gebhart/patrepeval huggingface dataset:
Detection of biological warfare agents with fiber-optic microsphere-based DNA arrays (2005)

Biological warfare agents (BWAs) pose significant threats to both military forces and civilian populations. The increased concern about bioterrorism has promoted the development of rapid, sensitive, and reliable detection systems to provide an early warning for detecting the release of BWAs. We have developed a high-density DNA array to detect BWAs in real environmental samples with fast response times and high sensitivity. An optical fiber bundle containing approximately 50,000 individual 3.1 &#956;m diameter fibers was chemically etched to yield an array of microwells and used as the substrate for the array. 50-mer single-stranded DNA probes designed to be specific for target BWAs were covalently attached to 3.1-&#956;m microspheres, and the microspheres were distributed into the microwells to form a randomized high-density DNA array. We demonstrated the applicability of this DNA array for the identification of Bacillus thuringiensis kurstaki, a BWA simulant, in real samples. PCR was used to amplify the sequences, introduce fluorescent labels into the target molecules, and provide a second level of specificity. After hybridization of test solutions to the array, analysis was performed by evaluating the specific responses of individual probes on the array.
Response of groundnut (Arachis hypogaea L.) to plant growth promoting Rhizobacteria in degraded soils (2018)

The effects of plant growth promoting Rhizobacteria (PGPR) on the growth, plant nutrient content and crop yield of groundnut (Arachis Hypogaea L.) cv. Golden were investigated under rainfed conditions in degraded lands within 2011 and 2014. The experiment was planned with a randomized complete block design having three replication. The two PGPR treatments alone or in combination with FYM were tested and compared with gypsum (alone), farm yard manure (FYM) (alone) and control. The data of 4 years showed that the use of PGPR and other amendments significantly increased plant growth, plant nutrient content, crop yield and soil fertility compared with the control. The (Gypsum, PGPR, FYM, and PGPR+FYM) applications increased cumulative grain yield by 3.94, 1.35, 7.08 and 10.34%, respectively.&nbsp; The straw yield increased by (1.29, 0.40, 2.17 and 4.15%) by the applications of gypsum, PGPR, FYM, and PGPR+FYM respectively compared with the control. In addition, organic matter content of soil with PGPR and other amendments significantly increased from 0.73 to 1.00%. Soil moisture content was enhanced from 23.40 to 28.20%. These amendments reduced soil pH from 8.14 to 7.80 and soil electrical conductivity (ECe) from 1.73 to 1.37 dS m-1. Overall, the results of this study indicated that the PGPR alone or in combination with FYM had the potential to increase growth and yield of groundnut and improve soil health of degraded soils. &nbsp; Key words: Plant growth promoting Rhizobacteria (PGPR), farm yard manure (FYM), gypsum, groundnut, degraded soils.
Macromol. Biosci. 11/2017 (2017)

Inside Front Cover: The genetically modified reporter bacteria Escherichia coli pTetR-LasR-pLuxR-GFP were entrapped into multi-component hydrogel microarrays to fabricate point-of-care biosensors for monitoring bacterial infections caused by Pseudomonas aeruginosa. The hybrid hydrogel was formed by combining the supramolecular self-assembly of a low molar mass gelator with Ca2+ mediated cross-linking of alginate. Upon exposure to relevant concentrations of the N-acyl homoserine lactone autoinducer secreted by Pseudomonas aeruginosa, the entrapped reporter bacteria exhibited a more than tenfold increase in fluorescence intensity due to the autoinducer-triggered green fluorescent protein expression. To enhance the signal to noise ratio, the reporter bacteria-loaded hydrogels were micropatterned. The sloping side-walls of pyramidal structures guide the sedimentation of the reporter bacteria and thus intensify the fluorescence signal at the tip of the pyramid to minimize the number of bacteria per well for high signal to noise ratio detection. The cover is prepared by Ping Li, Xiaoqiu Dou, Mareike Müller, Chuanliang Feng, Matthew Wook Chang, Martin Frettlöh and Holger Schönherr, article number 1700176.
Combined Opto-Electronical Simulation of Metal-Semiconductor-Metal (MSM) Photodetectors (1996)

A complete opto-electronical simulation of a metal-semiconductor-metal (MSM) photodetector is presented. We combined rigorous electromagnetic theory for modelling the light propagation with electronic device simulation methods. Different optical designs were compared with respect to efficiency and response times.
Softcopy Banding Visibility Assessment (2007)

