bluuebunny/crossref_metadata_2025 huggingface dataset:
A review of molecular dynamics simulations in the designing of effective shale inhibitors: application for drilling with water-based drilling fluids
Authors: Swai Rogers Evarist
Published: September 2020

When drilling for oil and gas, maintaining wellbore stability is of primary importance to reduce non-productive time and trouble cost. Shale swelling causes many problems related to stability when drilling with water-based drilling fluids (WBDF). For many years, it remains the number one cause of time wastage and well abandonment. Different shale samples have different chemical compositions that affect their behavior when in contact with water. This factor makes laboratory-based analysis and characterization of the swelling mechanisms and action of swelling inhibitors extremely challenging. Moreover, the need to replicate different conditions at which clay–water interactions might occur necessitates using a different technique. Molecular dynamics (MD) simulation can be used as a supplement technique to help interpret experimental studies, test and improve a theoretical model, and provide empirical data in high-pressure and high-temperature condition of the borehole. MD simulation applies Newton’s second law of motion to describe particles’ movement in a classical system. The technique can be performed on the time scale of nanoseconds, and in three dimensions, it is thus sufficient for the study of clay–water interaction at a molecular level. It provides a unique view of the clay mineral interlayer and surface activities. This work reviews the progress in MD simulations of clay swelling and its inhibition mechanisms for application in petroleum drilling operations.
Investigation of the anisotropic confinement-dependent brittleness of a Utah coal
Authors: Kim Bo-Hyun , Walton Gabriel , Larson Mark K. , Berry Steve
Published: September 2020

Changes of failure mechanism with increasing confinement, from extensional to shear-dominated failure, are widely observed in the rupture of intact specimens at the laboratory scale and in rock masses. In an analysis published in 2018, both unconfined and triaxial compressive tests were conducted to investigate the strength characteristics of 84 specimens of a Utah coal, including the spalling limits, the ratio of apparent unconfined compressive strength to unconfined compressive strength (UCS), the damage characteristics, and the post-yield dilatancy. These mechanical characteristics were found to be strongly anisotropic as a function of the orientation of the cleats relative to the loading direction, defined as the included angle. A total of four different included angles were used in the work performed in 2018. The authors found that the degree of anisotropic strength differed according to the included angle. However, the transition from extensional to shear failure at the given confinements was not clearly identified. In this study, a total of 20 specimens were additionally prepared from the same coal sample used in the previous study and then tested under both unconfined and triaxial compressive conditions. Because the authors already knew the most contrasting cases of the included angles from the previous work using the four included angles, they chose only two of the included angles (0° and 30°) for this study. For the triaxial compressive tests, a greater confining stress than the mean UCS was applied to the specimens in an attempt to identify the brittle-ductile transition of the coal. The new results have been compiled with the previous results in order to re-evaluate the confinement-dependency of the coal behavior. Additionally, the different confining stresses are used as analogs for different width-to-height (W/H) conditions of pillar strength. Although theW/Hratios of the specimens were not directly considered during testing, the equivalentW/Hratios of a pillar as a function of the confining stresses were estimated using an existing empirical solution. According to this relationship, theW/Hat which in situ pillar behavior would be expected to transition from brittle to ductile is identified.
La stéatopathie dysmétabolique
Authors: Zampaglione Lucia , Ferrari Jacopo , Goossens Nicolas
Published: September 2020

La stéatopathie dysmétabolique (NAFLD) est une maladie hépatique à évolution lente qui comprend un spectre allant de la stéatose hépatique non alcoolique, à la stéatohépatite non alcoolique (NASH) et dans les cas graves, la cirrhose. La NAFLD est la pathologie hépatique la plus répandue dans les pays occidentaux industrialisés, dont la Suisse, avec une prévalence en croissance rapide reflétant celle de l’obésité et du diabète de type 2. Un panel d’experts a récemment proposé l’utilisation d’une nomenclature alternative, la stéatose hépatique associée à un dysfonctionnement métabolique (MAFLD) dont l’utilisation reste discutée. Bien qu’il existe un pipeline de développement de médicaments très actif et que de nombreux médicaments sont actuellement en essai clinique de phase II et III, aucun traitement pharmacologique n’a encore été approuvé pour la NASH. Dans certains cas une chirurgie bariatrique pourra être discutée. Néanmoins, à l’heure actuelle, la prise en charge reste centrée sur les mesures hygiéno-diététiques et le suivi par le médecin de premier recours ou le spécialiste en fonction du stade d’hépatopathie et des comorbidités.
BLOCKS WITH SMALL-DIMENSIONAL BASIC ALGEBRA
Authors: SAMBALE BENJAMIN
Published: September 2020

