gebhart/patrepeval huggingface dataset:
Antimicrobial peptides: an overview of a promising class of therapeutics (2007)

Abstract Antibiotic resistance is increasing at a rate that far exceeds the pace of new development of drugs. Antimicrobial peptides, both synthetic and from natural sources, have raised interest as pathogens become resistant against conventional antibiotics. Indeed, one of the major strengths of this class of molecules is their ability to kill multidrug-resistant bacteria. Antimicrobial peptides are relatively small (6 to 100 aminoacids), amphipathic molecules of variable length, sequence and structure with activity against a wide range of microorganisms including bacteria, protozoa, yeast, fungi, viruses and even tumor cells. They usually act through relatively non-specific mechanisms resulting in membranolytic activity but they can also stimulate the innate immune response. Several peptides have already entered pre-clinical and clinical trials for the treatment of catheter site infections, cystic fibrosis, acne, wound healing and patients undergoing stem cell transplantation. We review the advantages of these molecules in clinical applications, their disadvantages including their low in vivo stability, high costs of production and the strategies for their discovery and optimization.
Tissue-Engineered Model of Human Osteolytic Bone Tumor (2017)

Ewing's sarcoma (ES) is a poorly differentiated pediatric tumor of aggressive behavior characterized by propensity to metastasize to bone. Interactions between the tumor and bone cells orchestrate a vicious cycle in which tumor cells induce osteoclast differentiation and activation to cause osteolytic lesions, broken bones, pain, and hypercalcemia. The lack of controllable models that can recapitulate osteolysis in ES impedes the development of new therapies and limits our understanding of how tumor cells invade bone. In response to this need, tissue-engineered models are now being developed to enable quantitative, predictive studies of human tumors. In this study, we report a novel bioengineered model of ES that incorporates the osteolytic process. Our strategy is based on engineering human bone containing both osteoclasts and osteoblasts within three-dimensional mineralized bone matrix. We show that the bone matrix is resorbed by mature osteoclasts while the new bone matrix is formed by osteoblasts, leading to calcium release and bone remodeling. Introduction of ES cell aggregates into the bone niche induced decreases in bone density, connectivity, and matrix deposition. Additionally, therapeutic reagents, such as zoledronic acid, which have demonstrated efficacy in ES treatment, inhibited bone resorption mediated by osteoclasts in the tumor model.
Arc Fault Detection Method Based on CZT Low-Frequency Harmonic Current Analysis (2017)

This paper presents a method for the detection of series arc faults in electrical circuits, which has been developed starting from an experimental characterization of the arc fault phenomenon and an arcing current study in several test conditions. Starting from this, the authors have found that is it possible to suitably detect arc faults by means of a high-resolution low-frequency harmonic analysis of current signal, based on chirp zeta transform, and a proper set of indicators. The proposed method effectiveness is shown by means of experimental tests, which were carried in both arcing and nonarcing conditions and in the presence of different loads, chosen according to the UL 1699 standard requirements.
High Purity Hydrogen Production with In-Situ Carbon Dioxide and Sulfur Capture in a Single Stage Reactor (2011)

