is less than 1 pm thick silicon nitride membrane. Almost all microfluidic devices are concerned with flow through very small passages and unintentional restrictions that lead to high-pressure gradients within the microchannels, which, in turn, cause deformations of the membranes. Knowledge of these deformations facilitates design and optimization of the microfluidic devices. We have developed a hybrid approach for accurate and precise characterization of microfluidic devices. This approach is based on Analytical, Computational, and Experimental Solutions (ACES) methodology. The experimental aspects of this methodology are based on laser interferometric measurements yielding displacement/deformation fields, while analytical and computational aspects are based on exact (closed form) and approximate (FEM) solutions, respectively. Comparison of analytical, computational, and experimental results indicates correlation to within 1%, for maximum deformations on the order of 1 μm. Continued advances in the methodology for characterization of the microfluidic devices will lead to development of robust devices, which will allow their integration with electronic actuation to enable a broad range of revolutionary new applications achievable with surface micromachining.
Postoperative single-sequence (PoSSe) MRI: imaging work-up for CT-guided or endoscopic drainage indication of collections after hepatopancreaticobiliary surgery (2021)

The PoSSe MRI approach is feasible in the early and intermediate postoperative setting after HPB surgery and shows a higher detection rate than sonography. Imaging work-up regarding drainage of collections was successful in all patients and our proposed PoSSe MRI algorithm provides an alternative to the standard work-up.
Enhanced Electrical Conductivity of Individual Conducting Polymer Nanobelts (2011)

A facile strategy for preparing 1D conducting polymer nanobelts with the width of the belts down to less than 50 nm is presented. Strong enhancement in the conductivity of individual polypyrrole (PPy) nanobelts is observed, due to lengthening of the π-conjugation length of PPy belts with decreasing belt width, as confirmed by micro-Raman measurements. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Beyond Traditional Structure-Based Drug Design: The Role of Iron Complexation, Strain, and Water in the Binding of Inhibitors for Hypoxia-Inducible Factor Prolyl Hydroxylase 2 (2019)

A combination of structure-based drug design and medicinal chemistry efforts led us from benzimidazole-2-carboxamide with modestly active hypoxia-inducible factor prolyl hydroxylase 2 inhibition to certain benzimidazole-2-pyrazole carboxylic acids that were more potent as well as orally efficacious stimulators of erythropoietin secretion in our in vivo mouse model. To better understand the structure-activity relationship, it was necessary to account for (i) the complexation of the ligand with the active site Fe<sup>2+</sup>, (ii) the strain incurred by the ligand upon binding, and (iii) certain key water interactions identified by a crystal structure analysis. With this more complete computational model, we arrived at an overarching paradigm that accounted for the potency differences between benzimidazole-2-carboxamide and benzimidazole-2-pyrazole carboxylic acid enzyme inhibitors. Moreover, the computational paradigm allowed us to anticipate that the bioisostere replacement strategy (amide → pyrazole), which had shown success in the benzimidazole series, was not generally applicable to other series. This illustrates that to fully reconcile the important ligand-active site interactions for certain targets, one often needs to move beyond traditional structure-based drug design (such as crystallographic analysis, docking, etc.) and appeal to a higher level of computational theory.
Acetabular Anteversion Changes Due to Spinal Deformity Correction: Bridging the Gap Between Hip and Spine Surgeons (2015)

Patients with spinopelvic malalignment had a high prevalence of excessively anteverted acetabular components. Sagittal spinal correction following total hip arthroplasty resulted in reduced acetabular anteversion, which may have implications for stability. Changes in anteversion are most closely related to changes in pelvic tilt in an almost one-to-one ratio.
Opposing Effects of Interleukin-36γ and Interleukin-38 on Trained Immunity (2023)

