gebhart/patrepeval huggingface dataset:
Controlling the self-assembly and material properties of β-sheet peptide hydrogels by modulating intermolecular interactions (2023)

Self-assembling peptides are a promising biomaterial with potential applications in medical de-vices and drug delivery. In the right combination of conditions, self-assembling peptides can form self-supporting hydrogels. Here, we describe how balancing attractive and repulsive intermo-lecular forces is critical for successful hydrogel formation. Electrostatic repulsion is tuned by al-tering the peptide’s net charge and intermolecular attractions are controlled through the degree of hydrogen bonding between specific amino acid residues. We find that an overall net peptide charge of +/-2 is optimal to facilitate the assembly of self-supporting hydrogels. If the net peptide charge is too low then dense aggregates form, while a high molecular charge inhibits the for-mation of larger structures. At constant charge, altering the terminal amino acids from glutamine to serine decreases the degree of hydrogen bonding within the assembling network. This tunes the viscoelastic properties of the gel, reducing the elastic modulus by two to three orders of magnitude. Finally, hydrogels could be formed from glutamine-rich, highly charged peptides by mixing the peptides in combinations with a resultant net charge of +/-2. These results illustrate how understanding and controlling self-assembly mechanisms through modulating intermolecular interactions can be exploited to derive a range of structures with tuneable properties.
Attack Detection and Localization in Smart Grid with Image-based Deep Learning (2021)

Smart grid's objective is to enable electricity and information to flow two-way while providing effective, robust, computerized, and decentralized energy delivery. This necessitates the use of state estimation-based techniques and real-time analysis to ensure that effective controls are deployed properly. However, the reliance on communication technologies makes such systems susceptible to sophisticated data integrity attacks imposing serious threats to the overall reliability of smart grid. To detect such attacks, advanced and efficient anomaly detection solutions are needed. In this paper, a two-stage deep learning-based framework is carefully designed by embedding power system's characteristics enabling precise attack detection and localization. First, we encode temporal correlations of the multivariate power system time-series measurements as 2D images using image-based representation approaches such as Gramian Angular Field (GAF) and Recurrence Plot (RP) to obtain the latent data characteristics. These images are then utilized to build a highly reliable and resilient deep Convolutional Neural Network (CNN)-based multi-label classifier capable of learning both low and high level characteristics in the images to detect and discover the exact attack locations without leveraging any prior statistical assumptions. The proposed method is evaluated on the IEEE 57-bus system using real-world load data. Also, a comparative study is carried out. Numerical results indicate that the proposed multi-class cyber-intrusion detection framework outperforms the current conventional and deep learning-based attack detection methods.
ChemInform Abstract: Synthesis of the Common C.1—C.13 Hydrophobic Domain of the B‐Type Amphidinolides. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Critical Dose for Strained Layer Configurations (1996)

We introduce an equilibrium critical Ge dose as stability criterion for strained SiGe structures, which is based on our new approach in equilibrium theory for strained layer relaxation reported in a recent paper. This critical dose concept for strained layers having a variable concentration of solute atoms in the host lattice is more appropriate to describe the condition for the occurrence of misfit dislocations than the simple criterion of a critical thickness. In addition we show how stable strained layer systems can be constructed beyond the “classical” critical thickness.
Time-of-flight PET image reconstruction using origin ensembles (2015)

