gebhart/patrepeval huggingface dataset:
Plasmonic nanochip for SERS chemical and biomedical sensing (2017)

The development of rapid, easy-to-use and highly sensitive DNA detection methods has received increasing interest for medical diagnostics and research purposes. Our laboratory has developed several chip-based DNA biosensors including molecular sentinel-on-chip (MSC), multiplex MSC, and inverse molecular sentinel-on-chip (iMS-on-Chip). These sensors use surface-enhanced Raman scattering (SERS) plasmonic chips, functionalized with DNA probes for single-step DNA detection. The sensing mechanisms is based on the hybridization of target sequences and DNA probes, resulting in a displacement of a SERS reporter from the chip surface. This distance increase results in change in SERS signal intensity from the reporter, thus indicating the capture, and therefore the presence, of the target nucleic acid sequence. The nucleic acid probes and the SERS chip, which compose the sensing platform, were designed for single-step DNA detection. The target sequences are detected by delivery of a sample solutions on a functionalized chip and characterization of the SERS signals, after 1 - 2 hr incubation. These techniques avoid labeling of the target sequence or washing to remove unreacted components, making them easy-to-use and cost effective. The use of SERS chip for medical diagnostics was demonstrated by detecting genetic biomarkers for respiratory viral infection and the DNA of dengue virus 4.
In vivo measurement of a new source of contrast, the dipolar relaxation time, <i>T</i><sub>1<i>D</i></sub>, using a modified inhomogeneous magnetization transfer (ihMT) sequence (2016)

The model and experiments described provide access to a new relaxation characteristic of tissue with potentially unique diagnostic information. Magn Reson Med 78:1362-1372, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Orthomolecular oncology: a mechanistic view of intravenous ascorbate's chemotherapeutic activity. (2002)

The effect of vitamin C in cancer has been a subject of great controversy; mainly because of the inconsistent results obtained by oral intakes of ascorbate when used as an anticancer agent. We believe the intravenous application of ascorbate will provide more consistent results in cancer patients since Vitamin C blood levels attained are substantially higher in a range proven cytotoxic to malignant cells. In this article we will present and discuss our proposed mechanism on the chemotherapeutic activity exhibited by ascorbate.
Heated Thick-Film Titania Exhaust Gas Oxygen Sensors (1984)

<div class="htmlview paragraph">This paper discusses laboratory propane burner and engine dynamometer durability testing of thick-film titania sensors whose resistance changes several orders of magnitude in response to changes in the partial pressure of oxygen around the stoichiometric point. Development has progressed to where porous titania films applied to alumina substrates exhibit switching and delay times equal to or faster than those achieved with zirconia based oxygen sensors (currently used in automotive exhaust applications) even after 50,000 equivalent miles of engine dynamometer testing. The titania film has been combined with a thick film heater such that good switching can be achieved over at least a 200°C to 850°C exhaust gas temperature range. This provides better engine control during idle and low engine speeds, and flexibility in locating the sensor further downstream in the exhaust.</div>
Characterization of <i>Mycobacterium tuberculosis</i> Mycothiol <i>S</i>-Conjugate Amidase (2003)

Mycothiol is comprised of N-acetylcysteine (AcCys) amide linked to 1D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside (GlcN-Ins) and is the predominant thiol found in most actinomycetes. Mycothiol S-conjugate amidase (Mca) cleaves the amide bond of mycothiol S-conjugates of a variety of alkylating agents and xenobiotics, producing GlcN-Ins and a mercapturic acid that can be excreted from the cell. Mca of Mycobacterium tuberculosis (Rv1082) was cloned and expressed as a soluble protein in Escherichia coli. The protein contained 1.4 +/- 0.1 equiv of zinc after purification, indicating that Mca is a metalloprotein with zinc as the native metal. Kinetic studies of Mca activity with 14 substrates demonstrated that Mca is highly specific for the mycothiol moiety of mycothiol S-conjugates and relatively nonspecific for the structure of the sulfur-linked conjugate. The deacetylase activity of Mca with GlcNAc-Ins is small but significant and failed to saturate at up to 2 mM GlcNAc-Ins, indicating that Mca may contribute modestly to the production of GlcN-Ins when GlcNAc-Ins levels are high. The versatility of Mca can be seen in its ability to react with a broad range of mycothiol S-conjugates, including two different classes of antibiotics. The mycothiol S-conjugate of rifamycin S was produced under physiologically relevant conditions and was shown to be a substrate for Mca in both oxidized and reduced forms. Significant activity was also seen with the mycothiol S-conjugate of the antibiotic cerulenin as a substrate for Mca.
Aerosol Jet® Direct-Write for Microscale Additive Manufacturing (2019)