Trained immunity is the process of long-term functional reprogramming (a <i>de facto</i> innate immune memory) of innate immune cells such as monocytes and macrophages after an exposure to pathogens, vaccines, or their ligands. The induction of trained immunity is mediated through epigenetic and metabolic mechanisms. Apart from exogenous stimuli, trained immunity can be induced by endogenous compounds such as oxidized LDL, urate, fumarate, but also cytokines including IL-1α and IL-1β. Here, we show that also recombinant IL-36γ, a pro-inflammatory cytokine of the IL-1-family, is able to induce trained immunity in primary human monocytes, demonstrated by higher cytokine responses and an increase in cellular metabolic pathways both regulated by epigenetic histone modifications. These effects could be inhibited by the IL-36 receptor antagonist as well as by IL-38, an anti-inflammatory cytokine of the IL-1 family which shares its main receptor with IL-36 (IL-1R6). Further, we demonstrated that trained immunity induced by IL-36γ is mediated by NF-κB and mTOR signaling. The inhibitory effect of IL-38 on IL-36γ-induced trained immunity was confirmed in experiments using bone marrow of IL-38KO and WT mice. These results indicate that exposure to IL-36γ results in long-term pro-inflammatory changes in monocytes which can be inhibited by IL-38. Recombinant IL-38 could therefore potentially be used as a therapeutic intervention for diseases characterized by exacerbated trained immunity.
Evidence for Resistance of Activated Sludge Flocs to Deflocculative DO Stress (2019)

In the published literature, deflocculation of aerobic biological flocs under low dissolved oxygen (DO) (<0.5 mg/L) conditions is typically reported as occurring as early as after 1 h of oxygen deficiency. However, results of this study involving aerobic sludge from three different sources repeatedly indicated a lack of deflocculation after 24 h of low DO conditions. This finding has led to the conclusion that low DO might not be a direct cause of deflocculation. In addition to the low DO conditions, the sludge samples were not re-fed throughout the experiment, but deflocculation was still not observed. An analysis of the soluble microbial products (SMP) and loosely and tightly bound extracellular polymeric substances (EPS) was performed to improve understanding of the sludge’s behavior in response to low DO conditions. Results indicated no increase in SMP content or change in the tightly bound EPS content upon extended periods of low DO. It was concluded that high proteins concentration in the bound EPS improved flocs stability, and so contributed to the maintenance of floc integrity during extended periods of low DO conditions.
Measurement and prediction of the glass transition temperature during processing of copper‐clad epoxy resin systems (1999)

Abstract The determination of the glass transition temperature of a cured resin system is necessary for the classification of the temperature region of usable service. For the printed circuit board industry, accurate and consistent properties of the copperclad laminates that are used as the substrate are essential. Variations in material properties of the finished laminates may become a hindrance in subsequent steps in the manufacturing of printed circuit boards and more importantly in the failure rate of the boards during service. In this research, a one‐dimensional finite difference method has been implemented with constitutive models to simulate the progression of the degree of cure and glass transition temperature during the processing of copper‐clad, multi‐layered, fiber mat reinforced, epoxy laminates. The numerical results have been compared to experimental measurements and it has been found that the simulation predicts the experimental observations quite well.
Event data-based computation-in-memory (CiM) configuration by co-designing integrated in-sensor and CiM computing for extremely energy-efficient edge computing (2022)

Abstract This paper discusses co-designing integrated in-sensor and in-memory computing based on the analysis of event data and gives a system-level solution. By integrating an event-based vision sensor (EVS) as a sensor and event-driven computation-in-memory (CiM) as a processor, event data taken by EVS are processed in CiM. In this work, EVS is used to acquire the scenery from a driving car and the event data are analyzed. Based on the EVS data characteristics of temporally dense and spatially sparse, event-driven SRAM-CiM is proposed for extremely energy-efficient edge computing. In the event-driven SRAM-CiM, a set of 8T-SRAMs stores multiple-bit synaptic weights of spiking neural networks. Multiply-accumulate operation with the multiple-bit synaptic weights is demonstrated by pulse amplitude modulation and pulse width modulation. By considering future EVS of high image resolution and high time resolution, the configuration of event-driven CiM for EVS is discussed.
Information Forests (2012)

