gebhart/patrepeval huggingface dataset:
Integration of Probability Based Ridge Variation Information with Local Ridge Orientation for Fingerprint Liveness Detection (2022)

Fingerprints are commonly used in biometric systems. However, the authentication of these systems became an open challenge because fingerprints can easily be fabricated. In this paper, a hybrid feature extraction approach named Integration of Probability Weighted Spatial Gradient with Ridge Orientation (IPWSGRo) has been proposed for fingerprint liveness detection. IPWSGRo integrates intensity variation and local ridge orientation information. Intensity variation is computed by using probability-weighted moments (PWM) and second order directional derivative filter. Moreover, the ridge orientation is estimated using rotation invariant Local Phase Quantization (LPQri) by retaining only the significant frequency components. These two feature vectors are quantized into predefined intervals to plot a 2-D histogram. The support vector machine classifier (SVM) is then used to determine the validity of fingerprints as either live or spoof. Results are obtained by applying the proposed technique on three standard databases of LivDet competition 2011, 2013, and 2015. Experimental results indicate that the proposed method is able to reduce the average classification error rates (ACER) to 5.7, 2.1, and 5.17% on LivDet2011, 2013, and 2015, respectively.
Inoculation of Swine with Foot-and-Mouth Disease SAP-Mutant Virus Induces Early Protection against Disease (2011)

Foot-and-mouth disease virus (FMDV) leader proteinase (L(pro)) cleaves itself from the viral polyprotein and cleaves the translation initiation factor eIF4G. As a result, host cell translation is inhibited, affecting the host innate immune response. We have demonstrated that L(pro) is also associated with degradation of nuclear factor κB (NF-κB), a process that requires L(pro) nuclear localization. Additionally, we reported that disruption of a conserved protein domain within the L(pro) coding sequence, SAP mutation, prevented L(pro) nuclear retention and degradation of NF-κB, resulting in in vitro attenuation. Here we report that inoculation of swine with this SAP-mutant virus does not cause clinical signs of disease, viremia, or virus shedding even when inoculated at doses 100-fold higher than those required to cause disease with wild-type (WT) virus. Remarkably, SAP-mutant virus-inoculated animals developed a strong neutralizing antibody response and were completely protected against challenge with WT FMDV as early as 2 days postinoculation and for at least 21 days postinoculation. Early protection correlated with a distinct pattern in the serum levels of proinflammatory cytokines in comparison to the levels detected in animals inoculated with WT FMDV that developed disease. In addition, animals inoculated with the FMDV SAP mutant displayed a memory T cell response that resembled infection with WT virus. Our results suggest that L(pro) plays a pivotal role in modulating several pathways of the immune response. Furthermore, manipulation of the L(pro) coding region may serve as a viable strategy to derive live attenuated strains with potential for development as effective vaccines against foot-and-mouth disease.
The development and use of real-time PCR for the quantification of nitrifiers in activated sludge (2002)

Chemical analytical data has long been used to monitor the performance of activated sludge plants even though the process relies on the performance of microorganisms. It is now evident that a rapid and reliable quantitative method is required, to be able to monitor the organisms responsible for nutrient transformation and their activities, allowing avenues for more efficient nutrient removal. The development of real-time or quantitative polymerase chain reaction (PCR) also known as TaqMan or 5'-nuclease assay has allowed the rapid, quantitative analysis of DNA templates, eliminating some of the variability traditionally associated with other quantitative techniques. In this study analysis of Nitrospira spp., one of the key organisms in nitrite oxidation in wastewater treatment, was used to validate real-time PCR for the their quantification in activated sludge. A probe and primer set, targeting the 16S rRNA gene of Nitrospira spp. was designed according to the constraints of the TaqMan specifications. Samples used to evaluate the method included DNA from the sludge from full-scale wastewater treatment plants and laboratory scale systems. The reproducibility, quantitative efficiency and specificity were assessed in the evaluation. It was concluded that the method is sensitive and reproducible but has some constraints on the quantitative efficiency. A survey of full-scale systems for Nitrospira spp. was carried out and the results are presented here.
Iterative equalization and decoding techniques for shallow water acoustic channels (2002)

