bluuebunny/crossref_metadata_2025 huggingface dataset:
PARP7 mono-ADP-ribosylates the agonist conformation of the androgen receptor in the nucleus
Authors: Kamata Teddy , Yang Chun-Song , Paschal Bryce M.
Published: July 2021

We recently described a signal transduction pathway that contributes to androgen receptor (AR) regulation based on site-specific ADP-ribosylation by PARP7, a mono-ADP-ribosyltransferase implicated in several human cancers. ADP-ribosylated AR is recognized by PARP9/DTX3L, a heterodimeric complex that contains an ADP-ribose reader (PARP9) and a ubiquitin E3 ligase (DTX3L). Here, we have characterized the cellular and biochemical requirements for AR ADP-ribosylation by PARP7. We found that the reaction requires nuclear localization of PARP7 and an agonist-induced conformation of AR. PARP7 contains a Cys3His1-type zinc finger (ZF), which also is critical for AR ADP-ribosylation. The Parp7 ZF is required for efficient nuclear import by a nuclear localization signal encoded in PARP7, but rescue experiments indicate the ZF makes a contribution to AR ADP-ribosylation that is separable from the effect on nuclear transport. ZF mutations do not detectably reduce PARP7 catalytic activity and binding to AR, but they do result in the loss of PARP7 enhancement of AR-dependent transcription of the MYBPC1 gene. Our data reveals critical roles for AR conformation and the PARP7 ZF in AR ADP-ribosylation and AR-dependent transcription.
An effective fault management scheme and comprehensive double line‐frequency ripple propagation analysis for MVDC networks
Authors: Sun Dongsen , Lu Xiaonan , Du Liang , Lu Fei
Published: July 2021

This paper proposes an effective fault management scheme for medium‐voltage direct current (MVDC) networks, which includes a virtual‐impedance‐based fault current limiter (VI‐FCL) on the DC side and a positive‐negative‐sequence (PNS) control scheme on the AC side. Depending on the fault current value, different protection strategies are adopted, which include either isolating the fault by opening circuit breakers or riding through the fault with the proposed VI‐FCL. It is known that unbalanced grid voltage can be found in conventional AC distribution feeders due to unbalanced loading conditions among three phases. The unbalanced grid voltage could induce double line‐frequency (2ω) ripples on both DC voltage and current, which could thereby trigger protection malfunction in the DC sub‐sections. Therefore, the PNS control scheme is used to eliminate the 2ω ripples of both DC voltages and currents caused by unbalanced AC voltages. Furthermore, a detailed 2ω mathematical model of the MVDC network under unbalanced AC voltage condition is derived to investigate how the 2ω ripple propagates across the network. A voltage source converter based multi‐terminal MVDC network is built to test DC faults with different fault currents, unbalanced AC voltages, and different control schemes. The test results verify both the proposed fault management scheme and the 2ω ripple propagation analysis.
A construction heuristic for finding an initial solution to a very large-scale capacitated vehicle routing problem
Authors: Vangipurapu Bapi Raju , Govada Rambabu
Published: July 2021

In this paper, a deterministic heuristic method is developed for obtaining an initial solution to an extremely large-scale capacitated vehicle routing problem (CVRP) having thousands of customers. The heuristic has three main objectives. First, it should be able to withstand the computational and memory problems normally associated with extremely large-scale CVRP. Secondly, the outputs should be reasonably accurate and should have a minimum number of vehicles. Finally, it should be able to produce the results within a short duration of time. The new method, based on the sweep algorithm, minimizes the number of vehicles by loading the vehicles nearly to their full capacity by skipping some of the customers as and when necessary. To minimize the total traveled distance, before the sweeping starts the customers are ordered based on both the polar angle and the distance of the customer from the depot. This method is tested on 10 sets of standard benchmark instances found in the literature. The results are compared with the results of the CW100 method by Arnold et al. [Comput. Oper. Res. 107 (2019) 32–42]. The results indicate that the new modified sweep algorithm produces an initial solution with a minimum number of vehicles and with reasonable accuracy. The deviation of the output from the best-known solution (BKS) is reasonable for all the test instances. When compared with the CW100 the modified sweep provides a better initial solution than CW100 whenever the capacity of the vehicle is more and the depot is located eccentrically. The heuristic does not face any memory problems normally associated with the solving of an extremely large-scale CVRP.
Performance Assessment of the Commercial CFD Software for the Prediction of the PWR Internal Flow
Authors: Lee Gong Hee , Bang Young Seok , Woo Sweng Woong , Cheong Ae Ju , Kim Do Hyeong , Kang Min Ku
Published: July 2021

