gebhart/patrepeval huggingface dataset:
Constructing Iboga Alkaloids via C–H Bond Functionalization: Examination of the Direct and Catalytic Union of Heteroarenes and Isoquinuclidine Alkenes (2015)

The iboga alkaloids have attracted considerable attention in both the scientific community and popular media due to their reported ability to reverse or markedly diminish cravings for, and self-administration of, the major drugs of abuse. We have developed three new intramolecular C-H functionalization procedures leading to the core seven-membered ring of the iboga skeleton, a cyclization that proved to be highly challenging. The electrophilic palladium salt Pd(CH3CN)4(BF4)2 was effective for the cyclization of diverse N-(2-arylethyl)isoquinuclidines with yields of 10-35%. A two-step, bromination-reductive Heck reaction protocol was also effective for the synthesis of ibogamine in 42% yield. Finally, a direct Ni(0)-catalyzed C-H functionalization provided the benzofuran analogues of ibogamine (74%) and epi-ibogamine (38%). Although each approach suffers from significant shortcomings, in combination, the methods described provide practical routes to diverse ibogamine analogues.
Active Adversarial Domain Adaptation (2020)

We propose an active learning approach for transferring representations across domains. Our approach, active adversarial domain adaptation (AADA), explores a duality between two related problems: adversarial domain alignment and importance sampling for adapting models across domains. The former uses a domain discriminative model to align domains, while the latter utilizes the model to weigh samples to account for distribution shifts. Specifically, our importance weight promotes unlabeled samples with large uncertainty in classification and diversity compared to la-beled examples, thus serving as a sample selection scheme for active learning. We show that these two views can be unified in one framework for domain adaptation and transfer learning when the source domain has many labeled examples while the target domain does not. AADA provides significant improvements over fine-tuning based approaches and other sampling methods when the two domains are closely related. Results on challenging domain adaptation tasks such as object detection demonstrate that the advantage over baseline approaches is retained even after hundreds of examples being actively annotated.
The KineSpring load absorber implant: rationale, design and biomechanical characterization (2010)

Osteoarthritis (OA) of the knee is the leading cause of disability in the adult population. Although a number of treatments for knee OA are available, none effectively prevent OA progression. Currently, a wide therapeutic gap exists for patients who have unsuccessfully exhausted conservative OA treatments but who are hesitant or ineligible to undergo invasive surgery. The KineSpring device is a novel, joint preserving, minimally invasive implant that reduces medial compartment loading without significantly impacting the loading of the lateral compartment. This article describes the rationale for and the design of the KineSpring device and summarizes results of initial biomechanical testing in an OA cadaver model.
Effects of Indole-3-Carbinol and Flavonoids Administered Separately and in Combination on Nitric Oxide Production and iNOS Expression in Rats (2010)

Beneficial effects of natural compounds are often attributed to modulation of NO production; however effects produced by plant extracts do not correlate with effects of purified components. The goal of our work was to study ability of flavonoids and indole-3-carbinol, as well as their combinations to modify NO production, iNOS gene and protein expression in rat tissues. Baicalein and luteolin decreased NO concentration in both intact and LPS-treated animals. Baicalein decreased iNOS gene expression. Luteolin decreased NO production in the liver and heart and number of iNOS-positive cells in the liver of LPS-treated animals. Combination of the two substances did not decrease the NO synthesis triggered by LPS, although it decreased iNOS gene expression. Quercetin decreased NO production in the heart, kidneys and blood of intact rats, but enhanced the LPS effect in testes, spleen and blood on NO production and iNOS protein expression in the liver. Indole-3-carbinol decreased NO concentration in the cerebellum, blood, lungs and skeletal muscles. The drug enhanced the LPS-triggered increase of NO production in all rat organs. It increased iNOS protein expression in intact liver; however it decreased the LPS-triggered outburst of the enzyme biosynthesis. Combination of indole3-carbinol with quercetin decreased NO production in LPS-treated animals however it slightly increased iNOS gene expression. Taken together our results suggest that modifications of NO level in tissues by a natural compound cannot be predicted from data about its effects on NOS expression or activity. Combination of substances can produce an effect differing from that of individual substances. This stresses importance of direct measurements of NO in the tissues.
Microarray Studies on the Effects of Palm Fruit Juice in Diabetic Nile Rats (2013)