We describe Information Forests, an approach to classification that generalizes Random Forests by replacing the splitting criterion of non-leaf nodes from a discriminative one - based on the entropy of the label distribution - to a generative one - based on maximizing the information divergence between the class-conditional distributions in the resulting partitions. The basic idea consists of deferring classification until a measure of “classification confidence” is sufficiently high, and instead breaking down the data so as to maximize this measure. In an alternative interpretation, Information Forests attempt to partition the data into subsets that are “as informative as possible” for the purpose of the task, which is to classify the data. Classification confidence, or informative content of the subsets, is quantified by the Information Divergence. Our approach relates to active learning, semi-supervised learning, mixed generative/discriminative learning.
Pancreatic Polypeptide-Producing Tumors (1984)

Eight patients with pancreatic polypeptide (PP)-producing islet cell tumors and one patient with pseudo-PP-producing tumors were examined. Their age range was 20 to 74 years. Clinical features included abdominal pain in four patients, weight loss in four patients, diarrhea in two patients, gastrointestinal bleeding in two patients, and jaundice in one patient. The range of the basal serum level of PP was 394 to 35,100 pg/mL. In two patients the PP-producing tumors were associated with multiple endocrine neoplasia. Two patients had diffuse hepatic metastases at the time of diagnosis and four patients had disease limited to the pancreas. Pancreaticoduodenectomy and 80% pancreatectomy were performed in four and two patients, respectively. Immunohistochemical staining was positive for PP and neuron-specific enolase in all cases and was negative for other peptides except in one specimen with microadenomatosis. Patients who underwent curative resection are asymptomatic with normal serum levels of PP.
Europium-Doped Cerium Oxide Nanoparticles for Microglial Amyloid Beta Clearance and Homeostasis (2022)

Alzheimer's disease (AD) is the most common neurodegenerative disorder. Pathologically, the disease is characterized by the deposition of amyloid beta (Aβ) plaques and the presence of neurofibrillary tangles. These drive microglia neuroinflammation and consequent neurodegeneration. While the means to affect Aβ plaque accumulation pharmacologically was achieved, how it affects disease outcomes remains uncertain. Cerium oxide (CeO<sub>2</sub>) reduces Aβ plaques, oxidative stress, inflammation, and AD signs and symptoms. In particular, CeO<sub>2</sub> nanoparticles (CeO<sub>2</sub>NPs) induce free-radical-scavenging and cell protective intracellular signaling. This can ameliorate the pathobiology of an AD-affected brain. To investigate whether CeO<sub>2</sub>NPs affect microglia neurotoxic responses, a novel formulation of europium-doped CeO<sub>2</sub>NPs (EuCeO<sub>2</sub>NPs) was synthesized. We then tested EuCeO<sub>2</sub>NPs for its ability to generate cellular immune homeostasis in AD models. EuCeO<sub>2</sub>NPs attenuated microglia BV2 inflammatory activities after Aβ<sub>1-42</sub> exposure by increasing the cells' phagocytic and Aβ degradation activities. These were associated with increases in the expression of the CD36 scavenger receptor. EuCeO<sub>2</sub>NPs facilitated Aβ endolysosomal trafficking and abrogated microglial inflammatory responses. We posit that EuCeO<sub>2</sub>NPs may be developed as an AD immunomodulator.
Additional information gained by positron emission tomography with 68Ga-DOTATOC for suspected unknown primary or recurrent neuroendocrine tumors (2015)

DOTATOC-PET/CT was useful for detecting NETs, especially when recurrence or metastases were suspected because of high hormone levels after surgery for a NET. It is unlikely, however, that additional information can be acquired in patients with no history of NET simply based on high hormone levels.
COMBINED ACTION OF SHORT PEPTIDES AND AMINO ACIDS ON THE ORGANOTYPIC TISSUE CULTERES OF THE YOUNG AND OLD ANIMALS GROWTH (2019)