We investigate the application of iterative equalization and decoding techniques to the shallow water acoustic channel. The first receiver is a joint decision feedback equalizer (DFE) and turbo decoder. The second receiver is a turbo equalizer, which jointly estimates the channel, performs MAP equalization, and decodes received symbols. Although the MAP equalizer is optimum for a known channel, channel estimation errors degrade the performance of the turbo equalizer. We compared the performance of both receivers under real channel conditions.
Displacement sensing using evanescent tunneling between guided resonances in photonic crystal slabs (2005)

Using both analytic theory and first-principles finite-difference time-domain simulations, we introduce a displacement sensing mechanism using photonic crystal slabs coupled in the near-field regime. In this regime, the operating characteristics are completely different from conventional resonant optical sensors, and high sensitivity can be obtained without the use of highly reflecting mirrors. This enables high displacement sensitivity combined with low sensitivity to wavelength and to structural disorders, thereby simplifying operation and fabrication of high-sensitivity displacement sensors.
Monoclonal antibodies which identify a genus-specific Listeria antigen (1988)

Fifteen murine monoclonal antibodies (MAbs) which react specifically with a protein antigen found in all species of Listeria were developed and characterized. These MAbs were tested extensively by both enzyme-linked immunosorbent assay and Western blot (immunoblot) analyses for cross-reaction with non-Listeria organisms, such as Staphylococcus, Streptococcus, Citrobacter, Pseudomonas, and Salmonella species, and were found to be nonreactive. The genus-specific antigen was identified as a heat-stable protein with a molecular weight in the range of 30,000 to 38,000 (under both reducing and nonreducing conditions), depending on the species of Listeria tested. In Listeria monocytogenes, L. innocua, L. ivanovii, and L. seeligeri the antigen has a molecular weight of approximately 30,000 to 34,000. In L. grayi and L. murrayi it has a molecular weight of approximately 35,000 to 38,000. In addition, several of the MAbs recognize lower-molecular-weight protein bands. There appear to be at least two groups of Listeria-specific MAbs based upon isotype and results of enzyme-linked immunosorbent assay and Western blot analyses. These MAbs have proven to be useful in the development of a diagnostic assay for Listeria species in food products.
Capsid-specific removal of circulating antibodies to adeno-associated virus vectors (2020)

Neutralizing antibodies directed against adeno-associated virus (AAV) are commonly found in humans. In seropositive subjects, vector administration is not feasible as antibodies neutralize AAV vectors even at low titers. Consequently, a relatively large proportion of humans is excluded from enrollment in clinical trials and, similarly, vector redosing is not feasible because of development of high-titer antibodies following AAV vector administration. Plasmapheresis has been proposed as strategy to remove anti-AAV antibodies from the bloodstream. Although safe and relatively effective, the technology has some limitations mainly related to the nonspecific removal of all circulating IgG. Here we developed an AAV-specific plasmapheresis column which was shown to efficiently and selectively deplete anti-AAV antibodies without depleting the total immunoglobulin pool from plasma. We showed the nearly complete removal of anti-AAV antibodies from high titer purified human IgG pools and plasma samples, decreasing titers to levels that allow AAV vector administration in mice. These results provide proof-of-concept of a method for the AAV-specific depletion of neutralizing antibodies in the setting of in vivo gene transfer.
On the Use of Acid-Base-Supported Catalysts for Hydroprocessing of Heavy Petroleum (2007)

The environmental regulation pressure is being increased to reduce precursors of pollution contaminants (sulfur, nitrogen, and aromatics) in fuels to lower levels. There are various processes to upgrade heavy and extra-heavy crude oils, such as solvent deasphalting, thermal conversion, catalytic conversion, distillation, and hydroprocessing. Hydroprocessing not only upgrades the crude oil but also produces synthetic crude oil that has a lower impurities content and a higher liquid yield of products. The fuels upgrading currently is achieved in refinery hydroprocessing units using different new-generation catalysts, along with several modifications of process conditions such as multistage reactors, type of catalyst loading, and reactor internals. However, it has been widely recognized that, for deep removal of these contaminants by hydroprocessing, research must be more oriented to the catalyst developments, rather than the process conditions. Actual commercial catalysts are based on well-known and studied active metals (CoMo, NiMo) and support (Al2O3). In addition, extensive research work has been performed with other supports (Al2O3−TiO2, Al2O3−ZrO2, etc.). Nevertheless, other promising acidic materials, such as zeolites, have received relatively less attention, and experimental reports on their use as part of the heavy oil hydroprocessing catalyst support are scarce in the literature. The objective of this contribution is then to discuss the use of acidic and/or basic materials as a support for the hydroprocessing catalyst, specifically for their possible application for the hydroprocessing of heavy oils, in cases where the desired product selectivity is toward gasoline and middle distillates.
Buildings-to-Grid Integration Framework (2018)

