gebhart/patrepeval huggingface dataset:
Efficient Transduction of Primary Vascular Cells by the Rare Adenovirus Serotype 49 Vector (2015)

Neointima formation and vascular remodeling through vascular smooth muscle cell migration and proliferation can limit the long-term success of coronary interventions, for example, in coronary artery bypass grafting (CABG). Ex vivo gene therapy has the potential to reduce unnecessary cell proliferation and limit neointima formation in vascular pathologies. To date, the species C adenovirus serotype 5 has been commonly used for preclinical gene therapy; however, its suitability is potentially limited by relatively poor tropism for vascular cells and high levels of preexisting immunity in the population. To avoid these limitations, novel species of adenovirus are being tested; here we investigate the potential of adenovirus 49 (Ad49) for use in gene therapy. Transduction of primary human vascular cells by a range of adenovirus serotypes was assessed; Ad49 demonstrated highest transduction of both vascular smooth muscle and endothelial cells. Gene transfer with Ad49 in vascular smooth muscle and endothelial cells was possible following short exposure times (<1 hr) and with low MOI, which is clinically relevant. Ex vivo delivery to surplus CABG tissue showed efficient gene transfer with Ad49, consistent with the in vitro findings. Luminal infusion of Ad49GFP into intact CABG samples ex vivo resulted in efficient vessel transduction. In addition, no seroprevalence rates to Ad49 were observed in a Scottish cohort of patients from cardiovascular clinics, thus circumventing issues with preexisting immunity. Our results show that Ad49 has tropism for vascular cells in vitro and ex vivo and demonstrate that Ad49 may be an improved vector for local vascular gene therapy compared with current alternatives.
Determination of alcohol- and sugar concentration in aqueous solutions using reflection terahertz time-domain spectroscopy (2007)

We use self-referencing reflection THz spectroscopy to measure the alcohol- and sugar concentration with high precision in small volumes of aqueous solutions, independent of carbonation and the contents of yeast or other small organic particles.
Transcribing piano music in the time domain (2016)

Automatic music transcription is the process of automatically inferring a high-level symbolic representation, such as music notation or piano-roll, from a music performance. It has many applications in music education, content-based music search, musicological analysis of non-notated music, and music enjoyment. Existing approaches often perform in the frequency domain, where the fundamental time-frequency resolution tradeoff prevents them from obtaining satisfactory transcription accuracies. In this project, we develop a novel approach in the time domain for piano transcription using convolutional sparse coding. It models the music waveform as a summation of piano note waveforms (dictionary elements) convolved with their temporal activations (onsets). The piano note waveforms are pre-recorded in a context-dependent way, i.e., for the specific piano to be transcribed in the specific environment. During transcription, the note waveforms are fixed, and their temporal activations are estimated and post-processed to obtain the pitch and onset transcription. This approach models temporal evolution of piano notes, and estimates pitches and onsets simultaneously in the same framework. Experiments show that it significantly outperforms a state-of-the-art frequency-domain music transcription method trained in the same context-dependent setting, in both transcription accuracy and time precision, in various scenarios including synthetic, anechoic, noisy, and reverberant environments.
Development of Hybrid Energy-Absorbing Reusable Terminal for Roadside Safety Applications (2005)

The hybrid energy-absorbing reusable terminal (HEART) is a newly developed crash cushion or end terminal to be used in highway safety applications to mitigate injuries to occupants of errant vehicles. HEART is composed of corrugated plates of high–molecular weight, high-density polyethylene (HMW-HDPE) supported on steel diaphragms that slide on a fixed rail. Kinetic energy from errant vehicles is converted to other energy forms through folding and deformation of the HMW-HDPE material. Many previous designs utilized plastic or permanent deformation of plastics or steels to accomplish this goal. However, HEART is a combination of plastic and steel that forms a largely self-restoring and largely reusable crash cushion. Consequently, HEART has a major life-cycle cost advantage over conventional crash cushion designs. HEART was developed through extensive use of finite element analysis with LS-DYNA. The simulation approach adopted for the development of HEART, construction details, and a description and results of crash tests performed so far to evaluate its performance are presented. Also discussed is some of the follow-up work currently under way for approval of HEART by FHWA as an acceptable crash cushion for use on the National Highway System.
Improvement of NADPH bioavailability in <i>Escherichia coli</i> by replacing NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase GapA with NADP+-dependent GapB from <i>Bacillus subtilis</i> and addition of NAD kinase (2013)