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Radiometric calibration methods from image sequences (2008)

In many computer vision systems, an image of a scene is assumed to directly reflect the scene radiance. However, this is not the case for most cameras as the radiometric response function which is a mapping from the scene radiance to the image brightness is nonlinear. In addition, the exposure settings of the camera are adjusted (often in the auto-exposure mode) according to the dynamic range of the scene changing the appearance of the scene in the images. Vignetting effect which refers to the gradual fading-out of an image at points near its periphery also contributes in changing the scene appearance in images.
In this dissertation, I present several algorithms to compute the radiometric properties of a camera which enable us to find the relationship between the image brightness and the scene radiance. First, I introduce an algorithm to compute the vignetting function, the response function, and the exposure values that fully explain the radiometric image formation process from a set of images of a scene taken with different and unknown exposure values. One of the key features of the proposed method is that the movement of the camera is not limited when taking the pictures whereas most existing methods limit the motion of the camera. Then I present a joint feature tracking and radiometric calibration scheme which performs an integrated radiometric calibration in contrast to previous radiometric calibration techniques which require the correspondences as an input which leads to a chicken-and-egg problem as precise tracking requires accurate radiometric calibration. By combining both into an integrated approach we solve this chicken-and-egg problem. Finally, I propose a radiometric calibration method suited for a set of images of an outdoor scene taken at a regular interval over a period of time. This type of data is a challenging problem because the illumination for each image is changing causing the exposure of the camera to change and the conventional radiometric calibration framework cannot be used for this type of data. The proposed methods are applied to radiometrically align images for seamless mosaics and 3D model textures, to create high dynamic range mosaics, and to build an adaptive stereo system.
Learning Descriptions of 2D Blob-Like Shapes for Object Recognition in X-Ray Images: An Initial Study (1994)

This paper describes a method for applying AQ15c to learning shape descriptions of 2D bloblike objects in x-ray images. The methodology and initial experimental results are discussed, along with comparisons to k-nearest neighbor and to feed-forward neural networks. The AQ15c learning method is shown to have distinct advantages over the aforementioned techniques in terms of higher or comprable classification accuracy, learning and recognition time, and understandability of learned concepts. This approach is well-suited for recognizing objects that can be isolated in the image using histogram and thresholding techniques and that have little internal structure. Key words: machine learning, machine vision, shape recognition, concept learning. Acknowledgments The authors would like to thank the many people whose useful discussions contributed to this work: Jerzy Bala, Eric Bloedorn, Ibrahim Imam, and Ali Hadjarian. The authors wish to also thank those who read preliminary drafts of this p...
Modeling of kinematic diffraction from a thin silicon film illuminated by a coherent, focused X-ray nanobeam (2010)

A rigorous model of a diffraction experiment utilizing a coherent, monochromatic, X-ray beam, focused by a Fresnel zone plate onto a thin, perfect, single-crystal layer is presented. In this model, first the coherent wave emanating from an ideal zone plate equipped with a direct-beam stop and order-sorting aperture is computed. Then, diffraction of the focused wavefront by a thin silicon film positioned at the primary focal spot is calculated. This diffracted wavefront is propagated to the detector position, and the intensity distribution at the detector plane is extracted. The predictions of this model agree quite well with experimental data measured at the Center for Nanoscale Materials nanoprobe instrument at Sector 26 of the Advanced Photon Source.
Identifying the primary reactions and products of fast pyrolysis of alkali lignin (2020)