The unique capabilities of Aerosol Jet® technology for noncontact material deposition with in-flight adjustment of ink rheology in microdroplets are explained based on first principles of physics. The suitable range of ink droplet size is determined from the effectiveness for inertial impaction when depositing onto substrate and convenience for pneumatic manipulation, in-flight solvent evaporation, etc. The existence of a jet Reynolds number window is shown by a fluid dynamics analysis of impinging jets for Aerosol Jet® printing with long standoff between nozzle and substrate, which defines the operation range of gas flow rate according to the nozzle orifice diameter. The time scale for ink droplets to remove volatile solvent is shown to just coincide that for them to travel in the nozzle channel toward substrate after meeting the coflowing sheath gas, enabling the in-flight manipulation of ink properties for high aspect-ratio feature printing. With inks being able to solidify rapidly, 3D structures, such as tall micropillars and thin-wall boxes, can be fabricated with Aerosol Jet® printing. Having mist droplets in the range of 1–5 μm also makes it possible to print lines of width about 10 μm.
X-Aptamers: A Bead-Based Selection Method for Random Incorporation of Druglike Moieties onto Next-Generation Aptamers for Enhanced Binding (2012)

By combining pseudorandom bead-based aptamer libraries with conjugation chemistry, we have created next-generation aptamers, X-aptamers (XAs). Several X-ligands can be added in a directed or random fashion to the aptamers to further enhance their binding affinities for the target proteins. Here we describe the addition of a drug (N-acetyl-2,3-dehydro-2-deoxyneuraminic acid), demonstrated to bind to CD44-HABD, to a complete monothioate backbone-substituted aptamer to increase its binding affinity for the target protein by up to 23-fold, while increasing the drug's level of binding 1-million fold.
Predrill Pore Pressure Prediction Using Seismic Data (2000)

Abstract An accurate knowledge of formation pore pressure is a key requirement for the safe and economic drilling of deepwater wells. A pre-drill estimate of pore pressure can be obtained from seismic velocities using a velocity to pore pressure transform. However, the velocities used are often not ideal. Seismic velocities used during seismic processing are designed to optimize the stack/migration result, with local fluctuations being smoothed out and the velocity sampling interval usually being too coarse for accurate pore pressure prediction. Various methods of determining seismic interval velocities from prestack seismic data are compared, and a velocity analysis approach suitable for pore pressure prediction is recommended. This is aimed at producing a pre-drill pore pressure cube from 3D seismic data, and uses seismic tomography to obtain an accurate velocity model. Seismic velocities obtained by conventional methods average the velocity over the seismic aperture and are therefore not suitable for pore pressure prediction in the presence of lateral variations, as may arise from the presence of dipping structures, lithology variations, salt layers of various thickness, fault blocks or variations in compaction and pore pressure. Reflection tomography gives improved spatial resolution of the seismic velocity field and thus allows a more reliable pre-drill pore pressure cube to be obtained. The method is used to predict pore pressure for a deep water Gulf of Mexico case study.
Reducing service failures by failure and workload aware load balancing in SaaS clouds (2013)

