gebhart/patrepeval huggingface dataset:
In Situ Transport Measurements Reveal Source of Mobility Enhancement of MoS2 and MoTe2 during Dielectric Deposition (2020)

Layered transition metal dichalcogenides (TMDs) and other two-dimensional (2D) materials are promising candidates for enhancing the capabilities of complementary metal-oxide-semiconductor (CMOS) technology. Field-effect transistors (FETs) made with 2D materials often exhibit mobilities below their theoretical limit, and strategies such as encapsulation with dielectrics grown by atomic layer deposition (ALD) have been explored to tune carrier concentration and improve mobility. While molecular adsorbates are known to dope 2D materials and influence charge scattering mechanisms, it is not well understood how ALD reactants affect 2D transistors during growth, motivating in situ or operando studies. Here, we report electrical characterization of MoS<sub>2</sub> and MoTe<sub>2</sub> FETs during ALD of MoO<sub>x</sub>. The field effect mobility improves significantly within the first five cycles of ALD growth using Mo(NMe<sub>2</sub>)<sub>4</sub> as the metal-organic precursor and H<sub>2</sub>O as the oxidant. Analyses of the in situ transconductance at the growth temperature and ex situ variable temperature transconductance measurements indicate that the majority of the mobility enhancement observed at the beginning of dielectric growth is due to screening of charged impurity scattering by the adlayer. Control experiments show that exposure to only H<sub>2</sub>O or O<sub>2</sub> induces more modest and reversible electronic changes in MoTe2 FETs, indicating that negligible oxidation of the TMD takes place during the ALD process. Due to the strong influence of the first <2 nm of deposition, when the dielectric adlayer may be discontinuous and still evolving in stoichiometry, this work highlights the need for further assessment of nucleation layers and initial deposition chemistry, which may be more important than the bulk composition of the oxide itself in optimizing performance and reproducibility.
LL-37 Opsonizes and Inhibits Biofilm Formation of Aggregatibacter actinomycetemcomitans at Subbactericidal Concentrations (2013)

ABSTRACT Host defense peptides are immediate responders of the innate immunity that express antimicrobial, immunoregulatory, and wound-healing activities. Neutrophils are a major source for oral host defense peptides, and phagocytosis by neutrophils is a major mechanism for bacterial clearance in the gingival tissue. Dysfunction of or reduction in the numbers of neutrophils or deficiency in the LL-37 host defense peptide was each previously linked with proliferation of oral Aggregatibacter actinomycetemcomitans which resulted in an aggressive periodontal disease. Surprisingly, A. actinomycetemcomitans shows resistance to high concentrations of LL-37. In this study, we demonstrated that submicrocidal concentrations of LL-37 inhibit biofilm formation by A. actinomycetemcomitans and act as opsonins and agglutinins that greatly enhance its clearance by neutrophils and macrophages. Improved uptake of A. actinomycetemcomitans by neutrophils was mediated by their opsonization with LL-37. Enhanced phagocytosis and killing of A. actinomycetemcomitans by murine macrophage-like RAW 264.7 cells were dependent on their preagglutination by LL-37. Although A. actinomycetemcomitans is resistant to the bactericidal effect of LL-37, our results offer a rationale for the epidemiological association between LL-37 deficiency and the expansion of oral A. actinomycetemcomitans and indicate a possible therapeutic use of cationic peptides for host defense.
Orc4 spatiotemporally stabilizes centromeric chromatin (2018)

Abstract Spatiotemporal regulation in DNA replication maintains kinetochore stability. The epigenetically regulated centromeres (CENs) in the budding yeast Candida albicans have unique DNA sequences, replicate early and are clustered throughout the cell cycle. In this study, the genome-wide occupancy of replication initiation protein Orc4 reveals its abundance at all CENs in C. albicans . Orc4 associates with four different DNA motifs, one of which coincides with tRNA genes. Hi-C combined with genome-wide replication timing analyses identify enriched interactions among early or late replicating Orc4-bound regions. A simulated polymer model of chromosomes reveals that early replicating and strongly enriched Orc4-bound sites localize towards the kinetochores. Orc4 is constitutively localized to CENs, and both Orc4 and Mcm2 stabilize CENPA. CENPA chaperone Scm3 localizes at the kinetochore during anaphase, coinciding with the loading time of CENPA. We propose that this spatiotemporal nuclear localization of Orc4, with Mcm2 and Scm3, recruits CENPA and stabilizes centromeric chromatin.
Number of Subunits Comprising the Epithelial Sodium Channel (1999)