This paper puts forth a mathematical framework for Buildings-to-Grid (BtG) integration in smart cities. The framework explicitly couples power grid and building's control actions and operational decisions, and can be utilized by buildings and power grids operators to simultaneously optimize their performance. Simplified dynamics of building clusters and building-integrated power networks with algebraic equations are presented---both operating at different time-scales. A model predictive control (MPC)-based algorithm that formulates the BtG integration and accounts for the time-scale discrepancy is developed. The formulation captures dynamic and algebraic power flow constraints of power networks and is shown to be numerically advantageous. The paper analytically establishes that the BtG integration yields a reduced total system cost in comparison with decoupled designs where grid and building operators determine their controls separately. The developed framework is tested on standard power networks that include thousands of buildings modeled using industrial data. Case studies demonstrate building energy savings and significant frequency regulation, while these findings carry over in network simulations with nonlinear power flows and mismatch in building model parameters. Finally, simulations indicate that the performance does not significantly worsen when there is uncertainty in the forecasted weather and base load conditions.
Amplified anticoagulant activity of tissue factor-targeted thrombomodulin (2006)

Tissue factor (TF) exposure is a potent pro-thrombotic trigger that initiates activation of the coagulation cascade, while thrombomodulin (TM) is a potent anticoagulant protein that limits the extent of activation. Both TF neutralizing antibodies and soluble TM (sTM) are effective anticoagulants. We have developed a novel anticoagulant fusion protein, Ab(TF)-TM, by fusing a TFneutralizing single-chain antibody, Ab(TF), to an active fragment of TM. Ab(TF)-TM is a novel anticoagulant targeting to sites of TF exposure with a dual mechanism of action. The Ab(TF) portion of the molecule inhibitsTF/factorVIIa mediated activation of FIX and FX, and the TM portion of the molecule acts as a cofactor for activation of protein C. In-vitro coagulation assays show that Ab(TF)-TM more potently inhibits TF-initiated coagulation (prothrombin time) than can its individual components, Ab(TF) (20-fold) and sTM (80-fold) alone, or in combination (10-fold). In contrast, the potency of Ab(TF)-TM in the activated partial thromboplastin and thrombin clotting time assays was similar to sTM alone. In a rat model of disseminated intravascular coagulation (DIC), intravenous injection of a human TF-containing thromboplastin reagent (0.5 ml/kg) resulted in an immediate death in approximately 60% of the animals and a clinical score of approximately 2.5. Pre-injection of Ab(TF)-TM or Ab(TF) and sTM, given alone or in combination, showed dose-dependent efficacy. At a dose of 0.7 nmol/kg, Ab(TF)-TM completely prevented death and reduced clinical scores by 79%, while neitherAb(TF) nor sTM, given alone or in combination, showed significant therapeutic effects. Calculated effective doses that reduced mortality by 50% relative to that in the control group (ED(50), nmol/kg) were 0.21 for Ab(TF)-TM, 3.2 for an equimolar mixture of Ab(TF) and sTM, 4.3 for sTM and 20 for Ab(TF). Thus, Ab(TF)-TM presented 10- to 100-fold enhancement of the anticoagulant potency, relative to the ED(50) in Ab(TF) and sTM given either alone or in combination, in a rat DIC model.
Cache-memory interfaces in compressed memory systems (2001)

We consider a number of cache/memory hierarchy design issues in systems with compressed random access memories (C-RAMs) In which compression and decompression occur automatically to and from main memory. Using a C-RAM as main memory, the bulk of main memory contents are stored in a compressed format and dynamically decompressed to handle cache misses at the next higher level of memory. This is the general approach adopted in IBM's memory expansion technology (MXT). The design of the main memory directory structures and storage allocation methods in such systems is described elsewhere; here, we focus on issues related to cache-memory interfaces. In particular, if the cache line size (of the cache or caches to which main memory data is transferred) is different than the size of the unit of compression in main memory, bandwidth and latency problems can occur. Another issue is that of guaranteed forward progress, that is, ensuring that modified lines can be written to the compressed main memory so that the system can continue operation even if overall compression deteriorates. We study several approaches for solving these problems, using trace-driven analysis to evaluate alternatives.
Process for simultaneous removal of SO.sub.2 and NO.sub.x from gas streams (1987)