Enzymatic synthesis of some industrially important compounds depends heavily on cofactor NADPH as the reducing agent. This is especially true in the synthesis of chiral compounds that are often used as pharmaceutical intermediates to generate the correct stereochemistry in bioactive products. The high cost and technical difficulty of cofactor regeneration often pose a challenge for such biocatalytic reactions. In this study, to increase NADPH bioavailability, the native NAD(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gapA gene in Escherichia coli was replaced with a NADP(+)-dependent gapB from Bacillus subtilis. To overcome the limitation of NADP(+) availability, E. coli NAD kinase, nadK was also coexpressed with gapB. The recombinant strains were then tested in three reporting systems: biosynthesis of lycopene, oxidation of cyclohexanone with cyclohexanone monooxygenase (CHMO), and an anaerobic system utilizing 2-haloacrylate reductase (CAA43). In all the reporting systems, replacing NAD(+)-dependent GapA activity with NADP(+)-dependent GapB activity increased the synthesis of NADPH-dependent compounds. The increase was more pronounced when NAD kinase was also overexpressed in the case of the one-step reaction catalyzed by CAA43 which approximately doubled the product yield. These results validate this novel approach to improve NADPH bioavailability in E. coli and suggest that the strategy can be applied in E. coli or other bacterium-based production of NADPH-dependent compounds.
Variable Cadence Walking and Ground Adaptive Standing With a Powered Ankle Prosthesis (2015)

This paper describes a control approach that provides walking and standing functionality for a powered ankle prosthesis, and demonstrates the efficacy of the approach in experiments with a unilateral transtibial amputee subject. Both controllers incorporate a finite-state structure that emulates healthy ankle joint behavior via a series of piecewise passive impedance functions. The walking controller additionally modifies impedance parameters based on estimated cadence, while the standing controller modulates the ankle equilibrium angle in order to adapt to the ground slope and user posture, and the supervisory controller selects between the walking and standing controllers. The system is shown to reproduce several essential biomechanical features of the healthy joint during walking, particularly relative to a passive prosthesis, and is shown to adapt to various cadences. The system is also shown to adapt to slopes over a range of ±15°, providing support to the user, as validated by quasi-static stiffness measurements recorded by the prosthesis. The subject is shown to place more weight on the powered prosthesis than on his passive prosthesis when standing on sloped surfaces, particularly at angles of 10° or greater. The authors also demonstrated that the prosthesis typically began providing support within 1 s of initial ground contact. Further, the supervisory controller was shown to effectively switch between walking and standing, as well as determine ground slope just prior to the transition from the standing controller to the walking controller, where the estimated ground slope was accurate to within 1.25° for all trials.
Molecular coevolution of coagulation factor VIII and von Willebrand factor (2021)

Ancestral sequence reconstruction provides a unique platform for investigating the molecular evolution of single gene products and recently has shown success in engineering advanced biological therapeutics. To date, the coevolution of proteins within complexes and protein-protein interactions is mostly investigated in silico via proteomics and/or within single-celled systems. Herein, ancestral sequence reconstruction is used to investigate the molecular evolution of 2 proteins linked not only by stabilizing association in circulation but also by their independent roles within the primary and secondary hemostatic systems of mammals. Using sequence analysis and biochemical characterization of recombinant ancestral von Willebrand factor (VWF) and coagulation factor VIII (FVIII), we investigated the evolution of the essential macromolecular FVIII/VWF complex. Our data support the hypothesis that these coagulation proteins coevolved throughout mammalian diversification, maintaining strong binding affinities while modulating independent and distinct hemostatic activities in diverse lineages.
Feasibility of Factory Calibration for Subcutaneous Glucose Sensors in Subjects With Diabetes (2014)

