gebhart/patrepeval huggingface dataset:
Chimeric Ply187 endolysin kills<i>Staphylococcus aureus</i>more effectively than the parental enzyme (2013)

Peptidoglycan hydrolases are an effective new source of antimicrobials. A chimeric fusion protein of the Ply187 endopeptidase domain and LysK SH3b cell wall-binding domain is a potent agent against Staphylococcus aureus in four functional assays.
Mice lacking the homeodomain transcription factor Nkx2.2 have diabetes due to arrested differentiation of pancreatic β cells (1998)

The endocrine pancreas is organized into clusters of cells called islets of Langerhans comprising four well-defined cell types: alpha beta, delta and PP cells. While recent genetic studies indicate that islet development depends on the function of an integrated network of transcription factors, the specific roles of these factors in early cell-type specification and differentiation remain elusive. Nkx2.2 is a member of the mammalian NK2 homeobox transcription factor family that is expressed in the ventral CNS and the pancreas. Within the pancreas, we demonstrate that Nkx2.2 is expressed in alpha, beta and PP cells, but not in delta cells. In addition, we show that mice homozygous for a null mutation of Nkx2.2 develop severe hyperglycemia and die shortly after birth. Immunohistochemical analysis reveals that the mutant embryos lack insulin-producing beta cells and have fewer glucagon-producing alpha cells and PP cells. Remarkably, in the mutants there remains a large population of islet cells that do not produce any of the four endocrine hormones. These cells express some beta cell markers, such as islet amyloid polypeptide and Pdx1, but lack other definitive beta cell markers including glucose transporter 2 and Nkx6.1. We propose that Nkx2.2 is required for the final differentiation of pancreatic beta cells, and in its absence, beta cells are trapped in an incompletely differentiated state.
Managing static leakage energy in microprocessor functional units (2002)

Static energy due to subthreshold leakage current is projected to become a major component of the total energy in high performance microprocessors. Many studies so far have examined and proposed techniques to reduce leakage in on-chip storage structures. In this study, static energy is reduced in the integer functional units by leveraging the unique qualities of dual threshold voltage domino logic. Domino logic has desirable properties that greatly reduce leakage current while providing fast propagation times. However due to the energy cost of entering the low leakage current state (sleep mode), domino logic has thus far been used only for leakage reduction in the longterm standby mode. We examine the utility of the sleep mode (while considering the aforementioned costs) when idle times are relatively short, one to a few hundred cycles, as is often the case for functional units. Using an analytical energy model suitable for architecture-level analysis, we explore the interaction of the application and technology, and the effect on energy and performance as the underlying parameters are varied, on a set of benchmarks. Our results show that if the leakage approaches the magnitude as projected in the literature, even for short idle intervals as few as ten cycles, an aggressive policy of activating the sleep mode at every idle period performs well and a more complex control strategy may not be warranted. We also propose a simple design, called Gradual Sleep, to reduce the energy impact of using the sleep mode for smaller idle periods.
A Circumferential Slot In-Line Virtual Impactor (2008)

An In-line Virtual Impactor is presented, which has an application as a pre-separator for sampling inlets, where the device scalps large particles from the aerosol size distribution. Numerical simulation was the principal tool employed in the design process, with physical experiments used to verify computational predictions. Performance investigations were primarily carried out for a configuration that provides a nominal cutpoint particle size of 10 μ m aerodynamic diameter at an inlet flow of 111 L/min and a major flow exhaust of 100 L/min; however, the concept is scalable in terms of both flow rates and cutpoint sizes. An inverted dual cone configuration contained within a tube provides a characteristic circumferential slot of width 2.54 mm (0.100 inches) and a slot length of 239 mm (9.42 inches) at the critical zone. The upper cone causes the flow to accelerate to an average throat velocity of 3.15 m/s, while the lower cone directs the major flow toward the exit port and minimizes recirculation zones that could cause flow instabilities in the major flow region. The cutpoint Stokes number is 0.73; however, the cutpoint can be adjusted by changing the geometrical spacing between the acceleration nozzle exit plane and a flow divider. When the system is operated at the major exhaust flow rate of 100 L/min, the pressure drop is 45 Pa. Good agreement is obtained between numerically predicted and experimentally observed performance.
Ultra-sensitive carbon nanotubes for single-molecule detection of DNA hybridization kinetics using conductance-based correlation spectroscopy (2011)