A process for simultaneous removal of SO.sub.2 and NO.sub.x from a gas stream that includes flowing the gas stream to a spray dryer and absorbing a portion of the SO.sub.2 content of the gas stream and a portion of the NO.sub.x content of the gas stream with ZnO by contacting the gas stream with a spray of an aqueous ZnO slurry; controlling the gas outlet temperature of the spray dryer to within the range of about a 0.degree. to 125.degree. F. approach to the adiabatic saturation temperature; flowing the gas, unreacted ZnO and absorbed SO.sub.2 and NO.sub.x from the spray dryer to a fabric filter and collecting any solids therein and absorbing a portion of the SO.sub.2 remaining in the gas stream and a portion of the NO.sub.x remaining in the gas stream with ZnO; and controlling the ZnO content of the aqueous slurry so that sufficient unreacted ZnO is present in the solids collected in the fabric filter to react with SO.sub.2 and NO.sub.x as the gas passes through the fabric filter whereby the overall feed ratio of ZnO to SO.sub.2 plus NO.sub.x is about 1.0 to 4.0 moles of ZnO per of SO.sub.2 and about 0.5 to 2.0 moles of ZnO per mole of NO.sub.x. Particulates may be removed from the gas stream prior to treatment in the spray dryer. The process further allows regeneration of ZnO that has reacted to absorb SO.sub.2 and NO.sub.x from the gas stream and acid recovery.
Regio‐ and Chemoselective 6′‐N‐Derivatization of Aminoglycosides: Bisubstrate Inhibitors as Probes To Study Aminoglycoside 6′‐<i>N</i>‐Acetyltransferases (2005)

Einfach zu komplexen nanomolaren Inhibitoren: Aminoglycosid-Coenzym-A-Derivate wurden durch eine effiziente regioselektive 6′-N-Modifizierung von Aminoglycosiden hergestellt (siehe Schema). Diese Bisubstrate sind fest bindende kompetitive Inhibitoren der Aminoglycosid-6′-N-Acetyltransferase, eines an der Antibiotikaresistenz beteiligten Enzyms.
Compact Organic Electro-Optic (EO) Modulator with Ultra Low Switching Voltage and Large Bandwidth Using Transparent Conducting Oxides (TCO) Bridge Electrodes (2009)

We report a new promising voltage-size performance record (0.6V-cm) of the organic EO modulator using transparent conducting oxides as the bridge electrodes. The comprehensive theoretical analysis predicts large electrical bandwidth (>40GHz) is achievable.
Removal of blends from boundary representation models (2002)

This paper reports an algorithm for deletion of blends (or fillets) from Boundary Representation (B-rep) solid models. Blend deletion is usually performed as the first step in feature recognition since it simplifies the model for recognition of volumetric features. The algorithm handles several blend types that include face-face, face-edge and vertex blends. It also handles interactions of blends with other blends and/or volumetric features. The main feature of our approach is the usage of the underlying blend structure in predicting the final topology. This results in fewer intersections and greater predictability than earlier face-deletion approaches, especially for large blend networks. Another unique feature of our algorithm is the recreation of new faces in certain situations of blend deletion.
Immunological mechanisms of exosome mediated therapeutic bioactivity in Duchenne muscular dystrophy (2020)