Linckelmann and Murphy have classified the Morita equivalence classes of p-blocks of finite groups whose basic algebra has dimension at most
$12$
. We extend their classification to dimension
$13$
and
$14$
. As predicted by Donovan’s conjecture, we obtain only finitely many such Morita equivalence classes.
Paternalism as Punishment
Authors: Birks David
Published: September 2020

In this article, I argue that even if we hold that at least some paternalistic behaviour is impermissible when directed towards innocent persons, in certain cases, the same behaviour is permissible when directed towards criminal offenders. I also defend the claim that in some cases it is morally preferable to behave paternalistically towards offenders as an alternative to traditional methods of punishment. I propose that the reason paternalistic behaviour is sometimes permissible towards an offender is the same reason that inflicting intentional harm on an offender is permissible – namely, that it is sometimes a morally justified method of punishing an offender for his wrongdoing.
Altered dynamic interactions within frontostriatal circuits reflect disturbed craving processing in internet gaming disorder
Authors: Zeng Ningning , Wang Min , Dong Haohao , Du Xiaoxia , Dong Guang-Heng
Published: September 2020

Background

Individuals with internet gaming disorder (IGD) are generally characterized by impaired executive control, persistent game-craving, and excessive reward-seeking behaviors. However, the causal interactions within the frontostriatal circuits underlying these problematic behaviors remain unclear. Here, spectral dynamic causal modeling (spDCM) was implemented to explore this issue.

Methods

Resting-state functional magnetic resonance imaging data from 317 online game players (148 IGD subjects and 169 recreational game users (RGUs)) were collected. Using independent component analysis, we determined six region of interests within frontostriatal circuits for further spDCM analysis, and further statistical analyses based on the parametric empirical Bayes framework were performed.

Results

Compared with RGUs, IGD subjects showed inhibitory effective connectivity from the right orbitofrontal cortex (OFC) to the right caudate and from the right dorsolateral prefrontal cortex to the left OFC; at the same time, excitatory effective connectivity was observed from the thalamus to the left OFC. Correlation analyses results showed that the directional connection from the right OFC to the right caudate was negatively associated with addiction severity.

Conclusions

These results suggest that the disrupted causal interactions between specific regions might contribute to dysfunctions within frontostriatal circuits in IGD, and the pathway from the right OFC to the right caudate could serve as a target for brain modulation in future IGD interventions.
An ASP approach for reasoning in a concept-aware multipreferential lightweight DL
Authors: Giordano Laura , Theseider Dupré Daniele
Published: September 2020

In this paper we develop a concept aware multi-preferential semantics for dealing with typicality in description logics, where preferences are associated with concepts, starting from a collection of ranked TBoxes containing defeasible concept inclusions. Preferences are combined to define a preferential interpretation in which defeasible inclusions can be evaluated. The construction of the concept-aware multipreference semantics is related to Brewka’s framework for qualitative preferences. We exploit Answer Set Programming (in particular,asprin) to achieve defeasible reasoning under the multipreference approach for the lightweight description logic ξ$\mathcal L_ \bot ^ + $.
Mi casa es tu casa? The Limits of Inter-systemic Dispute Resolution
Authors: Camarena Rodrigo , Condon Bradly J.
Published: September 2020

The ‘new NAFTA’ agreement between Canada, Mexico, and the United States maintained the system for binational panel judicial review of antidumping and countervailing duty determinations of domestic government agencies. In US–Mexico disputes, this hybrid system brings together Spanish and English-speaking lawyers from the civil and the common law to solve legal disputes applying domestic law. These panels raise issues regarding potential bicultural, bilingual, and bijural (mis)understandings in legal reasoning. Do differences in language, legal traditions, and legal cultures limit the effectiveness of inter-systemic dispute resolution? We analyze all of the decisions of NAFTA panels in US–Mexico disputes regarding Mexican antidumping and countervailing duty determinations and the profiles of the corresponding panelists. This case study tests whether one can actually comprehend the ‘other’. To what extent can a common law, English-speaking lawyer understand and apply Mexican law, expressed in Spanish and rooted in a distinct legal culture?
Chronic immobilization stress induces anxiety-related behaviors and	affects brain essential minerals in male rats
Authors: Sahin Zafer , Ozkurkculer Alpaslan , Kalkan Omer Faruk , Ozkaya Ahmet , Koc Aynur , Koca Raviye Ozen , Solak Hatice , Gormus Zulfikare Isik Solak , Kutlu Selim
Published: September 2020

