gebhart/patrepeval huggingface dataset:
Constrained phenylalanine analogues (1992)

Three Tic-containing (Tic = 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) model peptides were synthesized to assess the tendency of this constrained Phe analogue to fold into a beta-bend and a helical structure, and to adopt a preferred side-chain disposition. The results of the solution conformational analysis, performed by using Fourier transform infrared absorption and 1H nuclear magnetic resonance, indicate that in chloroform the -Aib-D-Tic-Aib-, -(Aib)2-D-Tic-(Aib)2-, and -L-Pro-D-Tic- sequences fold into intramolecularly H-bonded forms to a great extent. An X-ray diffraction analysis on p-BrBz-(Aib)2-DL-Tic-(Aib)2-OMe monohydrate and p-BrBz-L-Pro-D-Tic-NHMe allows us to conclude that, while the pentapeptide methylester forms an incipient (distorted) 3(10)-helix, the dipeptide methylamide adopts a type-II beta-bend conformation. In both cases, the D-Tic side-chain conformation is D, gauche(-). The implications for the use of the Tic residue in designing conformationally restricted analogues of bioactive peptides are briefly discussed.
Classroom to Clinic: Merging Education and Research to Efficiently Prototype Medical Devices (2013)

Innovation in patient care requires both clinical and technical skills, and this paper presents the methods and outcomes of a nine-year, clinical-academic collaboration to develop and evaluate new medical device technologies, while teaching mechanical engineering. Together, over the course of a single semester, seniors, graduate students, and clinicians conceive, design, build, and test proof-of-concept prototypes. Projects initiated in the course have generated intellectual property and peer-reviewed publications, stimulated further research, furthered student and clinician careers, and resulted in technology licenses and start-up ventures.
Size Independent pH Sensitivity for Ion Sensitive FinFETs Down to 10 nm Width (2019)

We investigate pH sensitivity dependence on width and length of ion sensitive field effect transistors (ISFETs) fabricated using CMOS FinFET technology. In the literature, there is currently no consensus about the pH sensitivity dependence on the FET geometrical dimensions. We observe no significant dependence of pH sensitivity on (Fin)FET widths (1000 to 10 nm) and lengths (1100 to 145 nm). The results indicate that it is possible to aggressively scale FETs, and create a dense array of pH sensors without any loss in sensitivity. These experimental findings are in accordance with our 3D TCAD modeling of electrolyte and (Fin)FET, which also show neither a degradation nor a boost in pH sensitivity when nano-scaling the FETs. Moreover, apart from ISFETs with SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> surface (32.3 ± 4.4 mV/pH), we report higher sensitivity with Ta <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> surface (51.2 ± 4.2 mV/pH), which is also a more robust material.
Comparative evaluation of modulation methods for a three-phase/switch buck power factor corrector concerning the input capacitor voltage ripple (2002)

For a three-phase three-switch buck-type PWM rectifier with unity power factor, the RMS value of the input filter capacitor voltage ripple is calculated for different modulation methods. A modulation method being optimal concerning the occurring switching losses and the RMS value of the capacitor voltage ripple is identified and guidelines for the dimensioning of the input filter are derived.
Optimal determination of the vapor pressure critical exponent (1978)

Abstract Correlations producing thermodynamic property tables employ the concepts of scaling with increasing frequency in the vapor‐liquid critical region. One of the important concepts is that the vapor pressure equation should provide infinite curvature and finite slope ψ c at the critical point. The vapor pressure critical exponent θ describes the divergent curvature in a power law expression. This paper provides an extensive study of θ. We have determined an optimal value of θ by two general approaches: a curve fit method (CFM) which employs least‐squares analyses, and a numerical derivative method (NDM). The CFM is interpolative but requires a vapor pressure equation, while the NDM is extrapolative but is independent of the vapor pressure equation. The vapor pressure equations, which satisfy scaling concepts most closely, exhibit a very flat minima for the CFM. As a result, the values of θ which provide reasonable correlations vary over an appreciable range (depending upon the compound, form of the equation, and the temperature range). The NDM did not present any particular difficulties. Our overall weighted average for θ is 0.199 with a standard deviation of 0.052, while the overall numerical average was 0.225 with a standard deviation of 0.045; the final recommended value of θ is 0.22 ± 0.04.
Apokalyptisches Denken in den USA: Die Bestseller-Serie "Left Behind" (2016)

