gebhart/patrepeval huggingface dataset:
Assessment of Small Bowel Crohn Disease: Noninvasive Peroral CT Enterography Compared with Other Imaging Methods and Endoscopy—Feasibility Study (2003)

A feasibility study was conducted to evaluate two biphasic computed tomographic (CT) enterography protocols, a noninvasive CT technique with water administered perorally and CT enteroclysis with methylcellulose administered through a nasojejunal tube, in 23 patients known or suspected to have Crohn disease. Results were compared with the results of fluoroscopic small bowel examination and terminal ileoscopy for the detection of active Crohn disease in the terminal ileum. Luminal distention did not differ significantly between the two CT protocols. Arterial phase imaging was noncontributory in 22 of 23 cases. The noninvasive peroral water CT enterography protocol had similar accuracy (12 of 15 cases, 80%) for enabling the detection of active Crohn disease in comparison with CT enteroclysis with nasojejunal tube (seven of eight, 88%) and fluoroscopic small bowel examination (17 of 23, 74%). No fistulas were missed with use of either CT technique. The authors conclude that noninvasive peroral portal venous phase CT enterography with use of water is an accurate and feasible technique for detecting active small bowel inflammation in patients with Crohn disease.
Diffuse Lung Disease in Young Children (2007)

This retrospective cohort study identifies a diverse spectrum of lung disorders, largely unique to young children. Application of a classification scheme grouped clinically distinct patients with variable age of biopsy and mortality. Standardized terminology and classification will enhance accurate description and diagnosis of these disorders.
Structure–Activity Relationships in 1,4-Benzodioxan-Related Compounds. 11. Reversed Enantioselectivity of 1,4-Dioxane Derivatives in α1-Adrenergic and 5-HT1A Receptor Binding Sites Recognition (2012)

5-HT(1A) receptor and α(1)-adrenoreceptor (α(1)-AR) binding sites recognized by the 1,4-dioxanes 2-4 display reversed stereochemical requirements. (S)-2 proved to be a potent 5-HT(1A) receptor agonist highly selective over α(1)-AR subtypes. Chirality influenced the anticancer activity of 3 and 4 in human prostate cancer cells (PC-3): (R)-4, eutomer at the α(1d)-AR subtype, was the most potent. The decreased effect of 4 and (R)-4 in α(1d)-AR silenced PC-3 cells confirmed that their anticancer activity was α(1d)-AR-dependent.
Feedback control of Layerwise Laser Melting using optical sensors (2010)

Layerwise Laser Melting (LLM) is a layerwise production technique enabling the production of complex metallic parts. Thin powder layers are molten according to a predefined scan pattern by means of a laser source. Nowadays constant process parameters are used throughout the build, leading for some geometries to an overly thick feature size or overheating at downfacing surfaces. In this paper a monitoring and control system is presented which enables monitoring the melt pool continously at high speed throughout the building process. The signals from the sensors can be incorporated in a real-time control loop, in this way enabling feedback control of the process parameters. In this paper the experimental set-up will be first shown. Next the dynamic relation between the melt pool and the process parameters is identified. Finally the proof of concept for feedback control is demonstrated with experimental results.
DGD-tolerant timing recovery for coherent receivers (2010)

The clock signal disappears for half-baud DGD with even power splitting between the polarizations for typical timing recoveries. A simple solution is analyzed for 16QAM using several timing error detectors.
Raman Scattering and Photoluminescence of Mg-Implanted GaN Films (2001)

As-grown highly resistive (>107 Ω cm) GaN samples were exposed to implantation of 24Mg+ ions with the energy of 120 keV and dose of 2 × 1014 cm—2. Isochronal rapid thermal annealing (RTA) was carried out for the Mg-implanted samples at 850, 950 and 1050 °C, respectively. Under z(x, x)z′ backscattering configuration, A1(LO) and E2(high) Raman modes of 735 cm—1 and 569 cm—1, respectively, were observed for the as-grown and Mg-implanted samples, but a Raman mode of 662 cm—1 appeared only in the implanted samples. We tentatively assigned the mode to a Mg acceptor-related vibration mode. Room temperature photoluminescence revealed that the as-grown films displayed a strong yellow luminescence of 560 nm (2.21 eV), while Mg-implanted samples only exhibited a broad blue-violet luminescence peaking at 400 nm (≈3.11 eV) which decreased with increasing RTA temperature. Our observation supported the Ga vacancy model responsible for yellow luminescence.
Semantic Multi-view Stereo: Jointly Estimating Objects and Voxels (2017)