Abstract. Alterations of essential elements in the brain are associated with the pathophysiology of many neuropsychiatric disorders. It is known that chronic/overwhelming stress may cause some anxiety and/or depression. We aimed to investigate the effects of two different chronic immobilization stress protocols on anxiety-related behaviors and brain minerals. Adult male Wistar rats were divided into 3 groups as follows ( n = 10/group): control, immobilization stress-1 (45 minutes daily for 7-day) and immobilization stress-2 (45 minutes twice a day for 7-day). Stress-related behaviors were evaluated by open field test and forced swimming test. In the immobilization stress-1 and immobilization stress-2 groups, percentage of time spent in the central area (6.38 ± 0.41% and 6.28 ± 1.03% respectively, p < 0.05) and rearing frequency (2.75 ± 0.41 and 3.85 ± 0.46, p < 0.01 and p < 0.05, respectively) were lower, latency to center area (49.11 ± 5.87 s and 44.92 ± 8.04 s, p < 0.01 and p < 0.01, respectively), were higher than the control group (8.65 ± 0.49%, 5.37 ± 0.44 and 15.3 ± 3.32 s, respectively). In the immobilization stress-1 group, zinc (12.65 ± 0.1 ppm, p < 0.001), magnesium (170.4 ± 1.7 ppm, p < 0.005) and phosphate (2.76 ± 0.1 ppm, p < 0.05) levels were lower than the control group (13.87 ± 0.16 ppm, 179.31 ± 1.87 ppm and 3.11 ± 0.06 ppm, respectively). In the immobilization stress-2 group, magnesium (171.56 ± 1.87 ppm, p < 0.05), phosphate (2.44 ± 0.07 ppm, p < 0.001) levels were lower, and manganese (373.68 ± 5.76 ppb, p < 0.001) and copper (2.79 ± 0.15 ppm, p < 0.05) levels were higher than the control group (179.31 ± 1.87 ppm, 3.11 ± 0.06 ppm, 327.25 ± 8.35 ppb and 2.45 ± 0.05 ppm, respectively). Our results indicated that 7-day chronic immobilization stress increased anxiety-related behaviors in both stress groups. Zinc, magnesium, phosphate, copper and manganese levels were affected in the brain.
Intermittency and Passive Scalar Nature of Electron Density Fluctuations in the High‐Latitude Ionosphere at Swarm Altitude
Authors: Consolini G. , De Michelis P. , Alberti T. , Coco I. , Giannattasio F. , Tozzi R. , Carbone V.
Published: September 2020

Some physical processes due to Sun‐Earth interaction can influence the configuration and the dynamics of the high‐latitude ionospheric plasma, particularly during geomagnetically disturbed periods. A possible consequence of this interaction is the occurrence of turbulent fluctuations that can be observed both in magnetic and electric fields and plasma density. Here, we focus on the intermittent nature of high‐latitude ionospheric electron density fluctuations during geomagnetically disturbed periods as observed by one of the satellites of the ESA‐Swarm constellation. The most obvious finding emerging from this study is the strong intermittent character of electron density fluctuations and the existence of an agreement between the anomalous scaling features of electron density fluctuations and those expected from a passive scalar quantity in fluid turbulence. This latter result supports the view of a passive scalar behavior of electron density in the high‐latitude ionosphere that can have significant implications in the field of Space Weather studies.
Interaction Between a Southwestward Propagating MSTID and a Poleward Moving WSA‐Like Plasma Patch on a Magnetically Quiet Night at Midlatitude China Region
Authors: Sun Longchang , Xu Jiyao , Zhu Yajun , Yuan Wei , Chen Zhiqing , Hao Yongqiang , Hu Lianhuan , Zhang Donghe , Guo Bing , Zhao Xiukuan
Published: September 2020

In this paper, we first investigate the effects of a postevening Weddell Sea Anomaly (WSA)‐like plasma patch on a southwestward propagating medium‐scale traveling ionospheric disturbance (MSTID) over Xinglong, China (40.4°N, 117.6°E; Mlat. ~30.4°N). We found that some of this kind of WSA‐like plasma patches moved northward from the equatorial ionization anomaly (EIA) regions to midlatitudes, as they traveled westward into China. During 2012–2016, these plasma patches frequently occurred during the period of May–August with a monthly occurrence rate of over 20%, causing nighttime plasma density enhancements (NPDEs) in midlatitudes of China. Over 50% of these structures were accompanied by concurrent MSTID and Es. We propose that an intense polarization electric field (PEF) associated with an MSTID/Es from the more northern regions of EIA could frequently drive these plasma patches poleward. On the night of 27 June 2014 (Kp < 2−), either an MSTID and an intense Es layer (the maximum foEs >12 MHz) occurred at the onset of the poleward motion of a WSA‐like plasma patch, lending credence to this possibility. The observed plasma patch was pushed poleward to interact with the observed MSTID, causing some poleward extending C‐shaped airglow depletions/enhancements of the MSTID in a transition region where the ionosphere changed from a collapse region to an uplifted one. We attributed those poleward extending airglow depletions to the interaction between the MSTID and the plasma patch because of the secondary gradient drift instability and those of airglow enhancements to the redistribution of plasma.
A Tsunami Warning System Based on Offshore Bottom Pressure Gauges and Data Assimilation for Crete Island in the Eastern Mediterranean Basin
Authors: Wang Yuchen , Heidarzadeh Mohammad , Satake Kenji , Mulia Iyan E. , Yamada Masaki
Published: September 2020

