gebhart/patrepeval huggingface dataset:
Privacy preserving probabilistic inference with Hidden Markov Models (2011)

Alice possesses a sample of private data from which she wishes to obtain some probabilistic inference. Bob possesses Hidden Markov Models (HMMs) for this purpose, but he wants the model parameters to remain private. This paper develops a framework that enables Alice and Bob to collaboratively compute the so-called forward algorithm for HMMs while satisfying their privacy constraints. This is achieved using a public-key additively homomorphic cryptosystem. Our framework is asymmetric in the sense that a larger computational overhead is incurred by Bob who has higher computational resources at his disposal, compared with Alice who has limited computing resources. Practical issues such as the encryption of probabilities and the effect of finite precision on the accuracy of probabilistic inference are considered. The protocol is implemented in software and used for secure keyword recognition.
289. Highly Inducible and Prostate Specific Oncolytic Adenovirus with E1A-AR Chimera (2005)

Top of pageAbstract
Previously, we demonstrated prostate-specific replication and passive cell lysis using E1A driven by a prostate-specific antigen promoter (PSA) and enhancer (PSE). However, the expression of E1A relies on promoters that utilize the androgen receptor (AR) for optimal function. Recently we have discovered that E1A and AR are mutually antagonistic in their transcriptional regulation. We demonstrate that a chimeric fusion of AR with the E1A converts an androgen receptor repressor to a co-activator. Here, we describe the features of conditionally replication-competent adenoviruses (CRADs) with E1A-AR chimeric expression in prostate cancer cells and non-prostate cancer cells.

We constructed a series of recombinant chimeric E1A-AR viruses including wild type AR (E1A-ARwt), transactivation domain (E1A-TAD), and a full-length AR with a point mutation in the ligand binding domain (E1A-ARC685Y), under the control of the prostate-specific enhancer (PSE) and rat probasin promoter (PBN). The E1A function of these viruses was evaluated in prostate cancer cells and non-prostate cancer cells using an adenovirus with Fiber-IRES-GFP lacking E1A as a reporter.

The wild type Ad5 with an E3-deletion replicates in both prostate cancer cells and non-prostate cancer cells. Replication of this virus is decreased by 50% by activated androgen receptors in the LNCaP cell line. The CRAD Ad5PSE-PBN-E1A displayed a rapidly inducible replication in prostate cancer cells in the presence of R1881, however, it had a delayed and relatively high expression in the absence of R1881. The chimeric CRADs Ad5PSE-PBN-E1A-AR and Ad5PSE-PBN-E1A-C685Y displayed marked induction of E1A in LNCaP (AR+), no induction in PC3 (AR-), and non-prostate cancer cells Hela in the presence of hormone, and no expression in any cell line in the absence of hormone. The cytopathic effect (CPE) of these chimeric viruses was also confirmed using crystal violet staining.

Our highly engineered E1A-AR chimeras not only convert a negative regulatory process into a positive regulatory process, but also greatly enhance the tissue specificity and the regulation of viral replication in the prostate. This strategy dramatically reduces toxicity in non-prostate tissue, while maintaining prostate specificity.
Total Synthesis of FR901464, an Antitumor Agent that Regulates the Transcription of Oncogenes and Tumor Suppressor Genes. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Multiple Forms of Phospholipase A2 in Arthritic Synovial Fluid (1989)

Phospholipase A2 (PLA2) has been purified to homogeneity from human arthritic synovial fluid. The activity resolved into multiple peaks by preparative HPLC. The most abundant peak (A) was present in synovial fluid from patients with rheumatoid arthritis, osteoarthritis, and psoriatic arthritis. A second major peak (B) was variable and lower in relative abundance, but was distinguishable from peak A by its stimulated activity in the presence of either 0.5 M Tris or 0.1% sodium deoxycholate (DOC), in addition to its longer HPLC column retention time. Both peaks required Ca2+ and showed optimal activity in DOC/phosphatidylcholine (PC) mixed micelle assays between pH 8.0 and 9.0. Both peaks showed higher activity with PC as substrate than with PI, however peak A exhibited higher activity with PE than PC. Upon preparative SDS-polyacrylamide gel electrophoresis, both peaks of PLA2 activity were resolved as proteins of approximately 14,000 Da. The N-terminal sequence obtained from purified peak A material matched that of a recent similar isolate (Hara et al. (1988) J. Biochem. 104, 326-328).
Video compression with tunable complexity via flexible syntax design (2007)