As the computer hardware technology develops the license applicants for nuclear power plant use the commercial CFD software with the aim of reducing the excessive conservatism associated with using simplified and conservative analysis tools. Even if some of CFD software developers and its users think that a state of the art CFD software can be used to solve reasonably at least the single-phase nuclear reactor safety problems, there is still the limitations and the uncertainties in the calculation result. From a regulatory perspective, Korea Institute of Nuclear Safety (KINS) has been presently conducting the performance assessment of the commercial CFD software for the nuclear reactor safety problems. In this study, in order to examine the prediction performance of the commercial CFD software with the porous model in the analysis of the scale-down APR+ (Advanced Power Reactor Plus) internal flow, simulation was conducted with the on-board numerical models in ANSYS CFX R.14 and FLUENT R.14. It was concluded that depending on the CFD software the internal flow distribution of the scale-down APR+ was locally somewhat different. Although there was a limitation in estimating the prediction performance of the commercial CFD software due to the limited number of the measured data, CFX R.14 showed the more reasonable predicted results in comparison with FLUENT R.14. Meanwhile, due to the difference of discretization methodology, FLUENT R.14 required more the computational memory than CFX R.14 for the same grid system. Therefore the CFD software suitable to the available computational resource should be selected for the massive parallel computation.
Climbing Performance in U23 and Professional Cyclists during a
Multi-stage Race
Authors: Leo Peter , Spragg James , Simon Dieter , Lawley Justin , Mujika Iñigo
Published: July 2021

The aim of this study was to analyze climbing performance across two editions of
a professional multistage race, and assess the influence of climb category,
prior workload, and intensity measures on climbing performance in U23 and
professional cyclists. Nine U23 cyclists (age 20.8±0.9 years) and 8
professional cyclists (28.1±3.2 years) participated in this study. Data
were divided into four types: overall race performance, climb category, climbing
performance metrics (power output, ascent velocity, speed), and workload and
intensity measures. Differences in performance metrics and workload and
intensity measures between groups were investigated. Power output, ascent
velocity, speed were higher in professionals than U23 cyclists for Cat 1 and Cat
2 (p≤0.001–0.016). Workload and intensity measures
(Worktotal, Worktotal∙km-1,
Elevationgain, eTRIMP and eTRIMP∙km-1) were
higher in U23 compared to professionals (p=0.002–0.014).
Climbing performance metrics were significantly predicted by prior workload and
intensity measures for Cat 1 and 2 (R2=0.27–0.89,
p≤0.001–0.030) but not Cat 3. These findings reveal that
climbing performance in professional road cycling is influenced by climb
categorization as well as prior workload and intensity measures. Combined, these
findings suggest that Cat 1 and 2 climbing performance could be predicted from
workload and intensity measures.
Perylene Monoimide as a Versatile Fluoroprobe: The Past, Present, and Future
Authors: Roy Rupam , Khan Aasif , Chatterjee Oendrila , Bhunia Sukomal , Koner Apurba Lal
Published: July 2021

Perylene dyes have transcended their role as simple colorants and have been reinvigorated as functional dyes. Based on the substitution at the peri-position by six-membered carboxylic imides, the perylene family is principally embellished with perylene diimides (PDIs) and perylene monoimides (PMIs). Perylene dyes are widely acclaimed and adorned on account of their phenomenal thermal, chemical, and photostability juxtaposed with their high absorption coefficient and near-unity fluorescence quantum yield. Although symmetric PDIs have always been in the limelight, their asymmetrical counterpart PMI is already rubbing shoulders, thanks to the consistent efforts of several scientific minds. Recently, there has been an upsurge in engendering PMI-based versatile organic architectures decked with intriguing photophysical properties and pertinent applications. In this review, the synthesis and photophysical features of various PMI-based derivatives along with their relevant applications in the arena of organic photovoltaics, photocatalysis, self-assembly, fluorescence sensing, and bio-imaging are accrued and expounded, hoping to enlighten the less delved but engrossing realm of PMIs.

Table of content:

1 Introduction

2 Advantages of PMI over PDI

3 Challenges in Working with PMI and Ways to Overcome

4 Various Aspects of Reactivity of Different Positions

5 Synthesis of the PMI core

6 Synthesis of PMI Derivatives

6.1 Bromination of PMI

6.2 Synthesis of PMI Derivatives using Coupling Reactions

6.2.1 Suzuki Coupling

6.2.2 Sonogashira Coupling

6.2.3 Buchwald–Hartwig Coupling Reaction

6.3 Nucleophilic Substitution Reactions

6.4 Peri-Annulation Reaction

7 Photophysical Properties of PMI

8 Singlet Fission Properties

9 Förster Resonance Energy Transfer with PMI

10 Symmetry Breaking Charge Transfer Properties

11 Panchromatic Light Absorption Properties of PMI

12 Acid/Base Sensitivity of PMI

13 NIR-Absorbing PMI

14 Achieving of Triplet State Using PMI

15 Solid-State Emissive PMI

16 Thermo-Responsive Materials with PMI

17 Photo-Responsive PMI Derivatives

18 Electrochemical Properties of Rylene Derivative

19 Self-Assembling Properties of PMI Derivatives

20 Applications of PMI in Solar Cells

21 PMIs in Bulk Heterojunction Solar Cells

22 PMIs in Dye-Sensitized Solar Cells

23 PMI as a Fluorescent Reporter

23.1 Application of PMI Derivatives for Bio-Imaging

23.2 Hydrophilic PMIs for Bio-Imaging

23.3 Aggregated PMI as NIR-Emissive Fluoroprobe for Bio-Imaging

24 Photocatalytic Hydrogen Generation using PMI

25 PMI-Based Organocatalysis

26 PMI Derivatives for Single-molecule Spectroscopy

27 Host–Guest Chemistry with PMI

28 Conclusions and Outlook
The Molecular Signature of High-intensity Training in the Human
Body
Authors: Wahl Patrick , Bloch Wilhelm , Proschinger Sebastian
Published: July 2021