Enhancement in the production of high purity hydrogen (H{sub 2}) from fuel gas, obtained from coal gasification, is limited by thermodynamics of the water gas shift (WGS) reaction. However, this constraint can be overcome by conducting the WGS in the presence of a CO{sub 2}-acceptor. The continuous removal of CO{sub 2} from the reaction mixture helps to drive the equilibrium-limited WGS reaction forward. Since calcium oxide (CaO) exhibits high CO{sub 2} capture capacity as compared to other sorbents, it is an ideal candidate for such a technique. The Calcium Looping Process (CLP) developed at The Ohio State University (OSU) utilizes the above concept to enable high purity H{sub 2} production from synthesis gas (syngas) derived from coal gasification. The CLP integrates the WGS reaction with insitu CO{sub 2}, sulfur and halide removal at high temperatures while eliminating the need for a WGS catalyst, thus reducing the overall footprint of the hydrogen production process. The CLP comprises three reactors - the carbonator, where the thermodynamic constraint of the WGS reaction is overcome by the constant removal of CO{sub 2} product and high purity H{sub 2} is produced with contaminant removal; the calciner, where the calcium sorbent is regenerated and a sequestration-ready CO{sub 2} stream is produced; and the hydrator, where the calcined sorbent is reactivated to improve its recyclability. As a part of this project, the CLP was extensively investigated by performing experiments at lab-, bench- and subpilot-scale setups. A comprehensive techno-economic analysis was also conducted to determine the feasibility of the CLP at commercial scale. This report provides a detailed account of all the results obtained during the project period.
Association of Serum Antibodies to Adherence Lectin with Invasive Amebiasis and Asymptomatic Infection with Pathogenic Entamoeba histolytica (1990)

The recognition of the Entamoeba histolytica galactose-inhibitable adherence lectin by antibodies was studied using sera obtained from subjects in South Africa with an amebic liver abscess or asymptomatically pathogenic or nonpathogenic E. histolytica infection and from uninfected regional controls. In addition, sera from healthy American controls or Americans known to be infected with other parasites were studied. Of the 95 sera containing antibodies to total parasite protein, 95% demonstrated antibodies to the 170-kDa heavy subunit but not to the 35-kDa light lectin subunit. All sera (n = 253) were tested by ELISA for antibodies to lectin: 99% from liver abscess patients and all 4 from individuals asymptomatically infected with pathogenic E. histolytica were positive; all from the 40 healthy American controls and the 29 infected with other parasites were negative (P less than .01). The prevalence of serum anti-lectin antibodies was identical (25%) in asymptomatic South Africans with either a nonpathogenic infection or a negative stool culture for E. histolytica. Thus, the presence of serum antibodies to lectin seems to indicate current or prior invasive amebiasis or asymptomatic intestinal infection with pathogenic E. histolytica.
Towards the Rational Design of Efficient Organic Structure‐Directing Agents for Zeolite Synthesis (2013)

Zeolites are crystalline microporous materials with application in diverse fields, especially in catalysis. The ability to prepare zeolites with targeted physicochemical properties for a specific catalytic application is a matter of great interest, because it allows the efficiency of the entire chemical process to be increased (higher product yields, lower undesired by-products, less energy consumption, and cost savings, etc). Nevertheless, directing the zeolite crystallization towards the material with the desired framework topology, crystal size, or chemical composition is not an easy task, since several variables influence the nucleation and crystallization processes. The combination of accumulated knowledge, rationalization, and innovation has allowed the synthesis of unique zeolitic structures in the last few years. This is especially true in terms of the design of organic and inorganic structure-directing agents (SDAs). In this Minireview we will present the rationale we have followed in our studies to synthesize new zeolite structures, while putting this in perspective with the advances made by other researchers of the zeolite community.
Phase conjugate interferometric measurement of thin film parameters (1989)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Mark Cronin-Golomb and Joseph Shamir, "Phase conjugate interferometric measurement of thin film parameters," Appl. Opt. 28, 5196-5197 (1989) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Plasma beam alignment for the large‐area substrates: Equipment and process (2005)

Abstract— We have developed an effective method for liquid‐crystal alignment of the large‐area substrates. This method is based on the oblique treatment of the alignment substrates with a “sheet” of accelerated plasma generated by the anode layer source of the “race track” geometry. During this treatment, the substrate or source is cyclically translated in the direction perpendicular to the plasma “sheet.” This method provides planar, tilted, and vertical liquid‐crystal alignment with excellent uniformity and reproducibility and easy axis control in the azimuthal and polar planes.
New insight into the material parameter B to understand the enhanced thermoelectric performance of Mg<sub>2</sub>Sn<sub>1−x−y</sub>Ge<sub>x</sub>Sb<sub>y</sub> (2015)