SLA violations are typically viewed as service failures. If service fails once, it will fail again unless remedial action is taken. In a virtualized environment, a common remedial action is to restart or reboot a virtual machine (VM). In this paper we present, a VM live-migration policy that is aware of SLA threshold violations of workload response time, physical machine (PM) and VM utilization as well as availability violations at the PM and VM. In the migration policy we take into account PM failures and VM (software) failures as well as workload features such as burstiness (coefficient of variation or CoV >1) which calls for caution during the selection of target PM when migrating these workloads. The proposed policy also considers migration of a VM when the utilization of the physical machine hosting the VM approaches its utilization threshold. We propose an algorithm that detects proactive triggers for remedial action, selects a VM (for migration) and also suggests a possible target PM. We show the efficacy of our proposed approach by plotting the decrease in the number of SLA violations in a system using our approach over existing approaches that do not trigger migration in response to non-availability related SLA violations, via discrete event simulation of a relevant case study.
A system to mine large-scale bilingual dictionaries from monolingual web pages (2007)

This paper describes a system that automatically mines EnglishChinese translation pairs from large amount of monolingual Chinese web pages. Our approach is motivated by the observation that many Chinese terms (e.g., named entities that are not stored in a conventional dictionary) are accompanied by their English translations in the Chinese web pages. In our approach, candidate translations are extracted using pre-defined templates. Transliterations and translation pairs are then identified using statistical learning methods. We compare several approaches to aligning transliterations and mining translations on more than 300GB Chinese web pages. In our experiments on MSN query log, we show that the mined bilingual dictionary greatly enlarges the coverage of an existing English-Chinese dictionary. It also improves query translation in cross-language information retrieval, leading to significantly higher retrieval effectiveness in on TREC collections.
Bandwidth enhancement of wavelength conversion viacross-gainmodulation by semiconductor optical amplifier cascade (1995)

The authors show experimentally and theoretically that the bandwidth for wavelength conversion through cross-gain modulation varies approximately linearly with the length of the amplifier. By cascading two similar semiconductor optical amplifiers, the small-signal wavelength conversion bandwidth is doubled.
Temperature Distribution in an Internal Reforming Molten Carbonate Fuel Cell. Influence of the Flow Direction of the Fuel in a Reforming Unit. (1992)

In order to minimize the cell-temperature gradient in an indirect internal reforming molten carbonate fuel cell (IIR-MCFC), three directions of fuel (CH4) flow in the reforming unit have been investigated. Temperature distribution in each type of stack was analyzed, and experiments were also conducted. As a result of the analysis, it was suggested that the temperature gradinent was minimized when the fuel in the reforming unit flowed perpendicular to the flow direction of the reformed gas in the anode gas channel while the cathode gas flowed in a diagonal direction to that of the reformed gas. The analytical results were compared with the experimental results, and reasonable agreement was obtained. As a consequence, it was found that the analytical method was useful for stack designing.
True background calibration technique for pipelinedADC (2000)

A digital background calibration technique for a pipelined analogue-to-digital converter (ADC) is presented. The calibration technique involves the use of a slow, but accurate, ADC in conjunction with a least-mean squares (LMS) algorithm to find the parameters, which correct for residue errors such as finite op-amp gain error, capacitor ratio mismatch and charge injection error in a non-ideal pipeline stage, resulting in a significant improvement in the INL and the DNL of the ADC.
Energy resolved X-ray grating interferometry (2013)

Although compatible with polychromatic radiation, the sensitivity in X-ray phase contrast imaging with a grating interferometer is strongly dependent on the X-ray spectrum. We used an energy resolving detector to quantitatively investigate the dependency of the noise from the spectral bandwidth and to consequently optimize the system—by selecting the best energy band matching the experimental conditions—with respect to sensitivity maximization and, eventually, dose. Further, since theoretical calculations of the spectrum are usually limited due to non-ideal conditions, an energy resolving detector accurately quantifies the spectral changes induced by the interferometer including flux reduction and beam hardening.
[Hepatitis B virus morphogenesis]. (2008)