The Nile rat (NR) models diet‐induced human type 2 diabetes (T2DM). In previous experiments (Brit J Nutr 106:1664, 2011), palm fruit juice (PFJ) blocked T2DM in male NR, while untreated rats exhibited advanced disease stages. The molecular mechanisms whereby PFJ exerts anti‐diabetic effects are unknown, prompting microarray gene expression analysis. Livers were obtained from NR undergoing 4 diet plans: hiCHO alone (diabetic control), 4800ppm resveratrol (RES) in food, 4800ppm PFJ in food, or 1500ppm PFJ in drinking water. Compared to hiCHO (most diabetic), hepatic liver gene expression profiles were enhanced for RES and PFJ‐ food , while PFJ‐ water gene expression changes were subtler. Random blood glucose was lowered (p&lt;0.05) in both PFJ groups, but only slightly by RES (n.s.). Compared to hiCHO, PFJ water had 17 genes up‐regulated, 29 down‐regulated. PFJ‐ food had 71 genes up‐regulated, 108 down‐regulated. RES had 90 genes upregulated, 76 down‐regulated. As a preliminary observation, the insulin signaling pathway, especially phosphatidylinositol (PI) 3‐ kinase, was significantly down‐regulated by PFJ‐ food and RES, PFJ‐ water being less marked. PI 3‐kinase has been reported to suppress glucose‐stimulated insulin secretion (Diabetes 51:87, 2002), suggesting PFJ and RES may modulate this activity in NRs to favor insulin secretion. Funding source: Foster Biomed Res Lab and the Malaysian Palm Oil Board
ChemInform Abstract: Synthesis of 3′‐Functionalized Oligonucleotides on a Single Solid Support. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Wave energy converter with enhanced amplitude response at frequencies coinciding with Swedish west coast sea states by use of a supplementary submerged body (2009)

The full-scale direct-driven wave energy converter developed at Uppsala University has been in offshore operation at the Swedish west coast since 2006. Earlier simulations have now been validated by full-scale experiment with good agreement. Based on that, a theoretical model for a passive system having optimum amplitude response at frequencies coinciding with Swedish west coast conditions has been developed. The amplitude response is increased by adding supplementary inertia by use of the additional mass from a submerged body. A sphere with neutral buoyancy is chosen as the submerged body and modeled as being below the motion of the waves. The model is based on potential linear wave theory and the power capture ratio is studied for real ocean wave data collected at the research test site. It is found that the power capture ratio for the two body system can be increased from 30% to 60% compared to a single body system. Increased velocity in the system also decreases the value for optimal load damping from the generator, opening up the possibility to design smaller units.
An Experimental Study on a Hot-Air-Based Anti-/De-Icing System for the Icing Protection of Aero-Engine Inlet Guide Vanes (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;In the present study, an experimental investigation was conducted to characterize a hot-air-based anti-/de-icing system for the icing protection of aero-engine inlet guide vanes(IGVs). The experimental study was conducted in a unique icing research tunnel available at Iowa State University (i.e., ISU-IRT). A hollowed IGV model embedded with U-shaped hot-air flowing conduit was designed and manufactured for the experimental investigations. During the experiments, while a high-speed imaging system was used to record the dynamic ice accretion or anti-/de-icing process over the surface of the IGV model for the test cases without and with the hot-air supply system being turned on, the corresponding surface temperature distributions on the IGV model were measured quantitatively by using a row of embedded thermocouples. In addition to investigating the characteristics of the convective heat transfer over the surface of the heated IGV model, a comprehensive parametric study was also conducted to evaluate the effects of the operation parameters of the hot-air-based anti-/de-icing system on its performance for IGV icing protection. The acquired ice accretion or anti-de-icing images were coordinated with the quantitative surface temperature measurements to elucidate the underlying physics. It was demonstrated clearly that, with proper operation parameters (i.e., by selecting proper heater temperature and mass flowrate of the hot-air stream), the hot-air-based anti-/de-icing system would be able to effectively prevent ice formation/accretion over the entire surface the IGV model.&lt;/div&gt;&lt;/div&gt;
Human Serine Protease HTRA1 Positively Regulates Osteogenesis of Human Bone Marrow-derived Mesenchymal Stem Cells and Mineralization of Differentiating Bone-forming Cells Through the Modulation of Extracellular Matrix Protein (2012)