Codecs such as H.264/AVC involve computationally intensive tasks that often prohibit the real-time implementation. It has been observed that the complexity of such video encoders can be tuned gracefully to a desired level through the use of a smaller set of macroblock types in mode decision and a lower motion vector precision in motion estimation. The rate-distortion performance, however, will be affected consequently. In this paper, we propose a flexible syntax mechanism (FSM) to tune the encoder complexity while maintaining a sufficient rate-distortion performance. The key idea inherit in the proposed FSM consists of two folds: first is the specification at the higher level of the bitstream syntax both the subset of macroblock types and the precision of motion vectors to be evaluated by the encoder, and second is the redesign of the entropy coders accordingly to effectively represent the selected macroblock types and the motion vectors. Since the entropy coding is optimized in terms of the bitrate consumption specifically for the subset of macroblock modes and the motion vector precision, the rate-distortion performance will be enhanced compared to the scenario where identical entropy codes are adopted regardless. Another advantage of our approach is the intrinsic scalability in complexity for the application of video encoding under different complexity constraints. The proposed approach may be considered for the next generation of video codecs with flexible complexity profiles.
MREIT conductivity imaging of the postmortem canine abdomen using CoReHA (2009)

Magnetic resonance electrical impedance tomography (MREIT) is a new bio-imaging modality providing cross-sectional conductivity images from measurements of internal magnetic flux densities produced by externally injected currents. Recent experimental results of postmortem and in vivo imaging of the canine brain demonstrated its feasibility by showing conductivity images with meaningful contrast among different brain tissues. MREIT image reconstructions involve a series of data processing steps such as k-space data handling, phase unwrapping, image segmentation, meshing, modelling, finite element computation, denoising and so on. To facilitate experimental studies, we need a software tool that automates these data processing steps. In this paper, we summarize such an MREIT software package called CoReHA (conductivity reconstructor using harmonic algorithms). Performing imaging experiments of the postmortem canine abdomen, we demonstrate how CoReHA can be utilized in MREIT. The abdomen with a relatively large field of view and various organs imposes new technical challenges when it is chosen as an imaging domain. Summarizing a few improvements in the experimental MREIT technique, we report our first conductivity images of the postmortem canine abdomen. Illustrating reconstructed conductivity images, we discuss how they discern different organs including the kidney, spleen, stomach and small intestine. We elaborate, as an example, that conductivity images of the kidney show clear contrast among cortex, internal medulla, renal pelvis and urethra. We end this paper with a brief discussion on future work using different animal models.
Storage Management Operations in Linked Uniform Shift-Register Loops (1976)

A new storage structure, called a uniform ladder, consists of a linear array of equal shift-register loops, each holding one record and linked by flow-steering switches. Data exchange across a loop boundary is mandatory if the controlling switch is on and forbidden if off. For MRU (Most Recently Used) storage management, the most important operation is the climbing of data to the top of the ladder from a depth of D loops, which takes only (D + 1)/2 record periods in the uniform ladder. Program switching is enhanced by efficient schemes for partial environmental exchanges and also by internal block transfers. A pushdown stack can be efficiently implemented by a change in the record storing technique.
Disturbed Flow Increases UBE2C (Ubiquitin E2 Ligase C) via Loss of miR-483-3p, Inducing Aortic Valve Calcification by the pVHL (von Hippel-Lindau Protein) and HIF-1α (Hypoxia-Inducible Factor-1α) Pathway in Endothelial Cells (2019)