The human hepatitis B virus (HBV) is a small hepatotropic enveloped virus associated with chronic infection that can lead to cirrhosis and hepatocellular carcinoma. The HBV genome is a DNA molecule contained in an icosahedral capsid. Although HBV is not a retrovirus, the replication of its genome involves reverse transcription. Another distinctive feature of HBV is the production, in great excess over virions, of non-infectious subviral particles (SVP) consisting of membrane phospholipids and the three envelope proteins (small [S], medium [M] and large [L]). These empty non-infectious particles are highly immunogenic, and their in vitro production is at the basis of the current vaccine against hepatitis B. Despite numerous studies that lead to a better understanding of the HBV replication, little is known about the morphogenesis of the virion and its associated SVP. Recent approaches suggest that the mechanisms responsable for assembly of the virions and the SVP could be distinct.
A Cortical Based Diagnosis System for MCI Based on sMRI Features Fusion (2018)

Alzheimer's disease (AD) is one of the most neurodegenerative disorders that target central nervous system with statistical results of more than 5 million sufferers among the Americans. According to the literature, discovering the disease in its early stage is considered as one of the main obstacles that face the scientists. The difficulty of this diagnostic task relied on a number of reasons including the variability of the disease's effect among its patients. This paper aims to study mild cognitive impairment (MCI), the type of impairment that found to increase the factor of achieving to AD. According to this study a cortical regions based computer-aided diagnosis (CAD) system can be presented that in turn serve the early diagnosis of AD. This goal is achieved by visualizing the personalized diagnosis of the MCI in each of the cortical regions separately. For this purpose, the proposed CAD system goes into four main stages: 1-preprocessing and cortex extraction, 2-cortex re-construction and shape-based feature extraction, 3-feature fusing, and 4-local/regional diagnosis followed by global diagnosis step. Evaluating the proposed system shows promising results with a maximum performance of 86.30%, 88.33%, and 84.88% for accuracy, specificity, and sensitivity, respectively.
A New Fast Framework for Early Detection of Prostate Cancer Without Prostate Segmentation (2018)

This paper presents a computer-aided diagnosis (CAD) system for early detection of prostate cancer from diffusion-weighted magnetic resonance imaging (DWI) acquired at six different b-values. Our system starts by defining a region of interest (ROI) that includes the prostate across the different slices of the input DWI volume. Then, the apparent diffusion coefficient (ADC) of the defined ROI is calculated, normalized and refined. Then, the probability density functions (PDFs) of the refined ADC volumes at the distinct b-values are constructed. Finally, the classification of prostate into either benign or malignant is achieved using a classification system of two stages. The proposed system is the first system of its type that has the ability to detect prostate cancer without any prior processing (e.g., the segmentation of the prostate region). Evaluation of the proposed system is done using DWI datasets acquired from 45 patients (20 benign and 25 malignant) at six distinct b-values. The acquisition of these DWI datasets is performed using two different scanners with distinct magnetic field strengths (1.5 Tesla and 3 Tesla). The resulting area under curve (AUC) is 0.77, which shows that the proposed system approaches the state-of-the-art performance without any prior processing.
Noise spatial nonuniformity and the impact of statistical image reconstruction in CT myocardial perfusion imaging (2012)

(1) Images reconstructed using FBP suffered from nonuniform spatial noise levels. This nonuniformity is another manifestation of the detrimental effects caused by short-scan reconstruction in CT MPI. (2) Images reconstructed using SIR had a much lower and more uniform noise level and thus can be used as a potential solution to address the FBP nonuniformity. (3) Given the improvement in the accuracy of the perfusion metrics when using SIR, it may be desirable to use a statistical reconstruction framework to perform low-dose dynamic CT MPI.
Translational Regulation of Utrophin by miRNAs (2011)

