gebhart/patrepeval huggingface dataset:
Targeted next generation sequencing in well-differentated/dedifferentiated liposarcoma (WD/DD LPS): Multiple gene amplifications but few mutations. (2015)

10550 Background: WD/DD LPS is a common soft tissue sarcoma with approximately 1500 new cases per year. Surgery is the mainstay of treatment but recurrences are frequent and limited systemic options make treatment challenging. ‘Tumor genotyping’ is becoming more common in clinical practice as it offers the hope of personalized targeted therapy. We wanted to evaluate the results and the clinical utility of available tumor genotyping panels in WD/DD LPS. Methods: MDACC patients (pt) who had their tumor analyzed by either Foundation One (FM) (244 gene panel for solid tumors, tumor only) or the institutional T200 panel (202 gene panel, tumor and normal) were included. There were 124 overlapping genes in these panels. FFPE sections were sequenced on the T200 panel using the Illumina HiSeq2000 platform. On average, the cutoff for calling variants on the T200 is 1%-5% for high coverage data ( > 500x) and 10-15% for lower coverage( < 200x). Results: Total of 20 pt samples were identified, 7 on T200 (1 WD+6 DD) and 13 on FM (5 WD+8 DD). Significant copy number alterations (CNA) were identified in all samples. Only recurrent, potentially clinically actionable CNA (out of the 166 identified) are tabulated below. In the 7 pt samples on T200, 27 mutations were detected: 8 genes (CTNNB1, MECOM, ZNF536, EGFR, EML4, CSMD3, PBRM1, PPP1R3A) were identified as deleterious (on Condel, PolyPhen and SIFT) and a truncating mutation was found in NF2. Of these only the EGFR and NF2 are known driver mutations and potentially actionable. These mutations have not been reported previously in DD LPS. On the FM panel, ZNF536, CSMD3 and PPP1R3Awere not evaluated (NE) and no mutations were reported. Conclusions: In this series, 20/20 (100%) of the WD/DD LPS had MDM2 and CDK4amplified. Additional recurrent novel deleterious genetic changes were identified, but further studies are needed to determine their therapeutic and pathogenetic significance. High Amplification ( ≥ 4) Gene T200 +FISH N = 7 FM N = 13 Previously reported in DD LPS (50 samples in cbioportal) MDM2 7 13 Y (90%) CDK4 7 13 Y (88%) DDR1 2 NE N AURKB 2 0 N ERBB2 2 0 N FLT4 2 0 Y (2%) FGFR4 2 0 N MAP2K4 2 0 N NOTCH1 3 0 N NOTCH4 2 NE N AKT1 2 0 Y (4%) MCL1 NE 2 Y (10%) High Deletion 2 0 N BRCA2
Expression and secretion of the human piacentaJ growth hormone inEscherichia coli (1989)

peer reviewed
On the Radiative Properties of Polydispersions : A Simplified Approach (1985)

Abstract In this paper an analysis is presented to predict the spectral absorption, extinction and scattering coefficients of polydispersions of carbon, different coals, and fly-ash particles. The normalization of the efficiency factors are given. Relatively simple, closed form expressions are derived for the spectral absorption and extinction coefficient. These simplified relations are promising for accurately predicting the radiative properties for use in multidimensional, spectral, radiative heat transfer analyses.
Sandwich-cultured hepatocytes: an in vitro model to evaluate hepatobiliary transporter-based drug interactions and hepatotoxicity (2020)

Sandwich-cultured hepatocytes (SCH) are a powerful in vitro tool that can be utilized to study hepatobiliary drug transport, species differences in drug transport, transport protein regulation, drug-drug interactions, and hepatotoxicity. This review provides an up-to-date summary of the SCH model, including a brief history of, and introduction to, the use of SCH, as well as methodology to evaluate hepatobiliary drug disposition. A summary of the literature that has utilized this model to examine the interplay between drug metabolizing enzymes and transport proteins, drug-drug interactions at the transport level, and hepatotoxicity as a result of altered hepatic transport also is provided.
Tissue boundary refinement in magnetic resonance images using contour-based scale space matching (1991)