Duchenne muscular dystrophy (DMD) is a lethal myodegenerative disease associated with chronic inflammation. Disruption in the balance between pro‐inflammatory and pro‐regenerative macrophage immunophenotypes contributes to disease progression. Standard‐of‐care is currently limited to anti‐inflammatory steroids, which marginally delay disease progression. We have recently characterized the therapeutic benefits of cardiosphere‐derived cells (CDCs), which are cardiac progenitor/stromal cells with immunomodulatory, pro‐myogenic, and anti‐fibrotic properties. CDCs partially reverse the key abnormalities of heart and skeletal muscle in mdx mice, findings which motivated two clinical trials (HOPE‐Duchenne and HOPE‐2) of CDCs in DMD patients. The bioactivity of CDCs is mediated by the secretion of lipid bilayer nanovesicles called exosomes, which transfer genetic material between cells to modify recipient cell behavior. We previously discovered macrophages are a primary feature in skeletal muscle of CDC‐exosome treated mdx mice, suggesting their presence is not pathological. Here, we sought to elucidate the role macrophages play in the repair of dystrophic skeletal muscle. Circulating monocytes, at least in part, traffic fluorescently‐labeled CDC‐exosomes to damaged muscle after intravenous delivery. Labeled CDC‐exosomes are detected in the interstitium adjacent to non‐muscle cells, macrophages, and surviving muscle fibers. Moreover, CDC‐exosomes confer a unique immunophenotype to mdx macrophages (M exo ). Next generation sequencing and pathway/network analysis indicate M exo share features of both M1 (pro‐inflammatory) and M2 (pro‐regenerative) macrophages. Indeed, media conditioned by M exo supports both myoblast proliferation and differentiation in vitro . Antibody chip array indicated M exo secrete many chemokines and cytokines known to promote inflammatory cell recruitment and modulation. In contrast to M1 and M2 macrophages, M exo secrete tissue inhibitor of matrix metalloproteinase‐2 (TIMP‐2). Interestingly, TIMP‐2 has been shown to promote myogenic differentiation of C2C12 myoblasts and may function in both ECM remodeling and myogenesis in vivo . Sequencing of small RNAs revealed that several miRNAs with known roles in myogenesis are uniquely enriched in M exo exosomes. Together, these data suggest CDC‐exosomes are trafficked to areas of muscle damage, in part, by circulating monocytes and modulate the mdx macrophage phenotype to support tissue regeneration. We propose that M exo macrophages mediate their pleiotropic effects via the secretion of cytokines, chemokines, and possibly exosomes. Modulation of mdx macrophage functions by CDC‐exosomes, to support muscle health, may represent a novel approach to treating DMD. Support or Funding Information Muscular Dystrophy Association, Coalition Duchenne, NIH R01 to EM
Abstract 15714: Intra-cardiac Pressure Estimation Using Subharmonic Aided Pressure Estimation (SHAPE) - A Clinical Evaluation (2020)

Introduction: Subharmonic aided pressure estimation (SHAPE) utilizes ambient pressure sensitivity of subharmonic signals from ultrasound contrast agents. The objective was to evaluate SHAPE with Definity (Lantheus Medical Imaging, Inc.) and Sonazoid (GE Healthcare) microbubbles for intra-cardiac pressure estimation. Hypothesis: Errors between SHAPE and pressures obtained during cardiac catheterization ≤ 5 mmHg. Methods: IRB approved this study. Consenting patients received an infusion of Definity (56 patients; 2 vials in 50 mL of saline; infusion rate: 4-10 mL/min) or Sonazoid (77 patients; rate (mL/hour) = 0.18 x weight in kg co-infused with saline at 120 mL/hour) during cardiac catheterization. Subharmonic data was acquired using a SonixTablet (PA 4/2 array; BK Ultrasound) synchronously with pressures from the left and right ventricles and the aorta (for left heart catheterizations only). Subharmonic data (in dB) was converted to pressure values (in mmHg) using calibration factors (mmHg/dB) based on data obtained from the aorta - utilizing pressures from the aorta either during the catheterization procedure or pressures obtained using a SphygmoCor (AtCor Medical Pty. Ltd.) device after the catheterization procedure. Clinically relevant pressures between the SHAPE technique and the pressure catheter were compared. Results: Correlation coefficient between the subharmonic and pressure data was -0.8 ± 0.1. With Definity, mean absolute errors ranged from 2.9 ± 1.5 to 5.0 ± 4.2 mmHg and from 4.4 ± 5.7 to 23.7 ± 28.3 mmHg for calibration factors utilizing aortic pressures from pressure catheter and SphygmoCor, respectively. For Sonazoid microbubbles, these errors ranged from 7.9 ± 12.0 to 10.1 ± 12.4 mmHg and from 7.2 ± 11.5 to 15.0 ± 23.2 mmHg, respectively. Two adverse events occurred during Definity infusion; these were resolved with return to baseline conditions. Conclusion: SHAPE may be useful for estimating intra-cardiac pressures noninvasively.
i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets (2011)

A web-server for the i-rDNA algorithm is available at http://metagenomics.atc.tcs.com/i-rDNA/