bluuebunny/crossref_metadata_2025 huggingface dataset:
Periodic bouncing of a plasmonic bubble in a binary liquid by competing solutal and thermal Marangoni forces
Authors: Zeng Binglin , Chong Kai Leong , Wang Yuliang , Diddens Christian , Li Xiaolai , Detert Marvin , Zandvliet Harold J. W. , Lohse Detlef
Published: June 2021

Significance

Plasmonic bubbles are relevant in biomedical diagnosis and therapy, catalysis, and micro- and nanomanipulation. Hitherto, their behavior has mainly been analyzed in pure liquids. However, in general, these applications of plasmonic bubbles take place in binary or multicomponent liquids. Here we show that plasmonic bubbles in a binary liquid display surprising phenomena, resulting from the emerging complicated physicochemical hydrodynamics of a vapor bubble in such binary liquids. Depending on the application, these phenomena can be either a benefit or a hindrance. Our results are also relevant for other bubble nucleation processes in multicomponent liquids, such as boiling, electrolysis, or catalysis.
Pseudocercospora fuligena (black leaf mould).
Authors: Baysal-Gurel Fulya
Published: June 2021

Pseudocercospora fuligena is not on an alert list or listed as a regulated pest.
Foxp3 enhancers synergize to maximize regulatory T cell suppressive capacity
Authors: Zong Xinying , Hao Xiaolei , Xu Beisi , Crawford Jeremy Chase , Wright Shaela , Li Jun , Zhang Yang , Bai Lu , He Minghong , Jiang Menglin , Fan Yiping , Connelly Jon P. , Pruett-Miller Shondra M. , Berns Hartmut , Janke Laura , Li Chunliang , Feng Yongqiang
Published: June 2021

T reg cells bearing a diverse antigen receptor repertoire suppress pathogenic T cells and maintain immune homeostasis during their long lifespan. How their robust function is determined genetically remains elusive. Here, we investigate the regulatory space of the cis-regulatory elements of T reg lineage–specifying factor Foxp3. Foxp3 enhancers are known as distinct readers of environmental cues controlling T reg cell induction or lineage stability. However, their single deficiencies cause mild, if any, immune dysregulation, leaving the key transcriptional mechanisms determining Foxp3 expression and thereby T reg cell suppressive capacity uncertain. We examined the collective activities of Foxp3 enhancers and found that they coordinate to maximize T reg cell induction, Foxp3 expression level, or lineage stability through distinct modes and that ablation of synergistic enhancers leads to lethal autoimmunity in young mice. Thus, the induction and maintenance of a diverse, stable T reg cell repertoire rely on combinatorial Foxp3 enhancers, suggesting broad, stage-specific, synergistic activities of cell-intrinsic factors and cell-extrinsic cues in determining T reg cell suppressive capacity.
Final report on APMP comparison in humidity APMP.T−K8: Dew point temperature +30 °C to +95 °C
Authors: Abe H , Kitano H , Lovell-Smith J , Achmadi A , Cheung C P , Choi B I , Hussain F , Jahan F , Norranim U , Sindhu A , Tsai S-F , Wang L
Published: June 2021

Main text

A key comparison in dew-point temperature in the range of +30 °C to +95 °C was carried out among the national standards held by NMIJ (pilot), MSL (coordinator), RCM-LIPI/SNSU-BSN, SCL, KRISS, NMIM, NMIA, NIMT, CMS/ITRI, and NMC, A*STAR. The purpose of the comparison was to establish the degree of equivalence between realizations of local scales of dew point temperature of humid gas among the participating national institutes. Although the comparison schedule was considerably delayed, no significant drift of the transfer standard was observed over the whole period of the comparison. The result of a chi-squared test demonstrated that the comparison was effective, and the results obtained in the comparison can be used as reliable supporting evidence for CMCs that each participant claims.

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database https://www.bipm.org/kcdb/.

The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Machine Learning Kinetic Energy Functional for a One-Dimensional Periodic System
Authors: Ren Hong-Bin , Wang Lei , Dai Xi
Published: June 2021

Kinetic energy (KE) functional is crucial to speed up density functional theory calculation. However, deriving it accurately through traditional physics reasoning is challenging. We develop a generally applicable KE functional estimator for a one-dimensional (1D) extended system using a machine learning method. Our end-to-end solution combines the dimensionality reduction method with the Gaussian process regression, and simple scaling method to adapt to various 1D lattices. In addition to reaching chemical accuracy in KE calculation, our estimator also performs well on KE functional derivative prediction. Integrating this machine learning KE functional into the current orbital free density functional theory scheme is able to provide us with expected ground state electron density.
Development of a 3He Gas Filling Station at the China Spallation Neutron Source
Authors: Qin Zecong , Huang Chuyi , Buck Z. N. , Kreuzpaintner W. , Amir S. M. , Salman A. , Ye Fan , Zhang Junpei , Jiang Chenyang , Wang Tianhao , Tong Xin
Published: June 2021