The human epithelial sodium channel (hENaC) is a hetero-oligomeric complex composed of three subunits, alpha, beta, and gamma. Understanding the structure and function of this channel and its abnormal behavior in disease requires knowledge of the number of subunits that comprise the channel complex. We used freeze-fracture electron microscopy and electrophysiological methods to evaluate the number of subunits in the ENaC complex expressed in Xenopus laevis oocytes. In oocytes expressing wild-type hENaC (alpha, beta, and gamma subunits), clusters of particles appeared in the protoplasmic face of the plasma membrane. The total number of particles in the clusters was consistent with the whole-cell amiloride-sensitive current measured in the same cells. The size frequency histogram for the particles in the clusters suggested the presence of an integral membrane protein complex composed of 17 +/- 2 transmembrane alpha-helices. Because each ENaC subunit has two putative transmembrane helices, these data suggest that in the oocyte plasma membrane, the ENaC complex is composed of eight or nine subunits. At high magnification, individual ENaC particles exhibited a near-square geometry. Functional studies using wild-type alphabeta-hENaC coexpressed with gamma-hENaC mutants, which rendered the functional channel differentially sensitive to methanethiosulfonate reagents and cadmium, suggested that the functional channel complex contains more than one gamma subunit. These data suggest that functional ENaC consists of eight or nine subunits of which a minimum of two are gamma subunits.
THE STRUCTURE AND ACTIVITY OF LEUPEPTINS AND RELATED ANALOGS (1971)

Leupeptins produced by various species of Actinomycetes, strongly inhibit proteases such as plasmin, trypsin and papainlj2'3). We previously reported4) the structures of two major components, acetyl-L-leucyl-L-
Scaling of multicast trees (1999)

One of the many benefits of multicast, when compared to traditional unicast, is that multicast reduces the overall network load. While the importance of multicast is beyond dispute, there have been surprisingly few attempts to quantify multicast's reduction in overall network load. The only substantial and quantitative effort we are aware of is that of Chuang and Sirbu [3]. They calculate the number of links L in a multicast delivery tree connecting a random source to m random and distinct network sites; extensive simulations over a range of networks suggest that L(m) &prop; m0.8. In this paper we examine the function L(m) in more detail and derive the asymptotic form for L(m) in k-ary trees. These results suggest one possible explanation for the universality of the Chuang-Sirbu scaling behavior.
531. Practical and Evidence-Based Considerations for Implementation of Bacterial Whole-Genome Sequencing Within Longitudinal Infection Control Practice (2019)

Abstract Background Whole-genome sequencing (WGS) of bacteria is becoming a routine tool within microbiology, yet its utility to help guide infection control (IC) practice longitudinally is underexplored. As with any technology adopted in the hospital, the integration of WGS into IC practice must be carefully managed and considered. We qualitatively report an evidence-based implementation workflow that considers WGS to help proactively guide IC professionals during investigation of infectious outbreaks. Methods We built upon lessons learned in an ongoing surveillance effort at a tertiary care hospital—utilizing retrospective WGS data within the Philips IntelliSpace Epidemiology system—to understand facilitators and barriers to the use of bacterial WGS longitudinally to inform IC workflow. Our team established a 9-month workgroup to study the practical aspects of implementing WGS in routine IC practice. From expert opinion collected via the workgroup, in addition to evidence from the literature, a workflow guidance document and checklist were codified. New ideas included incorporating education to promote the establishment of an IC triage process. Results Facilitators to implementation included ability to display genomic relatedness alongside relevant patient data to enable clinical actionability, ability to pivot time and resources rapidly when infections are a pseudo outbreak (false positive) or missed outbreak (false negative), opportunities for nuanced staff education, and willingness to be a first-of-kind adopter. Barriers were communication of genomic concepts to IC professionals and relevant institutional stakeholders, maintaining sharable notes of active investigations to promote data-sharing practices, and timing and review of relevant interventions into the facility workflow. Strategies to address these issues are considered. Conclusion This study provides a novel framework for adaptation of existing IC workflow strategies to leverage the utility of bacterial WGS, and it presents a schema to effectively engage relevant stakeholders, based on an analysis of the unique challenges inherent within IC practice. It also offers an innovative model for the development and implementation of IC workflows to account for, and adapt to, site-specific conditions. Disclosures All authors: No reported disclosures.
Multi-scale superpixel classification for optic cup localization (2014)