The Eastern Mediterranean Basin (EMB) is under the threat of tsunami events triggered by various causes including earthquakes and landslides. We propose a deployment of Offshore Bottom Pressure Gauges (OBPGs) around Crete Island, which would enable tsunami early warning by data assimilation for disaster mitigation. Our OBPG network consists of 12 gauges distributed around Crete Island, with a 100‐km interval, based on three criteria to select the locations. The station network must have a good azimuthal coverage and have enough (>50 km) distance from the coast, and the OBPGs are placed at the locations where the most energetic wave dynamics occur, which is confirmed by Empirical Orthogonal Function (EOF) analysis of pre‐calculated tsunami scenarios. We demonstrate three test cases comprising a hypothetical seismogenic tsunami in east Sicily, a hypothetical landslide tsunami in the Aegean Sea, and the real tsunami event of the May 2020 off the Crete earthquake. Our designed OBPG network achieves an accuracy of 88.5% for the hypothetical seismogenic tsunami and 87.3% for the hypothetical landslide tsunami with regard to the forecasting of first tsunami peak. For the real event of May 2020, it predicts the tsunami arrival at tide gauge NOA‐04 accurately; the observed and forecasted amplitudes of the first wave are 5.0 cm and 4.5 cm, respectively. The warning lead time for the May 2020 event was ~10 min. Therefore, our results reveal that the assimilation of OBPG data can satisfactorily forecast the amplitudes and arrival times for tsunamis in the EMB.
Mean Climate and Tropical Rainfall Variability in Aquaplanet Simulations Using the Model for Prediction Across Scales‐Atmosphere
Authors: Rios‐Berrios R. , Medeiros B. , Bryan G. H.
Published: September 2020

Aquaplanet experiments are important tools for understanding and improving physical processes simulated by global models; yet, previous aquaplanet experiments largely differ in their representation of subseasonal tropical rainfall variability. This study presents results from aquaplanet experiments produced with the Model for Prediction Across Scales‐Atmosphere (MPAS‐A)—a community model specifically designed to study weather and climate in a common framework. The mean climate and tropical rainfall variability simulated by MPAS‐A with varying horizontal resolution were compared against results from a recent suite of aquaplanet experiments. This comparison shows that, regardless of horizontal resolution, MPAS‐A produces the expected mean climate of an aquaplanet framework with zonally symmetric but meridionally varying sea‐surface temperature. MPAS‐A, however, has a stronger signal of tropical rainfall variability driven by convectively coupled equatorial waves. Sensitivity experiments with different cumulus parameterizations, physics packages, and vertical grids consistently show the presence of those waves, especially equatorial Kelvin waves, in phase with lower‐tropospheric convergence. Other models do not capture such rainfall‐kinematics phasing. These results suggest that simulated tropical rainfall variability depends not only on the cumulus parameterization (as suggested by previous studies) but also on the coupling between physics and dynamics of climate and weather prediction models.
Biofilm matrix disrupts nematode motility and predatory behavior
Authors: Chan Shepherd Yuen , Liu Sylvia Yang , Seng Zijing , Chua Song Lin
Published: September 2020

In nature, bacteria form biofilms by producing exopolymeric matrix that encases its entire community. While it is widely known that biofilm matrix can prevent bacterivore predation and contain virulence factors for killing predators, it is unclear if they can alter predator motility. Here, we report a novel “quagmire” phenotype, where Pseudomonas aeruginosa biofilms could retard the motility of bacterivorous nematode Caenorhabditis elegans via the production of a specific exopolysaccharide, Psl. Psl could reduce the roaming ability of C. elegans by impeding the slithering velocity of C. elegans. Furthermore, the presence of Psl in biofilms could entrap C. elegans within the matrix, with dire consequences to the nematode. After being trapped in biofilms, C. elegans could neither escape effectively from aversive stimuli (noxious blue light), nor leave easily to graze on susceptible biofilm areas. Hence, this reduced the ability of C. elegans to roam and predate on biofilms. Taken together, our work reveals a new function of motility interference by specific biofilm matrix components, and emphasizes its importance in predator–prey interactions.
Subjective mental health, incidence of depressive symptoms in later life, and the role of epigenetics: results from two longitudinal cohort studies
Authors: Perna Laura , Zhang Yan , Matias-Garcia Pamela R. , Ladwig Karl-Heinz , Wiechmann Tobias , Wild Beate , Waldenberger Melanie , Schöttker Ben , Mons Ute , Ihle Andreas , Kliegel Matthias , Schwettmann Lars , Peters Annette , Brenner Hermann
Published: September 2020

