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Phys Rev Lett 2021 Mar;126(12):120606

National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.

Symmetries are well known to have had a profound role in our understanding of nature and are a critical design concept for the realization of advanced technologies. In fact, many symmetry-broken states associated with different phases of matter appear in a variety of quantum technology applications. Such symmetries are normally broken in spatial dimension, however, they can also be broken temporally leading to the concept of discrete time symmetries and their associated crystals. Read More

J Chem Theory Comput 2021 Apr 8. Epub 2021 Apr 8.

Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.

Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range nonbonded interactions are calculated in molecular dynamics engines and in the current implementation of GIST have prevented precise comparisons between free energies estimated using GIST and those from other free energy methods such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a formalism by which particle mesh Ewald (PME)-based electrostatic energies and long-range Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the corresponding voxels they occupy in a manner consistent with the GIST approach. Read More

Chemphyschem 2021 Apr 7. Epub 2021 Apr 7.

Autonomous University of Madrid: Universidad Autonoma de Madrid, Chemistry, Ciudad Universitaria de Cantoblanco, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, SPAIN.

The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the anticancer mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin into the polar region of the lipid membrane is controlled, in a first moment, by long-range electrostatic interactions with the choline groups and, in a second step, by long-range electrostatic and hydrogen bond interactions with the phosphate groups. Read More

PeerJ 2021 25;9:e11069. Epub 2021 Mar 25.

Mare-Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigac˛ão Tecnologia e Inovac˛ão (ARDITI), Funchal, Madeira, Portugal.

Wide-ranging connectivity patterns of common bottlenose dolphins () are generally poorly known worldwide and more so within the oceanic archipelagos of Macaronesia in the North East (NE) Atlantic. This study aimed to identify long-range movements between the archipelagos of Macaronesia that lie between 500 and 1,500 km apart, and between Madeira archipelago and the Portuguese continental shelf, through the compilation and comparison of bottlenose dolphin's photo-identification catalogues from different regions: one from Madeira ( = 363 individuals), two from different areas in the Azores ( = 495 and 176), and four from different islands of the Canary Islands ( = 182, 110, 142 and 281), summing up 1791 photographs. An additional comparison was made between the Madeira catalogue and one catalogue from Sagres, on the southwest tip of the Iberian Peninsula ( = 359). Read More

Proc Natl Acad Sci U S A 2021 Apr;118(15)

Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark

Methylation of histone H3K9 is a hallmark of epigenetic silencing in eukaryotes. Nucleosome modifications often rely on positive feedback where enzymes are recruited by modified nucleosomes. A combination of local and global feedbacks has been proposed to account for some dynamic properties of heterochromatin, but the range at which the global feedbacks operate and the exact mode of heterochromatin propagation are not known. Read More

Opt Express 2021 Mar;29(7):10688-10697

Understanding the chiral light-matter interaction offers a new way to control the direction of light. Here, we present an unprecedently long-range transport of valley information of a 2D-layered semiconductor via the directional emission through a dielectric waveguide. In the evanescent near field region of the dielectric waveguide, robust and homogeneous transverse optical spin exists regardless of the size of the waveguide. Read More

Front Genet 2021 19;12:646179. Epub 2021 Mar 19.

Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.

Identifying causal regulatory variants and their target genes from the majority of non-coding disease-associated genetic loci is the main challenge in post-Genome-Wide Association Studies (GWAS) functional studies. Although chromosome conformation capture (3C) and its derivative technologies have been successfully applied to nominate putative causal genes for non-coding variants, many GWAS target genes have not been identified yet. This study generated a high-resolution contact map from epithelial ovarian cancer (EOC) cells with two H3K27ac-HiChIP libraries and analyzed the underlying gene networks for 15 risk loci identified from the largest EOC GWAS. Read More

Int J Mol Sci 2021 Mar 5;22(5). Epub 2021 Mar 5.

Univ. Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France.

About 8% of the human genome is covered with candidate -regulatory elements (cCREs). Disruptions of CREs, described as "-ruptions" have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator () regulatory elements were identified, but the regulatory mechanisms of the gene have yet to be fully elucidated. Read More

J Comp Neurol 2021 Apr 2. Epub 2021 Apr 2.

Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.

The basolateral amygdala (BLA), a region critical for emotional processing, is the limbic hub that is connected with various brain regions. BLA neurons are classified into different subtypes that exhibit differential projection patterns and mediate distinct emotional behaviors; however, little is known about their presynaptic input patterns. In this study, we employed projection-specific monosynaptic rabies virus tracing to identify the direct monosynaptic inputs to BLA subtypes. Read More

Neuroimage 2021 Mar 29;235:118013. Epub 2021 Mar 29.