High-intensity training is becoming increasingly popular outside of elite sport
for health prevention and rehabilitation. This expanded application of
high-intensity training in different populations requires a deeper understanding
of its molecular signature in the human body. Therefore, in this integrative
review, cellular and systemic molecular responses to high-intensity training are
described for skeletal muscle, cardiovascular system, and the immune system as
major effectors and targets of health and performance. Different kinds of
stimuli and resulting homeostatic perturbations (i. e., metabolic,
mechanical, neuronal, and hormonal) are reflected, taking into account their
role in the local and systemic deflection of molecular sensors and mediators,
and their role in tissue and organ adaptations. In skeletal muscle, a high
metabolic perturbation induced by high-intensity training is the major stimulus
for skeletal muscle adaptation. In the cardio-vascular system, high-intensity
training induces haemodynamic stress and deflection of the
Ca 2+ handling as major stimuli for
functional and structural adaptation of the heart and vessels. For the immune
system haemodynamic stress, hormones, exosomes, and O2 availability
are proposed stimuli that mediate their effects by alteration of different
signalling processes leading to local and systemic (anti)inflammatory responses.
Overall, high-intensity training shows specific molecular signatures that
demonstrate its high potential to improve health and physical performance.
Direct Access to S-Heterocycles by Scandium(III) Triflate Catalyzed Cyclization of Aromatic Thiols and Diols
Authors: Minakawa Maki , Minami Keisuke , Sato Yuya
Published: July 2021

A simple and environmentally friendly method to prepare S-heterocycles by cyclization of aromatic thiols and diols with H2O as a byproduct is described. The Sc(OTf)3-catalyzed dehydrative cyclizations of aromatic thiols and diols provided the corresponding thiopyran and thiophene derivatives. Control experiments were also performed to obtain insights into the reaction pathway
Expertise of Surgeons Publishing Novel Techniques in the Journal of Wrist Surgery
Authors: Cohen Lara L. , Massel Dustin H. , Geller Joseph S. , Chen David L. , Dodds Seth D.
Published: July 2021

Introduction Recent efforts to standardize reporting of surgeon experience in novel technique publications have recommended reporting of Tang level of expertise (LOE).

Question/Purpose The aim of this study was to document trends in LOE reporting for novel technique articles published in the Journal of Wrist Surgery and evaluate whether author experience affects novel research outcomes.

Methods A total of 261 articles published from 2018 to 2020 were reviewed. Articles describing novel surgical techniques were included and examined for Tang LOE. Author variables were collected online.

Results Eight percent (21/261) of articles discussed novel surgical techniques and one reported LOE. Nearly half (47.6%) of articles did not conduct statistical analysis. Four (19.0%) reported insignificant statistical results and 7 (33.3%) reported significant findings. All significant statistical findings were positive. Number of prior related publications by the senior author did not affect new technique result significance (p = 0.34).

Discussion From 2018 to 2020, only one article documented LOE. Authors' variables, including number of prior related publications, were not correlated with significant results in their new publications. This may suggest that an author's established experience in a novel technique, quantified by prior publications on the topic, does not make one more likely to achieve significantly better or worse outcomes in their reviewed Journal of Wrist Surgery study.

Conclusions Tang LOE is an important way for readers to classify expertise and should be reported, and potentially modified to better define contributing variables.
Trapeziectomy with Ligament Reconstruction and Tendon Interposition versus Trapeziometacarpal Joint Replacement for Thumb Carpometacarpal Osteoarthritis: A Systematic Review and Meta-Analysis
Authors: Qureshi Mobeen Khalid , Halim Usman Ali , Khaled Ahmad Sulaiman , Roche Simon John , Arshad Mohammed Shoaib
Published: July 2021

Background The trapeziometacarpal articulation in the thumb is a joint that is second-most commonly affected by osteoarthritis, and this can lead to considerable hand pain and disability. Currently, there is a multiplicity of surgical options available to address this problem, yet none has proven to be significantly superior to the others.

Objective This study aims to compare the outcome of trapeziectomy with ligament reconstruction and tendon interposition versus trapeziometacarpal joint replacement for thumb carpometacarpal osteoarthritis.

Materials and Methods A systematic review and meta-analysis was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement standards. The NICE Healthcare Databases Advanced Search (HDAS) tool was used to search articles. One randomized controlled trial (RCT), one prospective cohort study and two retrospective cohort studies were identified.

Results Our results demonstrate a significant difference in the Quick Disabilities of the Arm Shoulder and Hand (QDASH) score between the trapeziectomy with ligament reconstruction and tendon interposition (LRTI) and Joint Replacement groups with the joint replacement group exhibiting better QDASH scores than the LRTI group. We also found that those who had a joint replacement had a significantly better thumb opposition than those in the LRTI group, as demonstrated by a superior Kapandji score. However, the complication rate of joint replacement appears to be higher.