An algorithm for computationally focusing the tissue boundaries detected from magnetic resonance images is presented. The proposed approach is a novel, whole-contour-based technique for tracing edges selected at a coarse scale into successively finer scales to recover the needed precision. The tracing algorithm builds consensus through a fast pixel voting scheme. Also presented is a rigorous method for determining the appropriate itinerary when traversing scale space, beginning from the premise of a maximum pixel migration per unit change in scale parameter. This leads to an efficient method of processing images so as to maximize accuracy and minimize noise. Although the LoG (Laplacian of Gaussian) is used for many of the experiments, results using a novel edge detector which is mathematically superior to and faster to compute than the LoG and for which fewer steps are required to traverse the same effective span in scale space are presented. Experimental results on real data are presented, and other potential applications are discussed.
Method for Seismic Base Isolation of Liquid-Storage Tanks (1997)

A new method for seismic base isolation of ground-supported vertical cylindrical liquid-storage tanks is proposed in which the base plate is supported on a soil bed, and the tank wall is supported on a ring of vertically soft rubber bearings. The isolated system derives its flexibility from rocking and uplifting of the base, and derives its energy-dissipation capacity from base-plate yielding, soil damping, and hysteretic rubber damping. In this analysis, the tank-liquid system is represented by a lumped-mass-stick model, and the rubber bearings are represented by a series of nonlinear hysteretic axial springs. The partially uplifted base plate loaded by liquid is analyzed giving due consideration to the effects of membrane action and plastic yielding. Results demonstrate the ability of the isolation method in reducing significantly the overturning base moments and the axial compressive stresses in the tank wall, while still maintaining the values of base uplifts and plastic rotations in the base plate at reasonable levels.
Incorporation of amino acid-derived carbon into tylactone by Streptomyces fradiae GS14 (1984)

Washed cells from 72-h cultures of Streptomyces fradiae GS14 were used to examine the distribution of radiolabel from 14C-amino acids and related compounds into tylactone, CO2, and cells. Test compounds were categorized according to products of their oxidative degradation. Those compounds known to produce propionyl-coenzyme A by direct catabolic oxidation were designated as group I. Group II included those compounds oxidized to methylmalonyl-coenzyme A via succinyl-coenzyme A and the tricarboxylic acid cycle. Group III contained compounds known to be oxidized to acetoacetyl-coenzyme A. The total amount of label recovered after 60 min ranged from 3 to 65%. Although label from all test compounds except proline (group II) and lysine (group III) was incorporated into tylactone after 60 min, label from group I and group III compounds was incorporated at levels five times greater than label from group II compounds. From 55 to 75% of the recovered label from propionate (I), asparagine (II), glutamine (II), glutamate (II), alpha-ketoglutarate (II), and succinate (II) was recovered as 14CO2. From 75 to 95% of the recovered label from the remaining compounds tested was located in the cells. Based on the data, a pathway for the role of amino acids in the biosynthesis of tylactone is proposed.
Direct Reductive Amination versus Hydrogenation of Intermediates –A Comparison (2004)

Abstract The direct reductive amination of acetophenone with benzylamine or piperidine was studied in comparison with the hydrogenation of possible intermediates like a corresponding imine or enamine. No common features in terms of productivity and stereocontrol (in the case of chiral catalysts) have been found for both processes. Hence evaluation of efficient, selective and enantioselective catalysts for direct reductive amination appears to be a separate task.
Unified Optical Modeling (2010)

A great variety of optical modeling techniques have been proposed in the literature and some of them have been implemented in optics software. However, the approaches typically differ in their theoretical roots and notation. For instance geometrical optics is closely linked to ray tracing and laser beam propagation is linked to a scalar light field representation. Unified optical modeling aspires to place all significant modeling techniques into the same theoretical framework in order to enable a smooth combination of them in one and the same modeling task. We call the theoretical concept for unified optical modeling field tracing. Field tracing turns out to be the logical generalization of ray tracing and has been implemented in the field tracer software VirtualLab™.
Diameter Routing Extensions (2008)