The origin ensemble (OE) algorithm is a novel statistical method for minimum-mean-square-error (MMSE) reconstruction of emission tomography data. This method allows one to perform reconstruction entirely in the image domain, i.e. without the use of forward and backprojection operations. We have investigated the OE algorithm in the context of list-mode (LM) time-of-flight (TOF) PET reconstruction. In this paper, we provide a general introduction to MMSE reconstruction, and a statistically rigorous derivation of the OE algorithm. We show how to efficiently incorporate TOF information into the reconstruction process, and how to correct for random coincidences and scattered events. To examine the feasibility of LM-TOF MMSE reconstruction with the OE algorithm, we applied MMSE-OE and standard maximum-likelihood expectation-maximization (ML-EM) reconstruction to LM-TOF phantom data with a count number typically registered in clinical PET examinations. We analyzed the convergence behavior of the OE algorithm, and compared reconstruction time and image quality to that of the EM algorithm. In summary, during the reconstruction process, MMSE-OE contrast recovery (CRV) remained approximately the same, while background variability (BV) gradually decreased with an increasing number of OE iterations. The final MMSE-OE images exhibited lower BV and a slightly lower CRV than the corresponding ML-EM images. The reconstruction time of the OE algorithm was approximately 1.3 times longer. At the same time, the OE algorithm can inherently provide a comprehensive statistical characterization of the acquired data. This characterization can be utilized for further data processing, e.g. in kinetic analysis and image registration, making the OE algorithm a promising approach in a variety of applications.
Supplementary Figure 3 from Impact of Screening Test Performance and Cost on Mortality Reduction and Cost-effectiveness of Multimodal Ovarian Cancer Screening (2023)

&lt;p&gt;PDF file - 57K, CA125 Sensitivity Functions Estimated from PLCO and CARET Data&lt;/p&gt;
Binding of HIV-1 virions or gp120-anti-gp120 immune complexes to HIV-1-infected quiescent peripheral blood mononuclear cells reveals latent infection (1996)

HIV-1-infected quiescent CD4+ cells harbor the virus in an inactive state until subsequent activation. The possibility that HIV-1 itself and the virus envelope glycoprotein 120 (gp120) might be important agents of this activation was investigated. The present data indicate that binding of heat-inactivated HIV-1 (iHIV-1) to infected resting PBMCs was sufficient to activate NF-kappa B and AP-1, to induce transition from the G0/G1 stage of the cell cycle to the S/G2/M stage, to induce cell surface expression of CD25, to stimulate provirus integration, and to commit cells to produce virus. The cumulative amount of HIV-1 produced by iHIV-1-stimulated cells strictly depended on the concentration of p24gag in the virion preparations used for stimulation. Moreover, virus production was not evidenced in infected resting cells exposed to iHIV-1 previously incubated with soluble CD4 (sCD4), indicating that activation requires a contact between HIV-1 envelope glycoproteins and cell surface CD4. Although soluble gp120 did not stimulate virus production, we found that transition to the S/G2/M stage of the cell cycle, cell surface expression of activation Ags, and virus production were stimulated by cross-linking of CD4 by gp120-anti-gp120 immune complexes. Finally, incubation of gp120-anti-gp120 immune complexes with sCD4 inhibited these effects. These findings suggest that virions and gp120 anti-gp120 immune complexes found in infected patients at all times of infection can stimulate virus production in CD4+ cells harboring HIV-1 in an inducible state.
Parallel random number generation for VLSI systems using cellular automata (1989)

A novel random number generation (RNG) architecture of particular importance in VLSI for fine-grained parallel processing is proposed. It is demonstrated that efficient parallel pseudorandom sequence generation can be accomplished using certain elementary one-dimensional cellular automata (two binary states per site and only nearest-neighbor connections). The pseudorandom numbers appear in parallel from various cells in the cellular automaton on each clock cycle and pass standard empirical random number tests. Applications have been demonstrated in the design and analysis of special-purpose accelerators for Monte Carlo simulation of large intractable systems. In addition, significant advantages in pseudorandom built-in self-test of VLSI circuits using cellular automata based RNGs have been demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrical tuning of the spin–orbit interaction in nanowire by transparent ZnO gate grown by atomic layer deposition (2021)