The role of self-perceived general health in predicting morbidity and mortality among older people is established. The predictive value of self-perceived mental health and of its possible biological underpinnings for future depressive symptoms is unexplored. This study aimed to assess the role of mental health-related quality of life (HRQOL) and of its epigenetic markers in predicting depressive symptoms among older people without lifetime history of depression. Data were based on a subgroup (n = 1 492) of participants of the longitudinal ESTHER study. An epigenome-wide association study (EWAS) of mental HRQOL was conducted using DNA from baseline whole blood samples and logistic regression analyses were performed to assess the predictive value of methylation beta values of EWAS identified CpGs for incidence of depressive symptoms in later life. The methylation analyses were replicated in the independent KORA cohort (n = 890) and a meta-analysis of the two studies was conducted. Results of the meta-analysis showed that participants with beta values of cg27115863 within quartile 1 (Q1) had nearly a two-fold increased risk of developing depressive symptoms compared to participants with beta values within Q4(ORQ1vsQ4 = 1.80; CI 1.25–2.61). In the ESTHER study the predictive value of subjective mental health for future depressive symptoms was also assessed and for 10-unit increase in mental HRQOL scores the odds for incident depressive symptoms were reduced by 54% (OR 0.46; CI 0.40–0.54). These findings suggest that subjective mental health and hypomethylation at cg27115863 are predictive of depressive symptoms, possibly through the activation of inflammatory signaling pathway.
A 3-year follow-up study of atropine treatment for progressive myopia in Europeans
Authors: Polling Jan Roelof , Tan Emily , Driessen Sjoerd , Loudon Sjoukje E. , Wong Hoi-Lam , van der Schans Astrid , Tideman J. Willem L. , Klaver Caroline C. W.
Published: September 2020

Background

Atropine is the most powerful treatment for progressive myopia in childhood. This study explores the 3-year effectiveness of atropine in a clinical setting.

Methods

In this prospective clinical effectiveness study, children with progressive myopia ≥ 1D/year or myopia ≤ −2.5D were prescribed atropine 0.5%. Examination, including cycloplegic refraction and axial length (AL), was performed at baseline, and follow-up. Outcome measures were spherical equivalent (SER) and AL; annual progression of SER on treatment was compared with that prior to treatment. Adjustments to the dose were made after 1 year in case of low (AL ≥ 0.3 mm/year) or high response (AL < 0.1 mm/year) of AL.

Results

A total of 124 patients were enrolled in the study (median age: 9.5, range: 5–16 years). At baseline, median SER was −5.03D (interquartile range (IQR): 3.08); median AL was 25.14 mm (IQR: 1.30). N = 89 (71.8%) children were persistent to therapy throughout the 3-year follow-up. Median annual progression of SER for these children was −0.25D (IQR: 0.44); of AL 0.11 mm (IQR: 0.18). Of these, N = 32 (36.0%) had insufficient response and were assigned to atropine 1%; N = 26 (29.2%) showed good response and underwent tapering in dose. Rebound of AL progression was not observed. Of the children who ceased therapy, N = 9 were lost to follow-up; N = 9 developed an allergic reaction; and N = 17 (19.1%) stopped due to adverse events.

Conclusion

In children with or at risk of developing high myopia, a starting dose of atropine 0.5% was associated with decreased progression in European children during a 3-year treatment regimen. Our study supports high-dose atropine as a treatment option for children at risk of developing high myopia in adulthood.
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant
Authors: Wei Qingzhen , Wang Jinglei , Wang Wuhong , Hu Tianhua , Hu Haijiao , Bao Chonglai
Published: September 2020

Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29–78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.
Mapping cellular-scale internal mechanics in 3D tissues with thermally responsive hydrogel probes
Authors: Mok Stephanie , Al Habyan Sara , Ledoux Charles , Lee Wontae , MacDonald Katherine N. , McCaffrey Luke , Moraes Christopher
Published: September 2020

Local tissue mechanics play a critical role in cell function, but measuring these properties at cellular length scales in living 3D tissues can present considerable challenges. Here we present thermoresponsive, smart material microgels that can be dispersed or injected into tissues and optically assayed to measure residual tissue elasticity after creep over several weeks. We first develop and characterize the sensors, and demonstrate that internal mechanical profiles of live multicellular spheroids can be mapped at high resolutions to reveal broad ranges of rigidity within the tissues, which vary with subtle differences in spheroid aggregation method. We then show that small sites of unexpectedly high rigidity develop in invasive breast cancer spheroids, and in an in vivo mouse model of breast cancer progression. These focal sites of increased intratumoral rigidity suggest new possibilities for how early mechanical cues that drive cancer cells towards invasion might arise within the evolving tumor microenvironment.
Role of higher-order exchange interactions for skyrmion stability
Authors: Paul Souvik , Haldar Soumyajyoti , von Malottki Stephan , Heinze Stefan
Published: September 2020