In this paper, we present a multi-scale approach based on superpixel classification for optic cup localization. Our approach provides 3 major contributions. First, a contrast enhancement scheme is proposed to reduce illumination influence and enhance feature discrimination. Second, features are extracted from multiple superpixels scales for richer description of the optic cup. Third, a unique cup is localized by integrating the multi-scales together using majority voting. Our approach was validated on a clinical online dataset, ORIGA-light, of 650 population-based images. Overall, our approach is able to achieve a 0.248 non-overlap ratio (m <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ) and a 0.085 absolute CDR error (δ). Experimental results also shows that our multi-scale approach has a complementary effect to increase performance stability, and is able to achieve a higher accuracy when compared with the previous state-of-the-art superpixel-based method.
Reconstruction of Glucose in Plasma from Interstitial Fluid Continuous Glucose Monitoring Data: Role of Sensor Calibration (2007)

After the recalibration step, the relative error in reconstructing plasma glucose was reduced significantly. Results also demonstrate that further margins of improvement of plasma glucose reconstruction are possible by developing more sophisticated recalibration procedures.
yucca6, a Dominant Mutation in Arabidopsis, Affects Auxin Accumulation and Auxin-Related Phenotypes (2007)

Auxin plays critical roles in many aspects of plant growth and development. Although a number of auxin biosynthetic pathways have been identified, their overlapping nature has prevented a clear elucidation of auxin biosynthesis. Recently, Arabidopsis (Arabidopsis thaliana) mutants with supernormal auxin phenotypes have been reported. These mutants exhibit hyperactivation of genes belonging to the YUCCA family, encoding putative flavin monooxygenase enzymes that result in increased endogenous auxin levels. Here, we report the discovery of fertile dominant Arabidopsis hypertall1-1D and hypertall1-2D (yucca6-1D, -2D) mutants that exhibit typical auxin overproduction phenotypic alterations, such as epinastic cotyledons, increased apical dominance, and curled leaves. However, unlike other auxin overproduction mutants, yucca6 plants do not display short or hairy root phenotypes and lack morphological changes under dark conditions. In addition, yucca6-1D and yucca6-2D have extremely tall (>1 m) inflorescences with extreme apical dominance and twisted cauline leaves. Microarray analyses revealed that expression of several indole-3-acetic acid-inducible genes, including Aux/IAA, SMALL AUXIN-UP RNA, and GH3, is severalfold higher in yucca6 mutants than in the wild type. Tryptophan (Trp) analog feeding experiments and catalytic activity assays with recombinant YUCCA6 indicate that YUCCA6 is involved in a Trp-dependent auxin biosynthesis pathway. YUCCA6:GREEN FLUORESCENT PROTEIN fusion protein indicates YUCCA6 protein exhibits a nonplastidial subcellular localization in an unidentified intracellular compartment. Taken together, our results identify YUCCA6 as a functional member of the YUCCA family with unique roles in growth and development.
Feasibility of a Clutchless Dual-Shaft Hybrid Transmission System for Performance Applications (2016)

A novel hybrid-electric transmission concept was sought that yields higher acceleration and smoother gear-shifts compared to existing dual-clutch systems while improving the energy efficiency of the vehicle. After evaluating a range of strategies, the elimination of the clutch was identified as a viable method for reducing the vehicle's effective inertia and viscous losses. The proposed architecture implements a single electric motor, and two separate shafts for odd and even gears, to replace the functions of a clutch. High acceleration rates can be achieved using the electric motor when launching the vehicle. Furthermore, the torque from the electric motor (EM) and internal combustion engine (ICE) can be simultaneously delivered through the two shafts to sustain this high acceleration. A 0 to 100 km/hr time of 3.18 s was simulated for a 1600 kg vehicle using a 180 kW EM and 425 kW ICE. In addition, the EM can be used to match the speeds of consecutive gears on the two shafts to reduce jerk while shifting. Shift durations were found to vary between 0.2 and 0.9 s using this strategy. Other benefits include regenerative braking and the removal of the reverse gear since the EM can rotate in either direction. It was also found that the vehicle can be operated on only electric power in urban settings - represented by the NEDC driving cycle - if the battery is recharged through regenerative braking, and by the ICE the vehicle is stopped.
bnstruct: an R package for Bayesian Network structure learning in the presence of missing data (2016)

