gebhart/patrepeval huggingface dataset:
Gene Expression Profiling of Bulk CD138+ Plasma Cells in Preneoplastic Gammopathy/Asymptomatic Myeloma Identifies Distinct Subsets of Patients. (2005)

Abstract Gene expression profiling of plasma cells (GEP-PC) has provided major insights into myeloma pathobiology. However the data about GEP-PC in preneoplastic gammopathy (MGUS) or asymptomatic myeloma (AM) are limited, and gene expression patterns that might predict outcome in these patients have not been defined. We analyzed GEP (using U133Plus Affymetrix microarrays), of plasma cells isolated by immuno-magnetic bead selection with CD138 microbeads, from the bone marrow of patients with MGUS (n=16) and asymptomatic myeloma (AM; n=18) enrolled in a prospective South West Oncology Group (SWOG) observational study. Data from normal plasma cells (PCs) and from 105 myeloma PCs were included as controls. Myeloma PCs were randomly selected to include at least 15 patients from each of the 7 subgroups previously identified based on GEP of myeloma tumor cells (Zhan and Shaughnessy, ASH 2004). After the suppression of immunoglobulin (Ig) genes, there were 1297 genes that significantly differed in expression between MGUS-PCs and MM-PCs, and 1099 genes that differed between MGUS-PCs and normal PCs with a 1% false discovery rate. Hierarchical cluster analysis of all samples was performed using 1000 plasma cell signature genes that were most differentially expressed between normal and myeloma PCs. These data demonstrated that both MGUS and AM samples were distributed between normal and MM samples. A prediction analysis of microarrays (PAM) model (PNAS99:6567, 2002) utilizing 134 genes was then developed to determine if the signature from these genes in MGUS/AM was more similar to normal or to myeloma plasma cells. In this analysis, 11/16 (69%) of the MGUS samples were more similar to normal PC, compared to 6/18 (33%) of the AM samples (p=0.04). At present, there are no reliable phenotypic markers to distinguish between normal and malignant PCs within the bulk CD138+ population. Gene expression spikes for cyclin D1 and MAF/MAF-B were seen in both MGUS and AM cohorts, including in some patients with normal PC signature. These data provide the largest comparison to date, of GEP of PCs in preneoplastic versus malignant gammopathies and suggest that GEP may be a useful tool to prospectively identify subsets of patients within the MGUS/AM population with dominant normal PC or MM PC signatures, and potentially differing prognosis. Further analysis of differentially expressed genes between MGUS/MM PCs identified in this dataset may allow insights into the genomic changes in tumor cells underlying the malignant progression of myeloma.
Fabrication and characterization of gratings based on thermal shrinkable reactive cholesteric mesogens (2010)

Gratings were successfully fabricated by photolithography by using a particular reactive cholesteric liquid crystal at two different temperatures. The reflection band of the grating was found to be wider than that of a film having a single helical order, because the grating exhibited a binary helical order. Moreover, the surface topography of the grating was regulated by using photomasks with different pitches. The optical reflection spectrum of this grating structure spans two reflection spectra of cholesteric liquid crystal films that were prepared by UV curing at two heating temperatures. Experimental results reveal that the method proposed in this study can be used to produce broadband circular polarizing films.
Screen-printed flexible MRI receive coils (2016)

Magnetic resonance imaging is an inherently signal-to-noise-starved technique that limits the spatial resolution, diagnostic image quality and results in typically long acquisition times that are prone to motion artefacts. This limitation is exacerbated when receive coils have poor fit due to lack of flexibility or need for padding for patient comfort. Here, we report a new approach that uses printing for fabricating receive coils. Our approach enables highly flexible, extremely lightweight conforming devices. We show that these devices exhibit similar to higher signal-to-noise ratio than conventional ones, in clinical scenarios when coils could be displaced more than 18 mm away from the body. In addition, we provide detailed material properties and components performance analysis. Prototype arrays are incorporated within infant blankets for in vivo studies. This work presents the first fully functional, printed coils for 1.5- and 3-T clinical scanners.
Radiomic-Based Framework for Early Diagnosis of Lung Cancer (2019)

This paper proposes a new framework for pulmonary nodule diagnosis using radiomic features extracted from a single computed tomography (CT) scan. The proposed framework integrates appearance and shape features to get a precise diagnosis for the extracted lung nodules. The appearance features are modeled using 3D Histogram of Oriented Gradient (HOG) and higher-order Markov Gibbs random field (MGRF) model because of their ability to describe the spatial non-uniformity in the texture of the nodule regardless of its size. The shape features are modeled using Spherical Harmonic expansion and some basic geometric features in order to have a full description of the shape complexity of the nodules. Finally, all the modeled features are fused and fed to a stacked autoencoder to differentiate between the malignant and benign nodules. Our framework is evaluated using 727 nodules which are selected from the Lung Image Database Consortium (LIDC) dataset, and achieved classification accuracy, sensitivity, and specificity of 93.12%, 92.47%, and 93.60% respectively.
Biomechanical performance of leather and modern football helmets (2013)