We develop an InAs nanowire gate-all-around field-effect transistor using a transparent conductive zinc oxide (ZnO) gate electrode, which is in situ atomic layer deposited after growth of a gate insulator of Al2O3. We perform magneto-transport measurements and find a crossover from the weak localization effect to the weak antilocalization effect with an increasing gate voltage, which demonstrates that the Rashba spin–orbit coupling is tuned by the gate electrode. The efficiency of the gate tuning of the spin–orbit interaction is higher than those obtained for a two-dimensional electron gas, and as high as that for a gate-all-around nanowire metal-oxide-semiconductor field-effect transistor that was previously reported. The spin–orbit interaction is discussed in line with not only a conventionally used one-dimensional model but also with a recently proposed model that considers effects of microscopic band structures of materials.
The First Solution Structure of a Paramagnetic Copper(II) Protein:  The Case of Oxidized Plastocyanin from the Cyanobacterium Synechocystis PCC6803 (2001)

The NMR solution structure of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803 is here reported. The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross-peaks, 18 1D NOEs, 26 T(1) values, 96 dihedral angle constraints, and 18 H-bonds. The detection of broad hyperfine-shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root-mean-square deviation from the mean structure for the solution structure family is 0.72 +/- 0.14 and 1.16 +/- 0.17 A for backbone and heavy atoms, respectively. The structure is overall quite satisfactory and represents a breakthrough, in that it includes paramagnetic copper proteins among the metalloproteins for which solution structures can be afforded. The comparison with the available X-ray structure of a triple mutant is also performed.
Passive range measurement and discrepancy effects of distance for stereo scanning W-band radiometer (2010)

High resolution brightness temperature (BT) image of millimeter-wave radiometer is produced by mechanically scanning or by two dimensional antenna arrays for passive millimeter-wave (PMMW) range measurement. Similar to visible photogrammetry and stereo ranging, the range of target is estimated with stereo image pair taken by the radiometer. In this paper, we propose the range measurement method using 2-D scanning single radiometer for stereoscopic passive image. Two images are captured by scanning radiometer with baseline distance and range of the specific object can be determined by baseline distance with angular difference of an object from radiometric images. But there are many uncertainties for the range and range accuracy. We also have tested and analyzed this issue. In the experiment, range discrepancy effect dependent on target form of w-band scanning radiometer were tested and analyzed.
The Caenorhabditis elegans Ortholog of TRAP240, CeTRAP240/let-19, Selectively Modulates Gene Expression and Is Essential for Embryogenesis (2004)

Mediator complexes are large multiprotein assemblies that function in the regulation of eukaryotic gene transcription. In yeast, certain mediator subunits appear to comprise a subcomplex that acts in the regulation of a specific subset of genes. We investigated in a metazoan, Caenorhabditis elegans, the roles and interactions of two of those subunits, CeTRAP240/let-19 and CeTRAP230/dpy-22. We found that CeTRAP240/let-19 contains four domains that are conserved in the human TRAP240 protein and that one of those domains displays intrinsic transcriptional repression activity. Using RNA interference, we found that reduced expression of CeTRAP240/let-19 displayed a high penetrance of embryonic lethality in F1 progeny; animals that escaped embryonic arrest showed mutant phenotypes such as burst vulva and molting defects. CeTRAP240/let-19 appeared to affect specific genes, as CeTRAP240/let-19(RNAi) led to selectively reduced expression of a subset of reporter genes examined. Genetic experiments supported the view that CeTRAP240/let-19 and CeTRAP230/dpy-22, like their Drosophila and yeast counterparts, can operate on common pathways. Thus, a male tail phenotype caused by the pal-1(e2091) mutation was suppressed not only by CeTRAP230/dpy-22 mutants, as reported previously, but also by reduced expression of CeTRAP240/let-19. Additionally, CeTRAP240/let-19(RNAi) in a CeTRAP230/dpy-22 mutant background produced a strong synthetic lethal phenotype. Overall, our results establish specific roles of CeTRAP240/let-19 in C. elegans embryonic development and a functional interaction between CeTRAP240/let-19 and CeTRAP230/dpy-22. Interestingly, whereas this interaction has been conserved from yeast to mammals, the subcomplex modulates metazoan-specific genetic pathways, likely in addition to those also controlled in yeast.
Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses (2018)