Berenson-Allen Center for Non-invasive Brain Stimulation, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215 USA. Electronic address:

Resilience is the capacity of complex systems to persist in the face of external perturbations and retain their functional properties and performance. In the present study, we investigated how individual variations in brain resilience, which might influence response to stress, aging and disease, are influenced by genetics and/or the environment, with potential implications for the implementation of resilience-boosting interventions. Resilience estimates were derived from in silico lesioning of either brain regions or functional connections constituting the connectome of healthy individuals belonging to two different large and unique datasets of twins, specifically: 463 individual twins from the Human Connectome Project and 453 individual twins from the Colorado Longitudinal Twin Study. Read More

Sci Rep 2021 Mar 30;11(1):7182. Epub 2021 Mar 30.

School of Kinesiology, University of Minnesota, Minneapolis, MN, USA.

Among children learning to read braille, we asked whether the quantitative kinematics of scanning movements of the reading finger would be related to the proficiency of braille reading. Over a period of 12 months, we recorded the position and orientation of the reading fingers of eight congenitally or early blind children. We found that the strength of long-range power-law temporal correlations in the velocity fluctuations increased with performance in braille reading. Read More

NAR Genom Bioinform 2021 Mar 22;3(1):lqab017. Epub 2021 Mar 22.

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.

Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. Read More

J Comput Chem 2021 Mar 24. Epub 2021 Mar 24.

Institut des Sciences Moléculaires d'Orsay (ISMO) - UMR 8214. Bât. 520, Université Paris-Saclay, Orsay Cedex, France.

We present a comprehensive study of the most relevant numerical aspects influencing frequencies and intensities in the infrared spectrum of isolated polycyclic aromatic hydrocarbons (PAHs) regarding the overestimate of the IR CH-stretching bands. We use naphthalene as benchmark and show the validity of our results to different members of the PAH family. Our analysis relies on widely employed density functional theory methods and second-order vibrational perturbational theory for the computation of vibrational eigenstates. Read More

J Comput Chem 2021 Mar 23. Epub 2021 Mar 23.

Chemoinformatics & AI Research Group, Institute for Theoretical Medicine, Inc., Fujisawa, Japan.

A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Read More

J Biomol Struct Dyn 2021 Mar 22:1-14. Epub 2021 Mar 22.

Kaypeeyes Biotech Pvt. Ltd., Mysuru, Karnataka, India.

GH11 xylanases are versatile small-molecular-weight single-polypeptide chain monofunctional enzymes. This family of glycoside hydrolases has important applications in food, feed and chemical industries. We designed mutants for improved thermal stability with substitutions in the first six residues of the N-terminal region and evaluated the stability in silico. Read More

J Environ Sci (China) 2021 May 6;103:119-134. Epub 2020 Nov 6.

Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Key Lab of Environmental Optics & Technology, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.

Information on the vertical distribution of air pollutants is essential for understanding their spatiotemporal evolution underlying urban atmospheric environment. This paper presents the SO profiles based on ground-based Multi-Axis Differential Optical Absorption Spectroscopy (MAX-DOAS) measurements from March 2018 to February 2019 in Hefei, East China. SO decrease rapidly with increasing heights in the warm season, while lifted layers were observed in the cold season, indicating accumulation or long-range transport of SO in different seasons might occur at different heights. Read More

Sci Rep 2021 Mar 19;11(1):6462. Epub 2021 Mar 19.

CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, 230026, China.

We report the exact dimer phase, in which the ground states are described by product of singlet dimer, in the extended XYZ model by generalizing the isotropic Majumdar-Ghosh model to the fully anisotropic region. We demonstrate that this phase can be realized even in models when antiferromagnetic interaction along one of the three directions. This model also supports three different ferromagnetic (FM) phases, denoted as x-FM, y-FM and z-FM, polarized along the three directions. Read More

Cytogenet Genome Res 2021 Mar 16:1-9. Epub 2021 Mar 16.

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation,

Amplified sequences constitute a large part of mammalian genomes. A chromosome 1 containing 2 large (up to 50 Mb) homogeneously staining regions (HSRs) separated by a small inverted euchromatic region is present in many natural populations of the house mouse (Mus musculus musculus). The HSRs are composed of a long-range repeat cluster, Sp100-rs, with a repeat length of 100 kb. Read More

J Biol Phys 2021 Mar 13;47(1):49-59. Epub 2021 Mar 13.

Departamento de Física, Universidade Federal do Maranhão, São Luís, MA, Brazil.

In this work, we consider a ternary system formed by a surfactant with a lamellar phase (lecithin) that was doped with a solution of Laponite at 1% by volume. The inclusion of nanoparticles in the lamellar phase was investigated by the small-angle X-ray scattering (SAXS) technique, which revealed three types of structures according to the observed scattering pattern. The lamellar period increased linearly with hydration up to a certain limit; this type of behavior is not the same as that found for a similar system using AOT as a surfactant. Read More

Sci Rep 2021 Mar 11;11(1):5714. Epub 2021 Mar 11.

Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Rd., Guangzhou, 510150, China.

Noninvasive prenatal testing (NIPT) for single gene disorders remains challenging. One approach that allows for accurate detection of the slight increase of the maternally inherited allele is the relative haplotype dosage (RHDO) analysis, which requires the construction of parental haplotypes. Recently, the nanopore sequencing technologies have become available and may be an ideal tool for direct construction of haplotypes. Read More

IEEE Trans Pattern Anal Mach Intell 2021 Mar 9;PP. Epub 2021 Mar 9.