We present a label-free single-molecule based sensing platform using a carbon nanotube field-effect transistor. By point functionalizing a carbon nanotube through an electrochemical oxidation reaction, the conductance becomes sensitive and chemically reactive at a single point to which we can covalently attach a probe DNA molecule. Two-level fluctuations appear in the conductance of the carbon nanotube when it is immersed in a liquid buffer solution containing complementary target DNA. We show that the autocorrelation of the conductance can be used to extract DNA hybridization kinetics. The results are comparable to the one extracted through a hidden Markov model.
Stacked macro fiber piezoelectric composite generator for a spinal fusion implant (2014)

A manufacturing method was developed to create a piezoelectric 3-layer stacked, macro fiber composite generator operating in d33 mode to promote bone growth in spinal fusion surgeries. A specimen of 9 × 17 × 9 mm thick was constructed from 800 μm diameter PZT fibers and medical grade epoxy. Electromechanical testing was performed at three stages of manufacturing to determine the influence of these processes on power generation. An average peak power of over 335 μW was generated in the heat-treated specimen during simulated human body loads. The work provides insights into manufacturing methods for lowered source impedance power generation for a variety of applications.
Oculometric Assessment of Sensorimotor Impairment Associated with TBI (2016)

We conclude that multidimensional oculometric testing could be used as a sensitive screen for subtle neurological signs of subclinical neurological insults, to quantify functional impairment, to monitor deterioration or recovery, and to evaluate treatment efficacy.
System Call Interception Framework for Data Leak Prevention (2011)

In this paper, we describe the feasibility and practical study of the recently proposed idea for data leak prevention (DLP) based on end-point policy enforcement. The most reassuring way to prevent sensitive data leak is to thwart sensitive data export before it has a chance to occur. Using a System Call Interception (SCI) technique we investigate the possibility of automatically detecting and amending a non-desired, policy breaching behavior at the "intention" stage: as the corresponding system call is called by an application, but before the action has been accomplished. The SCI method is especially valuable for "black box" applications, for which source code is not available. In our system, we catalog the system calls involved in the DLP events, and reduce our SCI to the minimum necessary set of system calls associated with the sensitive, DLP-requiring tasks. We describe the system behavior for several different applications that we have studied to date.
Self-regulated four-phased charge pump with boosted wells (2003)

Charge pumps are useful to achieve on-chip boosted voltages in EPROM and other NVM devices. A new capacitive charge pump architecture is suggested which eliminates bulk effect by boosting the wells of transistors in the charge pump stages. In addition, the pump contains an internal voltage regulator, enabling it to supply a constant boosted output, regardless of process, environment and loading conditions. The pump operates from a 2.7V supply, provides up to 10mA at 8V and occupies 2 mm/sup 2/.
A Space Virtual-Vector Modulation With Voltage Balance Control for Nested Neutral-Point Clamped Converter Under Low Output Frequency Conditions (2016)

The recently-developed nested neutral-point clamped (NNPC) converter is a four-level converter for medium-voltage high-power applications. It has some merits such as operating over wide voltage ranges (2.4–7.2 kV) without switching devices in series and less diodes or capacitors when compared with classical four-level topologies. But it has severe voltage balancing problems under low output frequency conditions when conventional space vector modulation (SVM) or sinusoidal pulse width modulation (SPWM) is applied, which limits its wide applications. In order to solve this issue, a space virtual-vector modulation (SVVM) along with a voltage balance control (VBC) algorithm is proposed in this paper. It helps reduce the voltage ripples greatly and maintain them within an acceptable region under low output frequency conditions. Therefore, it guarantees even voltage stresses among switching devices and extends the NNPC converter's applications. Principles of the proposed SVVM and VBC algorithms are elaborated in detail, and the voltage balancing performance is investigated and compared with the cases where conventional SVM and SPWM with the same VBC are applied. The relationship curves between voltage ripples and flying capacitance, output power, and output frequency have been explored and compared for both conventional SVM and proposed SVVM. Simulation and experimental results are presented to verify the effectiveness of the proposed method.
Porous membrane controlled polymerization of nanofibers of polyaniline and its derivatives (2008)