Enrichment methodologies enable the analysis of minor members in multi-species transcriptomic data. We compared the standard enrichment of bacterial and eukaryotic mRNA to a targeted enrichment using an Agilent SureSelect (AgSS) capture for Brugia malayi, Aspergillus fumigatus, and the Wolbachia endosymbiont of B. malayi (wBm). Without introducing significant systematic bias, the AgSS quantitatively enriched samples, resulting in more reads mapping to the target organism. The AgSS-enriched libraries consistently had a positive linear correlation with their unenriched counterparts (r<sup>2</sup> = 0.559-0.867). Up to a 2,242-fold enrichment of RNA from the target organism was obtained following a power law (r<sup>2</sup> = 0.90), with the greatest fold enrichment achieved in samples with the largest ratio difference between the major and minor members. While using a single total library for prokaryote and eukaryote enrichment from a single RNA sample could be beneficial for samples where RNA is limiting, we observed a decrease in reads mapping to protein coding genes and an increase in multi-mapping reads to rRNAs in AgSS enrichments from eukaryotic total RNA libraries compared to eukaryotic poly(A)-enriched libraries. Our results support a recommendation of using AgSS targeted enrichment on poly(A)-enriched libraries for eukaryotic captures, and total RNA libraries for prokaryotic captures, to increase the robustness of multi-species transcriptomic studies.
Transferable Training Modules (2017)

Community health workers (promotores de salud) have the ability to empower communities to mitigate negative health outcomes. Current training efforts in environmental topics are lacking. This project addressed this gap by developing 4 transferable training modules on environmental health. By applying a series of surveys, interviews, and trainings, we evaluated their relevance. Partners provided favorable feedback for 3 of the 4 modules. It was also learned that the development method could be improved by engaging technically trained promotores de salud in the role of co-creators. This project has implications for environmental justice communities as it can lessen information disparities.
A Supersensitive CTC Analysis System Based on Triangular Silver Nanoprisms and SPION with Function of Capture, Enrichment, Detection, and Release (2018)

Detection of circulating tumor cells (CTCs) may be applied for diagnosis of early tumors like a liquid biopsy. However, the sensitivity remains a challenge because CTCs are extremely rare in peripheral blood. In this study, we developed a supersensitive CTC analysis system based on triangular silver nanoprisms (AgNPR) and superparamagnetic iron oxide nanoparticles (SPION) with function of capture, enrichment, detection, and release. The AgNPR was encoded with MBA (i.e., 4-mercaptobenzoic acid) and modified with rBSA (i.e., reductive bovine serum albumin) and FA (i.e., folic acid) generating organic/inorganic composite nanoparticle MBA-AgNPR-rBSA-FA, which has the function of surface-enhanced Raman scattering (SERS). The optimized SERS nanoparticles (i.e., MBA3-AgNPR-rBSA4-FA2) can be utilized for CTC detection in blood samples with high sensitivity and specificity, and the LOD (i.e., limit of detection) reaches to five cells per milliliter. In addition, the SPION was also modified with rBSA and FA generating magnetic nanoparticle SPION-rBSA-FA. Our supersensitive CTC analysis system is composed of MBA3-AgNPR-rBSA4-FA2 and SPION-rBSA-FA nanoparticles, which were applied for capture (via interaction between FA and FRα), enrichment (via magnet), and detection (via SERS) of cancer cells from blood samples. The results demonstrate that our supersensitive CTC analysis system has a better sensitivity and specificity than the SERS nanoparticles alone, and the LOD is up to 1 cell/mL. The flow cytometry and LSCM (i.e., laser scanning confocal microscope) results indicate the CTCs captured, enriched, and isolated by our supersensitive CTC analysis system can also be further released (via adding excessive free FA) for further cell expansion and phenotype identification.
Method for acquiring pressure measurements in presence of plasma-induced interference for supersonic flow control applications (2011)