The present study has identified key inhibitory mechanisms featuring miRNAs that regulate utrophin expression, and demonstrated that these mechanisms can be targeted to increase endogenous utrophin expression in cultured muscle cells. We suggest that miRNA-mediated inhibitory mechanisms could be targeted by methods similar to those described here as a novel strategy to increase utrophin expression as a therapy for DMD.
High efficiency hexagonal boron nitride neutron detectors with 1 cm2 detection areas (2020)

We report the realization of 1 cm2 hexagonal boron nitride (h-BN) thermal neutron detectors with an unprecedented detection efficiency of 59%. This was achieved through improvements in material quality, as reflected in a sixfold enhancement in the electron mobility and lifetime product and a threefold reduction in the surface recombination field, which resulted in a higher detection efficiency at a lower applied electric field over that of a previous state-of-the-art lateral detector with a detection area of 30 mm2. The attainment of 1 cm2 h-BN neutron detectors capable of retaining a high detection efficiency represents a significant milestone toward the practical applications of h-BN detectors.
Segregation of Multiple Talkers in the Vertical Plane: Implications for the Design of a Multiple Talker Display (2002)

Three experiments were conducted to evaluate the effect of spatial separation of multiple talkers in the vertical plane on speech intelligibility. The first experiment demonstrated a release from masking due to separation in the median plane, and that this release was not due to the presence of residual interaural time differences (ITDs). The second experiment showed that this release corresponded to an increase in signal level of 1.3 dB. The third experiment demonstrated that the increase in intelligibility due to separation in elevation and that due to separation in azimuth were not additive. Results are discussed in terms of their implications for the design of spatial audio displays.
3D porous chitosan–alginate scaffolds promote proliferation and enrichment of cancer stem-like cells (2016)

Cancer stem cells are increasingly becoming a primary target for new cancer treatment development. The ability to study their transient behavior in vitro will provide the opportunity for high-throughput testing of more effective therapies. We have previously demonstrated the use of 3D porous chitosan-alginate (CA) scaffolds to promote cancer stem-like cell (CSC) proliferation and enrichment in glioblastoma. Here we use 3D porous CA scaffolds to promote cancer stem-like cell enrichment in cell lines from prostate, liver, and breast cancers, and investigate the proliferation, morphology, and gene expressions of cells cultured in CA scaffolds as compared to 2D controls. The 3D CA scaffold cultures for all three cancer types showed reduced proliferation, formation of tumor spheroids, and increased expression of CSC associated mark genes (CD133 and NANOG), as opposed to monolayers. Additionally, we present a putative mechanism for the cancer stem-like cell enrichment on CA scaffolds. This study demonstrates that the cancer stem-like cell enrichment in CA scaffolds is a robust process that is not restricted to particular cancer types.
The Resonating Star Gyroscope: A Novel Multiple-Shell Silicon Gyroscope With Sub-5 deg/hr Allan Deviation Bias Instability (2009)

We report on the design, fabrication and characterization of a novel multiple-shell silicon vibratory microgyroscope. The resonating star gyroscope (RSG) is formed as a merged superposition of two square shells, yielding in-plane flexural modes that are utilized to sense rotation along the normal axis. The first prototypes of the single-shell RSG were implemented with 65 mum thick trench-refilled polysilicon structural material using the HARPSS process. These devices exhibited open-loop rate sensitivity of approximately 800 muV/deg/s. Despite high-aspect ratio sensing gaps, the device yielded poor sensitivity caused by low resonant-mode quality factors. To alleviate the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TED</sub> losses caused by the inevitable formation of voids in trench-refilled structural material, the RSG was implemented in (111) single crystalline silicon. A 2.5-mm multiple-shell RSG was fabricated in 40 mum-thick SOI device layer using a simple two-mask process. Multiple-shells enable a higher operating frequency and larger resonant mass, essential components for reducing the mechanical noise floor of the sensor. Experimental data of a high-Q (111) multiple-shell prototype indicates sub-5 deg/hr Brownian noise floor, with a measured Allan deviation bias drift of 3.5 deg/hr. The gyroscope exhibits an open-loop rate sensitivity of approximately 16.7 mV/deg/s in vacuum.