Dense 3D reconstruction from RGB images is a highly ill-posed problem due to occlusions, textureless or reflective surfaces, as well as other challenges. We propose object-level shape priors to address these ambiguities. Towards this goal, we formulate a probabilistic model that integrates multi-view image evidence with 3D shape information from multiple objects. Inference in this model yields a dense 3D reconstruction of the scene as well as the existence and precise 3D pose of the objects in it. Our approach is able to recover fine details not captured in the input shapes while defaulting to the input models in occluded regions where image evidence is weak. Due to its probabilistic nature, the approach is able to cope with the approximate geometry of the 3D models as well as input shapes that are not present in the scene. We evaluate the approach quantitatively on several challenging indoor and outdoor datasets.
Granulocyte-Macrophage Colony-Stimulating Factor for Cancer Treatment (1994)

In the 5 years since granulocyte-macrophage colony-stimulating factor (GM-CSF) was first tested clinically, a number of different strategies for its use have been evaluated in patients with malignant disease. These include using GM-CSF to support standard and high-dose chemotherapy, to accelerate myeloid reconstitution following marrow transplantation, to mobilize peripheral blood progenitor cells into the circulation for harvesting and transplantation, and in combination with cycle-specific chemotherapy drugs to enhance their cytotoxicity to leukemic cells. Early results were encouraging and data from randomized studies are now being reported. These are enabling an assessment of the value of these strategies for GM-CSF use in the management of cancer.
Evolution of Proteins and Gene Expression Levels are Coupled in Drosophila and are Independently Associated with mRNA Abundance, Protein Length, and Number of Protein-Protein Interactions (2005)

Organismic evolution requires that variation at distinct hierarchical levels and attributes be coherently integrated, often in the face of disparate environmental and genetic pressures. A central part of the evolutionary analysis of biological systems remains to decipher the causal connections between organism-wide (or genome-wide) attributes (e.g., mRNA abundance, protein length, codon bias, recombination rate, genomic position, mutation rate, etc) as well as their role-together with mutation, selection, and genetic drift-in shaping patterns of evolutionary variation in any of the attributes themselves. Here we combine genome-wide evolutionary analysis of protein and gene expression data to highlight fundamental relationships among genomic attributes and their associations with the evolution of both protein sequences and gene expression levels. Our results show that protein divergence is positively coupled with both gene expression polymorphism and divergence. We show moreover that although the number of protein-protein interactions in Drosophila is negatively associated with protein divergence as well as gene expression polymorphism and divergence, protein-protein interactions cannot account for the observed coupling between regulatory and structural evolution. Furthermore, we show that proteins with higher rates of amino acid substitutions tend to have larger sizes and tend to be expressed at lower mRNA abundances, whereas genes with higher levels of gene expression divergence and polymorphism tend to have shorter sizes and tend to be expressed at higher mRNA abundances. Finally, we show that protein length is negatively associated with both number of protein-protein interactions and mRNA abundance and that interacting proteins in Drosophila show similar amounts of divergence. We suggest that protein sequences and gene expression are subjected to similar evolutionary dynamics, possibly because of similarity in the fitness effect (i.e., strength of stabilizing selection) of disruptions in a gene's protein sequence or its mRNA expression. We conclude that, as more and better data accumulate, understanding the causal connections among biological traits and how they are integrated over time to constrain or promote structural and regulatory evolution may finally become possible.
Supplemental Tables from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA <i>In Situ</i> Hybridization Assay (2023)

&lt;p&gt;ISH product scores.&lt;/p&gt;
Retinopathy During the First 5 Years of Type 1 Diabetes and Subsequent Risk of Advanced Retinopathy (2022)