This study focused on the effect of temperature and residence time on the primary thermal decomposition reactions during a fast pyrolysis of softwood alkali lignin. The use of Py-GC/MS/FID (Micropyrolyser-Gas Chromatography/Mass Spectrometry/Flame Ionization Detector) allowed for rapid heating of the sample and detailed identification and quantification of the pyrolysis products at a temperature range of 400–600 °C, with residence times from 0.5–5 s. The identified primary pyrolysis products were mainly volatile guaiacyl-type compounds. There was a general increase in yield for the majority of the volatile compounds with increased temperature and time. The cleavage of the lignin polymer to linear carbonyl (acetaldehyde) and guaiacyl-type aromatic compounds increased with temperature, while that of catechol and cresol type was mainly favoured at 500 and 600 °C. Based on these results, a mechanistic pathway for the pyrolytic process was proposed, drawing a linkage from structural units of lignin to the formed primary products. In summary, our findings suggest that the primary decomposition reactions that occur under the fast pyrolysis conditions can be controlled by varying the process temperature and residence time, and deliver mechanistic insight into the product distribution from structurally complex lignin material.
Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase (2022)

Malaria is caused by infection with protozoan parasites of the <i>Plasmodium</i> genus, which is part of the phylum Apicomplexa. Most organisms in this phylum contain a relic plastid called the apicoplast. The apicoplast genome is replicated by a single DNA polymerase (apPOL), which is an attractive target for anti-malarial drugs. We screened small-molecule libraries (206,504 compounds) using a fluorescence-based high-throughput DNA polymerase assay. Dose/response analysis and counter-screening identified 186 specific apPOL inhibitors. Toxicity screening against human HepaRG human cells removed 84 compounds and the remaining were subjected to parasite killing assays using chloroquine resistant <i>P. falciparum</i> parasites. Nine compounds were potent inhibitors of parasite growth and may serve as lead compounds in efforts to discover novel malaria drugs.
Hybridized Local and Charge-Transfer Excited-State Emitter for a Blue Organic Solid-State Laser (2023)

The use of triplet excitons harvesting and short exciton lifetime organic emitters is important to improve the exciton utilization in organic semiconductor laser diodes. In this study, a hybridized local and charge-transfer (HLCT)-type molecule, 11-(3-(10-(4-(1-phenyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenyl)anthracen-9-yl)phenyl)-11H-benzofuro[3,2-b]carbazole (PhAnMBf), is used as an emitter for blue-emitting organic solid-state lasers (OSSLs). The short exciton lifetime and high photoluminescence quantum yield of the PhAnMBf emitter allowed the fabrication of an organic laser with an emission wavelength of 453 nm, a small full width at half-maximum of 1.2 nm, and a threshold of 105 nJ/pulse, corresponding to 44 μJ/cm2, on the distributed feedback substrate. The anthracene-based PhAnMBf material showed the potential of the HLCT emitter as an OSSL.
High-frequency performance of scaled carbon nanotube array field-effect transistors (2012)

We report the radio-frequency performance of carbon nanotube array transistors that have been realized through the aligned assembly of highly separated, semiconducting carbon nanotubes on a fully scalable device platform. At a gate length of 100 nm, we observe output current saturation and obtain as-measured, extrinsic current gain and power gain cut-off frequencies, respectively, of 7 GHz and 15 GHz. While the extrinsic current gain is comparable to the state-of-the-art, the extrinsic power gain is improved. The de-embedded, intrinsic current gain and power gain cut-off frequencies of 153 GHz and 30 GHz are the highest values experimentally achieved to date. We analyze the consistency of DC and AC performance parameters and discuss the requirements for future applications of carbon nanotube array transistors in high-frequency electronics.
SPECIAL FEATURE: TUTORIAL High-resolution Mass Spectrometry and Accurate Mass Measurements with Emphasis on the Characterization of Peptides and Proteins by Matrix-assisted Laser Desorption/Ionization Time-of-Ñight Mass Spectrometry (1997)

Fundamental concepts of high-resolution mass spectrometry as it relates to the issue of accurate mass measure-ments are presented. Important issues speciÐc to magnetic sector instruments, Fourier transform ion cyclotron resonance and time-of-Ñight (TOF) methods are discussed. Recent high-resolution TOF measurements on peptides and proteins, ionized by matrix-assisted laser desorption/ionization (MALDI), are presented and discussed in terms