At the China Spallation Neutron Source (CSNS), we have developed a custom gas-filling station, a glassblowing workshop, and a spin-exchange optical pumping (SEOP) system for producing high-quality 3He-based neutron spin filter (NSF) cells. The gas-filling station is capable of routinely filling 3He cells made from GE180 glass of various dimensions, to be used as neutron polarizers and analyzers on beamlines at the CSNS. Performance tests on cells fabricated at our gas-filling station are conducted via neutron transmission and nuclear-magnetic-resonance measurements, revealing nominal filling pressures, and a saturated 3He polarization in the region of 80%, with a lifetime of approximately 240 hours. These results demonstrate our ability to produce competitive NSF cells to meet the ever-increasing research needs of the polarized neutron research community.
Core-Excited Molecules by Resonant Intense X-Ray Pulses Involving Electron-Rotation Coupling
Authors: Zhu Yanping , Liu Yanrong , Zhao Xi , Kimberg Victor , Zhang Songbin
Published: June 2021

It has been reported that electron-rotation coupling plays a significant role in diatomic nuclear dynamics induced by intense VUV pulses [Phys. Rev. A 102 (2020) 033114; Phys. Rev. Res. 2 (2020) 043348]. As a further step, we present here investigations of the electron-rotation coupling effect in the presence of Auger decay channel for core-excited molecules, based on theoretical modeling of the total electron yield (TEY), resonant Auger scattering (RAS) and x-ray absorption spectra (XAS) for two showcases of CO and CH+ molecules excited by resonant intense x-ray pulses. The Wigner D-functions and the universal transition dipole operators are introduced to include the electron-rotation coupling for the core-excitation process. It is shown that with the pulse intensity up to 1016 W/cm2, no sufficient influence of the electron-rotation coupling on the TEY and RAS spectra can be observed. This can be explained by a suppression of the induced electron-rotation dynamics due to the fast Auger decay channel, which does not allow for effective Rabi cycling even at extreme field intensities, contrary to transitions in optical or VUV range. For the case of XAS, however, relative errors of about 10% and 30% are observed for the case of CO and CH+, respectively, when the electron-rotation coupling is neglected. It is concluded that conventional treatment of the photoexcitation, neglecting the electron-rotation coupling, can be safely and efficiently employed to study dynamics at the x-ray transitions by means of electron emission spectroscopy, yet the approximation breaks down for nonlinear processes as stimulated emission, especially for systems with light atoms.
Observation of Multiple Broadband Alfvénic Chirping Modes in HL-2A NBI Plasmas
Authors: Yu Liming , Chen Wei , Ji Xiaoquan , Shi Peiwan , Ding Xuantong , Shi Zhongbing , Ma Ruirui , Hou Yumei , Li Yonggao , Li Jiaxian , Cao Jianyong , Zhong Wulyu , Xu Min , Duan Xuru
Published: June 2021

Multiple broadband Alfvénic chirping modes (CMs), with frequencies in the wide range of f ∼ 35–150 kHz and chirping down rapidly, are found in HL-2A neutral beam injection plasmas, and the CMs can even coexist. The frequency chirping down process can be completed within ∼1 ms, and the frequency shift can reach 30–50 kHz. The CMs propagate in ion diamagnetic drift directions poloidally. The toroidal mode number is confirmed to be n = 1, 2, 3 and 4 for the f ∼ 35–65, 55–90, 70–120 and 100–150 kHz CMs, respectively. The CMs are more like to be energetic-particle continuum modes (EPMs), since the modes almost locate on the Alfvén continuum.
Nonlinear Hall Effect in Antiferromagnetic Half-Heusler Materials
Authors: Chen Cheng , Wang Huaiqiang , Yang Zhilong , Zhang Haijun
Published: June 2021

It has recently been demonstrated that various topological states, including Dirac, Weyl, nodal-line, and triple-point semimetal phases, can emerge in antiferromagnetic (AFM) half-Heusler compounds. However, how to determine the AFM structure and to distinguish different topological phases from transport behaviors remains unknown. We show that, due to the presence of combined time-reversal and fractional translation symmetry, the recently proposed second-order nonlinear Hall effect can be used to characterize different topological phases with various AFM configurations. Guided by the symmetry analysis, we obtain expressions of the Berry curvature dipole for different AFM configurations. Based on the effective model, we explicitly calculate the Berry curvature dipole, which is found to be vanishingly small for the triple-point semimetal phase, and large in the Weyl semimetal phase. Our results not only put forward an effective method for the identification of magnetic orders and topological phases in AFM half-Heusler materials, but also suggest these materials as a versatile platform for engineering the nonlinear Hall effect.
Itinerant Topological Magnons in SU(2) Symmetric Topological Hubbard Models with Nearly Flat Electronic Bands
Authors: Gu Zhao-Long , Li Jian-Xin
Published: June 2021

We show that a suitable combination of flat-band ferromagnetism, geometry and nontrivial electronic band topology can give rise to itinerant topological magnons. An SU(2) symmetric topological Hubbard model with nearly flat electronic bands, on a Kagome lattice, is considered as the prototype. This model exhibits ferromagnetic order when the lowest electronic band is half-filled. Using the numerical exact diagonalization method with a projection onto this nearly flat band, we can obtain the magnonic spectra. In the flat-band limit, the spectra exhibit distinct dispersions with Dirac points, similar to those of free electrons with isotropic hoppings, or a local spin magnet with pure ferromagnetic Heisenberg exchanges on the same geometry. Significantly, the non-flatness of the electronic band may induce a topological gap at the Dirac points, leading to a magnonic band with a nonzero Chern number. More intriguingly, this magnonic Chern number changes its sign when the topological index of the electronic band is reversed, suggesting that the nontrivial topology of the magnonic band is related to its underlying electronic band. Our work suggests interesting directions for the further exploration of, and searches for, itinerant topological magnons.
In the realm of the Hubble tension—a review of solutions
*
Authors: Di Valentino Eleonora , Mena Olga , Pan Supriya , Visinelli Luca , Yang Weiqiang , Melchiorri Alessandro , Mota David F , Riess Adam G , Silk Joseph
Published: June 2021