A new generalized material parameter<italic>B</italic>*, connecting weighted mobility, lattice thermal conductivity, and also the band gap, provides a new insight in pursuing high thermoelectric figure-of-merit<italic>ZT</italic>.
Production Of Omega-3 Long Chain Polyunsaturated Fatty Acids (Patent US 2015/0216828 A1) (2015)

A recombinant camelina plant or cell comprising one or more polynucleotides encoding a Δ6-desaturase, a Δ6-elongase and a Δ5-desaturase operably linked with one or more regulatory sequences.
Feedback Cancellation in Hearing Aids: a Computer Simulation Results from (1991)

Feedback cancellation in hearing aids involves estimating the feedback signal and subtracting it from the microphone input sig- nal. The feedback-cancellation system described in this paper updates the estimated feedback path whenever changes are detected in the feed- back behavior. When a change is detected, the normal hearing-aid pro- cessing is interrupted, a pseudorandom probe signal is injected into the system, and a set of filter coefficients are adjusted to give an esti- mate of the feedback path. The hearing aid is then returned to normal operation with the feedback-cancellation filter as part of the system. Two approaches are investigated for computing the filter coefficients: an LMS adaptive filter and a Wiener filter. Test results-are then pre- sented for a computer simulation of an in-the-ear (ITE) hearing aid. The simulation results indicate that more than 10 dB of cancellation can be obtained, and that the Wiener filter is more effective in the presence of strong interference.
A low-power all-digital PLL architecture based on phase prediction (2012)

We propose a new generalized all-digital phase-locked loop (ADPLL) architecture that allows to significantly save power through complexity reduction of its phase locking and detection mechanisms. The predictive nature of the ADPLL to estimate next edge occurrence of the reference clock is exploited here to reduce the timing range and thus complexity of the fractional part of the phase detection mechanism as implemented by a time-to-digital converter (TDC). In addition, the integer part, which counts the DCO clock edges, can be disabled to save power once the loop has achieved lock. The proposed architecture is verified through behavioral simulations. It can be widely used in fields of fractional-N frequency multiplication and frequency/phase modulation.
Microstructural Control of a 70% Silicon Nitride– 30% Barium Aluminum Silicate Self‐Reinforced Composite (2001)

The processing response of a 70% silicon nitride–30% barium aluminum silicate (70%‐Si 3 N 4 –30%‐BAS) ceramic‐matrix composite was studied using pressureless sintering, at temperatures ranging from 1740°C, which is below the melting point of BAS, to 1950°C. The relationship between the processing parameters and the microstructural constituents, such as morphology of the β‐Si 3 N 4 whisker and crystallization of the BAS matrix, was evaluated. The mechanical response of this array of microstructures was characterized for flexural strength, as well as fracture behavior, at test temperatures up to 1300°C. The indentation method was used to estimate the fracture resistance, and R ‐curves were obtained from modified compact‐tension samples of selected microstructures at room temperature.
All-optical serrodyne frequency shifter (2021)

We describe and demonstrate a method to induce a single-sideband serrodyne-like optical frequency shift in an all-fiber device. The time-varying phase-shift is generated by cross-phase modulation in a nonlinear fiber. Unlike electro-optic based serrodyne methods, which require a high-fidelity and high-bandwidth analog electrical ramp modulation signal, the proposed optical method uses a simple pulsed pump and can be made simultaneously both low-loss and polarization-independent. We demonstrate the technique by shifting a 1550 nm optical signal 150 MHz in a 1.5 dB insertion-loss polarization-independent frequency shifter and show a pathway to multi-GHz shifting frequencies.
Optimizing assembly and production of native bispecific antibodies by codon de-optimization (2016)