A novel, simple, and scalable technique to control the formation of the nanofibers of polyaniline and its derivatives via porous membrane controlled polymerization (PMCP) is reported. Through appropriate synthesis conditions, there are nearly 100% nanofibers formed with diameters tunable from 20nm to 250nm via the selection of pore diameter, monomer, counterions, and polymerization conditions. The nanofiber lengths vary from sub-micrometre to several micrometres. A single nanofiber can be easily isolated from the agglomeration. X-Ray diffraction patterns show that doped polyaniline nanofibers are substantially crystalline.
Preparation of Recombinant  -Thrombin: High-Level Expression of Recombinant Human Prethrombin-2 and Its Activation by Recombinant Ecarin (2004)

We have established a large-scale manufacturing system to produce recombinant human alpha-thrombin. In this system, a high yield of alpha-thrombin is prepared from prethrombin-2 activated by recombinant ecarin. We produced human prethrombin-2 using mouse myeloma cells and an expression plasmid carrying the chicken beta-actin promoter and mutant dihydrofolate reductase gene for gene amplification. To increase prethrombin-2 expression further, we performed fed-batch cultivation with the addition of vegetable peptone in 50 liters of suspension culture. After five feedings of vegetable peptone, the expression level of the recombinant prethrombin-2 reached 200 micro g/ml. Subsequently, the recombinant prethrombin-2 could be activated to alpha-thrombin by recombinant ecarin expressed in a similar manner. Finally, recombinant alpha-thrombin was purified to homogeneity by affinity chromatography using a benzamidine-Sepharose gel. The yield from prethrombin-2 in culture medium was approximately 70%. The activity of the purified recombinant alpha-thrombin, including hydrolysis of a chromogenic substrate, release of fibrinopeptide A, and activation of protein C, was indistinguishable from that of plasma-derived alpha-thrombin. Our system is suitable for the large-scale production of recombinant alpha-thrombin, which can be used in place of clinically available alpha-thrombin derived from human or bovine plasma.
Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants (2022)

Despite vaccine availability, the global spread of COVID-19 continues, largely facilitated by emerging SARS-CoV-2 mutations. Our earlier research documented that a specific combination of plant-derived compounds can inhibit SARS-CoV-2 binding to its ACE2 receptor and controlling key cellular mechanisms of viral infectivity. In this study, we evaluated the efficacy of a defined mixture of plant extracts and micronutrients against original SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants. The composition containing vitamin C, N-acetylcysteine, resveratrol, theaflavin, curcumin, quercetin, naringenin, baicalin, and broccoli extract demonstrated a highest efficacy by inhibiting the receptor-binding domain (RBD) binding of SARS-CoV-2 to its cellular ACE2 receptor by 90%. In vitro exposure of test pseudo-typed variants to this formula for 1 h before or simultaneously administrated to human pulmonary cells resulted in up to 60% inhibition in their cellular entry. Additionally, this composition significantly inhibited other cellular mechanisms of viral infectivity, including the activity of viral RdRp, furin, and cathepsin L. These findings demonstrate the efficacy of natural compounds against SARS-CoV-2 including its mutated forms through pleiotropic mechanisms. Our results imply that simultaneous inhibition of multiple mechanisms of viral infection of host cells could be an effective strategy to prevent SARS-CoV-2 infection.
Protective pan-ebolavirus combination therapy by two multifunctional human antibodies (2021)