In den Jahren 1995-2007 wurde in den USA eine sechzehnteilige Romanreihe mit dem Titel Left Behind veröffentlicht. Die einzelnen Bände führten wiederholt die US-amerikanischen Bestsellerlisten an und wurden weltweit insgesamt über 63 Millionen Mal verkauft. Die Autoren der Serie, Tim LaHaye und Jerry Jenkins, gehören einer apokalyptisch ausgerichteten Strömung der evangelikalen Bewegung an, welche als prämillenaristischer Dispensationalismus bezeichnet wird. In den Romanen stellen sie auf fiktive Weise die spezifische Endzeiterwartung dieser evangelikalen Gruppierung dar, welche von einer biblizistischen Auslegung der Johannes-Offenbarung geprägt ist. Diese führt zur Erwartung einer sieben Jahre andauernden Periode apokalyptischer Plagen, während welcher eine christliche Widerstandsgruppe gegen den Antichristen und seine Truppen kämpft. Am Ende der Apokalypse kehrt Jesus Christus zur Erde zurück, um all seine Feinde zu vernichten und alle „wahren ChristInnen" zu erlösen. Das Ziel der vorliegenden Diplomarbeit ist es, das in der Left Behind Serie zum Ausdruck gebrachte apokalyptische Denken des prämillenaristischen Dispensationalismus aus theologisch-ethischer Perspektive zu analysieren. Im Zuge dessen wird auch aufgezeigt, dass die Autoren die Romane nicht nur als Mittel zur Evangelisierung, sondern auch zur politischen Propaganda einsetzen. Im Rahmen der theologisch-ethischen Analyse wird dargestellt, inwiefern dies vor allem in Bezug auf die in der Serie zum Ausdruck gebrachte heilspartikularistische Vision der Left Behind Autoren, sowie die damit in Zusammenhang stehende positiven Sicht von Gewalt und Krieg problematisiert werden muss. Die Arbeit präsentiert dabei aktuelle Positionierungen aus der christlichen Theologie und Sozialethik zu den Themen Heilspartikularismus und Gewalt/Krieg und stellt diese der religiösen Botschaft der Left Behind Serie gegenüber. Eine abschließende ethische Betrachtung zeigt auf, worin der Unterschied zwischen der allgemeinen eschatologischen Ausgerichtetheit des christlichen Glaubens und der radikalen Endzeiterwartung apokalyptischer Gruppierungen liegt.
Chemistry-based RNA technologies: demonstration of usefulness of libraries of ribozymes and short hairpin RNAs (shRNAs) (2005)

Mechanism of action of hammerhead ribozymes has been investigated and their intracellular activities have been improved. Based on the improved ribozymes and more recently discovered natural RNAi, we have created libraries of both ribozymes and short hairpin RNAs (shRNAs). The introduction of a library of active ribozymes or shRNAs into cells, and the subsequent screening for phenotypic changes, allows the rapid identification of gene function.
High-Power Photonic Transmitter-Mixers with Integrated Wilkinson Power Combiner for Wireless Communication with High Data Rate (15 Gbps) at W-band (2012)

We demonstrate photonic transmitters-mixers integrated with Wilkinson power-combiners. Compared with single-ended operation, double-ended operation exhibits 5.5-dB higher output power over wide frequencies (65-100GHz). 15Gbps error-free wireless transmission with 6.6dBm output at 93 GHz is achieved.
Figure S1 from Oral IRAK-4 Inhibitor CA-4948 Is Blood-Brain Barrier Penetrant and Has Single-Agent Activity against CNS Lymphoma and Melanoma Brain Metastases (2023)

&lt;p&gt;Supplemental Figure 1. Myddosome signaling in normal human cerebral cortex.&lt;/p&gt;
Light-Weight Sequential SBL Algorithm: An Alternative to OMP (2023)

We present a Light-Weight Sequential Sparse Bayesian Learning (LWS-SBL) algorithm as an alternative to the orthogonal matching pursuit (OMP) algorithm for the general sparse signal recovery problem. The proposed approach formulates the recovery problem under the Type-II estimation framework and the stochastic maximum likelihood objective. We compare the computational complexity for the proposed algorithm with OMP and highlight the main differences. For the case of parametric dictionaries, a gridless version is developed by extending the proposed sequential SBL algorithm to locally optimize grid points near potential source locations and it is empirically shown that the performance approaches Cramer-Rao bound.´ Numerical results using the proposed approach demonstrate the support recovery performance improvements in different scenarios at a small computational price when compared to the OMP algorithm.
Carfilzomib Exerts Anti-Neoplastic Activity in Waldenstrom Macroglobulinemia. (2009)