The simplest ΛCDM model provides a good fit to a large span of cosmological data but harbors large areas of phenomenology and ignorance. With the improvement of the number and the accuracy of observations, discrepancies among key cosmological parameters of the model have emerged. The most statistically significant tension is the 4σ to 6σ disagreement between predictions of the Hubble constant, H
0, made by the early time probes in concert with the ‘vanilla’ ΛCDM cosmological model, and a number of late time, model-independent determinations of H
0 from local measurements of distances and redshifts. The high precision and consistency of the data at both ends present strong challenges to the possible solution space and demands a hypothesis with enough rigor to explain multiple observations—whether these invoke new physics, unexpected large-scale structures or multiple, unrelated errors. A thorough review of the problem including a discussion of recent Hubble constant estimates and a summary of the proposed theoretical solutions is presented here. We include more than 1000 references, indicating that the interest in this area has grown considerably just during the last few years. We classify the many proposals to resolve the tension in these categories: early dark energy, late dark energy, dark energy models with 6 degrees of freedom and their extensions, models with extra relativistic degrees of freedom, models with extra interactions, unified cosmologies, modified gravity, inflationary models, modified recombination history, physics of the critical phenomena, and alternative proposals. Some are formally successful, improving the fit to the data in light of their additional degrees of freedom, restoring agreement within 1–2σ between Planck 2018, using the cosmic microwave background power spectra data, baryon acoustic oscillations, Pantheon SN data, and R20, the latest SH0ES Team Riess, et al (2021 Astrophys. J.
908 L6) measurement of the Hubble constant (H
0 = 73.2 ± 1.3 km s−1 Mpc−1 at 68% confidence level). However, there are many more unsuccessful models which leave the discrepancy well above the 3σ disagreement level. In many cases, reduced tension comes not simply from a change in the value of H
0 but also due to an increase in its uncertainty due to degeneracy with additional physics, complicating the picture and pointing to the need for additional probes. While no specific proposal makes a strong case for being highly likely or far better than all others, solutions involving early or dynamical dark energy, neutrino interactions, interacting cosmologies, primordial magnetic fields, and modified gravity provide the best options until a better alternative comes along.
Binary acoustic trapping in a glass capillary
Authors: Fornell Anna , Baasch Thierry , Johannesson Carl , Nilsson Johan , Tenje Maria
Published: June 2021

Acoustic trapping is a useful method for handling biological samples in microfluidic systems. The aim of this work is twofold: first to investigate the physics behind acoustic trapping in a glass capillary and secondly to perform binary acoustic trapping. The latter is achieved by increasing the density of the fluid in the trapping channel. The trapping device consisted of a glass capillary with a rectangular inner cross-section (height 200 µm × width 2000 µm) equipped with a small piezoelectric transducer. The piezoelectric transducer was actuated at 4 MHz to generate a localised half-wavelength acoustic standing-wave-field in the capillary, comprising of a pressure field and a velocity field. Under acoustic actuation, only particles with higher density than the fluid, i.e. having a positive dipole scattering coefficient, were trapped in the flow direction. The numerical and analytical modelling of the system show that the trapping force which retains the particles against the flow depends only on the dipole scattering coefficient in the pressure nodal plane of the acoustic field. The analytical model also reveals that the retention force is proportional to the dipole scattering coefficient, which agrees with our experimental findings. Next, we showed that in a mixture of melamine particles and polystyrene particles in a high-density fluid it is possible to selectively trap melamine particles, since melamine particles have higher density than polystyrene particles.
A temperature gradient evaluation method for determining temperature dependent thermal conductivities
Authors: Wilhelmy Sönke , Zimare Anton , Lippmann Stephanie , Rettenmayr Markus
Published: June 2021

Details of an experimental set-up and an evaluation method for determining temperature dependent thermal conductivities from one-dimensional steady-state temperature distributions are presented. The method is validated by obtaining continuous values for the thermal conductivities of pure Ni in the temperature range between 440 K and 740 K, brass (Cu-30Zn) in the temperature range between 350 K and 650 K and a titanium aluminide (TiAl-TNM) in the temperature range between 400 K and 700 K. The results are in agreement with available literature data. The reported scatter in the literature on conductivities is caused by microstructural or/and compositional differences, which highlights the necessity for swift and accurate experimental determination of thermal properties. For this, the proposed temperature gradient evaluation method is especially suited as it allows the direct determination of thermal properties within large temperature intervals using only a single experimental run. The experimental effort for a comprehensive study of a material is thus drastically reduced as compared to the conventional method of determining thermal conductivity from measured thermal diffusivities and heat capacities. The experimental set-up additionally allows the independent determination of thermal diffusivity as function of temperature. No prior knowledge of any material properties of a given sample is necessary.
Cell spreading behaviors on hybrid nanopillar and nanohole arrays
Authors: Wu Xiaomin , Li Li , Wang Lu , Lei Zecheng , Yang Fan , Liu Ri , Wang Ying , Peng Kuiqing , Wang Zuobin
Published: June 2021