Mammalian high-temperature requirement serine protease A1 (HTRA1) is a secreted member of the trypsin family of serine proteases which can degrade a variety of bone matrix proteins and as such has been implicated in musculoskeletal development. In this study, we have investigated the role of HTRA1 in mesenchymal stem cell (MSC) osteogenesis and suggest a potential mechanism through which it controls matrix mineralization by differentiating bone-forming cells. Osteogenic induction resulted in a significant elevation in the expression and secretion of HTRA1 in MSCs isolated from human bone marrow-derived MSCs (hBMSCs), mouse adipose-derived stromal cells (mASCs), and mouse embryonic stem cells. Recombinant HTRA1 enhanced the osteogenesis of hBMSCs as evidenced by significant changes in several osteogenic markers including integrin-binding sialoprotein (IBSP), bone morphogenetic protein 5 (BMP5), and sclerostin, and promoted matrix mineralization in differentiating bone-forming osteoblasts. These stimulatory effects were not observed with proteolytically inactive HTRA1 and were abolished by small interfering RNA against HTRA1. Moreover, loss of HTRA1 function resulted in enhanced adipogenesis of hBMSCs. HTRA1 Immunofluorescence studies showed colocalization of HTRA1 with IBSP protein in osteogenic mASC spheroid cultures and was confirmed as being a newly identified HTRA1 substrate in cell cultures and in proteolytic enzyme assays. A role for HTRA1 in bone regeneration in vivo was also alluded to in bone fracture repair studies where HTRA1 was found localized predominantly to areas of new bone formation in association with IBSP. These data therefore implicate HTRA1 as having a central role in osteogenesis through modification of proteins within the extracellular matrix.
ModelArray: An R package for statistical analysis of fixel-wise data (2023)

Diffusion MRI is the dominant non-invasive imaging method used to characterize white matter organization in health and disease. Increasingly, fiber-specific properties within a voxel are analyzed using fixels. While tools for conducting statistical analyses of fixel-wise data exist, currently available tools support only a limited number of statistical models. Here we introduce ModelArray, an R package for mass-univariate statistical analysis of fixel-wise data. At present, ModelArray supports linear models as well as generalized additive models (GAMs), which are particularly useful for studying nonlinear effects in lifespan data. In addition, ModelArray also aims for scalable analysis. With only several lines of code, even large fixel-wise datasets can be analyzed using a standard personal computer. Detailed memory profiling revealed that ModelArray required only limited memory even for large datasets. As an example, we applied ModelArray to fixel-wise data derived from diffusion images acquired as part of the Philadelphia Neurodevelopmental Cohort (n = 938). ModelArray revealed anticipated nonlinear developmental effects in white matter. Moving forward, ModelArray is supported by an open-source software development model that can incorporate additional statistical models and other imaging data types. Taken together, ModelArray provides a flexible and efficient platform for statistical analysis of fixel-wise data.
Epigenetic memory in induced pluripotent stem cells (2010)

Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an 'epigenetic memory' of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment.
Surface Tiltmeter Fracture Mapping Reaches New Depths - 10,000 Feet and Beyond? (1998)

Abstract Recent improvements in tilt measurement techniques have greatly enhanced the resolution of hydraulic fracture-induced tilts, resulting in both greater mapping precision and an increase in the maximum mapping depth achievable with a surface tiltmeter array. With a previous depth limitation of around 6,000 ft., surface tiltmeter mapping was limited to areas with relatively shallow production. Application is greatly broadened now with a depth range down to 10,000 ft. In addition to the expanded depth range, there has been a marked improvement in the fracture mapping resolution. This paper begins with an overview of the tiltmeter fracture mapping concept, highlighting both the strengths of this technique and its limitations. Following that is a description of the technical advancements made over the last three years to allow fracture mapping at far greater depths. Finally, two brief case studies are presented to demonstrate fracture mapping at great depth, and also to provide insight on hydraulic fracture growth behavior in two different environments. As the case studies make clear, fracture growth is far more complex than is generally assumed. Better understanding of these complexities can lead to significantly enhanced fracture stimulation practices. P. 135
Cardiac CT blooming artifacts: clinical significance, root causes and potential solutions (2022)

This review paper aims to summarize cardiac CT blooming artifacts, how they present clinically and what their root causes and potential solutions are. A literature survey was performed covering any publications with a specific interest in calcium blooming and stent blooming in cardiac CT. The claims from literature are compared and interpreted, aiming at narrowing down the root causes and most promising solutions for blooming artifacts. More than 30 journal publications were identified with specific relevance to blooming artifacts. The main reported causes of blooming artifacts are the partial volume effect, motion artifacts and beam hardening. The proposed solutions are classified as high-resolution CT hardware, high-resolution CT reconstruction, subtraction techniques and post-processing techniques, with a special emphasis on deep learning (DL) techniques. The partial volume effect is the leading cause of blooming artifacts. The partial volume effect can be minimized by increasing the CT spatial resolution through higher-resolution CT hardware or advanced high-resolution CT reconstruction. In addition, DL techniques have shown great promise to correct for blooming artifacts. A combination of these techniques could avoid repeat scans for subtraction techniques.
Photocurrent Phenomena in Nanoribbon InAlN/GaN High Electron Mobility Transistors (2013)