Feasibility of factory calibration was demonstrated in subjects with diabetes using sensors based on "wired enzyme" technology, resulting in accuracy metrics similar to sensors calibrated with capillary blood glucose.
Model-Free Machine Learning in Biomedicine: Feasibility Study in Type 1 Diabetes (2016)

Although reinforcement learning (RL) is suitable for highly uncertain systems, the applicability of this class of algorithms to medical treatment may be limited by the patient variability which dictates individualised tuning for their usually multiple algorithmic parameters. This study explores the feasibility of RL in the framework of artificial pancreas development for type 1 diabetes (T1D). In this approach, an Actor-Critic (AC) learning algorithm is designed and developed for the optimisation of insulin infusion for personalised glucose regulation. AC optimises the daily basal insulin rate and insulin:carbohydrate ratio for each patient, on the basis of his/her measured glucose profile. Automatic, personalised tuning of AC is based on the estimation of information transfer (IT) from insulin to glucose signals. Insulin-to-glucose IT is linked to patient-specific characteristics related to total daily insulin needs and insulin sensitivity (SI). The AC algorithm is evaluated using an FDA-accepted T1D simulator on a large patient database under a complex meal protocol, meal uncertainty and diurnal SI variation. The results showed that 95.66% of time was spent in normoglycaemia in the presence of meal uncertainty and 93.02% when meal uncertainty and SI variation were simultaneously considered. The time spent in hypoglycaemia was 0.27% in both cases. The novel tuning method reduced the risk of severe hypoglycaemia, especially in patients with low SI.
A broad-band vibrational energy harvester utilizing symmetrical comb-drives coupled with strong charged electret (2017)

We have developed a broad-band vibrational energy harvester by utilizing symmetrical comb-drive electrodes that were coated with solid-ion electrets made of potassium-doped thermal silicon oxide film. The device was sealed in a vacuum package for high energy conversion to eliminate mechanical losses. With this device, we capture vibrations of any frequency as well as of impulse motions for power generation.
Burkholderia pseudomallei OMVs derived from infection mimicking conditions elicit similar protection to a live-attenuated vaccine (2021)

Burkholderia pseudomallei is a Gram-negative, facultative intracellular bacillus that causes the disease melioidosis. B. pseudomallei expresses a number of proteins that contribute to its intracellular survival in the mammalian host. We previously demonstrated that immunization with OMVs derived from B. pseudomallei grown in nutrient-rich media protects mice against lethal disease. Here, we evaluated if OMVs derived from B. pseudomallei grown under macrophage-mimicking growth conditions could be enriched with intracellular-stage proteins in order to improve the vaccine. We show that OMVs produced in this manner (M9 OMVs) contain proteins associated with intracellular survival yet are non-toxic to living cells. Immunization of mice provides significant protection against pulmonary infection similar to that achieved with a live attenuated vaccine and is associated with increased IgG, CD4<sup>+</sup>, and CD8<sup>+</sup> T cells. OMVs possess inherent adjuvanticity and drive DC activation and maturation. These results indicate that M9 OMVs constitute a new promising vaccine against melioidosis.
Crystal Growth and Spectroscopic Characterization of Tm-Doped Oxyapatites and Orthosilicates (1993)

The interest in diode pumped solid state lasers in the 2 μm region in recent years has been well documented. The need for compact, highly efficient sources has led to the study of new laser hosts which may improve performance. We have grown and analyzed the spectroscopic properties of two Tm3+-doped silicate oxyapatite hosts and one orthosilicate. These hosts are CaY4(SiO4)3O [CaYSOAP], CaLa4(SiO4)3O [CaLaSOAP], and Y2SiO5 [YSO or YOS]. The spectroscopic properties of these new hosts are compared with those of Tm3+:YAG, and indicate that these hosts may offer improvements to Tm3+:YAG in increasing tunability in the 2 μm region and in improving laser performance for the 2.3 μm transition. Preliminary laser results of a Tm:CaYSOAP laser are also presented.
Fast multiple reference frame motion estimation for H.264 (2005)

