bluuebunny/crossref_metadata_2025_split huggingface dataset:
Possible permanent Dirac- to Weyl-semimetal phase transition by ion implantation
Authors: Lee Won Jun , Salawu Yusuff Adeyemi , Kim Heon-Jung , Jang Chan Wook , Kim Sung , Ratcliff Thomas , Elliman Robert G. , Yue Zengji , Wang Xiaolin , Lee Sang-Eon , Jung Myung-Hwa , Rhyee Jong-Soo , Choi Suk-Ho 
Published: April 2022

AbstractThree-dimensional (3D) topological semimetals (TSMs) are a new class of Dirac materials that can be viewed as 3D graphene and are referred to as Dirac semimetals (DSMs) or Weyl semimetals (WSMs) depending on whether time reversal symmetry and/or inversion symmetry are protected, respectively. Despite some interesting results on Dirac- to Weyl-semimetal phase transitions under conditions of low temperature or strong magnetic field (B), all of them are reversible phenomena. Here, we report for the first time a possible permanent transition in a single TSM by ion implantation. A Dirac- to Weyl-semimetal phase transition in a Bi0.96Sb0.04 DSM results from inversion-symmetry breaking induced by implantation with nonmagnetic Au ions for implant fluences (ϕG) ≥ 3.2 × 1016 Au cm−2. This phenomenon is evidenced by the ϕG-dependent behavior of the Raman spectra and quantum-oscillation parameters extracted from magnetoresistance (MR) measurements, which show abrupt changes at ϕG ≥ 3.2 × 1016 Au cm−2. The verification of the transition is further supported by observations of negative MR in the longitudinal B // electric field orientation, indicating the existence of a chiral anomaly in Weyl fermions induced by implantation with nonmagnetic Au ions. In contrast, implantation with magnetic Mn ions exhibits no such particular behavior. Our findings demonstrate the first realization of a possible permanent DSM-to-WSM phase transition in a single material by the simple approach of implantation using nonmagnetic elements.
Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR
Authors: Gauto Diego F. , Macek Pavel , Malinverni Duccio , Fraga Hugo , Paloni Matteo , Sučec Iva , Hessel Audrey , Bustamante Juan Pablo , Barducci Alessandro , Schanda Paul 
Published: April 2022

AbstractLarge oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.
Learning meaningful representations of protein sequences
Authors: Detlefsen Nicki Skafte , Hauberg Søren , Boomsma Wouter 
Published: April 2022

AbstractHow we choose to represent our data has a fundamental impact on our ability to subsequently extract information from them. Machine learning promises to automatically determine efficient representations from large unstructured datasets, such as those arising in biology. However, empirical evidence suggests that seemingly minor changes to these machine learning models yield drastically different data representations that result in different biological interpretations of data. This begs the question of what even constitutes the most meaningful representation. Here, we approach this question for representations of protein sequences, which have received considerable attention in the recent literature. We explore two key contexts in which representations naturally arise: transfer learning and interpretable learning. In the first context, we demonstrate that several contemporary practices yield suboptimal performance, and in the latter we demonstrate that taking representation geometry into account significantly improves interpretability and lets the models reveal biological information that is otherwise obscured.
Interlayer magnetophononic coupling in MnBi2Te4
Authors: Padmanabhan Hari , Poore Maxwell , Kim Peter K. , Koocher Nathan Z. , Stoica Vladimir A. , Puggioni Danilo , (Hugo) Wang Huaiyu , Shen Xiaozhe , Reid Alexander H. , Gu Mingqiang , Wetherington Maxwell , Lee Seng Huat , Schaller Richard D. , Mao Zhiqiang , Lindenberg Aaron M. , Wang Xijie , Rondinelli James M. , Averitt Richard D. , Gopalan Venkatraman 
Published: April 2022

AbstractThe emergence of magnetism in quantum materials creates a platform to realize spin-based applications in spintronics, magnetic memory, and quantum information science. A key to unlocking new functionalities in these materials is the discovery of tunable coupling between spins and other microscopic degrees of freedom. We present evidence for interlayer magnetophononic coupling in the layered magnetic topological insulator MnBi2Te4. Employing magneto-Raman spectroscopy, we observe anomalies in phonon scattering intensities across magnetic field-driven phase transitions, despite the absence of discernible static structural changes. This behavior is a consequence of a magnetophononic wave-mixing process that allows for the excitation of zone-boundary phonons that are otherwise ‘forbidden’ by momentum conservation. Our microscopic model based on density functional theory calculations reveals that this phenomenon can be attributed to phonons modulating the interlayer exchange coupling. Moreover, signatures of magnetophononic coupling are also observed in the time domain through the ultrafast excitation and detection of coherent phonons across magnetic transitions. In light of the intimate connection between magnetism and topology in MnBi2Te4, the magnetophononic coupling represents an important step towards coherent on-demand manipulation of magnetic topological phases.
In vivo imaging of invasive aspergillosis with 18F-fluorodeoxysorbitol positron emission tomography
Authors: Kim Dong-Yeon , Pyo Ayoung , Ji Sehyeon , You Sung-Hwan , Kim Seong Eun , Lim Daejin , Kim Heejung , Lee Kyung-Hwa , Oh Se-Jeong , Jung Ye-rim , Kim Uh Jin , Jeon Subin , Kwon Seong Young , Kang Sae-Ryung , Lee Hyang Burm , Hyun Hoon , Kim So-Young , Moon Kyung-Sub , Lee Sunwoo , Kang Seung Ji , Min Jung-Joon 
Published: April 2022