With the increased national concern about concussions in football, recent research has focused on evaluating the impact performance of modern football helmets. Specifically, this technical note offers a biomechanical analysis of classic leather helmets compared with modern helmets. Furthermore, modern helmets were examined to illustrate the performance differences between the better- and worse-performing ones. A total of 1224 drop tests were performed from a range of drop heights and impact locations on 11 different helmet types (10 modern and 1 leather helmet model). The resulting head acceleration was used to assess the risk of concussion for each drop test. The results of this analysis demonstrate that modern helmets are significantly and substantially superior to leather helmets in all impact scenarios, and that notable differences exist among modern helmets.
Single-Site Emitter Localization via Multipath Fingerprinting (2012)

A novel method enabling single-site localization of wireless emitters in a rich multipath environment is presented. The localization is based on a novel fingerprinting technique exploiting the spatial-temporal characteristics of the multipath signals received by the base station antenna array. The fingerprint is based on a lower dimensional signal subspace of the spatial-temporal covariance matrix, capturing the dominant multipath signals. The performance is validated with both simulated and real data, demonstrating localization accuracy of about 1 m in typical indoor environments.
Diffraction-Aware Sound Localization for a Non-Line-of-Sight Source (2018)

We present a novel sound localization algorithm for a non-line-of-sight (NLOS) sound source in indoor environments. Our approach exploits the diffraction properties of sound waves as they bend around a barrier or an obstacle in the scene. We combine a ray tracing based sound propagation algorithm with a Uniform Theory of Diffraction (UTD) model, which simulate bending effects by placing a virtual sound source on a wedge in the environment. We precompute the wedges of a reconstructed mesh of an indoor scene and use them to generate diffraction acoustic rays to localize the 3D position of the source. Our method identifies the convergence region of those generated acoustic rays as the estimated source position based on a particle filter. We have evaluated our algorithm in multiple scenarios consisting of a static and dynamic NLOS sound source. In our tested cases, our approach can localize a source position with an average accuracy error, 0.7m, measured by the L2 distance between estimated and actual source locations in a 7m*7m*3m room. Furthermore, we observe 37% to 130% improvement in accuracy over a state-of-the-art localization method that does not model diffraction effects, especially when a sound source is not visible to the robot.
Microduplex Fe-Ni-Mo semihard magnet alloys (1984)

Cobalt-free, semihard magnet alloys based on the Fe-Ni-Mo system have been developed for potential substitution of Co-Fe base alloys such as Vicalloy I (52Co-38Fe-10V) for use in magnetic devices where ductility is required for processing into thin strips. Desirable magnetic properties for Fe-20Ni-4∼6 Mo alloys of Br∼4000–16 000 G, Hc∼20–220 Oe, Br/Bs∼0.8–0.99 can be achieved through processing which produces a microduplex, aligned and elongated multiphase structure. This structure is obtained by a combination of initial plastic deformation, two-phase decomposition in the (α+γ) region, final deformation, and final low temperature precipitation aging. The alloys are ductile and easy to process, and in the final aged condition have high strengths (0.2% yield strength=100∼200 ksi), which could be useful in applications where both magnetic and mechanical strength as well as ductility are required.
TFET-based cellular neural network architectures (2013)

It is well known that CMOS scaling trends are now accompanied by less desirable byproducts such as increased energy dissipation. To combat the aforementioned challenges, solutions are sought at both the device and architectural levels. With this context, this work focuses on embedding a low voltage device, a Tunneling Field Effect Transistor (TFET) within a Cellular Neural Network (CNN) - a low power analog computing architecture. Our study shows that TFET-based CNN systems, aside from being fully functional, also provide significant power savings when compared to the conventional resistor-based CNN. Our initial studies suggest that power savings are possible by carefully engineering lower voltage, lower current TFET devices without sacrificing performance. Moreover, TFET-based CNN reduces implementation footprints by eliminating the hardware required to realize output transfer functions. Application dynamics are verified through simulations. We conclude the paper with a discussion of desired device characteristics for CNN architectures with enhanced functionality.
Plasticity in memristive devices for spiking neural networks (2015)

Memristive devices present a new device technology allowing for the realization of compact non-volatile memories. Some of them are already in the process of industrialization. Additionally, they exhibit complex multilevel and plastic behaviors, which make them good candidates for the implementation of artificial synapses in neuromorphic engineering. However, memristive effects rely on diverse physical mechanisms, and their plastic behaviors differ strongly from one technology to another. Here, we present measurements performed on different memristive devices and the opportunities that they provide. We show that they can be used to implement different learning rules whose properties emerge directly from device physics: real time or accelerated operation, deterministic or stochastic behavior, long term or short term plasticity. We then discuss how such devices might be integrated into a complete architecture. These results highlight that there is no unique way to exploit memristive devices in neuromorphic systems. Understanding and embracing device physics is the key for their optimal use.
Highly versatile in-reflection photonic crystal fibre interferometer (2009)