Objective- Calcific aortic valve (AV) disease, characterized by AV sclerosis and calcification, is a major cause of death in the aging population; however, there are no effective medical therapies other than valve replacement. AV calcification preferentially occurs on the fibrosa side, exposed to disturbed flow (d-flow), whereas the ventricularis side exposed to predominantly stable flow remains protected by unclear mechanisms. Here, we tested the role of novel flow-sensitive UBE2C (ubiquitin E2 ligase C) and microRNA-483-3p (miR-483) in flow-dependent AV endothelial function and AV calcification. Approach and Results- Human AV endothelial cells and fresh porcine AV leaflets were exposed to stable flow or d-flow. We found that UBE2C was upregulated by d-flow in human AV endothelial cells in the miR-483-dependent manner. UBE2C mediated OS-induced endothelial inflammation and endothelial-mesenchymal transition by increasing the HIF-1α (hypoxia-inducible factor-1α) level. UBE2C increased HIF-1α by ubiquitinating and degrading its upstream regulator pVHL (von Hippel-Lindau protein). These in vitro findings were corroborated by immunostaining studies using diseased human AV leaflets. In addition, we found that reduction of miR-483 by d-flow led to increased UBE2C expression in human AV endothelial cells. The miR-483 mimic protected against endothelial inflammation and endothelial-mesenchymal transition in human AV endothelial cells and calcification of porcine AV leaflets by downregulating UBE2C. Moreover, treatment with the HIF-1α inhibitor (PX478) significantly reduced porcine AV calcification in static and d-flow conditions. Conclusions- These results suggest that miR-483 and UBE2C and pVHL are novel flow-sensitive anti- and pro-calcific AV disease molecules, respectively, that regulate the HIF-1α pathway in AV. The miR-483 mimic and HIF-1α pathway inhibitors may serve as potential therapeutics of calcific AV disease.
Graphene-Borate as an Efficient Fire Retardant for Cellulosic Materials with Multiple and Synergetic Modes of Action (2017)

To address high fire risks of flamable cellulosic materials, that can trigger easy combustion, flame propagation, and release of toxic gases, we report a new fire-retardant approach using synergetic actions combining unique properties of reduced graphene oxide (rGO) and hydrated-sodium metaborates (SMB). The single-step treatment of cellulosic materials by a composite suspension of rGO/SMB was developed to create a barrier layer on sawdust surface providing highly effective fire retardant protection with multiple modes of action. These performances are designed considering synergy between properties of hydrated-SMB crystals working as chemical heat-sink to slow down the thermal degradation of the cellulosic particles and gas impermeable rGO layers that prevents access of oxygen and the release of toxic volatiles. The rGO outer layer also creates a thermal and physical barrier by donating carbon between the flame and unburnt wood particles. The fire-retardant performance of developed graphene-borate composite and mechanism of fire protection are demonstrated by testing of different forms of cellulosic materials such as pine sawdust, particle-board, and fiber-based structures. Results revealed their outstanding self-extinguishing behavior with significant resistance to release of toxic and flammable volatiles suggesting rGO/SMB to be suitable alternative to the conventional toxic halogenated flame-retardant materials.
Synthetic aperture ultrasonic testing apparatus with shear and longitudinal wave modes (1986)

First Page
Pericarp Fiber Separation from Corn Flour Using Sieving and Air Classification (2008)

ABSTRACT In the dry‐grind process, starch in ground corn (flour) is converted to ethanol, and the remaining corn components (protein, fat, fiber, and ash) form a coproduct called distillers dried grains with solubles (DDGS). Fiber separation from corn flour would produce fiber as an additional coproduct that could be used as combustion fuel, cattle feed, and as feedstock for producing valuable products such as “cellulosic” ethanol, corn fiber gum, oligosaccharides, phytosterols, and polyols. Fiber is not fermented in the dry‐grind corn process. Its separation before fermentation would increase ethanol productivity in the fermenter. Recently, we showed that the elusieve process, a combination of sieving and elutriation (air flow), was effective in fiber separation from DDGS. In this study, we evaluated the elusieve process for separating pericarp fiber from corn flour. Corn flour remaining after fiber separation was termed “enhanced corn flour”. Of the total weight of corn flour, 3.8% was obtained as fiber and 96.2% was obtained as enhanced corn flour. Neutral detergent fiber (NDF) of corn flour, fiber, and enhanced corn flour (dry basis) were 9.0, 61.5, and 5.7%, respectively. Starch content of corn flour, fiber, and enhanced corn flour (dry basis) were 68.8, 23.5, and 71.3%, respectively. Final ethanol concentration from enhanced corn flour (14.12% v/v) was marginally higher than corn flour (13.72% v/v). No difference in ethanol yields from corn flour and enhanced corn flour was observed. The combination of sieving and air classification can be used to separate pericarp fiber from corn flour. The economics of fiber separation from corn flour using the elusieve process would be governed by the production of valuable products from fiber and the revenues generated from the valuable products.
Capacitively-driven and piezoresistively-sensed CMOS-MEMS resonators (2012)