Although nanopillars (NPs) provide a promising tool for capturing tumor cells, the effect of mixing NPs with other nanopatterns on cell behavior remains to be further studied. In this paper, a method of fabricating silicon nanoscale topographies by combining laser interference lithography with metal assisted chemical etching was introduced to investigate the behaviors and pseudopodia of A549 cells on the topologies. It was found that cells had a limited manner in spreading with small cell areas on the silicon nanopillar (SiNP) arrays, but a good manner in spreading with large cell areas on the silicon nanohole (SiNH) arrays. When on the hybrid SiNP/SiNH arrays, cells had medium cell areas and they arranged orderly along the boundaries of SiNPs and SiNHs, as well as 80% of cells displayed a preference for SiNPs over SiNHs. Furthermore, the lamellipodia and filopodia are dominant in the hybrid SiNP/SiNH and SiNP arrays, respectively, both of them are dominant in the SiNH arrays. In addition, the atomic force acoustic microscopy was also employed to detect the subsurface features of samples. The results suggest that the hybrid SiNP/SiNH arrays have a targeted trap and elongation effect on cells. The findings provide a promising method in designing hybrid nanostructures for efficient tumor cell traps, as well as regulating the cell behaviors and pseudopodia.
Self-Assembly of DNA molecules in magnetic Fields
Authors: Gao Mingyan , Hu Jing , Wang Jianfei , Liu Mengnan , Zhu Xiaona , Saeed Sadaf , Hu Cuihua , Song Zhengxun , Xu Hongmei , Wang Zuobin
Published: June 2021

In this work, a rich variety of self-assembled DNA patterns were obtained in the magnetic field. Herein, atomic force microscopy (AFM) was utilized to investigate the effects of the concentration of DNA solution, intensity and direction of magnetic field and modification of mica surface by different cations on the self-assembly of DNA molecules. It was found that owning to the change of the DNA concentration, even under the same magnetic field, the DNA self-assembly results were different. The in situ test results showed that the DNA self-assembly in an magnetic field was more likely to occur in liquid phase than in gas phase. In addition, whether in a horizontal or vertical magnetic field, a single stretched dsDNA was obtained in a certain DNA concentration and magnetic field intensity. Besides, the modification of cations on the mica surface significantly increased the force between the DNA molecules and mica surface, and further changed the self-assembly of DNA molecules under the action of magnetic field.
Ice melts—the question
Authors: Featonby David
Published: June 2021

How does the comparative density of ice and water affect water levels as ice melts in different circumstances? This article attempts to demonstrate this.
Using smartphone cameras and ambient light sensors in distance learning: the attenuation law as experimental determination of gamma correction
Authors: Onorato Pasquale , Rosi Tommaso , Tufino Eugenio , Caprara Caterina , Malgieri Massimiliano
Published: June 2021

In times of the explosion of distance learning, because of emergency due to the pandemic, smartphone sensors and cameras are extremely valuable for teachers as they allow students to perform significant experimental activities in their own homes. The open-source software Tracker can be used in combination with the smartphone camera to perform measurements not only of mechanics activities, but also of optics. In the latter case, it is not always easy for students to understand how the pixel brightness which can be inferred from the taken photos are related to actual physical light intensity. In this paper we present a simple experiment to verify the exponential decay in the intensity of light going through successive sheets of a material (the Lambert law) with two different methods, i.e. using either the smartphone light sensor or the smartphone camera and Tracker. Besides its theoretical significance, the experiment constitutes a useful tool for calibrating the camera/Tracker combination to use it for different experiments.
Evaluation of secondary electron intensities for dopant profiling in ion implanted semiconductors: a correlative study combining SE, SIMS and ECV methods
Authors: Shyam Kumar C N , Tabean Saba , Morisset Audrey , Wyss Philippe , Lehmann Mario , Haug Franz-Josef , Jeangros Quentin , Hessler-Wyser Aïcha , Valle Nathalie , Wirtz Tom , Eswara Santhana
Published: June 2021

This study evaluates the secondary electron (SE) dopant contrast in scanning electron microscopy (SEM) and helium ion microscopy (HIM) on boron implanted silicon sample. Complementary techniques like secondary ion mass spectrometry and electrochemical capacitance voltage (ECV) measurements are used to understand the dopant profile and active dopant distribution before and after a thermal firing, a step carried out to remove implantation damage and to electrically activate the implanted boron. Thermal firing resulted in an activation efficiency of 33%. HIM showed higher contrast than SEM having more defined peak with a lower background contribution. Variations in dopant concentration near the peak maximum were observed in ECV measurements, which was not observed in the intensity profiles from both SEM and HIM. This study demonstrates the effectiveness of SE dopant profiling as a quick tool to map the electrically active dopant concentrations even in far-from-equilibrium materials such as ion implanted samples.
From sub- to superdiffusion: fractional Brownian motion of membraneless organelles in early C. elegans embryos
Authors: Benelli Rebecca , Weiss Matthias
Published: June 2021