Conclusion Our study reveals that while both treatment options are valid, the limited body of evidence currently available shows that joint replacement carries more risks and thus should not replace the current standard treatment of trapeziectomy with LRTI. This study highlights the need for more trials to be performed to more accurately compare the two treatment modalities. For the time being, we advocate that joint replacement is only performed by surgeons who perform this procedure regularly to reduce the risk of complications.
Risk Factors of Arterial Events in Patients with Venous Thromboembolism: A Systematic Review and Meta-Analysis
Authors: Noumegni Steve Raoul , Hoffmann Clément , Tromeur Cécile , Didier Romain , Bressollette Luc , Lacut Karine , Couturaud Francis
Published: July 2021

Background If recent studies suggested that arterial ischemic events in patients with venous thromboembolism (VTE) are more frequent than in the general population without VTE, whether patients with VTE have different risk factors of arterial events than classic known cardiovascular risk factors remain undefined. Through this systematic review and meta-analysis, we aimed to identify risk factors of arterial ischemic events in patients with VTE.

Methods We searched PubMed, EMBASE, and Cochrane databases to identify cohort studies published between January 1, 2000, and December 31, 2020, reporting risk factors of arterials ischemic events in patients with VTE. Random-effect models meta-analysis served to get the pooled hazard ratio (HR) and 95% confidence interval (CI) of each risk factor identified.

Results We screened 1,467 records of which 18 were finally included in systematic review and 10 in meta-analyses. Adjusted HR for 9 factors were included in meta-analysis. Male gender (HR: 1.38; 95% CI: 1.28–1.49), diabetes (HR: 1.65; 95% CI: 1.28–2.12), hypertension (HR: 1.38; 95% CI: 1.04–1.84), previous atherothrombotic event (HR: 3.22; 95% CI: 1.12–9.23), chronic kidney disease (HR: 1.41; 95% CI: 1.05–1.88), cancer (HR: 1.72; 95% CI: 1.41–2.09), and unprovoked VTE (HR: 1.88; 95% CI: 1.37–2.57) were the identified risk factors of arterial events in VTE population after meta-analysis.

Conclusion Risk factors of arterial events in patients with VTE include usual cardiovascular risk factors and other risk factors that are related to VTE such as cancer and unprovoked VTE.
Buchtipp: Neuauflage beleuchtet alle Facetten des Personalmanagements
Authors: Fischer Ingo
Published: July 2021

Auch das Personalmanagement im Krankenhaus wandelt sich. Die demografischen Veränderungen, die Finanzierung des Pflegedienstes, Pflegepersonaluntergrenzen und die in der Medizin zunehmende Digitalisierung sind Grund genug, die etablierte Publikation „Personalmanagement im Krankenhaus“ mit einer fünften Auflage zu aktualisieren und zu erweitern. Die vorliegende Publikation richtet sich insbesondere an Führungskräfte und Führungsnachwuchskräfte im Gesundheitswesen, da zunehmend Vorgesetzte das operative Personalmanagement tragen und umsetzen.
Jonas Schreyögg zu Trägermodellen: „Wir müssen künftig in anderen Kategorien denken“
Authors: Kohrs Jens
Published: July 2021

Nach der weiter anhaltenden Bildung von Verbünden und Netzwerken sieht der Hamburger Gesundheitsökonom Prof. Dr. Jonas Schreyögg in der Rekommunalisierung die nächste Entwicklungsphase im deutschen Krankenhaussektor. Im Gespräch mit kma erläutert er, was er davon hält und warum vor der Frage nach der Trägerkonstellation etwas viel Wichtigeres geklärt werden sollte.
Using passive pumping to make small vacuum systems that can sustain cold atoms for months
Authors: McConnon Aili
Published: July 2021

New vacuum technology for laser-cooled atoms reliably sustains cold atoms for over 200 days with no signs of degradation.
Influence of particle non-dilute effects on its dispersion in particle-laden blast wave systems
Authors: V. Marayikkottu Akhil , A. Levin Deborah
Published: July 2021

Even though the interaction of blast waves with dense particle distributions is ubiquitous in nature and in industry, the underlying physics of the multiphase system evolution is not clearly understood. A canonical multiphase system composed of an embedded monodisperse distribution of spherical particles in a spherical, high-energy gaseous charge is studied numerically using an Eulerian–Lagrangian approach to elucidate the role of non-dilute particle effects on the dynamics of the two-phase flow system. The direct simulation Monte Carlo method is modified to model inelastic particle–particle collisions and to model the gaseous flow inter-leaving through complex structures of monodisperse dense distributions of spherical particles to obtain parameters that are fit to semi-empirical particle cloud drag laws that account for aerodynamic interactions. The study reveals that inter-particle collisions decrease the total particle kinetic energy at early stages of the particle-laden blast wave system evolution, but near-particle interaction increases the particle kinetic energy at this stage. In contrast, at later stages of evolution, collisions tend to retain more kinetic energy, while the aerodynamic interactions tend to dissipate particle kinetic energy.
Controlled and deterministic creation of synthetic antiferromagnetic domains by focused ion beam irradiation
Authors: Samad Fabian , Hlawacek Gregor , Arekapudi Sri Sai Phani Kanth , Xu Xiaomo , Koch Leopold , Lenz Miriam , Hellwig Olav
Published: July 2021