A foundry-oriented capacitively-driven CMOS-MEMS resonator using differentially piezoresistive sensing has been demonstrated for the first time to enable feedthrough cancellation with more than 20 dB noise floor reduction as compared to purely capacitive transduction. The resonators are formed by high-Q SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> structure (Q >; 5,500) using metal wet etching and XeF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> release processes while polysilicon (originally CMOS gate poly) embedded inside the resonator structure serves as piezoresistive element for vibratory detection. In addition, such composite structure enabling electrical isolation accomplishes decoupling of capacitive and piezoresistive transductions, allowing the selection (or switching) of the preferred transduction scheme using the same resonator device. The resonators with capacitive drive and differentially piezoresistive sense configuration have been demonstrated with Q >; 4,000 and more than 28 dB signal-to-feedthrough ratio. CMOS-MEMS oxide resonators with differentially piezoresistive sensing provide an excellent alternative to purely capacitive transduction for integrated oscillator applications.
Corrosion detection in welds and heat-affected zones using ultrasonic Lamb waves (2006)

Measurements are reported on the amplitude of ultrasonic Lamb waves reflected from a single 20 mm-diameter flat-bottomed hole located adjacent to the weld of a 6 mm-thick butt welded steel plate. The hole was introduced to simulate the presence of corrosion defects in the heat-affected zone, and served to assess the suitability of using the fundamental So Lamb waves as a means for remote detection of corrosion in fluid-filled storage tanks. Measurements were made using a prototype, omnidirectional multi-element transducer developed at Imperial College, and also using a single edge-mounted transducer. Detection of a hole was only possible when using the plate tester at oblique incidence angles, because of the inability to discriminate weld echoes from those due to the hole at normal or near-normal incidence. Detection of holes was also limited to those with a minimum depth of approximately 3 mm by the presence of coherent background noise. Measurements using a single edge-mounted transducer demonstrated that preferential waveguide propagation of the So mode occurred along the weld, in a manner coined 'weld-guided waves'. This permitted easy detection of a 2 mm deep-hole located adjacent to the weld at a distance of 1 m from the transducer. It is likely that a practical surface-mounted transducer based on the S 0 waveguide mode of operation could be developed for the inspection of corrosion defects within the heat-affected zone of fluid-filled tanks. It is probable that such a device would have a range of many metres, be simple in construction, and that the method would be relatively unaffected by the presence of fluid and inherently sensitive because of the suppression of other propagation modes.
A tactile enhancement instrument for minimally invasive surgery (2005)

We developed a surgical probe with tactile and auditory feedbacks. Despite the moderate system gain achievable with the initial prototype, the system could measurably improve users' ability to detect small cuts in cartilage-like elastic surfaces.
Characterization of Hepatitis C Virus Recombinants with Chimeric E1/E2 Envelope Proteins and Identification of Single Amino Acids in the E2 Stem Region Important for Entry (2012)

The hepatitis C virus (HCV) envelope proteins E1 and E2 play a key role in host cell entry and represent important targets for vaccine and drug development. Here, we characterized HCV recombinants with chimeric E1/E2 complexes in vitro. Using genotype 1a/2a JFH1-based recombinants expressing 1a core-NS2, we exchanged E2 with functional isolate sequences of genotypes 1a (alternative isolate), 1b, and 2a. While the 1a-E2 exchange did not impact virus viability, the 2a-E2 recombinant was nonviable. After E2 exchange from three 1b isolates, long delays were observed before spread of infection. For recovered 1b-E2 recombinants, single E2 stem region amino acid changes were identified at residues 706, 707, and 710. In reverse genetic studies, these mutations increased infectivity titers by ~100-fold, apparently without influencing particle stability or cell binding although introducing slight decrease in particle density. In addition, the 1b-E2 exchange led to a decrease in secreted core protein of 25 to 50%, which was further reduced by the E2 stem region mutations. These findings indicated that compensatory mutations permitted robust infectious virus production, without increasing assembly/release. Studies of E1/E2 heterodimerization showed no differences in intracellular E1/E2 interaction for chimeric constructs with or without E2 stem region mutations. Interestingly, the E2 stem region mutations allowed efficient entry, which was verified in 1a-E1/1b-E2 HCV pseudoparticle assays. A CD81 inhibition assay indicated that the mutations influenced a late step of the HCV entry pathway. Overall, this study identified specific amino acids in the E2 stem region of importance for HCV entry and for production of infectious virus particles.
Fabrication of a monolithically integrated multiple wavelength Fabry-Perot filter array using transparent etch stop layers for accurate wavelength determination (2006)