Transition-metal interfaces and multilayers are a promising class of systems to realize nanometer-sized, stable magnetic skyrmions for future spintronic devices. For room temperature applications, it is crucial to understand the interactions which control the stability of isolated skyrmions. Typically, skyrmion properties are explained by the interplay of pair-wise exchange interactions, the Dzyaloshinskii-Moriya interaction and the magnetocrystalline anisotropy energy. Here, we demonstrate that higher-order exchange interactions – which have so far been neglected – can play a key role for the stability of skyrmions. We use an atomistic spin model parametrized from first-principles and compare three different ultrathin film systems. We consider all fourth-order exchange interactions and show that, in particular, the four-site four spin interaction has a large effect on the energy barrier preventing skyrmion and antiskyrmion collapse into the ferromagnetic state. Our work opens perspectives to stabilize topological spin structures even in the absence of Dzyaloshinskii-Moriya interaction.
A predictable conserved DNA base composition signature defines human core DNA replication origins
Authors: Akerman Ildem , Kasaai Bahar , Bazarova Alina , Sang Pau Biak , Peiffer Isabelle , Artufel Marie , Derelle Romain , Smith Gabrielle , Rodriguez-Martinez Marta , Romano Manuela , Kinet Sandrina , Tino Peter , Theillet Charles , Taylor Naomi , Ballester Benoit , Méchali Marcel
Published: September 2020

DNA replication initiates from multiple genomic locations called replication origins. In metazoa, DNA sequence elements involved in origin specification remain elusive. Here, we examine pluripotent, primary, differentiating, and immortalized human cells, and demonstrate that a class of origins, termed core origins, is shared by different cell types and host ~80% of all DNA replication initiation events in any cell population. We detect a shared G-rich DNA sequence signature that coincides with most core origins in both human and mouse genomes. Transcription and G-rich elements can independently associate with replication origin activity. Computational algorithms show that core origins can be predicted, based solely on DNA sequence patterns but not on consensus motifs. Our results demonstrate that, despite an attributed stochasticity, core origins are chosen from a limited pool of genomic regions. Immortalization through oncogenic gene expression, but not normal cellular differentiation, results in increased stochastic firing from heterochromatin and decreased origin density at TAD borders.
Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication
Authors: Dutta Prasun , Talenti Andrea , Young Rachel , Jayaraman Siddharth , Callaby Rebecca , Jadhav Santosh Kumar , Dhanikachalam Velu , Manikandan Mayakannan , Biswa Bhim B. , Low Wai Y. , Williams John L. , Cook Elizabeth , Toye Phil , Wall Eileen , Djikeng Appolinaire , Marshall Karen , Archibald Alan L. , Gokhale Suresh , Kumar Satish , Hume David A. , Prendergast James G. D.
Published: September 2020

More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. Here, we sequence the genomes of 79 water buffalo across seven breeds and compare patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication.
Brain stimulation in zero gravity: transcranial magnetic stimulation (TMS) motor threshold decreases during zero gravity induced by parabolic flight
Authors: Badran Bashar W. , Caulfield Kevin A. , Cox Claire , Lopez James W. , Borckardt Jeffrey J. , DeVries William H. , Summers Philipp , Kerns Suzanne , Hanlon Colleen A. , McTeague Lisa M. , George Mark S. , Roberts Donna R.
Published: September 2020

We are just beginning to understand how spaceflight may impact brain function. As NASA proceeds with plans to send astronauts to the Moon and commercial space travel interest increases, it is critical to understand how the human brain and peripheral nervous system respond to zero gravity. Here, we developed and refined head-worn transcranial magnetic stimulation (TMS) systems capable of reliably and quickly determining the amount of electromagnetism each individual needs to detect electromyographic (EMG) threshold levels in the thumb (called the resting motor threshold (rMT)). We then collected rMTs in 10 healthy adult participants in the laboratory at baseline, and subsequently at three time points onboard an airplane: (T1) pre-flight at Earth gravity, (T2) during zero gravity periods induced by parabolic flight and (T3) post-flight at Earth gravity. Overall, the subjects required 12.6% less electromagnetism applied to the brain to cause thumb muscle activation during weightlessness compared to Earth gravity, suggesting neurophysiological changes occur during brief periods of zero gravity. We discuss several candidate explanations for this finding, including upward shift of the brain within the skull, acute increases in cortical excitability, changes in intracranial pressure, and diffuse spinal or neuromuscular system effects. All of these possible explanations warrant further study. In summary, we documented neurophysiological changes during brief episodes of zero gravity and thus highlighting the need for further studies of human brain function in altered gravity conditions to optimally prepare for prolonged microgravity exposure during spaceflight.
Dual similarity solutions of MHD stagnation point flow of Casson fluid with effect of thermal radiation and viscous dissipation: stability analysis
Authors: Lund Liaquat Ali , Omar Zurni , Khan Ilyas , Baleanu Dumitru , Nisar Kottakkaran Sooppy
Published: September 2020