We report a simple and highly versatile photonic crystal fiber (PCF) interferometer that operates in reflection mode. The device consists of a short section of PCF fusion spliced at the distal end of a standard single mode fiber. The air-holes of the PCF are intentionally collapsed over a microscopic region around the splice. The collapsed region broadens the propagating mode because of diffraction. This allows the coupling and recombination of two PCF modes. Depending on the PCF structure two core modes or a core and a cladding mode can be excited. In either case the devices exhibit sinusoidal interference patterns with fringe spacing depending on the PCF length. The interferometers are highly stable over time and can operate at high temperatures with minimal degradation. The interferometers are suitable for highresolution sensing of strain, refractive index (biosensing), gases, volatile organic compounds, etc.
Giant magnetoresistance in Co/Cu multilayers: Influence of Co thickness at the first antiferromagnetic maximum (1996)

The dependence of the magnetoresistive properties of Co/Cu multilayers on the thickness of the Co layers is described for the case when the Cu layer thickness is 9 Å, corresponding to the first antiferromagnetic maximum. Both the width and the height of the peaks in the magnetoresistance/field curves decrease with increasing Co layer thickness in the range 5–50 Å. This leads to an optimum Co layer thickness of 30–40 Å that maximizes the sensitivity to changes in magnetic field. This result may have practical significance for applications that require the relative lack of hysteresis that is found at the first antiferromagnetic maximum.
Planar diffractive elements as Bragg volume holograms versus surface relief gratings (1997)

A method for designing and fabricating optical systems based on planar holographic optics is presented. The planar optical system is usually composed of two (or more) holographic optical elements which are fabricated onto the same substrate. This paper compares and contrasts the two principal fabrication methods of holographic elements as Bragg volume holograms or as surface relief gratings. Various examples of planar holographic optical systems are presented, and their advantages over regular optical systems are illustrated.
Effect of a Water Rinse on ‘Labile’ Fluoride and Other Ions in Plaque and Saliva before and after Conventional and Experimental Fluoride Rinses (2001)

Labile reservoirs are important in maintaining ion concentrations in oral fluids, especially after a fluoride dentifrice application, where a persistent increase in fluid fluoride can mitigate or reverse caries progression. In this study, the effect of experimental and conventional fluoride rinses on the in vitro and in vivo water-induced release of fluoride, calcium, phosphate, acetate and hydrogen ions from oral reservoirs was examined. At the start of each experiment, 13 subjects rinsed either with a conventional 228-ppm fluoride NaF rinse, a 228-ppm fluoride controlled-release rinse (CR rinse) or received no rinse. Sixty minutes later upper and lower molar plaque samples and 1-min saliva samples were collected. The subjects then rinsed with deionized water for 1 min, and 7 min later, a second set of samples was collected (in vivo study). Plaque fluid and clarified saliva were then recovered from samples by centrifugation, and the remaining plaque mass was sequentially extracted with water and acid to measure the water-extracted and total whole-plaque fluoride (in vitro study). All the samples were analyzed using microtechniques for pH, free calcium, phosphate, organic acids (plaque fluid) and fluoride (plaque fluid, centrifuged saliva and plaque extracts). Results showed that in vivo water rinsing decreased acetate and phosphate in plaque fluid, and fluoride in plaque fluid and saliva, but had no effect on plaque fluid pH. In vivo water rinsing, however, increased plaque fluid free calcium, apparently due to water-induced loss of calcium-binding ions. Water- or fluoride-rinse-induced changes in plaque fluid concentration were greater at the lower molar site, suggesting that rinse pooling may influence ion distribution. Before the water rinse, plaque fluid, saliva and whole-plaque total fluoride values were 1.7, 2 and 4 times higher after the CR rinse compared to the NaF rinse. Furthermore, the CR rinse deposited approximately 11 times more water-extracted fluoride compared to the NaF rinse, suggesting a 'more efficient' precipitation of 'labile' or 'loosely bound fluoride'. The results presented here, and in previous studies, suggest the possibility of formulating effective fluoride dentifrices with a lower fluoride content than is currently in use.
Assay of Spent Fuel by a Simple Reactivity Method (1983)

A new method for the assay of spent-fuel assemblies has been developed that eliminates the need for external isotopic neutron sources, yet retains the advantages of an active interrogation system. The assay is accomplished by changing the reactivity of the system and correlating the measurements to burnup.
A study of hormonal effects in cervical smear samples using Raman spectroscopy (2017)