Lung cancer is the most common cause of cancer death worldwide. However, it is hard even for experienced doctors to distinguish them from the massive CT slices. The currently existing nodule datasets are limited in both scale and category, which is insufficient and restricts its applications greatly. Read More

J Chem Phys 2021 Mar;154(9):094119

Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg.

Dynamics of flexible molecules are often determined by an interplay between local chemical bond fluctuations and conformational changes driven by long-range electrostatics and van der Waals interactions. This interplay between interactions yields complex potential-energy surfaces (PESs) with multiple minima and transition paths between them. In this work, we assess the performance of the state-of-the-art Machine Learning (ML) models, namely, sGDML, SchNet, Gaussian Approximation Potentials/Smooth Overlap of Atomic Positions (GAPs/SOAPs), and Behler-Parrinello neural networks, for reproducing such PESs, while using limited amounts of reference data. Read More

J Pediatr Surg 2021 Feb 13. Epub 2021 Feb 13.

Department of Pediatric Surgery, Skåne University Hospital Lund, Lund University, Lund, Sweden. Electronic address:

Background/purpose: In Hirschsprung disease (HD) surgery, confirming ganglionic bowel is essential. A faster diagnostic method than the current frozen biopsy is desirable. This study investigated whether aganglionic and ganglionic intestinal wall can be distinguished from each other by ultra high frequency ultrasound (UHF ultrasound). Read More

Viruses 2021 02 12;13(2). Epub 2021 Feb 12.

Fish Health Branch, Leetown Science Center, US Geological Survey Kearneysville, WV 25430, USA.

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (), a freshwater teleost, and belongs to the genus . At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Read More

Ultrasonics 2021 Feb 21;114:106407. Epub 2021 Feb 21.

Department of Engineering Science & Mechanics, Penn State, United States. Electronic address:

The propagation of ultrasonic guided waves in cortical bone has potential to inform medical caregivers about the condition of the bone structure. However, as waveguides, human long bones such as the tibia are complex in terms of their material behavior and their geometric features. They exhibit anisotropic elasticity and internal damping. Read More

J Infect Chemother 2021 Mar 1. Epub 2021 Mar 1.

Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, 10700, Thailand. Electronic address:

Introduction: Vancomycin-resistant Enterococcus faecium (VREfm) carrying vanA was first isolated from patient at Siriraj Hospital, Thailand in 2004. Since then, VREfm isolates have been detected increasingly in this 2500-bed university hospital. To understand the epidemiology of vanA VREfm in this setting, the isolates collected during 2004-2013 were characterized. Read More

Chem Pharm Bull (Tokyo) 2021 ;69(3):237-245

Institute of Nature and Environmental Technology, Kanazawa University.

As a background sampling site in western Japan, the Kanazawa University Wajima Air Monitoring Station (KUWAMS) continuously observes the air pollutants, including PM, PM, organic carbon (OC) and element carbon (EC). Data for September 2019 to April 2020 were compared with data for September 2018 to April 2019. The mean concentrations of both PM and PM were 4. Read More

Cerebellum Ataxias 2021 Feb 24;8(1). Epub 2021 Feb 24.

Service de Neuroimagerie, Centre Hospitalier National d'Ophtalmologie des 15-20, Quinze-Vingt, 28, rue de Charenton, 75012, Paris, France.

Background: Transcranial direct current stimulation (tDCS) of the cerebellum dynamically modulates cerebello-thalamo-cortical excitability in a polarity-specific manner during motor, visuo- motor and cognitive tasks. It remains to be established whether tDCS of the cerebellum impact also on resting-state intrinsically connected networks (ICNs). Such impact would open novel research and therapeutical doors for the neuromodulation of ICNs in human. Read More

Environ Pollut 2020 Aug 18;263(Pt A):114574. Epub 2020 Apr 18.

State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China. Electronic address:

Persistent organic pollutants (POPs) can undergo long-range atmospheric transport (LRAT) and deposit in remote areas. How persistent are POPs in remote areas? To answer this question, we measured two parent-DDTs and eight metabolites in soil and air along a transect in the Qinghai-Tibet Plateau, China, to quantitatively evaluate the degree of degradation of DDTs. DDTs were ubiquitous in soil and air with the total DDT concentrations (ΣDDTs) ranging 37. Read More

Environ Pollut 2021 May 11;276:116728. Epub 2021 Feb 11.

Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, 02882-1197, United States. Electronic address:

The North Pacific-Arctic Oceans are important compartments for semi-volatile organic compounds' (SVOCs) global marine inventory, but whether they act as a "source" or "sink" remains controversial. To study the air-sea exchange and fate of SVOCs during their poleward long-range transport, low-altitude atmosphere and surface seawater were measured for polycyclic aromatic hydrocarbons (PAHs) by passive sampling from July to September in 2014. Gaseous PAH concentrations (0. Read More