In this paper, the rate of heat transfer of the steady MHD stagnation point flow of Casson fluid on the shrinking/stretching surface has been investigated with the effect of thermal radiation and viscous dissipation. The governing partial differential equations are first transformed into the ordinary (similarity) differential equations. The obtained system of equations is converted from boundary value problems (BVPs) to initial value problems (IVPs) with the help of the shooting method which then solved by the RK method with help of maple software. Furthermore, the three-stage Labatto III-A method is applied to perform stability analysis with the help of a bvp4c solver in MATLAB. Current outcomes contradict numerically with published results and found inastounding agreements. The results reveal that there exist dual solutions in both shrinking and stretching surfaces. Furthermore, the temperature increases when thermal radiation, Eckert number, and magnetic number are increased. Signs of the smallest eigenvalue reveal that only the first solution is stable and can be realizable physically.
Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7
Authors: Greenfield Julia , Shang Xiaoran , Luo Heng , Zhou Yan , Linden Sara B. , Heselpoth Ryan D. , Leiman Petr G. , Nelson Daniel C. , Herzberg Osnat
Published: September 2020

The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.
Abrogation of atypical neurogenesis and vascular-derived EphA4 prevents repeated mild TBI-induced learning and memory impairments
Authors: Greer Kisha , Basso Erwin Kristobal Gudenschwager , Kelly Colin , Cash Alison , Kowalski Elizabeth , Cerna Steven , Ocampo Collin Tanchanco , Wang Xia , Theus Michelle H.
Published: September 2020

Brain injury resulting from repeated mild traumatic insult is associated with cognitive dysfunction and other chronic co-morbidities. The current study tested the effects of aberrant neurogenesis in a mouse model of repeated mild traumatic brain injury (rmTBI). Using Barnes Maze analysis, we found a significant reduction in spatial learning and memory at 24 days post-rmTBI compared to repeated sham (rSham) injury. Cell fate analysis showed a greater number of BrdU-labeled cells which co-expressed Prox-1 in the DG of rmTBI-injured mice which coincided with enhanced cFos expression for neuronal activity. We then selectively ablated dividing neural progenitor cells using a 7-day continuous infusion of Ara-C prior to rSham or rmTBI. This resulted in attenuation of cFos and BrdU-labeled cell changes and prevented associated learning and memory deficits. We further showed this phenotype was ameliorated in EphA4f./f/Tie2-Cre knockout compared to EphA4f./f wild type mice, which coincided with altered mRNA transcript levels of MCP-1, Cx43 and TGFβ. These findings demonstrate that cognitive decline is associated with an increased presence of immature neurons and gene expression changes in the DG following rmTBI. Our data also suggests that vascular EphA4-mediated neurogenic remodeling adversely affects learning and memory behavior in response to repeated insult.
Author Correction: A thrombolytic therapy using diagnostic ultrasound combined with RGDS-targeted microbubbles and urokinase in a rabbit model
Authors: Guan Lina , Wang Chunmei , Yan Xue , Liu Liyun , Li Yanhong , Mu Yuming
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Establishing Virulence Associated Polyphosphate Kinase 2 as a drug target for Mycobacterium tuberculosis
Authors: Singh Mamta , Tiwari Prabhakar , Arora Garima , Agarwal Sakshi , Kidwai Saqib , Singh Ramandeep
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Connexin26 mediates CO2-dependent regulation of breathing via glial cells of the medulla oblongata
Authors: van de Wiel Joseph , Meigh Louise , Bhandare Amol , Cook Jonathan , Nijjar Sarbjit , Huckstepp Robert , Dale Nicholas
Published: September 2020