We study layered synthetic antiferromagnets (SAFs) with out-of-plane interface anisotropy, where the layer-wise antiferromagnetic (AF) alignment is induced by interlayer exchange coupling (IEC). By applying low energy He+ focused ion beam irradiation to the SAF, a depth-dependent reduction of the IEC and anisotropy can be achieved due to layer intermixing. As a consequence, after irradiation, a specific field reversal sequence of the SAF is energetically preferred. When tuning the pristine SAF to exhibit an inverted field reversal, we are thus able to create AF domains in the irradiated regions. When irradiated with a fluence gradient, these AF domains can be further deterministically manipulated by an external magnetic field. Among other applications, this could be utilized for engineering a controllable and local magnetic stray field landscape, for example, at AF domain walls, within the otherwise stray field free environment provided by the SAF.
Motion analysis of a trapped ion chain by single photon self-interference
Authors: Cerchiari G. , Araneda G. , Podhora L. , Slodička L. , Colombe Y. , Blatt R.
Published: July 2021

We present an optical scheme to detect the oscillations of a two-ion string confined in a linear Paul trap. The motion is detected by analyzing the intensity correlations in the fluorescence light emitted by one or two ions in the string. We present measurements performed under continuous Doppler cooling and under pulsed illumination. We foresee several direct applications of this detection method, including motional analysis of multi-ion species or coupled mechanical oscillators and sensing of mechanical correlations.
High pressure structural evolution of cubic solid solution YbInO3
Authors: Kaiwart Rahul , Dwivedi Abhilash , Shukla R. , Velaga Srihari , Grover V. , Poswal H. K.
Published: July 2021

The structural evolution of cubic (c) solid solution YbInO3 (space group Ia3¯) under pressure has been investigated using synchrotron based angle dispersive x-ray diffraction measurements and density functional theory based first principles calculations. A first order irreversible structural phase transition is observed at ∼15 GPa. The ambient cubic phase coexists with the high pressure phase up to the highest pressure achieved in the experiment, i.e., 42 GPa. Based on experimental and theoretical investigations, the high pressure phase of c-YbInO3 is proposed to be an orthorhombic solid solution structure having the space group Pnma. In the high pressure Pnma phase, the coordination of Yb1/In1 (general site 4c) atoms with respect to O atoms increases from six to eight, while Yb2/In2 (special site 4b) atoms remain in six coordination. Our theoretical calculations show that distorted octahedra (YbO6 and InO6), sitting at the general position in c-YbInO3, change its geometry toward regular octahedra with increasing pressure, which gives rise to the phase transformation.
Broadband visible two-dimensional spectroscopy of molecular dyes
Authors: Mewes Lars , Ingle Rebecca A. , Al Haddad Andre , Chergui Majed
Published: July 2021

Two-dimensional Fourier transform spectroscopy is a promising technique to study ultrafast molecular dynamics. Similar to transient absorption spectroscopy, a more complete picture of the dynamics requires broadband laser pulses to observe transient changes over a large enough bandwidth, exceeding the inhomogeneous width of electronic transitions, as well as the separation between the electronic or vibronic transitions of interest. Here, we present visible broadband 2D spectra of a series of dye molecules and report vibrational coherences with frequencies up to ∼1400 cm−1 that were obtained after improvements to our existing two-dimensional Fourier transform setup [Al Haddad et al., Opt. Lett. 40, 312–315 (2015)]. The experiment uses white light from a hollow core fiber, allowing us to acquire 2D spectra with a bandwidth of 200 nm, in a range between 500 and 800 nm, and with a temporal resolution of 10–15 fs. 2D spectra of nile blue, rhodamine 800, terylene diimide, and pinacyanol iodide show vibronic spectral features with at least one vibrational mode and reveal information about structural motion via coherent oscillations of the 2D signals during the population time. For the case of pinacyanol iodide, these observations are complemented by its Raman spectrum, as well as the calculated Raman activity at the ground- and excited-state geometry.
Nuclear–electronic orbital methods: Foundations and prospects
Authors: Hammes-Schiffer Sharon
Published: July 2021

The incorporation of nuclear quantum effects and non-Born–Oppenheimer behavior into quantum chemistry calculations and molecular dynamics simulations is a longstanding challenge. The nuclear–electronic orbital (NEO) approach treats specified nuclei, typically protons, quantum mechanically on the same level as the electrons with wave function and density functional theory methods. This approach inherently includes nuclear delocalization and zero-point energy in molecular energy calculations, geometry optimizations, reaction paths, and dynamics. It can also provide accurate descriptions of excited electronic, vibrational, and vibronic states as well as nuclear tunneling and nonadiabatic dynamics. Nonequilibrium nuclear–electronic dynamics simulations beyond the Born–Oppenheimer approximation can be used to investigate a wide range of excited state processes. This Perspective provides an overview of the foundational NEO methods and enumerates the prospects for using these methods as building blocks for future developments. The conceptual simplicity and computational efficiency of the NEO approach will enhance its accessibility and applicability to diverse chemical and biological systems.
A new route of synthesizing atomically thin 2D materials embedded in bulk oxides
Authors: Hwang Jeongwoon , Kim Jongchan , Nie Yifan , Lee Byoung Hun , Ahn Jinho , Kim Jiyoung , Sung Myung Mo , Cho Kyeongjae
Published: July 2021