Fractional Brownian motion (FBM) is a prevalent Gaussian stochastic process that has frequently been linked to subdiffusive motion in complex fluids, e.g. inside living cells. In contrast, examples for a superdiffusive FBM in complex fluids are sparse, and a covering of all FBM regimes in the same sample is basically lacking. Here we show that membraneless organelles in the single-cell state of C. elegans embryos, so-called p-granules, constitute an experimental example in which the whole range of FBM processes, from the sub- to the superdiffusive regime, can be observed. The majority of p-granules is subdiffusive, featuring an antipersistent velocity autocorrelation function (VACF). A smaller fraction of trajectories shows normal diffusion or even superdiffusion with a persistent VACF. For all trajectories, from sub- to superdiffusive, the VACF, its characteristic values, and the trajectories’ power-spectral density are well matched by FBM predictions. Moreover, static localization errors, a frequent problem in single-particle tracking experiments, are shown to not affect the conclusion that p-granule motion is best described by FBM from the sub- to the superdiffusive regime.
Suspended nanocrystalline diamond ridge waveguides designed for the mid-infrared
Authors: Rahmati A T , Mashanovich G Z , Nezhad M P
Published: June 2021

A comprehensive study and design of air-clad suspended ridge diamond waveguides for operation across the 2.5–16 µm spectral range is presented, specifically targeting nanocrystalline diamond (NCD) thin films directly grown on silicon substrates. Three film thicknesses of 520, 1000 and 2000 nm are considered, to cover overlapping sub-bands of 2.5–5, 4–9 and 8–16 µm, respectively. Within each sub-band, the waveguide dimensions for single mode quasi-TE operation are found and the waveguide material losses and bending losses are estimated at each design point. In addition, in each case the minimum required undercut depth and etch hole placement for optical isolation of the waveguide mode from the silicon substrate is also quantified. We also estimate the losses associated with scattering from surface roughness, which is an unavoidable byproduct of the NCD thin film growth process. Our results indicate that despite the relatively low film thickness-to-wavelength ratio, mechanically stable waveguides with good optical confinement and low material and bending losses can be realised to cover the full 2.5–16 µm range. In addition, scattering loss estimations predict a drastic drop in roughness-induced scattering losses above 6 µm, even for relatively rough films. In addition to highlighting the utility of suspended NCD as a versatile platform for mid-infrared integrated photonics, the approaches and results presented here can be used to inform the design of suspended air-clad waveguides in other material platforms.
Self-imaging vectorial singularity networks in 3d structured light fields
Authors: Droop Ramon , Otte Eileen , Denz Cornelia
Published: June 2021

We transfer on-demand structuring of three-dimensional scalar amplitude and phase patterns to polarization-structured, vectorial light fields and its singularities. Our approach allows inheriting non-diffracting as well as self-imaging propagation properties to tailored singular ellipse fields, including self-replicating amplitude, polarization, and singularity configurations. It is experimentally realized by amplitude, phase and polarization modulation of the angular spectrum of the light field. We demonstrate the customization of complex singularity formations embedded in three-dimensionally (3d) tailored vectorial field. Our findings show that embedded networks of polarization singularities can be customized to propagate in a robust way along curved trajectories, creating and annihilating during propagation. This 3d structuring of vectorial singular light fields opens new perspectives for in-depth singularity studies and for advancing applications as optical micro-manipulation and material machining.
Magnetic sensors-A review and recent technologies
Authors: Khan Mohammed Asadullah , Sun Jian , Li Bodong , Przybysz Alexander , Kosel Jürgen
Published: June 2021

Magnetic field sensors are an integral part of many industrial and biomedical applications, and their utilization continues to grow at a high rate. The development is driven both by new use cases and demand like internet of things as well as by new technologies and capabilities like flexible and stretchable devices. Magnetic field sensors exploit different physical principles for their operation, resulting in different specifications with respect to sensitivity, linearity, field range, power consumption, costs etc. In this review, we will focus on solid state magnetic field sensors that enable miniaturization and are suitable for integrated approaches to satisfy the needs of growing application areas like biosensors, ubiquitous sensor networks, wearables, smart things etc. Such applications require a high sensitivity, low power consumption, flexible substrates and miniaturization. Hence, the sensor types covered in this review are Hall Effect, Giant Magnetoresistance, Tunnel Magnetoresistance, Anisotropic Magnetoresistance and Giant Magnetoimpedance.
BERTMHC: improved MHC–peptide class II interaction prediction with transformer and multiple instance learning
Authors: Cheng Jun , Bendjama Kaïdre , Rittner Karola , Malone Brandon
Published: June 2021

Motivation

Increasingly comprehensive characterization of cancer-associated genetic alterations has paved the way for the development of highly specific therapeutic vaccines. Predicting precisely the binding and presentation of peptides to major histocompatibility complex (MHC) alleles is an important step toward such therapies. Recent data suggest that presentation of both class I and II epitopes are critical for the induction of a sustained effective immune response. However, the prediction performance for MHC class II has been limited compared to class I.

Results

We present a transformer neural network model which leverages self-supervised pretraining from a large corpus of protein sequences. We also propose a multiple instance learning (MIL) framework to deconvolve mass spectrometry data where multiple potential MHC alleles may have presented each peptide. We show that pretraining boosted the performance for these tasks. Combining pretraining and the novel MIL approach, our model outperforms state-of-the-art models based on peptide and MHC sequence only for both binding and cell surface presentation predictions.