This document describes two(2) extensions to the current diameter
routing scheme. The first extension describes an explicit routing
mechanism that MAY be employed by Diameter nodes to allow specific
stateful Diameter proxies to remain in the path of all messages
exchanges constituting a Diameter session. The second extension
describes a realm based redirection scheme as an alternative to host
based redirection described in [RFC3588].
Medical Imaging Systems (2020)

This open access book gives a complete and comprehensive introduction to the fields of medical imaging systems, as designed for a broad range of applications. The authors of the book first explain the foundations of system theory and image processing, before highlighting several modalities in a dedicated chapter. The initial focus is on modalities that are closely related to traditional camera systems such as endoscopy and microscopy. This is followed by more complex image formation processes: magnetic resonance imaging, X-ray projection imaging, computed tomography, X-ray phase-contrast imaging, nuclear imaging, ultrasound, and optical coherence tomography.
Downregulation of miR-193a-5p correlates with lymph node metastasis and poor prognosis in colorectal cancer (2014)

Downregulation of miR-193a-5p correlates with lymph node metastasis and poor survival of CRC. miR-193a-5p may be a useful biomarker for CRC diagnosis, metastasis and prognosis prediction.
Neural Taylor Approximations: Convergence and Exploration in Rectifier Networks (2016)

Modern convolutional networks, incorporating rectifiers and max-pooling, are neither smooth nor convex; standard guarantees therefore do not apply. Nevertheless, methods from convex optimization such as gradient descent and Adam are widely used as building blocks for deep learning algorithms. This paper provides the first convergence guarantee applicable to modern convnets, which furthermore matches a lower bound for convex nonsmooth functions. The key technical tool is the neural Taylor approximation -- a straightforward application of Taylor expansions to neural networks -- and the associated Taylor loss. Experiments on a range of optimizers, layers, and tasks provide evidence that the analysis accurately captures the dynamics of neural optimization. The second half of the paper applies the Taylor approximation to isolate the main difficulty in training rectifier nets -- that gradients are shattered -- and investigates the hypothesis that, by exploring the space of activation configurations more thoroughly, adaptive optimizers such as RMSProp and Adam are able to converge to better solutions.
Decision Forests for Classification, Regression, Density Estimation, Manifold Learning and Semi-Supervised Learning (2011)

This paper presents a unified, efficient model of random decision forests which can be applied to a number of machine learning, computer vision and medical image analysis tasks. Our model extends existing forest-based techniques as it unifies classification, regression, density estimation, manifold learning, semi-supervised learning and active learning under the same decision forest framework. This means that the core implementation needs be written and optimized only once, and can then be applied to many diverse tasks. The proposed model may be used both in a generative or discriminative way and may be applied to discrete or continuous, labelled or unlabelled data. The main contributions of this paper are: 1) proposing a single, probabilistic and efficient model for a variety of learning tasks; 2) demonstrating margin-maximizing properties of classification forests; 3) introducing density forests for learning accurate probability density functions; 4) proposing efficient algorithms for sampling from the forest generative model; 5) introducing manifold forests for non-linear embedding and dimensionality reduction; 6) proposing new and efficient forest-based algorithms for transductive and active learning. We discuss how alternatives such as random ferns and extremely randomized trees stem from our more general model. This paper is directed at both students who wish to learn the basics of decision forests, as well as researchers interested in our new contributions. It presents both fundamental and novel concepts in a structured way, with many illustrative examples and real-world applications. Thorough comparisons with state of the art algorithms such as support vector machines, boosting and Gaussian processes are presented and relative advantages and disadvantages discussed.The many synthetic examples and existing commercial applications demonstrate the validity of the proposed model and its flexibility. Powerpoint slides (with many examples and animations) are also available from http://research.microsoft.com/groups/vision/decisionforests.aspx
Intratumoral lymphatics are essential for the metastatic spread and prognosis in squamous cell carcinomas of the head and neck region. (2003)