Conventional mechanical or chemical exfoliation approach of 2D material synthesis is largely dependent on the inherent structure of the parent material, i.e., whether it is a layered structure or a 3D bulk structure with embedded 2D substructures. A recent experiment demonstrated that unprecedented atomically thin metal oxides without bulk layered structures can be synthesized by using liquid metals. Supported by an experimental realization of atomically thin W layers through the metal atomic layer deposition method, we propose a new type of transition metal (TM)-based 2D materials that can be stabilized at the oxide interfaces with oxide substrates and overlayers. Based on the ab initio density functional theory calculations, we show that most of the TM elements can form unprecedented atomically thin 2D materials by the surface oxygen passivation, which is available from the oxide substrate and the overlayer. The stabilized 2D TM layers show diverse electronic and magnetic properties. Our results suggest a novel way to extend 2D materials study and a possible application of those 2D TM layers embedded in oxides.
Self-learning hybrid Monte Carlo method for isothermal–isobaric ensemble: Application to liquid silica
Authors: Kobayashi Keita , Nagai Yuki , Itakura Mitsuhiro , Shiga Motoyuki
Published: July 2021

Self-learning hybrid Monte Carlo (SLHMC) is a first-principles simulation that allows for exact ensemble generation on potential energy surfaces based on density functional theory. The statistical sampling can be accelerated with the assistance of smart trial moves by machine learning potentials. In the first report [Nagai et al., Phys. Rev. B 102, 041124(R) (2020)], the SLHMC approach was introduced for the simplest case of canonical sampling. We herein extend this idea to isothermal–isobaric ensembles to enable general applications for soft materials and liquids with large volume fluctuation. As a demonstration, the isothermal–isobaric SLHMC method was used to study the vibrational structure of liquid silica at temperatures close to the melting point, whereby the slow diffusive motion is beyond the time scale of first-principles molecular dynamics. It was found that the static structure factor thus computed from first-principles agrees quite well with the high-energy x-ray data.
Interface optical phonons in double-channel AlGaN/GaN heterostructures: The ternary mixed crystal effect and size effect
Authors: Zhou X. J. , Gu Z. , Xing Y.
Published: July 2021

Considering the anisotropy of wurtzite semiconductors, the interface optical phonons in double-channel AlGaN/GaN heterostructures are investigated by using a dielectric continuous model and transfer matrix method. Also, the ternary mixed crystal effect and size effect on the dispersion relations and electrostatic potentials of phonons are analyzed in detail. The results show that there are six branches of interface phonon modes in a double-channel heterostructure. For some values of Al composition, however, the phonon mode with the highest frequency may not exist, especially when the thicknesses of materials and the wave vectors of phonons are small. The ternary mixed crystal effect and size effect not only influence the values of phonon frequency and electrostatic potential, but also change the vibration mode of interface phonons. This suggests that the interface phonon vibrations can be controlled to reduce their adverse effects by changing the Al composition of AlGaN and the thickness of each layer in a double-channel heterostructure.
Flow near porous media boundaries including inertia and slip: A one-domain approach
Authors: Valdés-Parada F. J. , Lasseux D.
Published: July 2021

This work addresses the macroscopic modeling of flow near porous media boundaries. This includes the vicinity with a fluid channel (i.e., a fracture), another rigid porous medium, or an impervious non-deformable solid. The analysis is carried out for one-phase, steady, incompressible, inertial, and isothermal flow of a Newtonian fluid, considering slip effects at the solid–fluid interfaces. A one-domain approach is proposed, employing a simplified version of the volume averaging method, while conceiving the system as two homogeneous regions separated by an inter-region. The upscaling procedure yields a closed macroscopic model including a divergence-free average (filtration) velocity for the mass balance equation and a unique momentum equation having a Darcy structure. The latter involves apparent permeability tensors that are constant in the homogeneous regions and position-dependent in the inter-region. All the permeability tensors are determined from the solution of coupled closure problems that are part of the developments. The derived model is validated by comparisons with direct numerical simulations in several two-dimensional configurations, namely, two porous media of contrasted properties in direct contact or separated by a fracture, the boundaries being either flat or wavy and a porous medium in contact with a flat or corrugated solid wall or separated from the latter by a fluid layer. The simplicity and versatility of the derived model make it an interesting alternative to existing one- and two-domain approaches developed so far.
Dynamics of a buoyant pulsating bubble near two crossed walls
Authors: Li Shi-Min , Liu Yun-Long , Wang Qianxi , Zhang A-Man
Published: July 2021

The dynamics of a buoyant pulsating bubble near two crossed perpendicular rigid boundaries (a horizontal and a vertical wall) are studied using the boundary element method combined with the method of mirror images. The Kelvin impulse and the elastic mesh velocity method are used to calculate the direction and volume of the liquid jet generated during bubble collapse. The numerical results show good agreement with experiments. An increase in buoyancy causes a local high-pressure zone at the root of the jet to move toward the bottom of the bubble, causing the jet to rotate upward toward the vertical wall. At a certain position, with the change in buoyancy, the dimensionless bubble volume at the instant of jet impact reaches a minimum when the jet direction is horizontal, with a peak in the dimensionless jet velocity occurring. A comprehensive parametric study of jet characteristics, including jet direction, velocity, and relative volume (the volume ratio of the jet to the bubble at the instant of jet impact), is carried out in terms of buoyancy and the standoff distances to the two walls. The Blake criterion can be used to judge whether a bubble jet is pointing obliquely upward or downward, provided that it deviates significantly from the horizontal direction. Depending on the buoyancy, the jet characteristics at different standoff distances are found to exhibit three distinct patterns of behavior. Finally, we discuss the changes in the jet velocity and relative volume as the buoyancy is varied.
First-principles correction scheme for linear-response time-dependent density functional theory calculations of core electronic states
Authors: Bussy Augustin , Hutter Jürg
Published: July 2021