AbstractInvasive aspergillosis is a critical complication in immunocompromised patients with hematologic malignancies or with viral pneumonia caused by influenza virus or SARS‑CoV‑2. Although early and accurate diagnosis of invasive aspergillosis can maximize clinical outcomes, current diagnostic methods are time-consuming and poorly sensitive. Here, we assess the ability of 2-deoxy-2-18F-fluorosorbitol (18F-FDS) positron emission tomography (PET) to specifically and noninvasively detect Aspergillus infections. We show that 18F-FDS PET can be used to visualize Aspergillus fumigatus infection of the lungs, brain, and muscles in mouse models. In particular, 18F-FDS can distinguish pulmonary aspergillosis from Staphylococcus aureus infection, both of which induce pulmonary infiltrates in immunocompromised patients. Thus, our results indicate that the combination of 18F-FDS PET and appropriate clinical information may be useful in the differential diagnosis and localization of invasive aspergillosis.
Probing the seismic cycle timing with coseismic twisting of subduction margins
Authors: Corbi F. , Bedford J. , Poli P. , Funiciello F. , Deng Z. 
Published: April 2022

AbstractAssessing the timing of great megathrust earthquakes is together crucial for seismic hazard analysis and deemed impossible. Geodetic instrumentation of subduction zones has revealed unexpected deformation patterns at subduction segments adjacent to those that hosted recent mega-earthquakes: coastal sites move landward with faster velocities than before the earthquake. Here, we show observations from the largest and best-monitored megathrust earthquakes, and from a scaled analog model, to reveal that these events create coseismic and postseismic deformation patterns typical of a complete gear-like rotation about a vertical axis, hereafter called twisting. We find that such twisting alters the interseismic velocity field of adjacent subduction segments depending on the time since the last earthquake. Early interactions accelerate while late interactions decelerate local kinematics. This finding opens the possibility of using megathrust earthquakes, the characteristics of the twisting pattern, and the ensuing geodetic velocity changes, as a proxy for estimating the timing of the seismic cycle at unruptured segments along the margin.
Evidence for oxygen-conserving diamond formation in redox-buffered subducted oceanic crust sampled as eclogite
Authors: Aulbach Sonja , Stachel Thomas 
Published: April 2022

AbstractCratonic eclogite is the product of oceanic crust subduction into the subcontinental lithospheric mantle, and it also is a fertile diamond source rock. In contrast to matrix minerals in magma-borne xenoliths, inclusions in diamond are shielded from external fluids, retaining more pristine information on the state of the eclogite source at the time of encapsulation. Vanadium is a multi-valent element and a widely used elemental redox proxy. Here, we show that that xenolithic garnet has lower average V abundances than garnet inclusions. This partly reflects crystal-chemical controls, whereby higher average temperatures recorded by inclusions, accompanied by enhanced Na2O and TiO2 partitioning into garnet, facilitate V incorporation at the expense of clinopyroxene. Unexpectedly, although diamond formation is strongly linked to metasomatism and xenoliths remained open systems, V concentrations are similar for bulk eclogites reconstructed from inclusions and from xenoliths. This suggests an oxygen-conserving mechanism for eclogitic diamond formation, and implies that eclogite is an efficient system to buffer fO2 over aeons of lithospheric mantle modification by subduction-derived and other fluids.
Ferroelectricity coexisted with p-orbital ferromagnetism and metallicity in two-dimensional metal oxynitrides
Authors: Ai Haoqiang , Li Feifei , Bai Haoyun , Liu Dong , Lo Kin Ho , Yang Shengyuan A. , Kawazoe Yoshiyuki , Pan Hui 
Published: April 2022