Supplementary data are available at Bioinformatics online.
Chemoselective Peptide Backbone Diversification and Bioorthogonal Ligation by Ruthenium‐Catalyzed C−H Activation/Annulation (2021)

Abstract The field of peptide derivatization by metal‐catalyzed C−H activation has been mostly directed to modify the side chains, but poor attention has been given to the peptide backbone. Here we report a ruthenium‐catalyzed C−H activation/annulation process that can chemoselectively modify the peptide backbone producing functionalized isoquinolone scaffolds with high regioselectivity in a rapid and step‐economical manner. This strategy is characterized by racemization‐free conditions and the production of fluorescent peptides, and peptide conjugates to drugs, natural products and other peptide fragments, providing a chemical approach for the construction of novel peptide‐pharmacophore conjugates. Mechanistic studies suggest that amide bonds of peptide backbone act as the bidentate directing group to promote the C−H activation/annulation process. This report provides an unprecedented example of peptide backbone diversification and bioorthogonal ligation exploiting the power of ruthenium‐catalyzed C−H activation. magnified image
Monte Carlo simulation of high-field electron transport in alternating-current thin-film electroluminescent devices (1993)

We present an ensemble Monte Carlo simulation of electron transport in bulk ZnS at high electric fields. Scattering mechanisms associated with polar optical phonons, acoustic phonons (through deformation potential coupling), intervalley scattering, and impurities (neutral and ionized) are included in a nonparabolic multi-valley model. The simulated results show that energetic electrons are available for impact excitation at fields exceeding 1 MV/cm, and that transient effects are negligible in explaining measured efficiencies in ACTFEL devices.... ACTFEL, Electroluminescence, Monte Carlo, High-Field Transport, ZnS.
A Systematic Ex-Vivo Study of the Anti-Proliferative/Cytotoxic Bioactivity of Major Olive Secoiridoids’ Double Combinations and of Total Olive Oil Phenolic Extracts on Multiple Cell-Culture Based Cancer Models Highlights Synergistic Effects (2023)

Several individual olive oil phenols (OOPs) and their secoiridoid derivatives have been shown to exert anti-proliferative and pro-apoptotic activity in treatments of human cancer cell lines originating from several tissues. This study evaluated the synergistic anti-proliferative/cytotoxic effects of five olive secoiridoid derivatives (oleocanthal, oleacein, oleuropein aglycone, ligstroside aglycone and oleomissional) in all possible double combinations and of total phenolic extracts (TPEs) on eleven human cancer cell lines representing eight cell-culture-based cancer models. Individual OOPs were used to treat cells for 72 h in half of their EC<sub>50</sub> values for each cell line and their synergistic, additive or antagonistic interactions were evaluated by calculating the coefficient for drug interactions (CDI) for each double combination of OOPs. Olive oil TPEs of determined OOPs' content, originating from three different harvests of autochthonous olive cultivars in Greece, were evaluated as an attempt to investigate the efficacy of OOPs to reduce cancer cell numbers as part of olive oil consumption. Most combinations of OOPs showed strong synergistic effect (CDIs < 0.9) in their efficacy, whereas TPEs strongly impaired cancer cell viability, better than most individual OOPs tested herein, including the most resistant cancer cell lines evaluated.
Regimes of bandwidth enhancement in coupled-cavity semiconductor laser using photon–photon resonance (2019)