Linear-response time-dependent density functional theory (LR-TDDFT) for core level spectroscopy using standard local functionals suffers from self-interaction error and a lack of orbital relaxation upon creation of the core hole. As a result, LR-TDDFT calculated x-ray absorption near edge structure spectra needed to be shifted along the energy axis to match experimental data. We propose a correction scheme based on many-body perturbation theory to calculate the shift from first-principles. The ionization potential of the core donor state is first computed and then substituted for the corresponding Kohn–Sham orbital energy, thus emulating Koopmans’s condition. Both self-interaction error and orbital relaxation are taken into account. The method exploits the localized nature of core states for efficiency and integrates seamlessly in our previous implementation of core level LR-TDDFT, yielding corrected spectra in a single calculation. We benchmark the correction scheme on molecules at the K- and L-edges as well as for core binding energies and report accuracies comparable to higher order methods. We also demonstrate applicability in large and extended systems and discuss efficient approximations.
Multi-channel distorted-wave Born approximation for rovibrational transition rates in molecular collisions
Authors: Selim Taha , Christianen Arthur , van der Avoird Ad , Groenenboom Gerrit C.
Published: July 2021

Modeling protoplanetary disks and other interstellar media that are not in local thermal equilibrium require the knowledge of rovibrational transition rate coefficients of molecules in collision with helium and hydrogen. We present a computational method based on the numerically exact coupled-channel (CC) method for rotational transitions and a multi-channel distorted-wave Born approximation (MC-DWBA) for vibrational transitions to calculate state-to-state rate coefficients. We apply this method to the astrophysically important case of CO2–He collisions, using newly computed ab initio three-dimensional potential energy surfaces for CO2–He with CO2 distorted along the symmetric and asymmetric stretch (ν1 and ν3) coordinates. It is shown that the MC-DWBA method is almost as accurate as full CC calculations, but more efficient. We also made computations with the more approximate vibrational coupled-channel rotational infinite-order sudden method but found that this method strongly underestimates the vibrationally inelastic collision cross sections and rate coefficients for both CO2 modes considered.
Targeting Axl favors an antitumorigenic microenvironment that enhances immunotherapy responses by decreasing Hif-1α levels
Authors: Goyette Marie-Anne , Elkholi Islam E. , Apcher Chloé , Kuasne Hellen , Rothlin Carla V. , Muller William J. , Richard Darren E. , Park Morag , Gratton Jean-Philippe , Côté Jean-François
Published: July 2021

Significance

A significant pool of HER2
+
breast cancer patients are either unresponsive or become resistant to standards of care. New therapeutic approaches exploiting the tumor microenvironment, including immunotherapies, are attractive. Hypoxia shapes the tumor microenvironment toward therapy resistance and metastasis. Here, we report a role for AXL receptor tyrosine kinase in the hypoxic response by promoting HIF-1α expression. Interfering with Axl in a preclinical model of HER2
+
breast cancer normalizes the blood vessels and promotes a proinflammatory microenvironment that enhances immunotherapy response to reduce the primary and metastatic tumor burdens. Clinical trials so far suggest that achieving immunotherapy responses in HER2
+
cancers might be challenging, and our data might provide an important insight to circumvent a roadblock.
The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection
Authors: Kim Seohyun , Park Jin-Sup , Lee Jaehoon , Lee Kiseok Keith , Park Ok-Sun , Choi Hee-Seung , Seo Pil Joon , Cho Hyung-Taeg , Frost Jennifer M. , Fischer Robert L. , Choi Yeonhee
Published: July 2021

The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. InArabidopsis, genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. AnalyzingArabidopsisplants homozygous for a loss-of-functiondme-2allele, we show that DME influences many aspects of sporophytic growth and development.dme-2mutants exhibited delayed seed germination, variable root hair growth, aberrant cellular proliferation and differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence and stomatal precursor cells, and inflorescence meristem (IM) resurrection. We also show that sporophytic DME activity exerts a profound effect on the transcriptome of developingArabidopsisplants, including discrete groups of regulatory genes that are misregulated indme-2mutant tissues, allowing us to potentially link phenotypes to changes in specific gene expression pathways. These results show that DME plays a key role in sporophytic development and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activities during the sporophytic life cycle inArabidopsis.
Capture and delivery of tail-anchored proteins to the endoplasmic reticulum
Authors: Farkas Ákos , Bohnsack Katherine E.
Published: July 2021