When production of bispecific antibodies requires the co-expression and assembly of three or four polypeptide chains, low expression of one chain can significantly limit assembly and yield. κλ bodies, fully human bispecific antibodies with native IgG structure, are composed of a common heavy chain and two different light chains, one kappa and one lambda. No engineering is applied to force pairing of the chains, thus both monospecific and bispecific antibodies are secreted in the supernatant. In this context, stoichiometric expression of the two light chains allows for maximal assembly of the bispecific antibody. In this study, we selected a κλ body with suboptimal characteristics due to low kappa chain expression. Codon optimization to increase expression of the kappa chain did not improve bispecific yield. Surprisingly, progressive introduction of non-optimal codons into the sequence of the lambda chain resulted in lowering its expression for an optimal tuning of the relative distribution of monospecific and bispecific antibodies. This codon de-optimization led to doubling of the κλ body yield. These results indicate that assembly of different proteins into a recombinant complex is an interconnected process and that reducing the expression of one polypeptide can actually increase the overall yield.
Characterization of the binding and neutralizing properties of monoclonal antibodies against JCV (2013)

Antibody-based immunity to JC polyomavirus (JCV) is not well understood and monoclonal Antibodies (mAbs) that functionally neutralize the infectivity of JCV have not been documented. (1). Virus Like Particles (VLP)-based ELISAs can detect JCV-binding antibodies that do not necessarily neutralize the infectivity of JCV. Therefore, functional neutralization-based serology will be needed to validate candidate JCV VLP vaccines and therapeutic McAbs. (2). The neutralizing activity of McAbs can be specific for particular genotypes and clinical strains. Hence, VLPs from multiple genotypes may be needed to formulate a vaccine that could protect against diverse JCV strains circulating in patients with progressive multifocal encephalopathy (PML).
Using embedded element patterns for the analysis of small arrays (2016)

The embedded element pattern of an infinite array is one approach used to model finite size arrays greater than 10 × 10. For smaller array sizes however, using a single embedded element pattern may not suffice since the coupling results in large variations in the currents across elements. In this paper we try to determine if using all nine embedded element patterns of a 3 × 3 rectangular array to form the array radiation pattern compares favorably with the results from full-wave analysis with Antenna Toolbox. The results indicate that such an approximation is indeed valid.
Mechanisms of Incorporation for <scp>D</scp>-Amino Acid Probes That Target Peptidoglycan Biosynthesis (2019)

Bacteria exhibit a myriad of different morphologies, through the synthesis and modification of their essential peptidoglycan (PG) cell wall. Our discovery of a <u>f</u>luorescent <u>D</u>-<u>a</u>mino <u>a</u>cid (FDAA)-based PG labeling approach provided a powerful method for observing how these morphological changes occur. Given that PG is unique to bacterial cells and a common target for antibiotics, understanding the precise mechanism(s) for incorporation of (F)DAA-based probes is a crucial determinant in understanding the role of PG synthesis in bacterial cell biology and could provide a valuable tool in the development of new antimicrobials to treat drug-resistant antibacterial infections. Here, we systematically investigate the mechanisms of FDAA probe incorporation into PG using two model organisms <i>Escherichia coli</i> (Gram-negative) and <i>Bacillus subtilis</i> (Gram-positive). Our in vitro and in vivo data unequivocally demonstrate that these bacteria incorporate FDAAs using two extracytoplasmic pathways: through activity of their D,D-transpeptidases, and, if present, by their L,D-transpeptidases and not via cytoplasmic incorporation into a D-Ala-D-Ala dipeptide precursor. Our data also revealed the unprecedented finding that the DAA-drug, D-cycloserine, can be incorporated into peptide stems by each of these transpeptidases, in addition to its known inhibitory activity against D-alanine racemase and D-Ala-D-Ala ligase. These mechanistic findings enabled development of a new, FDAA-based, in vitro labeling approach that reports on subcellular distribution of muropeptides, an especially important attribute to enable the study of bacteria with poorly defined growth modes. An improved understanding of the incorporation mechanisms utilized by DAA-based probes is essential when interpreting results from high resolution experiments and highlights the antimicrobial potential of synthetic DAAs.
Statistics of Four-Wave Mixing Crosstalk (1995)