Abstract Abstract 4916 Introduction Proteasome inhibition represents a valid therapeutical approach in several tumors and its use has been validated in Waldenstrom's macroglobulinemia (WM), where single-agent Bortezomib has been successfully tested in phase 2 clinical trials. Nevertheless, a significant fraction of patients relapse, or develop significant toxicity due to high toxicity in non-transformed cells. Therefore preclinical evaluation of new proteasome inhibitor with a more selective inhibition of neoplastic cells is needed in order to increase efficacy and improve patient outcome. We tested Carfilzomib, a tetrapeptide epoxyketone selective inhibitor of the chymotrypsin-like activity of the immunoproteasome and constitutive proteasome in WM. Methods WM and IgM secreting low-grade lymphoma cell lines (BCWM.1, MEC1, RL) were used. Expression of imunoproteasome and constitutive proteasome subunits (beta1, beta2, beta5; LMP2, MECL1, LMP7) were detected primary WM cells and cell lines by an ELISA-based assay. Cytotoxicity and DNA synthesis were measured by thymidine uptake and MTT, respectively. Cell signaling and apoptotic pathways were determined by Western Blot. Determination of the additive or synergistic effect of drugs combination was calculated using the CalcuSyn software based on the Chou-Talalay method. Results Primary CD19 bone-marrow derived WM cells express higher level of the immunopreoteasome as compared to the constitutive proteasome. Carfilzomib inhibited the chymotrypsin-like activity of both the immunoproteasome (LMP7) and the constitutive proteasome (beta5) and in WM cells, in a dose-dependent manner; leading to inhibition of proliferation (IC50: 5nM; 48h) and induction of cytotoxicity (IC50: 7.5nM; 48h) in WM cells. Carfilzomib mediated apoptosis in WM by increasing PARP-, caspase-9- and -3-cleavage; as well as by inducing activation of c-jun-N-terminal kinase and ER-stress in a dose-dependent manner. Moreover, combination of Carfilzomib and bortezomib induced synergistic cytotoxicity in WM cells, as shown by enhanced PARP-, caspase-9- and -3-cleavage; and synergy in inhibiting the chymotrypsin-like activity of the immunoproteasome and constitutive proteasome. Conclusion Taken together, these findings provide the pre-clinical rational for testing Carfilzomib in Waldenstrom Macroglobulinemia. Disclosures Aujay: Proteolix: Employment, Equity Ownership. Demo:Proteolix: Employment, Equity Ownership. Ghobrial:Millennium: Honoraria, Research Funding, Speakers Bureau; Celgene: Consultancy, Honoraria, Speakers Bureau; Novartis: Honoraria, Speakers Bureau.
Surface Reconstructions of Lamellar ABC Triblock Copolymer Mesostructures (2003)

We show that the near surface structure of lamellar ABC triblock copolymer mesostructures can deviate considerably from the “ideal” surface anticipated from the bulk structure of the material. Varying the molecular architecture and the surface energy difference between the respective blocks, we show that such surface reconstructions are caused by a complex balance of enthalpic and entropic contributions to the free energy of the system. The results are compared to the well-known surface behavior of classical crystals and experimental conditions for what may be called “block copolymer surface science” are discussed.
Spectral And Temporal Characteristics Of Light Sources (1988)

The spectral and temperal characteristics of light sources are important considerations to optimize the performance of a lighting system to meet the needs of the receiver. The output of sources varies by wave length and may peak in the ultra violet, visible or infra-red portion of the spectrum. Variations in the supply frequency (dc, 60 hertz, etc) and the wave shaping provided by the ballast needed for some lamps plus the lamp operation characteristics will produce changes in output with time. Proper selection of the lamp and its ballast when required can achieve optimum performance to meet the receiver needs and any added system requirements.
Black into green: A BIG opportunity for North Dakota’s oil and gas producers (2019)