AbstractTwo-dimensional (2D) multiferroics have attracted increasing interests in basic science and technological fields in recent years. However, most reported 2D magnetic ferroelectrics are based on the d-electron magnetism, which makes them rather rare due to the empirical d0 rule and limits their applications for low magnetic phase transition temperature. In this work, we demonstrate that the ferroelectricity can coexist with the p-electron-induced ferromagnetism without the limitation of d0 rule and metallicity in a family of stable 2D MXene-analogous oxynitrides, X2NO2 (X = In, Tl). Remarkably, the itinerant character of p electrons can lead to the strong ferromagnetic metallic states. Furthermore, a possible magnetoelectric effect is manifested in a Tl2NO2/WTe2 heterostructure through the interface engineering. Our findings provide an alternative possible route toward 2D multiferroics and enrich the concept of ferroelectric metals.
Best practices for the interpretation and reporting of clinical whole genome sequencing
Authors: Austin-Tse Christina A. , Jobanputra Vaidehi , Perry Denise L. , Bick David , Taft Ryan J. , Venner Eric , Gibbs Richard A. , Young Ted , Barnett Sarah , Belmont John W. , Boczek Nicole , Chowdhury Shimul , Ellsworth Katarzyna A. , Guha Saurav , Kulkarni Shashikant , Marcou Cherisse , Meng Linyan , Murdock David R. , Rehman Atteeq U. , Spiteri Elizabeth , Thomas-Wilson Amanda , Kearney Hutton M. , Rehm Heidi L. ,   Medical Genome Initiative*
Published: April 2022

AbstractWhole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
Simultaneous adsorption of As(III) and Cd(II) by ferrihydrite-modified biochar in aqueous solution and their mutual effects
Authors: Tian Xiaosong , Xie Qing , Chai Guanqun , Li Guanghui 
Published: April 2022

AbstractA simply synthetic ferrihydrite-modified biochar (Fh@BC) was applied to simultaneously remove As(III) and Cd(II) from the aqueous solution, and then to explore the mutual effects between As(III) and Cd(II) and the corresponding mechanisms. The Langmuir maximum adsorption capacities of As(III) and Cd(II) in the single adsorbate solution were 18.38 and 18.18 mg g−1, respectively. It demonstrated that Fh@BC was a potential absorbent material for simultaneous removal of As(III) and Cd(II) in aqueous solution. According to the XRF, SEM–EDS, FTIR, XRD, and XPS analysis, the mechanisms of simultaneous removal of As(III) and Cd(II) by Fh@BC could be attributable to the cation exchange, complexation with R-OH and Fe-OH, and oxidation. Moreover, the mutual effect experiment indicated that Cd(II) and As(III) adsorption on Fh@BC in the binary solution exhibited competition, facilitation and synergy, depending on their ratios and added sequences. The mechanisms of facilitation and synergy between Cd(II) and As(III) might include the electrostatic interaction and the formation of both type A or type B ternary surface complexes on the Fh@BC.
A systematic review and meta-analysis on the association between CD36 rs1761667 polymorphism and cardiometabolic risk factors in adults
Authors: Yazdanpanah Zeinab , Mozaffari‐Khosravi Hassan , Mirzaei Masoud , Sheikhha Mohammad Hasan , Salehi-Abargouei Amin 
Published: April 2022

AbstractThe cluster of differentiation 36 (CD36) is one of the main receptors implicated in the pathogenesis of the cardiovascular disease. This study aimed to assess the association between CD36 rs1761667 polymorphism and cardiometabolic risk factors including body mass index (BMI), waist circumference (WC), total cholesterol (TC), triglyceride, HDL-C, LDL-C, blood pressure and fasting blood glucose (FBG). PubMed, EMBASE, Scopus, web of science, and Google Scholar were searched up to December 2021. Subgroup and meta-regression analyses were conducted to explore sources of heterogeneity. Eighteen eligible studies (6317 participants) were included in the study. In the overall analysis, a significant association was found between rs1761667 polymorphism of CD36 and TG in allelic (p < 0.001), recessive (p = 0.001) and homozygous (p = 0.006) models. A relationship between this polymorphism and HDL-C and FBG level was observed in the recessive genetic model. In the subgroup analysis, the A allele was associated with impaired lipid profiles (TC, LDL-C and HDL-C) in the Asian population. The influences of health status, design of the study, confounders, and other sources of heterogeneity should be considered when interpreting present findings. Cohort studies with large sample size and in different ethnicities are needed to confirm the relationship between rs1761667 SNP and cardiometabolic risk factors.
Adolescent’s self-reported weight and its association with media impact on decision to lose weight and body thinness perception
Authors: Al-Hazzaa Hazzaa M. , Al-Awadhi Balqees A. , Al-Dashti Yousef A. , Alajmi Fahhad A. , Almansour Fawaz D. , Al-Haifi Ahmed R. 
Published: April 2022