These data suggest that individuals with any sign of retinopathy within the first 5 years of T1D onset may be at higher risk of long-term development of advanced DR, especially PDR. Identification of early-onset DR may influence prognosis and help guide therapeutic management to reduce the risk of future visual loss in these individuals.
A high time-resolution two-tap CMOS lock-in pixel image sensor for time-resolved measurements and its applications (2016)

A CMOS lock-in pixel image sensor with embedded storage diodes in a pixel and lateral electric field modulator (LEFM) is developed for time-resolved measurements such as a fluorescence lifetime imaging microscopy (FLIM) and near-infrared spectroscopy (NIRS). The time-resolved CMOS image sensor (CIS) with two-tap lock-in pixels achieves a very high time resolution of 10ps when images are averaged over 30 frames, a very short intrinsic response time of 180ps at 374nm, and a low temporal random noise of 1.75e-rms with true correlated double sampling (CDS) operation. In addition, by using the LEFM and optimized process, a very high extinction ratio of approximately 94% at 472nm laser diode is achieved. The usefulness of the proposed CIS is demonstrated by the device simulations and the measurements. Then, we confirmed that the developed imager is very suitable for the scientific applications such as a biomedical imaging and multifunctional cameras.
Models of visual appearance for analyzing and editing images and videos (2012)

The visual appearance of an image is a complex function of factors such as scene geometry, material reflectances and textures, illumination, and the properties of the camera used to capture the image. Understanding how these factors interact to produce an image is a fundamental problem in computer vision and graphics. This dissertation examines two aspects of this problem: models of visual appearance that allow us to recover scene properties from images and videos, and tools that allow users to manipulate visual appearance in images and videos in intuitive ways. In particular, we look at these problems in three different applications. 
First, we propose techniques for compositing images that differ significantly in their appearance. Our framework transfers appearance between images by manipulating the different levels of a multi-scale decomposition of the image. This allows users to create realistic composites with minimal interaction in a number of different scenarios. We also discuss techniques for compositing and replacing facial performances in videos. 
Second, we look at the problem of creating high-quality still images from low-quality video clips. Traditional multi-image enhancement techniques accomplish this by inverting the camera's imaging process. Our system incorporates feature weights into these image models to create results that have better resolution, noise, and blur characteristics, and summarize the activity in the video. 
Finally, we analyze variations in scene appearance caused by changes in lighting. We develop a model for outdoor scene appearance that allows us to recover radiometric and geometric information about the scene from images. We apply this model to a variety of visual tasks, including color-constancy, background subtraction, shadow detection, scene reconstruction, and camera geo-location. We also show that the appearance of a Lambertian scene can be modeled as a combination of distinct three-dimensional illumination subspaces—a result that leads to novel bounds on scene appearance, and a robust uncalibrated photometric stereo method.
Steric Stabilization of Lipid/Polymer Particle Assemblies by Poly(ethylene glycol)-Lipids (2007)

Biocompatible and biodegradable assemblies consisting of spherical particles coated with lipid layers were prepared from sub-micrometer poly(lactic acid) particles and lipid mixtures composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-3-trimethylammonium-propane. These original colloidal assemblies, named LipoParticles, are of a great interest in biotechnology and biomedicine. Nevertheless, a major limitation of their use is their poor colloidal stability toward ionic strength. Indeed, electrostatic repulsions failed to stabilize LipoParticles in aqueous solutions containing more than 10 mM NaCl. By analogy with the extensive use of poly(ethylene glycol) (PEG)-lipid conjugates to improve the circulation lifetime of liposomes in vivo, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)] with various PEG chain lengths was added to the lipid formulation. Here, we show that LipoParticle stabilization was enhanced at least up to 150 mM NaCl (for more than 1 year at 4 degrees C). To determine the structure of PEG-modified LipoParticles as a function of the PEG chain length and the PEG-lipid fraction in the lipid formulation, a thorough physicochemical characterization was carried out by means of many techniques including quasi-elastic light scattering, zeta potential measurements, transmission electron microscopy, 1H NMR spectroscopy, and small-angle X-ray scattering. Finally, an attempt was made to link the resulting structural data to the colloidal behavior of PEG-modified LipoParticles.
Papillomavirus-like Particles in Equine Medicine (2023)