Abstract Ebolaviruses cause a severe and often fatal illness with the potential for global spread. Monoclonal antibody-based treatments that have become available recently have a narrow therapeutic spectrum and are ineffective against ebolaviruses other than Ebola virus (EBOV), including medically important Bundibugyo (BDBV) and Sudan (SUDV) viruses. Here we report the development of a therapeutic cocktail comprising two broadly neutralizing human antibodies rEBOV-515 and rEBOV-442 that recognize non-overlapping sites on the ebolavirus glycoprotein (GP). Antibodies in the cocktail exhibited synergistic neutralizing activity and resisted viral escape, and they were optimized for their Fc-mediated effector function activities. The cocktail protected non-human primates from ebolavirus disease caused by EBOV, BDBV, or SUDV with high therapeutic effectiveness. High-resolution structures of the cocktail antibodies in complex with GP revealed the molecular determinants for neutralization breadth and potency. This study provides advanced preclinical data to support clinical development of this cocktail for pan-ebolavirus therapy.
Memory requirements for future Internet routers with essentially-perfect QoS guarantees (2010)

The theory of a future Internet network which achieves essentially-perfect QoS guarantees for all QoS-enabled traffic flows for all loads ≤ 100% of capacity has recently been established. A scheduling algorithm with a bounded normalized service lead/lag (NSLL) is used to schedule traffic flows within the routers. An 'Application-Specific Token-Buffer Traffic Shaper' is used at the traffic sources, to achieve a bounded NSLL on incoming bursty traffic flows. An 'Application-Specific Playback Queue' is used to perfectly regenerate the original busty traffic flows at every destination. Under these conditions, it has been established that every QoS-enabled flow: (i) is delivered with essentially-perfect end-to-end QoS guarantees, and (ii) buffers O(K) cells/packets per router, where K is the bound on the NSLL. In this paper, we reduce the router buffering requirements significantly, so that each router buffers ≤ one cell/packet per QoS-enabled traffic flow, a reduction of up to 1K-10K over existing technologies. The proposed technology can be incorporated into new routers with negligible hardware cost, and is compatible with existing IntServ, DiffServ, MPLS and RSVP-TE protocols.
New cross-strain protective influenza vaccine using self-attenuated influenza virus (2016)

Abstract Live attenuated vaccines (LAVs) are derived from disease-causing pathogens and are effective way for prevention of infectious disease. Classical LAVs are produced experimentally by repeated passaging of a virus in cultured cells, but this method is not always reliable and safe because in some cases, there is a reversion to wild-type virulence. Several methods have been employed to improve them, but the efficacy and safety are still a challenge. In this study, we have developed a self-attenuated RNA virus expressing a functional and mammalian species-specific artificial microRNA. Using influenza virus as a model, we designed an artificial miR-93 cassette for insertion into NS gene segment of influenza viral genome, which produces a specific amiRNA for inhibiting NP gene expression that would result in a virus which is attenuated in mammalian cells. The resulting engineered self-attenuated influenza virus, PR8-amiR-93NP, produced mature and functional artificial microRNA against NP in mammalian cells, but could be propagated at a high yield with the traditional influenza virus production method in embryonated chicken eggs. Furthermore, PR8-amiR-93NP was attenuated by 100 fold in mice compared with its wild-type counterpart. In animal experiments, intranasal vaccination with PR8-amiR-93NP induces antigen-specific antibody responses and protective immunity against heterologous influenza virus strains. In conclusion, our results demonstrated that this self-attenuation approach provides a safe and effective platform for generation of live attenuated influenza vaccine, as a next generation nasal spray influenza vaccine.
A Novel Optical Instrument for Estimating Size Segregated Aerosol Mass Concentration in Real Time (2009)

A novel optical instrument has been developed that estimates size segregated aerosol mass concentration (i.e., PM 10 , PM 4 , PM 2.5 , and PM 1 ) over a wide concentration range (0.001–150 mg/m 3 ) in real time. This instrument combines photometric measurement of the particle cloud and optical sizing of single particles in a single optical system. The photometric signal is calibrated to approximate the PM 2.5 fraction of the particulate mass, the size range over which the photometric signal is most sensitive. The electrical pulse heights generated by light scattering from particles larger than 1 micron are calibrated to approximate the aerodynamic diameter of an aerosol of given physical properties, from which the aerosol mass distribution can be inferred. By combining the photometric and optical pulse measurements, this instrument can estimate aerosol mass concentrations higher than typical single particle counting instruments while providing size information and more accurate mass concentration information than traditional photometers. Experiments have shown that this instrument can be calibrated to measure aerosols with very different properties and yet achieve reasonable accuracy.
Kinetics of Nested Inorganic Fullerene-like Nanoparticle Formation (1998)