Four-wave mixing (FWM) is the dominant nonlinear effect in intensity-modulated wavelength-division multiplexed (WDM) optical communication systems using dispersion-shifted fiber (DSF). In WDM systems with equally spaced channels all the product terms generated by FWM in the bandwidth of the system fall at the channel frequencies. The mixing products generated at the channel frequencies coherently interfere with the signals, giving rise to crosstalk. Due to the coherent nature of FWM interference in equally spaced WDM systems, a single mixing product generated on one of the channels with a power 20 dB lower than the signal power is enough to cause a ±1 dB fluctuation in the received power [1].
Preparation and Properties of High Performance Nanocomposite Bipolar Plate for Fuel Cell (2007)

The thin polymer composite bipolar plates (the thickness < 1.5 mm) for use in polymer electrolyte membrane fuel cells (PEMFCs) containing vinyl ester resin, graphite powder, organoclay have been fabricated by bulk molding compound (BMC) process. Organoclay prepared by ionic exchange of montmorillonite (MMT) with three different Mw of diamine intercalating agents was used to reinforce the mechanical properties of the composite bipolar plates. Results indicate that the basal spacing and content of MMT varied with Mw of POP-diamines are critical in determining the resultant mechanical properties for bipolar plates. The flexural strength and the unnotched impact strength of the plate were ca. 38 % (from 30.21 MPa to 45.66 MPa) and ca. 30 % (from 58.11 J/m to 80.21 J/m) higher than the pristine graphite plate, respectively, as the basal spacing of MMT (2 phr) was increased from 1.71 to 5.43 nm. The limiting oxygen index (L.O.I.) and the UL-94 test revealed that the bipolar plate possesses excellent flame retardant with L.O.I. higher than 50 and UL-94-V0. In addition, the electrical conductivity of the bipolar plates with different MMT contents and basal spacing of MMT is higher than 100 S/cm.
Improved Stoneley Wave Inversion Method for Fracture Evaluation (2017)

Abstract The conductivity and density of fractures intersecting a borehole strongly influence well productivity, making fracture characterization an important aspect of reservoir management. A Stoneley-wave inversion process is presented to estimate borehole washout volume and fracture conductivity. In addition to identifying conductive fractures, the ability to detect borehole washout volume can impact other well operations, such as cementing or geomechanical property estimation, in situations where placing a caliper tool in the borehole is not desirable. Low-frequency Stoneley wave reflections are commonly used to locate and evaluate fractures crossing a fluid-filled, open borehole. However, other mechanisms, such as the reflection from bed boundaries or changes in borehole size, can also induce secondary pressure waves. The inversion of reflectivity over a frequency bandwidth can be used to determine whether a secondary wave is likely the result of a conductive fracture, borehole washout, or the combination of both a washout and a fracture. The integration of additional information from other logs, such as borehole images, caliper, slowness, etc., is used to further distinguish fractures from bedding effects. This paper describes the theoretical considerations and signal-processing techniques used in this integrated approach, and results from the analysis of field data are presented. The inversion bandwidth ranges from a minimum frequency of 300 to 500 Hz to a maximum of several kHz and is automatically adjusted based on data quality. Several wells were studied using forward modeling and numeric inversion. A comparison of inversion results to borehole images and caliper logs shows depth registration errors typically of 0.3 m (1 ft) or less. The inversion of all reflectivity measurements over the specified bandwidth distinguishes borehole washouts (stronger high-frequency response) from conductive fractures (stronger low-frequency response) and thus provides a more reasonable estimate of fracture conductivity compared to conventional wide-band integrated-amplitude reflection analyses.
Automated Scoring of a Summary-Writing Task Designed to Measure Reading Comprehension (2013)

We introduce a cognitive framework for measuring reading comprehension that includes the use of novel summary writing tasks. We derive NLP features from the holistic rubric used to score the summaries written by students for such tasks and use them to design a preliminary, automated scoring system. Our results show that the automated approach performs well on summaries written by students for two different passages. 1