Tail-anchored (TA) proteins fulfill diverse cellular functions within different organellar membranes. Their characteristic C-terminal transmembrane segment renders TA proteins inherently prone to aggregation and necessitates their posttranslational targeting. The guided entry of TA proteins (GET in yeast)/transmembrane recognition complex (TRC in humans) pathway represents a major route for TA proteins to the endoplasmic reticulum (ER). Here, we review important new insights into the capture of nascent TA proteins at the ribosome by the GET pathway pretargeting complex and the mechanism of their delivery into the ER membrane by the GET receptor insertase. Interestingly, several alternative routes by which TA proteins can be targeted to the ER have emerged, raising intriguing questions about how selectivity is achieved during TA protein capture. Furthermore, mistargeting of TA proteins is a fundamental cellular problem, and we discuss the recently discovered quality control machineries in the ER and outer mitochondrial membrane for displacing mislocalized TA proteins.
Impaired respiratory burst contributes to infections in PKCδ-deficient patients
Authors: Neehus Anna-Lena , Moriya Kunihiko , Nieto-Patlán Alejandro , Le Voyer Tom , Lévy Romain , Özen Ahmet , Karakoc-Aydiner Elif , Baris Safa , Yildiran Alisan , Altundag Engin , Roynard Manon , Haake Kathrin , Migaud Mélanie , Dorgham Karim , Gorochov Guy , Abel Laurent , Lachmann Nico , Dogu Figen , Haskologlu Sule , İnce Erdal , El-Benna Jamel , Uzel Gulbu , Kiykim Ayca , Boztug Kaan , Roderick Marion R. , Shahrooei Mohammad , Brogan Paul A. , Abolhassani Hassan , Hancioglu Gonca , Parvaneh Nima , Belot Alexandre , Ikinciogullari Aydan , Casanova Jean-Laurent , Puel Anne , Bustamante Jacinta
Published: July 2021

Patients with autosomal recessive protein kinase C δ (PKCδ) deficiency suffer from childhood-onset autoimmunity, including systemic lupus erythematosus. They also suffer from recurrent infections that overlap with those seen in patients with chronic granulomatous disease (CGD), a disease caused by defects of the phagocyte NADPH oxidase and a lack of reactive oxygen species (ROS) production. We studied an international cohort of 17 PKCδ-deficient patients and found that their EBV-B cells and monocyte-derived phagocytes produced only small amounts of ROS and did not phosphorylate p40phox normally after PMA or opsonized Staphylococcus aureus stimulation. Moreover, the patients’ circulating phagocytes displayed abnormally low levels of ROS production and markedly reduced neutrophil extracellular trap formation, altogether suggesting a role for PKCδ in activation of the NADPH oxidase complex. Our findings thus show that patients with PKCδ deficiency have impaired NADPH oxidase activity in various myeloid subsets, which may contribute to their CGD-like infectious phenotype.
Nernst–Planck–Poisson analysis of electrolyte-gated organic field-effect transistors
Authors: Delavari Najmeh , Tybrandt Klas , Berggren Magnus , Piro Benoît , Noël Vincent , Mattana Giorgio , Zozoulenko Igor
Published: July 2021

Electrolyte-gated organic field-effect transistors (EGOFETs) represent a class of organic thin-film transistors suited for sensing and biosensing in aqueous media, often at physiological conditions. The EGOFET device includes electrodes and an organic semiconductor channel in direct contact with an electrolyte. Upon operation, electric double layers are formed along the gate-electrolyte and the channel-electrolyte interfaces, but ions do not penetrate the channel. This mode of operation allows the EGOFET devices to run at low voltages and at a speed corresponding to the rate of forming electric double layers. Currently, there is a lack of a detailed quantitative model of the EGOFETs that can predict device performance based on geometry and material parameters. In the present paper, for the first time, an EGOFET model is proposed utilizing the Nernst-Planck-Poisson equations to describe, on equal footing, both the polymer and the electrolyte regions of the device configuration. The generated calculations exhibit semi-qualitative agreement with experimentally measured output and transfer curves.
Electron scattering by magnetic impurity in Weyl semimetals
Authors: Díaz-Fernández Álvaro , Domínguez-Adame Francisco , de Abril Oscar
Published: July 2021

Weyl semimetals are prominent examples of topologically protected quantum matter. These materials are the three-dimensional counterparts of graphene and great efforts are being devoted to achieve a thorough understanding of their fundamental physics. In this work, we aim at contributing to this end by discussing the effect of a single magnetic impurity in Weyl semimetals as a first step towards considering a larger number of point-like impurities. We find that resonances appear in the local density of states (LDOS) with a Friedel-like behaviour, oscillating as a function of distance. By studying the spin-resolved LDOS, we can observe non-trivial and anisotropic spin textures where the spin components perpendicular to the spin of the impurity wind around the latter, until the spin becomes completely parallel to the impurity right at the impurity’s location. Friedel oscillations also play a relevant role in the form of the spin textures, forming an oscillatory pattern. We believe our results can pave the way to further studies which consider the presence of a large number of random magnetic impurities.
Test beam study of SiPM-on-tile configurations
Authors: Belloni A. , Chen Y.M. , Dyshkant A. , Edberg T.K. , Eno S. , Freeman J. , Krohn M. , Lai Y. , Lincoln D. , Los S. , Mans J. , Reichenbach G. , Uplegger L. , Uzunyan S.A. , Zutshi V.
Published: July 2021

Light yield and spatial uniformity for a large variety of configurations of scintillator tiles were studied. The light from each scintillator was collected by a Silicon Photomultiplier (SiPM) directly viewing the produced scintillation light (SiPM-on-tile technique).
The varied parameters included tile transverse size, tile thickness, tile wrapping material, scintillator composition, and SiPM model.
These studies were performed using 120 GeV protons at the Fermilab Test Beam Facility. External tracking allowed the position of each proton penetrating a tile to be measured. The results were compared to a GEANT4 simulation of each configuration of scinitillator, wrapping, and SiPM.