Multiple reference frame motion compensation is a new feature introduced in H.264/MPEG-4 AVC to improve video coding performance. However, the computational cost of multiple reference frame motion estimation (MRF-ME) is very high. We propose an algorithm that takes into account the correlation/continuity of motion vectors among different reference frames. We also show that the algorithm effectively reduces the computations of MRF-ME, and achieves similar coding gain compared to the full-search approach.
Wettability Engendered Templated Self-assembly (WETS) for Fabricating Multiphasic Particles (2015)

Precise control over the geometry and chemistry of multiphasic particles is of significant importance for a wide range of applications. In this work, we have developed one of the simplest methodologies for fabricating monodisperse, multiphasic micro- and nanoparticles possessing almost any composition, projected shape, modulus, and dimensions as small as 25 nm. The synthesis methodology involves the fabrication of a nonwettable surface patterned with monodisperse, wettable domains of different sizes and shapes. When such patterned templates are dip-coated with polymer solutions or particle dispersions, the liquids, and consequently the polymer or the particles, preferentially self-assemble within the wettable domains. Utilizing this phenomenon, we fabricate multiphasic assemblies with precisely controlled geometry and composition through multiple, layered depositions of polymers and/or particles within the patterned domains. Upon releasing these multiphasic assemblies from the template using a sacrificial layer, we obtain multiphasic particles. The templates can then be readily reused (over 20 times in our experiments) for fabricating a new batch of particles, enabling a rapid, inexpensive, and easily reproducible method for large-scale manufacturing of multiphasic particles.
Recovering device drivers (2004)

This article presents a new mechanism that enables applications to run correctly when device drivers fail. Because device drivers are the principal failing component in most systems, reducing driver-induced failures greatly improves overall reliability. Earlier work has shown that an operating system can survive driver failures [Swift et al. 2005], but the applications that depend on them cannot. Thus, while operating system reliability was greatly improved, application reliability generally was not. To remedy this situation, we introduce a new operating system mechanism called a shadow driver. A shadow driver monitors device drivers and transparently recovers from driver failures. Moreover, it assumes the role of the failed driver during recovery. In this way, applications using the failed driver, as well as the kernel itself, continue to function as expected. We implemented shadow drivers for the Linux operating system and tested them on over a dozen device drivers. Our results show that applications and the OS can indeed survive the failure of a variety of device drivers. Moreover, shadow drivers impose minimal performance overhead. Lastly, they can be introduced with only modest changes to the OS kernel and with no changes at all to existing device drivers.
Miniature cryosorption vacuum pump for portable instruments (1994)

This article describes the design, construction, and laboratory testing of a low power, low-weight, and compact cryosorption vacuum pump for backing, roughing, or other intermediate pressure applications. Novel features of this pump include a high-temperature, low-pressure desorption cycle allowing useful pumping capacities of many gases at 77 K, and the use of a miniature cryorefrigerator. The laboratory test pump used a cold finger cooled by a single stage helium Stirling cycle refrigerator having a 1 W capacity at 70 K, weighing between 1.6 and 2.0 kg, and consuming less than 45 W of electrical power. Calculations show that pumping rates for N2 at 1×10−4 Torr could be up to 10 Torr ℓ s−1 short-term, and approximately 0.5 Torr ℓ s−1 continuously. Our laboratory working model showed that it was possible to pump at pressures down to approximately 2×10−5 Torr using a type 5A molecular sieve. Pumping rates for air of up to 5 Torr ℓ min−1 were achieved. Using desorption at 363 K and 2×10−1 Torr, the capacity of type 5A molecular sieve was determined to be approximately 16 Torr ℓ g−1 at 1×10−4 Torr. It is anticipated that such a pump would be useful in certain portable instruments such as portable gas chromatograph-mass spectrometers used for occupational health applications, or other applications where weight, available power, and pumping requirements were compatible.
Reversible photoresponsive hydrogels based on spiropyran (2014)