Availability and implementation

Our source code is available at https://github.com/s6juncheng/BERTMHC under a noncommercial license. A webserver is available at https://bertmhc.privacy.nlehd.de/

Supplementary information

Supplementary data are available at Bioinformatics online.
TIGA: target illumination GWAS analytics
Authors: Yang Jeremy J , Grissa Dhouha , Lambert Christophe G , Bologa Cristian G , Mathias Stephen L , Waller Anna , Wild David J , Jensen Lars Juhl , Oprea Tudor I
Published: June 2021

Motivation

Genome-wide association studies can reveal important genotype–phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study.

Results

Here, we describe rational ranking, filtering and interpretation of inferred gene–trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene–trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene–trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.

This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists.

Availability and implementation

Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Comparison of laparoscopic versus robot-assisted versus transanal total mesorectal excision surgery for rectal cancer: a retrospective propensity score-matched cohort study of short-term outcomes
Authors: Hol J C , Burghgraef T A , Rutgers M L W , Crolla R M P H , van Geloven N A W , Hompes R , Leijtens J W A , Polat F , Pronk A , Smits A B , Tuynman J B , Verdaasdonk E G G , Consten E C J , Sietses C
Published: June 2021

Background

Laparoscopic total mesorectal excision (TME) surgery for rectal cancer has important technical limitations. Robot-assisted and transanal TME (TaTME) may overcome these limitations, potentially leading to lower conversion rates and reduced morbidity. However, comparative data between the three approaches are lacking. The aim of this study was to compare short-term outcomes for laparoscopic TME, robot-assisted TME and TaTME in expert centres.

Methods

Patients undergoing rectal cancer surgery between 2015 and 2017 in expert centres for laparoscopic, robot-assisted or TaTME were included. Outcomes for TME surgery performed by the specialized technique in the expert centres were compared after propensity score matching. The primary outcome was conversion rate. Secondary outcomes were morbidity and pathological outcomes.

Results

A total of 1078 patients were included. In rectal cancer surgery in general, the overall rate of primary anastomosis was 39.4, 61.9 and 61.9 per cent in laparoscopic, robot-assisted and TaTME centres respectively (P < 0.001). For specialized techniques in expert centres excluding abdominoperineal resection (APR), the rate of primary anastomosis was 66.7 per cent in laparoscopic, 89.8 per cent in robot-assisted and 84.3 per cent in TaTME (P < 0.001). Conversion rates were 3.7 , 4.6 and 1.9 per cent in laparoscopic, robot-assisted and TaTME respectively (P = 0.134). The number of incomplete specimens, circumferential resection margin involvement rate and morbidity rates did not differ.

Conclusion

In the minimally invasive treatment of rectal cancer more primary anastomoses are created in robotic and TaTME expert centres.
Subacromial spacer implantation: an alternative to arthroscopic superior capsular reconstruction. A systematic review
Authors: Osti Leonardo , Milani Lorenzo , Ferrari Silvana , Maffulli Nicola
Published: June 2021

Introduction

This systematic review evaluated and compared the use of a subacromial spacer implantation (SSI) with arthroscopic superior capsular repair (ASCR) in the management of massive irreparable rotator cuff tears (MIRCTs) with an assessment of clinical and imaging outcomes.

Sources of data

This systematic review was carried out following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched in PubMed, Medline and Embase database literature using the keywords ‘subacromial spacer’, ‘subacromial balloon’, ‘subacromial device’, ‘arthroscopy’, ‘superior capsular reconstruction’, ‘irreparable rotator cuff tears’, ‘satisfaction’ and ‘quality of life’.

Areas of agreement

We included a total of 29 articles (14 about SSI and 15 about ASCR) dealing with outcomes, satisfaction and patients’ quality of life.

Areas of controversy

The use of a subacromial spacer showed similar results in terms of patients’ satisfaction and quality of life when compared with ASCR.

Growing points

SSI can be implanted quickly and has a low complication rate. It can therefore be considered a good alternative for the management of MIRCTs.

Areas timely for developing research

The subacromial spacer is a biodegradable implant easily implanted at arthroscopy. It can lead good clinical and imaging outcomes in MIRCTs. Similarly, ASCR can be performed with either an autograft or synthetic allograft transplantation, with satisfactory results. Long-term prospective studies are needed to compare SSI and ASCR to verify their effectiveness.
Interactive rather than independent effect of APOE and sex potentiates tau deposition in women
Authors: Wang Yi-Ting T , Pascoal Tharick A , Therriault Joseph , Kang Min Su , Benedet Andréa L , Savard Melissa , Tissot Cécile , Lussier Firoza Z , Arias Jaime Fernandez , Mathotaarachchi Sulantha , Rajah Maria Natasha , Gauthier Serge , Rosa-Neto Pedro ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: June 2021