A new perspective on carbon economics is developed and applied to demonstrate that oil and natural gas producers in North Dakota (ND) have an opportunity to make a profitable transition to wind energy producers. ND's oil and gas producers can fund this black into green (BIG) transition by: first, investing a fraction of their revenues into wind energy farms; and second, reinvesting a portion of revenues from the wind-generated electricity. Over a period of 40 years, 100% of the greenhouse gas emissions associated with the production and consumption of ND's oil and gas could be offset with an investment of 10% of both hydrocarbons' value and a reinvestment of three cents per kilowatt-hour of wind-generated electricity. At the end of the 40-year period, the resultant 155-gigawatt wind farm would have offset 13.4 × 109 tons of carbon dioxide equivalent and cost $9.90/ton of offset carbon dioxide equivalent. This BIG example demonstrates the financial and environmental benefits of ND's oil and gas producers transforming into renewable energy producers; hence regulators, hydrocarbon producers, and utilities should take note and think BIG. The reconfigurable, Excel-based model used herein is provided to allow readers to extend this example from ND to other regions, hydrocarbons, and green energy sources.
Adaptive Multimedia Mining on Distributed Stream Processing Systems (2010)

We present an application for distributed semantic concept detection in multimedia streams. The streams are mined using Support Vector Machine based concept detectors (classifiers) deployed on a distributed stream processing system. We organize the classifiers into a hierarchical topology based on semantic relationships between the concepts of interest, and use the system resource manager to place the topology across a set of processing nodes. We then develop distributed game theoretic optimization strategies for dynamic adaptation of individual classifier operating characteristics in order to maximize end-to-end application utility under varying resource availability. As part of this paper, we will demonstrate the principles behind large-scale multimedia stream mining, and showcase the design, development, deployment, and distributed adaptation of such applications on a large scale cluster. A video demonstration of the system can be found at: http://childman.bol.ucla.edu/ICDM/demovideoicdm2009.swf.
Poly Lactic-co-Glycolic Acid-Coated Toluidine Blue Nanoparticles for the Antibacterial Therapy of Wounds (2021)

Bacterial infections in wounded skin are associated with high mortality. The emergence of drug-resistant bacteria in wounded skin has been a challenge. Toluidine blue (TB) is a safe and inexpensive photosensitizer that can be activated and used in near-infrared photodynamic therapy to effectively kill methicillin-resistant <i>Staphylococcus aureus</i> (MRSA). However, its aggregation-induced quenching effect largely affects its clinical applications. In this study, TB nanoparticles (NPs) were synthesized using an ultrasound-assisted coating method. Their physicochemical and biological properties were studied and evaluated by scanning electron microscopy and Fourier-transform infrared spectroscopy. The TBNPs had a broad-spectrum antibacterial activity against Gram-positive bacteria (MRSA) and Gram-negative bacteria (<i>E. coli</i>). In addition, MTT, hemolysis, and acute toxicity tests confirmed that TBNPs had good biocompatibility. The TBNPs exhibited a high photodynamic performance under laser irradiation and efficiently killed <i>E. coli</i> and MRSA through generated reactive oxygen species, which destroyed the cell wall structure. The potential application of TBNPs in vivo was studied using an MRSA-infected wound model. The TBNPs could promote wound healing within 7 days, mainly by reducing the inflammation and promoting collagen deposition and granulation tissue formation. In conclusion, the TBNPs offer a promising strategy for clinical applications against multiple-drug resistance.
Leukoreduction of blood transfusions—There is such a thing as a free lunch* (2010)

University of Rochester School of Medicine; Rochester, NY The authors have not disclosed any potential conflicts of interest.
Refined Requirements for Protein Regions Important for Activity of the TALE AvrBs3 (2015)

AvrBs3, the archetype of the family of transcription activator-like (TAL) effectors from phytopathogenic Xanthomonas bacteria, is translocated by the type III secretion system into the plant cell. AvrBs3 localizes to the plant cell nucleus and activates the transcription of target genes. Crucial for this is the central AvrBs3 region of 17.5 34-amino acid repeats that functions as a DNA-binding domain mediating recognition in a "one-repeat-to-one base pair" manner. Although AvrBs3 forms homodimers in the plant cell cytosol prior to nuclear import, it binds DNA as a monomer. Here, we show that complex formation of AvrBs3 proteins negatively affects their DNA-binding affinity in vitro. The conserved cysteine residues at position 30 of each repeat facilitate AvrBs3 complexes via disulfide bonds in vitro but are also required for the gene-inducing activity of the AvrBs3 monomer, i.e., activation of plant gene promoters. Our data suggest that the latter is due to a contribution to protein plasticity and that cysteine substitutions to alanine or serine result in a different DNA-binding mode. In addition, our studies revealed that extended parts of both the N-terminal and C-terminal regions of AvrBs3 contribute to DNA binding and, hence, gene-inducing activity in planta.
Resonant normal-incidence separate-absorption-charge-multiplication Ge/Si avalanche photodiodes (2009)