Papillomaviruses (PVs) are a family of small DNA tumor viruses that can induce benign lesions or cancer in vertebrates. The observation that animal PV capsid-proteins spontaneously self-assemble to empty, highly immunogenic virus-like particles (VLPs) has led to the establishment of vaccines that efficiently protect humans from specific PV infections and associated diseases. We provide an overview of PV-induced tumors in horses and other equids, discuss possible routes of PV transmission in equid species, and present recent developments aiming at introducing the PV VLP-based vaccine technology into equine medicine.
Fuel governor for controlled autoignition engines (2023)

Methods and systems for controlling combustion performance of an engine are provided. A desired fuel quantity for a first combustion cycle is determined. One or more engine actuator settings are identified that would be required during a subsequent combustion cycle to cause the engine to approach a target combustion phasing. If the identified actuator settings are within a defined acceptable operating range, the desired fuel quantity is injected during the first combustion cycle. If not, an attenuated fuel quantity is determined and the attenuated fuel quantity is injected during the first combustion cycle.
Correction: Corrigendum: Revealing the planar chemistry of two-dimensional heterostructures at the atomic level (2015)

Nature Communications 6, Article number: 7482 (2015); Published 23 June 2015; Updated 21 August 2015 The financial support for this Article was not fully acknowledged. The Acknowledgements should have included the following: The atomic force microscope used in these studies was acquired under the program ‘Understanding Charge Separation and Transfer at Interfaces in Energy Materials (EFRC:CST)’, an Energy Frontier Research Center funded by the U.
Visible GaN lasers for quantum sensing and communication applications (2019)

We report on GaN lasers with extremely narrow linewidth (&lt;1MHz) at ‘magic wavelengths’ for cold-atom interferometry quantum sensors, and high frequency (GHz) operation for specialised telecommunication applications.
Stochastic EMC/EMI Experiments Optimization Using Resampling Techniques (2016)

Recent studies have shown high interest in statistical methods dedicated to the prediction of the maximum confidence levels in simulations and measurements for risk assessment in electromagnetic compatibility. In particular, it has been shown that one of the main issues remains the access to a number of samples allowing the assessment of the risks in regards to test setup random variables. In this paper, it is argued that a real-time bootstrapping module enables to optimize the number of experiments while estimating the maximum confidence levels of the accessible samples. An efficient technique is presented to substitute the full experimental requirements to a simple and low time-consuming mathematical algorithm. The benefits expected of this method are illustrated throughout experimental shielding effectiveness power measurements. Based upon an optimized statistical approach, the first statistical moments (e.g., mean and standard deviation) of power received inside a cabinet are provided jointly with an accurate assessment of power's quantiles, leading to a better evaluation of extreme values.
Peptidomimetic-Based Multidomain Targeting Offers Critical Evaluation of Aβ Structure and Toxic Function (2018)

The prevailing hypothesis stipulates that the preamyloid oligomers of Aβ are the main culprits associated with the onset and progression of Alzheimer's disease (AD), which has prompted efforts to search for therapeutic agents with the ability to inhibit Aβ oligomerization and amyloidogenesis. However, clinical progress is impeded by the limited structural information about the neurotoxic oligomers. To address this issue, we have adopted a synthetic approach, where a library of oligopyridylamide-based small molecules was tested against various microscopic events implicated in the self-assembly of Aβ. Two oligopyridylamides bind to different domains of Aβ and affect distinct microscopic events in Aβ self-assembly. The study lays the foundations for a dual recognition strategy to simultaneously target different domains of Aβ for further improvement in antiamyloidogenic activity. The data demonstrate that one of the most effective oligopyridylamides forms a high affinity complex with Aβ, which sustains the compound's activity in cellular milieu. The oligopyridylamide was able to rescue cells when introduced 24 h after the incubation of Aβ. The rescue of Aβ toxicity is potentially a consequence of the colocalization of the oligopyridylamide with Aβ. The synthetic tools utilized here provide a straightforward strategic framework to identify a range of potent antagonists of Aβ-mediated toxic functions. This approach could be a powerful route to the design of candidate drugs for various amyloid diseases that have so far proven to be "untargetable".
Mapping Student Development in Culturally Contextualized Design (2015)