In this paper we describe a method of fabricating a Fabry-Perot filter array consisting of four distinct wavelengths using a stopping layer, which in turn is discriminately measured. Precise control of the oxide thickness is demonstrated by using reflectance to measure center wavelengths (CWL) between 645nm-822nm with full width half maximum (FWHM) values of 15 nm. These parameters are used to confirm good narrow band filter characteristics. The physical and chemical properties of an oxide layer converted from a silicon-carbon-nitride (SiCN) etch stop layer (ESL) is reported for both as-deposited and the resultant oxidized film. The filter array can be fabricated directly on top of silicon photo diodes, to form a complete multi-wavelength sensor system. Fabricating a multi-wavelength filter array using etch-stop layers can provide better thickness control and across wafer uniformity compared to a timed-etch approach.
Grafted MXene/polymer electrolyte for high performance solid zinc batteries with enhanced shelf life at low/high temperatures (2021)

Solid electrolytes based on the polymer-grafted MXene eliminate the dendrites and hydrogen evolution of ZIBs, and endow the ZIBs with up to 90 days of shelf life.
Cold Sintering Process of Composites: Bridging the Processing Temperature Gap of Ceramic and Polymer Materials (2016)

Co‐sintering ceramic and thermoplastic polymer composites in a single step with very high volume fractions of ceramics seems unlikely, given the vast differences in the typical sintering temperatures of ceramics versus polymers. These processing limitations are overcome with the introduction of a new sintering approach, namely “cold sintering process” (CSP). CSP utilizes a transient low temperature solvent, such as water or water with dissolved solutes in stoichiometric ratios consistent with the ceramic composition, to control the dissolution and precipitation of ceramics and effect densification between room temperature and ≈200 °C. Under these conditions, thermoplastic polymers and ceramic materials can be jointly formed into dense composites. Three diphasic composite examples are demonstrated to show the overall diversity of composite material design between organic and inorganic oxides, including the microwave dielectric Li 2 MoO 4 –(C 2 F 4 ) n , electrolyte Li 1.5 Al 0.5 Ge 1.5 (PO 4 ) 3 –(CH 2 CF 2 ) x [CF 2 CF(CF 3 )] y , and semiconductor V 2 O 5 –poly(3,4‐ethylenedioxythiophene) polystyrene sulfonate composites. Cold sintering is more general and shall have a major impact on the processing of composite materials for many different applications, mechanical, thermal, and electronic, to mention a few possibilities. CSP concepts open up new composite material design and device integration schemes, impacting a wide variety of applications.
Potato Patatin Generates Short-Chain Fatty Acids from Milk Fat that Contribute to Flavour Development in Cheese Ripening (2015)

The potato lipase, patatin, has long been thought of as essentially inactive towards triacylglycerols. Recently, technology has been developed to isolate potato proteins in native form as food ingredients at industrial scale. Characterisation of native patatin obtained in this way revealed that this enzyme activity towards triacylglycerols has been underestimated. This enables the application of patatin in cheese ripening, which is described in this study. When patatin is added to milk during cheese making, the lipase preferentially releases short-chain fatty acids that contribute to cheese flavour in a dose-dependent manner. Fortuitously, the lipase activity is found mainly in the curd. The release of the short-chain fatty acids matches the activity profile of patatin towards homotriacylglycerols of defined chain length. Residual patatin in the whey fraction can be inactivated effectively by heat treatment that follows Arrhenius kinetics. The results are discussed in terms of cheese making, patatin substrate preference and implications for the use of patatin more generally in food emulsions.