The operation of pulsed-plasma actuators for flow control is often associated with the presence of charged species in the flow and severe electromagnetic interference with external circuitry. These effects can lead to time-resolved transducer pressure measurements that are contaminated with electromagnetic interference effects or even transducer damage due to the interaction with charged species. A new technique is developed that enables high-bandwidth pressure measurements to be made in the presence of such rapidly switched plasma actuators. The technique is applied for the specific configuration of a pulsed-plasma jet actuator (spark jet) that is used to control the unsteadiness of a shock wave/boundary layer interaction generated by a compression ramp in a Mach 3 flow. The critical component of the technique involves using a pulsed-ground electrode to drain the charged species from the plasma jet before they reach the pressure transducer. The pulsed-ground electrode was shown to drain charged species into the pulsed ground prior to interacting with the transducer, which made it possible to make measurements without damaging the transducer. The resulting signals were still contaminated by electromagnetic interference spikes and so a data-processing technique was used to remove the artifacts and recover a largely uncontaminated power spectrum. The signal processing scheme used interpolation schemes previously developed for laser Doppler velocimetry applications. The data-processing procedure is demonstrated with a benchmark case in which the electromagnetic interference was isolated from the pulsed-plasma jet actuation effect. It is shown that the data-processing procedure removed the contamination from the electromagnetic interference at all frequencies but for the pulsing frequency and its higher harmonics.
Association of periodontal disease with systemic health indices in dogs and the systemic response to treatment of periodontal disease (2011)

Increasing severity of attachment loss was associated with changes in systemic inflammatory variables and renal indices. A decrease in CRP concentration after treatment was correlated with the severity of PD. The BUN concentration increased significantly after treatment of PD. There is a need for continued research into the systemic impact of PD.
Materials and Molecular Research Division annual report 1975. [Summaries of research activities at Lawrence Berkeley Laboratory, University of California] (1975)

Separate abstracts were prepared for the four sections. (JFP)
12: Algorithmen I, Übung, SS 2019, 05.06.2019 (2019)

12 | 0:00:00 Start 0:10:03 Adaptives Sortieren 0:10:59 Insertion Sort: Adaptiv? 0:11:41 Insertion Sort: Erwartete Laufzeit 0:14:09 Natural Merge Sort 0:15:03 Erwartete Anzahl von Runs 0:19:51 Split Sort 0:22:41 Schnelle Mediansuche für Quicksort 0:33:01 Sortieralgorithmen in aktuellen Programmiersprachen Addison Wesley, 2005
Design and development of CoCrFeNiTa eutectic high entropy alloys (2020)

High entropy alloys (HEA) are an emerging class of metallic materials that have shown the potential to outsmart conventional alloy systems in terms of different physical and mechanical properties. Development of eutectic microstructure in high entropy alloys can help in obtaining even better combination of mechanical properties due to fine distribution of phases. Eutectic high entropy alloys have been developed in the present study by addition of tantalum to the CoCrFeNi system. Pseudo binary phase diagram of CoCrFeNi–Ta was calculated with the help of Thermocalc software. Different alloy compositions were prepared by arc melting under argon atmosphere. Development of lamellar microstructure consisting of FCC and Laves phase was confirmed by the microstructural and crystal structure characterization carried out with the help of SEM and XRD. Necessary changes in the calculated phase diagram, in the light of microstructure and crystal structure characterization results, has been proposed. To evaluate the effect of eutectic microstructure on the mechanical properties of developed alloys, mechanical characterization was carried out with the help of compression tests and hardness tests. Development of eutectic microstructure consisting of FCC and Laves has helped in significantly improving the yield strength of developed alloys without causing drastic decrease in ductility. Completely eutectic alloys have shown better combination of mechanical properties in comparison to the respective hypoeutectic and hypereutectic high entropy alloys. It is believed that development of complete eutectic microstructure in high entropy alloys can help in obtaining alloys with significantly improved combination of strength and ductility.