The apolipoprotein E gene (APOE) is the most important genetic risk factor for sporadic Alzheimer disease, with the ε4 allele being associated with increased cerebral amyloid-β and tau pathologies. Although APOE has been suggested to have a stronger effect in women as compared to men, there is a lack of comprehensive assessment on how the interactive effect of APOE and sex modulates regional vulnerability to tau accumulation. We previously have shown the regional vulnerability to the interactive effect of tau and APOE, yet the sex difference was not specifically addressed. In this study, we leveraged PET imaging data from the Translational Biomarkers in Aging and Dementia cohort at McGill University Research Centre for Studies in Aging to elucidate the APOE-by-sex interactive effect on tau burden. We hypothesized sex-dependent regional vulnerability to tau deposition. PET radiopharmaceuticals [18F]AZD4694 and [18F]MK6240 were used to assess amyloid-β and tau level respectively in 277 subjects from the Translational Biomarkers in Aging and Dementia cohort. We found that the interaction between APOE and sex, rather than their independent main effects, was associated with abnormal tau accumulation in medial temporal regions. Specifically, we found that female APOEε4 carriers showed significantly higher tau burden in early tau deposition regions including the hippocampus, entorhinal and parahippocampal cortices, after accounting for age, educational attainment, clinical diagnosis and neocortical amyloid load. We replicated these findings in 221 subjects from the Alzheimer’s Disease Neuroimaging Initiative cohort, in which a different tau-PET radioligand, [18F]flortaucipir, was used to assess tau burden. In conclusion, this study provides evidence from two cohort studies that interactive rather than independent effect of APOE and sex potentiates early tau deposition in women. Our results have important implications for clinical trials and practice, which should take into consideration both APOEε4 carriage status and sex for identifying individuals with the highest probability of developing tau accumulation and clinical progression.
LncRNA PCBP1-AS1 correlated with the functional states of cancer cells and inhibited lung adenocarcinoma metastasis by suppressing the EMT progression
Authors: Li Zhihua , Pan Cheng , Wang Zhibo , Deng Xiaheng , Zhu Quan , Wu Weibing , Chen Liang
Published: June 2021

The development of single-cell RNA sequencing (scRNA-seq) provided us an unprecedented chance to identify novel oncogenes or tumor suppressors at single-cell resolution. Long non-coding RNAs (lncRNAs) related to the functional states of cancer cells might play vital roles in the progression of lung adenocarcinoma (LUAD). In this study, lncRNAs that were associated with the functional states of LUAD cells identified in scRNA-seq studies were screened based on the CancerSEA database. Differential gene expression analysis and survival analysis were performed in TCGA, GEO and our JSPH databases. Finally, transwell and tail vein metastasis assays were used to reveal the functions of our identified novel prognostic lncRNAs. A total of 849 lncRNAs were initially identified. Among them, 11 lncRNAs were found significantly associated with LUAD prognosis in the TCGA database. Two of them (PCBP1-AS1 and ZSCAN16-AS1) were further validated in independent GEO datasets. ScRNA-seq analysis showed that PCBP1-AS1 and ZSCAN16-AS1 were significantly negatively correlated with most of the functional states of LUAD cells, especially with metastasis. Functionally, PCBP1-AS1 was aberrantly downregulated in LUAD cells and tumor tissues. Knockdown of PCBP1-AS1 significantly promoted the migration and invasion of LUAD cells. Consistently, PCBP1-AS1 overexpression suppressed the metastasis of LUAD in vitro and in vivo. Besides, PCBP1-AS1 inhibition induced decreased E-cadherin expression and increased N-cadherin, Vimentin and Snail expression. In conclusion, PCBP1-AS1 could suppress the metastasis of LUAD by targeting the epithelial–mesenchymal transition pathway and might serve as a prognostic biomarker and a potential therapeutic target of LUAD.
Adenosine A2A Receptors Contribute to the Radial Migration of Cortical Projection Neurons through the Regulation of Neuronal Polarization and Axon Formation
Authors: Alçada-Morais Sofia , Gonçalves Nélio , Moreno-Juan Verónica , Andres Belén , Ferreira Sofia , Marques Joana M , Magalhães Joana , Rocha João M M , Xu Xinli , Partidário Matilde , Cunha Rodrigo A , López-Bendito Guillermina , Rodrigues Ricardo J
Published: June 2021

Cortical interneurons born in the subpallium reach the cortex through tangential migration, whereas pyramidal cells reach their final position by radial migration. Purinergic signaling via P2Y1 receptors controls the migration of intermediate precursor cells from the ventricular zone to the subventricular zone. It was also reported that the blockade of A2A receptors (A2AR) controls the tangential migration of somatostatin+ interneurons. Here we found that A2AR control radial migration of cortical projection neurons. In A2AR-knockout (KO) mouse embryos or naïve mouse embryos exposed to an A2AR antagonist, we observed an accumulation of early-born migrating neurons in the lower intermediate zone at late embryogenesis. In utero knockdown of A2AR also caused an accumulation of neurons at the lower intermediate zone before birth. This entails the presently identified ability of A2AR to promote multipolar–bipolar transition and axon formation, critical for the transition of migrating neurons from the intermediate zone to the cortical plate. This effect seems to require extracellular ATP-derived adenosine since a similar accumulation of neurons at the lower intermediate zone was observed in mice lacking ecto-5′-nucleotidase (CD73-KO). These findings frame adenosine as a fine-tune regulator of the wiring of cortical inhibitory and excitatory networks.
Recovery From COVID-19-Related Olfactory Disorders and Quality of Life: Insights From an Observational Online Study
Authors: Ferdenzi Camille , Bousquet Christophe , Aguera Pierre-Emmanuel , Dantec Morgane , Daudé Christelle , Fornoni Lesly , Fournel Arnaud , Kassan Aurélien , Mantel Marylou , Moranges Maëlle , Moussy Erwan , Richard Ortegón Stéphane , Rouby Catherine , Bensafi Moustafa
Published: June 2021