In this work the impedance of separate-absorption-charge-multiplication Ge/Si avalanche photodiodes (APD) is characterized over a large range of bias voltage. An equivalent circuit with an inductive element is presented for modeling the Ge/Si APD. All the parameters for the elements included in the equivalent circuit are extracted by fitting the measured S(22) with the genetic algorithm optimization. Due to a resonance in the avalanche region, the frequency response of the APD has a peak enhancement when the bias voltage is relatively high, which is observed in the measurement and agrees with the theoretical calculation shown in this paper.
Mode partition noise in vertical cavity surface emitting lasers (2002)

In vertical cavity surface emitting lasers (VCSELs), a single longitudinal mode is supported in a cavity that can allow multiple transverse modes. In contrast to edge emitting lasers where multiple modes are longitudinal with nearly identical transverse profile, transverse modes can have significant differences in their coupling efficiency. Hence, mode selective loss (MSL) is easily introduced and mode partition noise (MPN) is more significant to the intensity noise of VCSELs. In this paper, we discuss the relevant time scales of the mode partition dynamics of VCSELs and explain the low frequency dependence of the relative intensity noise (RIN) spectrum.
Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe (2017)

Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically mapped and compared cleavage and polyadenylation sites (PASs) in two yeast species, <i>S. cerevisiae</i> and <i>S. pombe</i> Although >80% of the mRNA genes in each species were found to display APA, <i>S. pombe</i> showed greater 3' UTR size differences among APA isoforms than did <i>S. cerevisiae</i> PASs in different locations of gene are surrounded with distinct sequences in both species and are often associated with motifs involved in the Nrd1-Nab3-Sen1 termination pathway. In <i>S. pombe,</i> strong motifs surrounding distal PASs lead to higher abundances of long 3' UTR isoforms than short ones, a feature that is opposite in <i>S. cerevisiae</i> Differences in PAS placement between convergent genes lead to starkly different antisense transcript landscapes between budding and fission yeasts. In both species, short 3' UTR isoforms are more likely to be expressed when cells are growing in nutrient-rich media, although different gene groups are affected in each species. Significantly, 3' UTR shortening in <i>S. pombe</i> coordinates with up-regulation of expression for genes involved in translation during cell proliferation. Using <i>S. pombe</i> strains deficient for Pcf11 or Pab2, we show that reduced expression of 3'-end processing factors lengthens 3' UTR, with Pcf11 having a more potent effect than Pab2. Taken together, our data indicate that APA mechanisms in <i>S. pombe</i> and <i>S. cerevisiae</i> are largely different: <i>S. pombe</i> has many of the APA features of higher species, and Pab2 in <i>S. pombe</i> has a different role in APA regulation than its mammalian homolog, PABPN1.
Influence of Particle Geometry on Gastrointestinal Transit and Absorption following Oral Administration (2017)

Geometry has been considered as one of the important parameters in nanoparticle design because it affects cellular uptake, transport across the physiological barriers, and in vivo distribution. However, only a few studies have been conducted to elucidate the influence of nanoparticle geometry in their in vivo fate after oral administration. This article discloses the effect of nanoparticle shape on transport and absorption in gastrointestinal (GI) tract. Nanorods and nanospheres were prepared and labeled using fluorescence resonance energy transfer molecules to track the in vivo fate of intact nanoparticles accurately. Results demonstrated that nanorods had significantly longer retention time in GI tract compared with nanospheres. Furthermore, nanorods exhibited stronger ability of penetration into space of villi than nanospheres, which is the main reason of longer retention time. In addition, mesenteric lymph transported 1.75% nanorods within 10 h, which was more than that with nanospheres (0.98%). Fluorescent signals arising from nanoparticles were found in the kidney but not in the liver, lung, spleen, or blood, which could be ascribed to low absorption of intact nanoparticles. In conclusion, nanoparticle geometry influences in vivo fate after oral delivery and nanorods should be further investigated for designing oral delivery systems for therapeutic drugs, vaccines, or diagnostic materials.