Head and neck squamous cell carcinomas (HNSCCs) frequently disseminate to regional lymph nodes. To investigate the possible mechanisms involved, we studied the expression of cancer cell adhesion molecules together with lymphatic vascular and blood vascular markers in a panel of 97 primary HNSCC tumors and correlated expression levels with conventional clinicopathological parameters and with long-term prognosis. In particular, we measured the density of intratumoral and peritumoral lymph vessels as assessed with the marker lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) and the density of tumor CD44, a receptor up-regulated in many metastatic cancers. Intratumoral LYVE-1(+) lymphatic vessels were clearly associated with a higher risk for local relapse as well as with poor disease-specific prognosis (P = 0.02 and 0.0009, respectively). In contrast, a high density of peritumoral LYVE-1(+) vessels was a sign of favorable survival (P = 0.05). Strong primary tumor CD44 expression was associated with a poor prognosis, an increased risk of local recurrence (P = 0.03 and 0.02, respectively), and an increase in resistance to radiation therapy (P = 0.03). CD44 was the only factor with an independent prognostic value for the disease-specific overall survival (P = 0.04). Our results suggest that intratumoral lymphatics play a greater role than peritumoral lymphatics in nodal metastasis of HNSCC and that tumor CD44 levels can predict sensitivity to radiation therapy. These parameters may be useful predictive and prognostic tools in the clinical management of HNSCC.
A RESONANT SISO SENSOR BASED ON A COUPLED ARRAY OF MICROELECTROMECHANICAL OSCILLATORS (2006)

This work details the preliminary development and testing of a novel, single input -single output (SISO) resonant microsensor, which exploits vibration localization in a coupled-oscillator architecture to allow for the detection of multiple analytes with a single platform. The work includes a brief description of a preliminary sensor design and its operating principles, an outline of a lumped mass analog that proves convenient for analysis and predictive design, and preliminary experimental results, recently obtained from a first-generation device, which verify the sensor's feasibility.
Adenylate Kinase and AMP Signaling Networks: Metabolic Monitoring, Signal Communication and Body Energy Sensing (2009)

Adenylate kinase and downstream AMP signaling is an integrated metabolic monitoring system which reads the cellular energy state in order to tune and report signals to metabolic sensors. A network of adenylate kinase isoforms (AK1-AK7) are distributed throughout intracellular compartments, interstitial space and body fluids to regulate energetic and metabolic signaling circuits, securing efficient cell energy economy, signal communication and stress response. The dynamics of adenylate kinase-catalyzed phosphotransfer regulates multiple intracellular and extracellular energy-dependent and nucleotide signaling processes, including excitation-contraction coupling, hormone secretion, cell and ciliary motility, nuclear transport, energetics of cell cycle, DNA synthesis and repair, and developmental programming. Metabolomic analyses indicate that cellular, interstitial and blood AMP levels are potential metabolic signals associated with vital functions including body energy sensing, sleep, hibernation and food intake. Either low or excess AMP signaling has been linked to human disease such as diabetes, obesity and hypertrophic cardiomyopathy. Recent studies indicate that derangements in adenylate kinase-mediated energetic signaling due to mutations in AK1, AK2 or AK7 isoforms are associated with hemolytic anemia, reticular dysgenesis and ciliary dyskinesia. Moreover, hormonal, food and antidiabetic drug actions are frequently coupled to alterations of cellular AMP levels and associated signaling. Thus, by monitoring energy state and generating and distributing AMP metabolic signals adenylate kinase represents a unique hub within the cellular homeostatic network.
Chemiluminescence microscopy reveals functional heterogeneity in single neutrophils undergoing oxygen burst (1988)

Activated polymorphonuclear leukocytes (PMN) respond to various triggers with an oxygen burst, during which the release of reactive oxygen species (ROS) plays a key role in microbial killing. The biological function of the ROS-associated light emissions is not known. However, this particularly weak cell-derived chemiluminescence (CL) may serve as a parameter for the identification of PMN activation. In this study we describe a novel technique which we termed CL microscopy. A microscope-based low-light image-processing system was applied which was sensitive enough to detect single photons, capable of two-dimensional signal accumulation, and digital image analysis. This technique permitted, for the first time, the visualization of the oxygen burst in single cells. Furthermore, quantitative evaluation of cell-derived luminol-enhanced CL revealed functional heterogeneity. Single-cell investigations of activated living PMN of normal human donors showed clear differences in kinetics and intensity of the oxygen burst related to different stimuli. The chemical agent (phorbol 12-myristate 13-acetate) induced CL in 83% of PMN. In contrast, the complement-mediated phagocytic stimulation by opsonized zymosan gave much higher light intensities of individual cells, but only in part of the PMN population (30%). CL microscopy presents a new and highly sensitive technique with considerable potential for single-cell analysis in immunological research.
Comparison of capillary and venous blood for malaria detection using two PCR-based assays in febrile patients in Sierra Leone (2021)