High electron mobility transistors (HEMTs) based on InAlN/GaN nanoribbon (NR) structures appear as a new technology which can deliver record current densities. Ultraviolet (UV) photodetectors based on ungated InAlN/GaN NR HEMT structures have a gain in the range of the 10 5 –10 7 , a sublinear behaviour with the excitation power and a UV/visible contrast of more than three orders of magnitude. In spite of the larger surface-to-volume ratio, sublinearities and persistent photocurrent effects are less intense in NR structures compared to planar devices, and they decrease at higher excitation power. The asymmetric NR morphology does not induce a preferential coupling of polarized light in the NR structure; since light is mostly absorbed in the GaN buffer layer and photogenerated charges are efficiently collected by the HEMT channel.
Automatic 3D reconstruction of manifold meshes via delaunay triangulation and mesh sweeping (2016)

In this paper we propose a new approach to incrementally initialize a manifold surface for automatic 3D reconstruction from images. More precisely we focus on the automatic initialization of a 3D mesh as close as possible to the final solution; indeed many approaches require a good initial solution for further refinement via multi-view stereo techniques. Our novel algorithm automatically estimates an initial manifold mesh for surface evolving multi-view stereo algorithms, where the manifold property needs to be enforced. It bootstraps from 3D points extracted via Structure from Motion, then iterates between a state-of-the-art manifold reconstruction step and a novel mesh sweeping algorithm that looks for new 3D points in the neighborhood of the reconstructed manifold to be added in the manifold reconstruction. The experimental results show quantitatively that the mesh sweeping improves the resolution and the accuracy of the manifold reconstruction, allowing a better convergence of state-of-the-art surface evolution multi-view stereo algorithms.
Statistical feedback control of a plasma etch process (1994)

This paper presents the methodology developed for the automatic feedback control of a silicon nitride plasma etch process. The methodology provides an augmented level of control for semiconductor manufacturing processes, to the level that the operator inputs the required process quality characteristics (e.g. etch rate and uniformity values) instead of the desired process conditions (e.g., specific RF power, pressure, gas flows). The optimal equipment settings are determined from previously generated process/equipment models. The control algorithm is driven by the in-situ measurements, using in-line sensors monitoring each wafer. The sensor data is subjected to Statistical Quality Control (SQC) to determine if deviations from the required process observable values can be attributed to noise in the system or are due to a sustained anomalous behavior of the equipment. Once a change in equipment behavior is detected, the process/equipment models are adjusted to match the new state of the equipment. The updated models are used to run subsequent wafers until a new SQC failure is observed. The algorithms developed have been implemented and tested, and are currently being used to control the etching of wafers under standard manufacturing conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Parallel Multi-channel Biologic Signal Processing (2005)

We are building a prototype intelligent cardiovascular monitor (ICM) using the process trellis software architecture for parallel, real-time monitors. This paper describes our experience with the signal processing portion of the ICM. We implemented two versions of the multi-state Kalman filtering algorithm for simultaneous, multi-channel, biologic signal processing. One version had a separate process for each signal. This paper concentrates on a version which parallelized the analysis of a single signal. Unfortunately, unresolvable data dependencies within the Kalman filtering algorithm severely limited the performance gains. The process trellis is a software framework for combining heterogeneous, black-box processes (written in C) into a realtime monitor that executes on a parallel computer [6]. The process trellis itself is implemented in the machine-independent parallel programming language C-Linda@ [7].
Optimizing resource utilization using transformations (2002)

A transformational approach aimed at improving the resource utilization in high level synthesis is introduced. The current implementation combines retiming and associativity in a single framework. This combination of transformations results in considerable area improvements, as is amply demonstrated by benchmark examples. A novel learning while searching iterative improvement probabilistic algorithm has been developed and is used to resolve the associated NP-complete combinatorial optimization problem. The effectiveness of the proposed algorithms and the transformations is demonstrated using standard benchmark examples, with the aid of statistical analysis, and through a comparison with estimated minimal bounds. The proposed algorithm has proven to be very effective in reaching the optimal solution as well as in runtime.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>