Education Management and Organizations from the U-M. Her research focuses on organizational change by exploring deep-seated inequalities
A Bulky Glycocalyx Fosters Metastasis Formation by Promoting G1 Cell Cycle Progression (2017)

Abstract Metastasis depends upon cancer cell growth and survival within the metastatic niche. Tumors which remodel their glycocalyces, by overexpressing bulky glycoproteins like mucins, exhibit a higher predisposition to metastasize, but the role of mucins in oncogenesis remains poorly understood. Here we report that a bulky glycocalyx promotes the expansion of disseminated tumor cells in vivo by fostering integrin adhesion assembly to permit G1 cell cycle progression. We engineered tumor cells to display glycocalyces of various thicknesses by coating them with synthetic mucin-mimetic glycopolymers. Cells adorned with longer glycopolymers showed increased metastatic potential, enhanced cell cycle progression, and greater levels of integrin-FAK mechanosignaling and Akt signaling in a syngeneic mouse model of metastasis. These effects were mirrored by expression of the ectodomain of cancer-associated mucin MUC1. These findings functionally link mucinous proteins with tumor aggression, and offer a new view of the cancer glycocalyx as a major driver of disease progression.
Characterization of the Focal Cooling Necessary to Suppress Spontaneous Epileptiform Activity (2007)

It has been established that focal cooling to suppress epileptiform activity has become a real and viable option. However, the specific thermal parameters necessary to suppress epileptiform activity have only begun to be quantitatively defined. In 2002 it was reported that a 41 year-old man with medically intractable epilepsy undertook surgery to remove his tumor and resect adjacent epileptogenic tissue. Electrocorticography was performed before resection. Cold saline was impinged on the resulting interictal spike foci resulting in transient, complete cessation of spiking. We present a transient post-operative heat transfer analysis of the cold saline impingement on the surface of brain. An approximate temporal and spatial temperature distribution of the perfused human brain response to surface cooling was developed. The realistic extent of cooling below the brain surface due to impinging saline was quantified. The sensitivity of cooling penetration depth to (a) saline exit velocity from the syringe, and (b) syringe inside diameter, was evaluated. A parametric study was performed to characterize the effects of brain metabolism and blood perfusion on surface cooling. The required thermal parameters necessary to suppress epileptiform activity through focal cooling are here quantitatively approximated, i.e. heat flux removal and maximum and realistic cooling penetration depths. The relatively shallow penetration depth suggests that the spreading depolarization associated with epileptiform activity may be abolished through focal cooling without affecting the deeper neurons responsible for motor activity.
How to train your ViT? Data, Augmentation, and Regularization in Vision\n Transformers (2021)

Vision Transformers (ViT) have been shown to attain highly competitive\nperformance for a wide range of vision applications, such as image\nclassification, object detection and semantic image segmentation. In comparison\nto convolutional neural networks, the Vision Transformer's weaker inductive\nbias is generally found to cause an increased reliance on model regularization\nor data augmentation ("AugReg" for short) when training on smaller training\ndatasets. We conduct a systematic empirical study in order to better understand\nthe interplay between the amount of training data, AugReg, model size and\ncompute budget. As one result of this study we find that the combination of\nincreased compute and AugReg can yield models with the same performance as\nmodels trained on an order of magnitude more training data: we train ViT models\nof various sizes on the public ImageNet-21k dataset which either match or\noutperform their counterparts trained on the larger, but not publicly available\nJFT-300M dataset.\n
Enhanced vesicular stomatitis virus (VSVΔ51) targeting of head and neck cancer in combination with radiation therapy or ZD6126 vascular disrupting agent (2012)

Our data suggest that the combinations of VSVΔ51 with either IR or ZD6126 are potentially novel therapeutic opportunities for HNSCC.