No difference was found in malaria detection between venous and capillary blood using two different PCR-based detection assays. This data gives support for use of capillary blood, a material which can be obtained easier by less invasive methods, for PCR-based malaria diagnostics, independent of the platform.
New Trends in Palladium‐Catalyzed Transfer Hydrogenations Using Formic Acid (2005)

Abstract In the presence of a catalytic amount of organic bases, Pd‐catalyzed transfer hydrogenations with formic acid were found to be facile processes. These new conditions produce innocuous carbon dioxide as the by‐product compared to the use of ammonium formate, which generates ammonia and carbon dioxide as gaseous by‐products which recombine to create unsafe conditions. When the substrate is basic enough to form salts with formic acid, no additional base is necessary. In certain cases, the product of the reaction was used to accelerate the transfer hydrogenation process.
Exploiting Dimensions of the MIMO Wireless Channel: Multidimensional Link Adaptation (2005)

In this paper, we propose an adaptive radio interface scheme for systems that employ multiple antennas. This is in contrast to the adaptive interface of single-antenna systems like in current packet data cellular systems. We propose groups of transmission parameters called modulation, coding and antenna schemes (MCAS) that are chosen according to the current conditions of the wireless channel, in order to maximize the performance in terms of good put, while maintaining a certain level of reliability.
A Simple Route to 2-AlkenethioicO-Esters and 2-Alkenedithioic Esters [Thiono- and Dithioesters, 37] (1985)

The reaction of the copper(I) derivative of dimethyl methanephosphonic ester with O-alkyl carbonochloridothioates affords O-alkyl (dimethoxyphosphinyl)-thioacetates. These compounds as well as the corresponding dithioesters react with aldehydes in a Horner-Emmons reaction to give O-alkyl 2-alkenethioates or alkyl 2-alkenedithioates, respectively.
Quantitative ultrasonic characterization of lesion composition and remodeling in atherosclerotic rabbit aorta. (1993)

We have previously shown that high-frequency, high-resolution ultrasound can characterize the acoustic properties and composition of fatty plaques in cholesterol-fed rabbits. To determine whether quantitative ultrasound can delineate the regression of atherosclerotic lesions by detecting a change in their composition from fatty to fibrous types induced by alterations in dietary regimen, we fed six New Zealand White rabbits a 2% cholesterol diet for 3 months, followed by a standard diet for 3 additional months to promote the development of fibrous intimal lesions. Segments of aortas were excised, and backscattered radiofrequency data were acquired from 400 to 600 independent sites in each specimen with an acoustic microscope operated at 50 MHz. Control data were provided by measuring backscatter from adjacent portions of the aortas devoid of lesions. Histological and immunocytochemical analyses of the fibrous intimal lesions confirmed the presence of smooth muscle cells and abundant connective tissue with little appreciable lipid. Backscatter from normal aortic segments (-30.7 +/- 1.0 dB) was approximately 10-fold greater than that from fibrous lesions (-42.4 +/- 1.0 dB; P < .05). We previously reported that integrated backscatter from fatty lesions was -50.6 +/- 0.7 dB, or approximately 10-fold less than that from fibrous lesions (P < .05). Values for integrated backscatter from the media of each tissue type were approximately equal (-30.0 +/- 1.7 versus -30.7 +/- 1.6 versus -33.4 +/- 0.8 dB for normal versus fibrous versus fatty tissues, respectively; P = not significant).(ABSTRACT TRUNCATED AT 250 WORDS)
Concept Evolution Modeling Using Semantic Vectors (2016)

We propose a method for a concept-centric semantic analysis of an evolving corpus, highlighting the persistent concepts, emergence of new concepts, and the changes in the semantic associations between concepts. We report our findings on a corpus of computer science literature that spans six decades, revealing interesting patterns about the progress of the discipline.