Raman spectroscopy is a powerful tool that has the potential to be used as a screening method for cervical cancer. It is a label-free, low-cost method providing a biochemical fingerprint of a given sample. The objective of this study was to address patient-to-patient variability contributed by hormonal effects due to the menstrual cycle, the use of hormone-based contraceptives (HC) and the onset of menopause, and to determine if these changes would affect the ability to successfully identify dyskaryotic cells. Raman spectra were recorded from unstained ThinPrep cervical samples (45 cytology negative and 15 high-grade dyskaryosis (high-grade squamous intraepithelial lesion, HSIL) samples using a HORIBA Jobin Yvon XploRA system. HPV DNA testing was also performed. Clinical data collected included date of the last menstrual period, the use of HC and/or menopausal status. Spectral changes were observed depending on the day of the menstrual cycle and on the use of HC. Despite this, HSIL could be discriminated from normal cells regardless of the day on which the sample was taken or the use of HC.
Synthetic Retinoids: Structure–Activity Relationships (2009)

Retinoid signalling pathways are involved in numerous processes in cells, particularly those mediating differentiation and apoptosis. The endogenous ligands that bind to the retinoid receptors, namely all-trans-retinoic acid (ATRA) and 9-cis-retinoic acid, are prone to double-bond isomerisation and to oxidation by metabolic enzymes, which can have significant and deleterious effects on their activities and selectivities. Many of these problems can be overcome through the use of synthetic retinoids, which are often much more stable, as well as being more active. Modification of their molecular structures can result in retinoids that act as antagonists, rather than agonists, or exhibit a large degree of selectivity for particular retinoid-receptor isotypes. Several such selective retinoids are likely to be of value as pharmaceutical agents with reduced toxicities, particularly in cancer therapy, as reagents for controlling cell differentiation, and as tools for elucidating the precise roles that specific retinoid signalling pathways play within cells.
Large maximal cliques enumeration in sparse graphs (2008)

Here we study a variant of maximal clique enumeration problem by incorporating a minimum size criterion. We describe preprocessing techniques to reduce the graph size. This is of practical interest since enumerating maximal cliques is a computationally hard problem and the execution time increases rapidly with the input size. We discuss basics of an algorithm for enumerating large maximal cliques which exploits the constraint on minimum size of the desired maximal cliques. Social networks are prime examples of large sparse graphs where enumerating large maximal cliques is of interest. We present experimental results on the social network formed by the call detail records of one of the world's largest telecom service providers. Our results show that the preprocessing methods achieve significant reduction in the graph size. We also characterize the execution behaviour of our large maximal clique enumeration algorithm.
Beyond Oil and Gas: The Methanol Economy (2011)

Nature's photosynthesis uses the sun's energy with chlorophyll in plants as a catalyst to recycle carbon dioxide and water into new plant life. Only given sufficient geological time can new fossil fuels be formed naturally. Today, anthropogenic CO2 emissions, mainly from the burning of fossil fuels, also far outpace nature's CO2 recycling capabilities, contributing significantly to the current global warming problem. To supplement and dramatically accelerate the natural CO2 recycling process, chemical recycling of carbon dioxide from natural and industrial sources as well as varied human activities or even from the air itself to methanol or dimethyl ether (DME) and their varied products including hydrocarbons can be achieved via its capture and subsequent reductive conversion in the framework of the Methanol Economy.
Superresolution tomography using a moving detection system and convex projections (1992)

Tomographic imaging systems such as those used in PET and SPECT are typically limited in their performance by the size of the detectors used in acquiring the data. By analogy to findings in the context of optical image-plane applications, 1-2 we show that, by moving a tomographic detection system to expand the measurement set, image detail can be recovered by methods such as convex projections. It is demonstrated that, by underrelaxing the data constraints in a convex projection algorithm, excellent results can be obtained in the presence of the high levels of quantum noise typically encountered in the motivating applications. In addition, the method presented is shown to be robust to reasonable misspecifications of the spatial response functions of the imaging system. A “wobbling” PET system is used for purposes of demonstration; however, the concept can be applied in a variety of ways to various tomographic imaging configurations to improve achievable spatial resolution, either in image space or in projection space.
SSCH (2004)

Capacity improvement is one of the principal challenges in wireless networking. We present a link-layer protocol called Slotted Seeded Channel Hopping, or SSCH, that increases the capacity of an IEEE 802.11 network by utilizing frequency diversity. SSCH can be implemented in software over an IEEE 802.11-compliant wireless card. Each node using SSCH switches across channels in such a manner that nodes desiring to communicate overlap, while disjoint communications mostly do not overlap, and hence do not interfere with each other. To achieve this, SSCH uses a novel scheme for distributed rendezvous and synchronization. Simulation results show that SSCH significantly increases network capacity in several multi-hop and single-hop wireless networking scenarios.