Although olfactory disorders (OD) are among the most significant symptoms of COVID-19, recovery time from COVID-19-related OD and their consequences on the quality of life remain poorly documented. We investigated the characteristics and behavioral consequences of COVID-19-related OD using a large-scale study involving 3111 French respondents (78% women) to an online questionnaire over a period of 9 months covering different epidemic waves (from 8 April 2020 to 13 January 2021). In the patients who subjectively recovered from COVID-19-related OD (N = 609), recovery occurred on average after 16 days and most of the time within 1 month (“normal” recovery range); 49 subjectively recovered in 1–2.5 months, and several cases took up to 6.5 months. Among the patients with ongoing OD (N = 2502), 974 were outside the “normal” recovery range (persistent OD) and reported OD for 1–10 months. Developing a persistent OD was more likely with increasing age and in women and was more often associated with parosmia and phantosmia. The deleterious impact of COVID-19-related OD on the quality of life was significantly aggravated by OD duration and was more pronounced in women. Because persistent OD is not infrequent after COVID-19, has deleterious consequences on the quality of life, and receives few solutions from the health practitioners, it would be beneficial to implement screening and treatment programs to minimize the long-term behavioral consequences of COVID-19-related OD.
Increased Household Secondary Attacks Rates With Variant of Concern Severe Acute Respiratory Syndrome Coronavirus 2 Index Cases
Authors: Buchan Sarah A , Tibebu Semra , Daneman Nick , Whelan Michael , Vanniyasingam Thuva , Murti Michelle , Brown Kevin A
Published: June 2021

We compared secondary attack rates in households with B.1.1.7 variant of concern (VOC) versus non-VOC index cases in a matched cohort in Ontario, Canada. The secondary attack rate for VOC index cases was 1.31 times higher than non-VOC index cases. This increase was particularly accentuated for asymptomatic or presymptomatic index cases.
High Prevalence of Anti–Severe Acute Respiratory Syndrome Coronavirus 2 (Anti–SARS-CoV-2) Antibodies After the First Wave of Coronavirus Disease 2019 (COVID-19) in Kinshasa, Democratic Republic of the Congo: Results of a Cross-sectional Household-Based Survey
Authors: Nkuba Antoine N , Makiala Sheila M , Guichet Emilande , Tshiminyi Paul M , Bazitama Yannick M , Yambayamba Marc K , Kazenza Benito M , Kabeya Trésor M , Matungulu Elysee B , Baketana Lionel K , Mitongo Naomi M , Thaurignac Guillaume , Leendertz Fabian H , Vanlerberghe Veerle , Pelloquin Raphaël , Etard Jean-François , Maman David , Mbala Placide K , Ayouba Ahidjo , Peeters Martine , Muyembe Jean-Jacques T , Delaporte Eric , Ahuka Steve M
Published: June 2021

Background

In October 2020, after the first wave of coronavirus disease 2019 (COVID-19), only 8290 confirmed cases were reported in Kinshasa, Democratic Republic of the Congo, but the real prevalence remains unknown. To guide public health policies, we aimed to describe the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) antibodies in the general population in Kinshasa.

Methods

We conducted a cross-sectional, household-based serosurvey between 22 October 2020 and 8 November 2020. Participants were interviewed at home and tested for antibodies against SARS-CoV-2 spike and nucleocapsid proteins in a Luminex-based assay. A positive serology was defined as a sample that reacted with both SARS-CoV-2 proteins (100% sensitivity, 99.7% specificity). The overall weighted, age-standardized prevalence was estimated and the infection-to-case ratio was calculated to determine the proportion of undiagnosed SARS-CoV-2 infections.

Results

A total of 1233 participants from 292 households were included (mean age, 32.4 years; 764 [61.2%] women). The overall weighted, age-standardized SARS-CoV-2 seroprevalence was 16.6% (95% CI: 14.0–19.5%). The estimated infection-to-case ratio was 292:1. Prevalence was higher among participants ≥40 years than among those <18 years (21.2% vs 14.9%, respectively; P < .05). It was also higher in participants who reported hospitalization than among those who did not (29.8% vs 16.0%, respectively; P < .05). However, differences were not significant in the multivariate model (P = .1).

Conclusions

The prevalence of SARS-CoV-2 is much higher than the number of COVID-19 cases reported. These results justify the organization of a sequential series of serosurveys by public health authorities to adapt response measures to the dynamics of the pandemic.
Reporting of Infectious Diseases in the United States During the Coronavirus Disease 2019 (COVID-19) Pandemic
Authors: Crane Matthew A , Popovic Aleksandra , Panaparambil Rohan , Stolbach Andrew I , Romley John A , Ghanem Khalil G
Published: June 2021

Reporting of infectious diseases other than COVID-19 has been greatly decreased throughout the COVID-19 pandemic. We find this decrease varies by routes of transmission, reporting state, and COVID-19 incidence at the time of reporting. These results underscore the need for continual investment in routine surveillance efforts despite pandemic conditions.