Abstract In the last decade, different solutions were proposed to boost the transmission bitrate of semiconductor lasers. Here, we focus on applying optical feedback to a semiconductor laser from an external cavity in order to induce enhancement of the modulation bandwidth up to 50 GHz as well as resonant modulation (RM) around frequencies approaching 60 GHz. High-speed modulation up to 90 Gbps under none-return to zero operation and a 45 Gbaud using pulse amplitude modulation-4 signals are predicted. Both types of improving the modulation performance of the laser are attributed to the photon–photon resonance (PPR) effect. The regimes of the external power reflectivity that correspond to both types of modulation response are specified. Comprehensive simulations are introduced to correlate the PPR frequency to the RM frequencies of the non-modulated coupled-cavity laser. Dependencies of the enhanced BW and PPR frequency on the cavity length and bias current are elucidated.
The effect of exercise on fatigue and physical functioning in breast cancer patients during and after treatment and at 6 months follow-up: A meta-analysis (2017)

Breast cancer is the leading cause of cancer in women worldwide. Exercise interventions may improve physical and psychological factors during and after active breast cancer treatment. The aim of this systematic review was to assess the current knowledge regarding the efficacy of physical exercise with respect to fatigue and self-reported physical functioning. Systematic searches in Cochrane Library, Medline, Embase, Cinahl, PsycINFO, AMED and PEDro. After assessing the quality of the studies, we identified 25 randomized controlled trials that included 3418 breast cancer patients. An increase in physical functioning and a decrease in fatigue were observed after a physical exercise intervention, with an SMD of 0.27 (0.12, 0.41) and -0.32 (-0.49, - 0.14), respectively. There were slightly higher improvements in physical functioning and fatigue when the patients received the intervention after adjuvant breast cancer treatment. The 6-month follow-up data showed a small favourable difference for the physical exercise group for both physical functioning and fatigue. This systematic review found that an exercise intervention program can produce short-term improvements in physical functioning and can reduce fatigue in breast cancer patients. However, more studies are needed to confirm the time-dependent observations in this study.
Low-complexity digital pre-emphasis technique for next generation optical transceiver (2015)

We experimentally verified the effectiveness of a novel digital pre-emphasis technique to compensate limited DAC bandwidth for next generation flexible systems. A gain larger than 1dB/0.1nm OSNR at the 7%-FEC limit has been experimentally verified for 8, 16 and 32QAM.
Cloning and expression in Saccharomyces cerevisiae of a Trichoderma reesei β-mannanase gene containing a cellulose binding domain (1995)

International audience
Comparative study of open-loop transmit diversity schemes with four antennas in DFT-precoded OFDMA using turbo FDE and iterative channel estimation (2012)

This paper compares the block error rate (BLER) performance of open-loop (OL) transmit diversity schemes with four antennas in the uplink for discrete Fourier transform (DFT)-precoded orthogonal frequency division multiple access (OFDMA). One candidate is a quasi-orthogonal (QO) - space-time block code (STBC) in which four-branch minimum mean-square error combining (MMSEC) is achieved at the cost of residual inter-code interference (ICI). Another candidate is a combination of STBC and selection diversity called time switched transmit diversity (TSTD) or frequency switched transmit diversity (FSTD). We assume a turbo frequency domain equalizer (FDE) associated with iterative decision-feedback channel estimation (DFCE) at a receiver to reduce the influences of the residual ICI and channel estimation (CE) error. From the extensive link-level simulation results, we show that a combination of STBC and TSTD (FSTD) is suitable as four-antenna OL transmit diversity scheme for DFT-precoded OFDMA using turbo FDE and iterative DFCE.
Weakly Coupled Multi Core Fibers with Optimum Design to Realize Selectively Ecitation of Individual Super-modes (2012)

A design of the weakly coupled 7 core fibers was optimized for the mode division multipleing transmission. By localizing super-modes, high spatial density would be successfully realized with simple setup utilizing the multi core connectors.
Inter-Slice Mobility Management in 5G: Motivations, Standard Principles, Challenges, and Research Directions (2022)

Mobility management in a sliced 5G network introduces new and complex challenges. In a network-sliced environment, user mobility has to be managed among not only different base stations or access technologies but also different slices. Managing user mobility among slices, or inter-slice mobility, motivates the need for new solutions. This article, presented as a tutorial, focuses on the problem of inter-slice mobility from the perspective of 3GPP standards for 5G. It provides a detailed overview of the relevant 3GPP standard principles. Accordingly, key technical gaps, challenges, and corresponding research directions are identified toward achieving seamless inter-slice mobility within the current 3GPP network slicing framework.