The possibility of using photo-stimulus to control actuation is very appealing as light can provide contactless stimulation, is biocompatible and can be applied in a non-invasive and highly precise manner. Photo-responsive hydrogels are highly favoured for making light-stimulated polymer actuators as they have the ability to undergo significant volumetric changes in response to an external light stimulus.[1] Hydrogels possess biocompatibility and a degree of flexibility, very similar to natural tissue, due to their significant water content. Photo-responsive engineered hydrogels can be made to collapse and thereby release a percentage of their water content upon light irradiation.\nThe most widely used photo-sensitive molecules for photo-actuation of hydrogels are spiropyrans as they allow for reversible conformational, hydrophobicity/hydrophilicity and polarity changes upon irradiation with light of particular wavelengths.[2] Taking advantage of this photo-induced change of hydrophilic/hydrophobic character, photoresponsive gels based on N-isopropylacrylamide and spiropyran have been realised.[1,3]\nIn this work, a new generation of photoresponsive hydrogels are proposed, based on N-isopropylacrylamide copolymerised with pendant spiropyran groups and acrylic acid. These hydrogels actuate on the following principle: When the hydrogel is immersed in water, the copolymerised acrylic acid dissociates and the proton is taken by the spiropyran unit present in the copolymer causing it to change from spiropyran (SP) to the protonated merocyanine (MCH+) form. When the copolymer is irradiated with light matching the absorbance of MCH+, the MCH+ switches back to the closed hydrophobic SP form, releasing a proton in the process; As result of the formation of the more hydrophobic SP isomer, dehydration of the main polymer chain occurs and the hydrogel shrinks. When the light source is removed, the SP is spontaneously reprotonated and the hydrogel reswells.\nDue to the relative pKa values of acrylic acid, and of the spiropyran and merocyanine isomers, the protonation and deprotonation processes occur internally within the gel and there is no need for an external source of protons. In contrast to previous formulations, these gels do not show degradation of their photo-induced shrinking ability after multiple washings in deionised water and repeated switching over a two month period. Moreover, improved reswelling performance of these hydrogels has been realised by inducing porosity through the use of poly(ethylene glycol) as a pore forming agent. In this way, significantly faster kinetics for the hydrogel shrinking and re-swelling processes have been obtained compared to conventional hydrogels.\n1. Sugiura, S. et al., Sens. Act. A 2007, 140, 176. 2. Florea, L.; Diamond, D.; Benito-Lopez, F. Macromol. Mater. Eng. 2012, 297, 1148. 3. Ziolkowski, B.; Florea, L.; Theobald, J.; Benito-Lopez, F.; Diamond, D. Soft Matter 2013, 9, 8754.
Novel immunoassay for the measurement of complexed prostate-specific antigen in serum. (1998)

Serum prostate-specific antigen (PSA) is an effective diagnostic tool for detection of prostate cancer (CaP) at an early and potentially curable stage, but specificity is low. Studies have shown that the proportion of serum PSA complexed with alpha-1-antichymotrypsin (ACT) is higher in men with CaP than in men with benign prostate disease. We developed a novel immunoassay for complexed PSA based on the unique binding properties of a monoclonal antibody that fails to bind free PSA in the presence of antibodies specific for free PSA. The assay measured mixtures of free and complexed PSA accurately, and the measured values of free + complexed PSA in artificial mixtures and in patient sera were equivalent to the measured value of total PSA. Both the serum concentration and the proportion of complexed PSA was substantially higher in patients with CaP compared with patients with benign prostate disease. The cPSA assay may have utility in improving specificity in screening for prostate cancer.
Optimum Pilot Symbol Assisted Modulation (2007)

Optimum detectors for pilot symbol assisted modulation (PSAM) signals in Rayleigh and Rician fading channels are derived. Conventional PSAM as used on Rayleigh fading channels is also employed on Rician fading channels. It is shown that the conventional PSAM receiver is optimal for binary phase shift keying in Rayleigh fading but suboptimal for Rician fading and suboptimal for 16-ary quadrature amplitude modulation in Rayleigh fading. The optimum PSAM signal detector uses knowledge of the specular component and also jointly processes the pilot symbols and the data symbol. The performance of the optimum detector is analyzed and compared with that of the conventional detector. It is concluded that substantial gains can be achieved by exploiting knowledge of the specular component while joint processing of the data symbol with the pilot symbols may offer small benefits.