Banding is a printer artifact perceived as one dimensional luminance variations across the print-out caused by different mechanical problems such as vibration of different printer components in laser electrophotographic (EP) printers or media advance errors in inkjet printers. In the printing industry, banding is considered to be one of the worst defects that dominates overall perceived image quality. Understanding the visibility of banding will help us in developing strategies to reduce the banding artifact. We developed a soft-copy environment to conduct various experiments for investigating the visibility of banding in laser EP printers. This environment includes the methodology to duplicate the print on the monitor, and a banding extraction technique. This technique enables us to freely adjust the magnitude of banding of any printer. We validated the accuracy of this methodology by conducting a banding matching experiment. We used this platform to conduct banding visibility assessment experiments. One of them was a banding discrimination experiment. The results showed that for the printers investigated, a reduction of 6.5% in the banding magnitude will be just noticeable by an average observer. We were also able to find the detection thresholds of banding in grayscale images for three laser electrophotographic printers. The detection threshold of the best printer was about 50% of its original banding. So there is still plenty of room to reduce the visibility of the banding artifact. We were also able to compare the banding visibility of different printers quantitatively by conducting a cross-platform experiment. This methodology can form the basis for a metric for visibility of banding in laser EP printers. With some modifications, these techniques could also be adapted to other printer technologies such as ink jet printers.
Abstract 4723: Innovative cancer treatment of human lung cancer cells PC-9 with a synthetic retinoid Am80 and EGCG via inhibition of HDAC4 and HDAC5 (2016)

Abstract A synthetic new retinoid Am80 (tamibarotene) is used for treatment of acute promyelocytic leukemia (APL) patients with resistance of all-trans-retinoic acid (ATRA). To potentiate efficacy of Am80, we challenged combination treatment of Am80 and EGCG on human lung cancer cell line PC-9. It is now well accepted that EGCG acts as synergist with numerous anticancer compounds, and that the average reduction of tumor volume for in vivo genograft mouse models implanted using various human cancer cell lines was 70.3% with combinations of 13 anticancer compounds and EGCG. We previously reported that combinations of NSAIDs (sulindac and celecoxib) or other retinoids (ATRA, 13-cis-RA and 9-cis-RA) and EGCG synergistically induced apoptosis of the cells along with strong expression of growth arrest and DNA-damage inducible gene 153 (GADD153) and death receptor (DR5) gene. Our objective was to investigate the mechanism of the synergistic induction for GADD153-DR5 apoptosis pathway. The proteomic analysis of lysine-acetylated proteins was conducted with a shotgun analysis using nanoLC-ESI-MS/MS in PC-9 cells. We found that the numbers of acetylated proteins were different: 551 acetylated proteins were found in non-treated cells, 331 proteins in cells treated with combination, and 59 proteins were common in both cases. Acetylation was mainly found in non-histone proteins, chaperons, transcription factors, and enzymes. The combination increased acetylated p53 (Lys382) about 3-fold compared with non-treated cells. In addition, combination significantly decreased the protein amounts of histone deacetylase (HDAC) 4 and HDAC 5 to 50% and 20%, respectively, but not HDAC6 among Class II HDACs. Class I HDACs (HDAC1, 2, and 3) were not decreased. All the results suggest that combination of Am80 and EGCG induces GADD153-DR5 apoptotic pathway, and reduces the amounts of HDAC4 and HDAC5 resulting in changing protein acetylation. Citation Format: Masami Suganuma, Yukiko Oya, Sonthaya Umsumarng, Keisuke Iida, Anchalee Rawangkhan, Ryo Sakai, Hiroyuki Kagechika, Koichi Shudo, Hirota Fujiki. Innovative cancer treatment of human lung cancer cells PC-9 with a synthetic retinoid Am80 and EGCG via inhibition of HDAC4 and HDAC5. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4723.
Multi-cell uplink-downlink beamforming throughput duality based on Lagrangian duality with per-base station power constraints (2008)

Despite significant research efforts in beamforming, the maximum achievable downlink throughput with beamforming in a multi-cell environment is not available due to difficulty in finding optimal downlink beamforming. Thus, to reformulate the problem into a more solvable form, we derive dual uplink throughput optimization problem to multi-cell downlink beam- forming throughput maximization with per-base station (BS) power constraints based on Lagrangian duality. The optimal downlink beamforming is shown to be a minimum mean squared error (MMSE) beamforming in the dual uplink. It is also shown that the dual uplink problem achieves the same optimal throughput as the primal downlink problem.
MiREDiBase: a manually curated database of validated and putative editing events in microRNAs (2020)

Abstract MicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase .
Effects of Superplasticizers in Highly Alkaline Model Suspensions Containing Silica Fume (1998)

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Authentication Indicator in Kerberos Tickets (2017)