AbstractThis study investigated the accuracy of self-reported weight among Kuwaiti adolescents and the associations of self-reported weight and calculated BMI with the impact of media use on adolescent’s decision to lose weight and body thinness perception. A total of 706 Kuwaiti adolescents (363 females) 15–18 year-olds were randomly selected from schools. Weight and height were self-reported by the adolescents and measured by the researchers. A specifically designed questionnaire reported the impact of media use on adolescent’s decision to lose weight and body thinness perception. There were significant (p < 0.001) relationships between measured and reported weight (r = 0.947), height (r = 0.777), and calculated BMI (r = 0.623). Intraclass correlation coefficients (95% CI) between self-reported and measured weight and height were 0.973 (0.968–0.977) and 0.867 (0.839–0.891), respectively. The mean differences between self-reported and measured weight (1.26 kg) and BMI (0.478 kg/m2) were relatively small. Females under-reported their weight and the calculated BMI from estimated weight and height was underestimated by adolescents with overweight/obesity. The impact of media use on the adolescent’s perception of being thin relative to the accuracy of the calculated BMI was significant (p = 0.043–0.001). The age-adjusted odds ratio of the calculated (underestimated) BMI in adolescents without overweight/obesity was 0.437 (95% CI = 0.257–0.741; p = 0.002). It was concluded that the validity of self-reported weight was high. Adolescents with overweight/obesity were more likely to underestimate their weight and calculated BMI. Educating adolescents about proper lifestyles and weight loss through media appears warranted.
On evaluation metrics for medical applications of artificial intelligence
Authors: Hicks Steven A. , Strümke Inga , Thambawita Vajira , Hammou Malek , Riegler Michael A. , Halvorsen Pål , Parasa Sravanthi 
Published: April 2022

AbstractClinicians and software developers need to understand how proposed machine learning (ML) models could improve patient care. No single metric captures all the desirable properties of a model, which is why several metrics are typically reported to summarize a model’s performance. Unfortunately, these measures are not easily understandable by many clinicians. Moreover, comparison of models across studies in an objective manner is challenging, and no tool exists to compare models using the same performance metrics. This paper looks at previous ML studies done in gastroenterology, provides an explanation of what different metrics mean in the context of binary classification in the presented studies, and gives a thorough explanation of how different metrics should be interpreted. We also release an open source web-based tool that may be used to aid in calculating the most relevant metrics presented in this paper so that other researchers and clinicians may easily incorporate them into their research.
RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels
Authors: Hillary Luke S , Adriaenssens Evelien M , Jones David L , McDonald James E 
Published: April 2022

Abstract
The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with &gt;10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.
A weighted block cooperative sparse representation algorithm based on visual saliency dictionary
Authors: Chen Rui , Li Fei , Tong Ying , Wu Minghu , Jiao Yang 
Published: April 2022

AbstractUnconstrained face images are interfered by many factors such as illumination, posture, expression, occlusion, age, accessories and so on, resulting in the randomness of the noise pollution implied in the original samples. In order to improve the sample quality, a weighted block cooperative sparse representation algorithm is proposed based on visual saliency dictionary. First, the algorithm uses the biological visual attention mechanism to quickly and accurately obtain the face salient target and constructs the visual salient dictionary. Then, a block cooperation framework is presented to perform sparse coding for different local structures of human face, and the weighted regular term is introduced in the sparse representation process to enhance the identification of information hidden in the coding coefficients. Finally, by synthesising the sparse representation results of all visual salient block dictionaries, the global coding residual is obtained and the class label is given. The experimental results on four databases, that is, AR, extended Yale B, LFW and PubFig, indicate that the combination of visual saliency dictionary, block cooperative sparse representation and weighted constraint coding can effectively enhance the accuracy of sparse representation of the samples to be tested and improve the performance of unconstrained face recognition.
A robust sparse representation algorithm based on adaptive joint dictionary
Authors: Tong Ying , Chen Rui , Wu Minghu , Jiao Yang 
Published: April 2022

AbstractSparse representation based on dictionary construction and learning methods have aroused interests in the field of face recognition. Aiming at the shortcomings of face feature dictionary not ‘clean’ and noise interference dictionary not ‘representative’ in sparse representation classification model, a new method named as robust sparse representation is proposed based on adaptive joint dictionary (RSR‐AJD). First, a fast low‐rank subspace recovery algorithm based on LogDet function (Fast LRSR‐LogDet) is proposed for accurate low‐rank facial intrinsic dictionary representing the similar structure of human face and low computational complexity. Then, the Iteratively Reweighted Robust Principal Component Analysis (IRRPCA) algorithm is used to get a more precise occlusion dictionary for depicting the possible discontinuous interference information attached to human face such as glasses occlusion or scarf occlusion etc. Finally, the above Fast LRSR‐LogDet algorithm and IRRPCA algorithm are adopted to construct the adaptive joint dictionary, which includes the low‐rank facial intrinsic dictionary, the occlusion dictionary and the remaining intra‐class variant dictionary for robust sparse coding. Experiments conducted on four popular databases (AR, Extended Yale B, LFW, and Pubfig) verify the robustness and effectiveness of the authors’ method.