Recently, a model for the growth mechanism of inorganic fullerene-like (IF) nanoparticles of MS2 (M = Mo, W) from the respective oxides was presented (Feldman, Y.; Frey, G. L.; Homyonfer, M.; Lyakhovitskaya, V.; Margulis, L.; Cohen, H.; Hodes, G.; Hutchison, J. L.; Tenne, R. J. Am. Chem. Soc. 1996, 118, 5362). According to this model, sulfidization of oxide particles of <150 nm leads to the formation of a sulfide encapsulate with oxide core, which is progressively converted into a hollow IF nanoparticle. Using transmission electron microscopy, the sulfidization of a group of oxide nanoparticles is demonstrated step by step. This study provides direct evidence for the quasi spiral growth of the sulfide layers into the oxide nanoparticle core. However, the mechanism for the formation of the first closed sulfide layer which engulfs the oxide encapsulate remained a puzzle thus far. The analysis of the kinetics of simultaneous reduction and sulfidization of WO3 powders suggests the occurrence of a unique driving force for the fast growth of the first curved sulfide layer (001) around an oxide nanoparticle. According to the present model, a synergy between the reduction and sulfidization processes which occurs in a very narrow window of parameters leads to the formation of the first one or two closed sulfide layers. The present study is not limited to the sulfides. The formation of IF−WSe2 (Tsirlina, T.; Feldman, Y.; Homyonfer, M.; Sloan, J.; Hutchison, J. L.; Tenne, R. Fullerene Sci. Technol. 1998, 6, 157) is found to be consistent with the same kind of model.
Biometric driven initiative system for passive continuous authentication (2011)

In this paper, a passive continuous authentication system based on both the hard and the soft biometrics is implemented. The passive continuous authentication system keeps verifying the user without interrupting the user concentrating on his work. It also provides the capacity for the machine to recognize who is in front of the terminal, reduces the potential security leak of the user is temporarily absent front the terminal, and denies the invader to login the system with the stolen account and password. Our system forces to logoff the user when the authentication result identifies the user leaves his seat, but the system won't logoff the user if the user only turns his face to some other directions. The reliability of the system is verified by 7 registered users. According to the experimental results, combining the soft and the hard biometrics in our theoretical framework achieves the goal of continuous authentication efficiently and correctly.
Recent developments in spinel at NRL (Conference Presentation) (2017)

Transparent magnesium aluminate spinel (MgAl2O4) ceramic has excellent transmission from the UV to mid-wave IR. It is rugged with strength that is 5x that of glass. Spinel also has better IR transmission compared to sapphire and ALON. Because of its superior mechanical and optical properties, it is considered as a sensor window for numerous military platforms. At the Naval Research Laboratory (NRL), we have focused on process developments to facilitate wider acceptance of spinel for various applications. These developments include purification of spinel to reduce the absorption and scattering losses, as well as new processes to make conformal spinel windows and also to reduce manufacturing and finishing costs. In this presentation, we will provide an update on all the spinel activities at NRL
Enriching spoken language translation with dialog acts (2008)

Current statistical speech translation approaches predominantly rely on just text transcripts and do not adequately utilize the rich contextual information such as conveyed through prosody and discourse function. In this paper, we explore the role of context characterized through dialog acts (DAs) in statistical translation. We demonstrate the integration of the dialog acts in a phrase-based statistical translation framework, employing 3 limited domain parallel corpora (Farsi-English, Japanese-English and Chinese-English). For all three language pairs, in addition to producing interpretable DA enriched target language translations, we also obtain improvements in terms of objective evaluation metrics such as lexical selection accuracy and BLEU score.