This document updates RFC 4120, as it specifies an extension in the
Kerberos protocol. It defines a new authorization data type, AD-
AUTHENTICATION-INDICATOR. The purpose of introducing this data type is
to include an indicator of the strength of a client's
authentication in service tickets so that application services can use
it as an input into policy decisions.
Correlations between pyrolysis combustion flow calorimetry and conventional flammability tests with halogen‐free flame retardant polyolefin compounds (2008)

Abstract Seven halogen‐free flame retardant (FR) compounds were evaluated using pyrolysis combustion flow calorimetry (PCFC) and cone calorimetry. Performance of wires coated with the compounds was evaluated using industry standard flame tests. The results suggest that time to peak heat release rate (PHRR) and total heat released (THR) in cone calorimetry (and THR and temperature at PHRR in PCFC) be given more attention in FR compound evaluation. Results were analyzed using flame spread theory. As predicted, the lateral flame spread velocity was independent of PHRR and heat release capacity. However, no angular dependence of flame spread velocity was observed. Thus, the thermal theory of ignition and flame spread, which assumes that ignition at the flame front occurs at a particular flame and ignition temperature, provides little insight into the performance of the compounds. However, results are consistent with a heat release rate greater than about 66kW/m 2 during flame propagation for sustained ignition of insulated wires containing mineral fillers, in agreement with a critical heat release rate criterion for burning. Mineral fillers can reduce heat release rate below the threshold value by lowering the flaming combustion efficiency and fuel content. A rapid screening procedure using PCFC is suggested by logistic regression of the binary (burn/no‐burn) results. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Measuring the electrical resistivity and contact resistance of vertical carbon nanotube bundles for application as interconnects (2011)

Carbon nanotubes (CNT) are known to be materials with potential for manufacturing sub-20 nm high aspect ratio vertical interconnects in future microchips. In order to be successful with respect to contending against established tungsten or copper based interconnects, though, CNT must fulfil their promise of also providing low electrical resistance in integrated structures using scalable integration processes fully compatible with silicon technology. Hence, carefully engineered growth and integration solutions are required before we can fully exploit their potentialities. This work tackles the problem of optimizing a CNT integration process from the electrical perspective. The technique of measuring the CNT resistance as a function of the CNT length is here extended to CNT integrated in vertical contacts. This allows extracting the linear resistivity and the contact resistance of the CNT, two parameters to our knowledge never reported separately for vertical CNT contacts and which are of utmost importance, as they respectively measure the quality of the CNT and that of their metal contacts. The technique proposed allows electrically distinguishing the impact of each processing step individually on the CNT resistivity and the CNT contact resistance. Hence it constitutes a powerful technique for optimizing the process and developing CNT contacts of superior quality. This can be of relevant technological importance not only for interconnects but also for all those applications that rely on the electrical properties of CNT grown with a catalytic chemical vapor deposition method at low temperature.
Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units (2012)

Monogenic diseases are frequent causes of neonatal morbidity and mortality, and disease presentations are often undifferentiated at birth. More than 3500 monogenic diseases have been characterized, but clinical testing is available for only some of them and many feature clinical and genetic heterogeneity. Hence, an immense unmet need exists for improved molecular diagnosis in infants. Because disease progression is extremely rapid, albeit heterogeneous, in newborns, molecular diagnoses must occur quickly to be relevant for clinical decision-making. We describe 50-hour differential diagnosis of genetic disorders by whole-genome sequencing (WGS) that features automated bioinformatic analysis and is intended to be a prototype for use in neonatal intensive care units. Retrospective 50-hour WGS identified known molecular diagnoses in two children. Prospective WGS disclosed potential molecular diagnosis of a severe GJB2-related skin disease in one neonate; BRAT1-related lethal neonatal rigidity and multifocal seizure syndrome in another infant; identified BCL9L as a novel, recessive visceral heterotaxy gene (HTX6) in a pedigree; and ruled out known candidate genes in one infant. Sequencing of parents or affected siblings expedited the identification of disease genes in prospective cases. Thus, rapid WGS can potentially broaden and foreshorten differential diagnosis, resulting in fewer empirical treatments and faster progression to genetic and prognostic counseling.
Intrinsic Tailing of Resistive States Distributions in Amorphous HfO<sub><italic>x</italic></sub> and TaO<sub><italic>x</italic></sub> Based Resistive Random Access Memories (2015)

We report on the ineffectiveness of programming oxide-based resistive random access memory (OxRAM) at low current with a program and verify algorithm due to intrinsic relaxation of the verified distribution to the natural state distribution obtained by single-pulse programming without verify process. Based on oxygen defect formation thermodynamics and on their diffusion barriers in amorphous HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> and TaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> , we describe the intrinsic nature of tailing of the verified low resistive state and high resistive state distributions. We introduce different scenarios to explain fast distribution widening phenomenon, which is a fundamental limitation for OxRAM current scaling and device reliability.
Pseudomonas aeruginosaExoenzyme S Stimulates Murine Lymphocyte Proliferation In Vitro (1999)

The exuberant immunoinflammatory response that is associated with Pseudomonas aeruginosa infection is the major source of the morbidity and mortality in cystic fibrosis (CF) patients. Previous studies have established that an exoproduct of P. aeruginosa (exoenzyme S) is a mitogen for human T lymphocytes and activates a larger percentage of T cells than most superantigens, which may contribute to the immunoinflammatory response. An animal model would facilitate studies of the pathophysiologic consequences of this activation. As a first step toward developing an animal model, the murine lymphocyte response to exoenzyme S was examined. When stimulated with exoenzyme S, splenocytes isolated from naive mice entered S phase and proliferated. The optimum response occurred after 2 to 3 days in culture, at 4 x 10(5) cells per well and 5.0 micrograms of exoenzyme S per ml. The response was not due to lipopolysaccharide, since Rhodobacter sphaeroides lipid A antagonist did not block the response. Other preparations of exoenzyme S stimulated lymphocyte proliferation, since the response to recombinant exoenzyme S (rHisExo S) cloned from strain 388 was similar to the response to exoenzyme S from strain DG1. There was evidence that genetic variability influenced the response, since A/J, CBA/J, and C57BL/6 mice were high responders and BALB/cJ mice were low responders following stimulation with exoenzyme S. Both splenic T and B lymphocytes entered the cell cycle in response to exoenzyme S. Thus, murine lymphocytes, like human lymphocytes, respond to P. aeruginosa exoenzyme S, which supports the development of a murine model that may facilitate our understanding of the role that exoenzyme S plays in the pathogenesis of P. aeruginosa infections in CF patients.
Relevance of charges and polymer mechanical stiffness in the mechanism and kinetics of formation of liponanoparticles probed by the supported bilayer model approach (2019)

In specific conditions, co-incubation of polymer nanoparticles and phospholipid vesicles leads to the formation of lipid bilayer coated nanoparticles usable as biocompatible drug delivery systems for co-encapsulation of two drugs. In this work, we focused on the preparation and characterization of liponanoparticles obtained by co-incubation of poly(d,l, lactic acid) (PDLLA) and neutral (POPC) or cationic (POPC/DOTAP) liposomes. The comparison of the behavior of the various studied vesicles co-incubated with nanoparticles highlighted the role of electrostatic interactions. Although the bilayer adsorbed at the surface of polymer nanoparticles was not visible by cryoTEM, zeta-potential measurements and fluorescence confocal microscopy showed evidence of the formation of hybrid nanoparticles in the presence of cationic vesicles. Using silicon dioxide and Langmuir-Schaefer transferred polymer layer-coated surfaces, a thorough analysis of the process of formation of a phospholipid bilayer at the surface of a PDLLA film was performed by combining QCM-D and AFM experiments, taking into account the nature and properties of the support, and the concentration and charge of the lipids. Contrarily to POPC vesicles, cationic ones formed a bilayer on the PDLLA layer in water, but their fast rupture on the soft material did not allow complete nanoparticle surface coverage. This work demonstrates the role of charges and polymer mechanical stiffness in the mechanism and kinetics of formation of PDLLA liponanoparticles in pure water.
Amplifying ion signal levels for MS/MS and MSn applications in native MS experiments in negative ion mode using cVSSI techniques (2022)

Capillary vibrating sharp-edge spray ionization (cVSSI) has been investigated for its utility in tandem mass spectrometry (MS) and multistage tandem MS (MSn) experiments for native MS analyses in negative ion mode. Compared with capillary electrosprayionization (cESI) and heated electrospray ionization, cVSSI provided significant increases (up to >1000 fold) in ion signal levels. Signal-to-noise ratio (S/N) show a reduction in difference where cVSSI provides an increase of up to 7 fold. Performing MS3 experiments on all biomolecules examined here showed that more fragment ions could be identified from the cVSSI experiments. Additionally, the ion intensity levels of fragment ions observed with all ionization sources exceeds the S/N advantage of the precursor ions. Tracking MS/MS product ions as a function of analyte concentration reveals an ~10 fold sensitivity advantage for the cVSSI approach when compared with the other ionization sources. Taken together, the results highlight the importance of the total ion signal advantage provided by cVSSI (as opposed to S/N) and are discussed in light of ion utilization considerations. Finally, separate experiments demonstrate that the ion signal level advantages hold even for samples for which small amounts of organic solvent are used to improve ionization.