Breathing is highly sensitive to the PCO2 of arterial blood. Although CO2 is detected via the proxy of pH, CO2 acting directly via Cx26 may also contribute to the regulation of breathing. Here we exploit our knowledge of the structural motif of CO2-binding to Cx26 to devise a dominant negative subunit (Cx26DN) that removes the CO2-sensitivity from endogenously expressed wild type Cx26. Expression of Cx26DN in glial cells of a circumscribed region of the mouse medulla - the caudal parapyramidal area – reduced the adaptive change in tidal volume and minute ventilation by approximately 30% at 6% inspired CO2. As central chemosensors mediate about 70% of the total response to hypercapnia, CO2-sensing via Cx26 in the caudal parapyramidal area contributed about 45% of the centrally-mediated ventilatory response to CO2. Our data unequivocally link the direct sensing of CO2 to the chemosensory control of breathing and demonstrates that CO2-binding to Cx26 is a key transduction step in this fundamental process.
Author Correction: The planctomycete Stieleria maiorica Mal15T employs stieleriacines to alter the species composition in marine biofilms
Authors: Kallscheuer Nicolai , Jeske Olga , Sandargo Birthe , Boedeker Christian , Wiegand Sandra , Bartling Pascal , Jogler Mareike , Rohde Manfred , Petersen Jörn , Medema Marnix H. , Surup Frank , Jogler Christian
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The 2019/20 Australian wildfires generated a persistent smoke-charged vortex rising up to 35 km altitude
Authors: Khaykin Sergey , Legras Bernard , Bucci Silvia , Sellitto Pasquale , Isaksen Lars , Tencé Florent , Bekki Slimane , Bourassa Adam , Rieger Landon , Zawada Daniel , Jumelet Julien , Godin-Beekmann Sophie
Published: September 2020

The Australian bushfires around the turn of the year 2020 generated an unprecedented perturbation of stratospheric composition, dynamical circulation and radiative balance. Here we show from satellite observations that the resulting planetary-scale blocking of solar radiation by the smoke is larger than any previously documented wildfires and of the same order as the radiative forcing produced by moderate volcanic eruptions. A striking effect of the solar heating of an intense smoke patch was the generation of a self-maintained anticyclonic vortex measuring 1000 km in diameter and featuring its own ozone hole. The highly stable vortex persisted in the stratosphere for over 13 weeks, travelled 66,000 km and lifted a confined bubble of smoke and moisture to 35 km altitude. Its evolution was tracked by several satellite-based sensors and was successfully resolved by the European Centre for Medium-Range Weather Forecasts operational system, primarily based on satellite data. Because wildfires are expected to increase in frequency and strength in a changing climate, we suggest that extraordinary events of this type may contribute significantly to the global stratospheric composition in the coming decades.
A spiropyran functionalized fluorescent probe for mitochondria targeting and imaging of endogenous hydrogen sulfide in living cells
Authors: Liu Qiaoling , Zhao Ying , Zhang Yan , Xie Kaixin , Liu Ruirong , Ren Borong , Yan Yanmei , Li Lin
Published: September 2020

A turn-on spiropyran functionalized fluorescein derivative (FMC) is developed for targeting HS− in mitochondria.
A covalent deprotection strategy for assembling supramolecular coordination polymers from metal–organic cages
Authors: Schneider Matthew L. , Linder-Patton Oliver M. , Bloch Witold M.
Published: September 2020

A covalent deprotection strategy facilitates the self-polymerisation of amine-functionalised Cu4L4 metal–organic cages into supramolecular coordination polymers with tunable porosity.
Precise engineering of apoferritin through site-specific host–guest binding
Authors: Wang Xuewei , Du Ke , Heng Hao , Chen Weijian , Li Xiao , Wei Xiaoxuan , Feng Fude , Wang Shu
Published: September 2020

An efficient non-covalent method for precise engineering of the apoferritin surface at twelve two-fold channels is established using a PEGylated porphyrin.
A bimolecular i-motif mediated FRET strategy for imaging protein homodimerization on a living tumor cell surface
Authors: Kan Ailing , Liu Xiaoting , Xu Xiaowen , Zhang Nan , Jiang Wei
Published: September 2020

Proximity-induced folding of two identical half-i's into bimolecular i-motifs leads to FRET for imaging membrane protein homodimerization with an improved matching-degree.
Cu–tetracatechol metallopolymer catalyst for three component click reactions and β-borylation of α,β-unsaturated carbonyl compounds
Authors: Joshi Saurabh , Yip Yong Jie , Türel Tankut , Verma Sandeep , Valiyaveettil Suresh
Published: September 2020

A Cu-tetracatechol polymer catalyst is easy to prepare, works in aqueous media and is recyclable with good catalytic efficiencies. This metallopolymer showed high conversion efficiencies for both click and β-borylation reactions with good recyclability.
Micronization of CL-20 using supercritical and liquefied gases
Authors: Zharkov Mikhail N. , Kuchurov Ilya V. , Zlotin Sergei G.
Published: September 2020

Liquid and supercritical CO2 and TFE have been systematically studied as media for CL-20 recrystallization to estimate their potential for the selective preparation of ultrafine particles.
Molecular dynamics simulation of CO2-switchable surfactant regulated reversible emulsification/demulsification processes of a dodecane–saline system
Authors: Zhang Lihu , Lu Xiancai , Liu Xiandong , Li Qin , Cheng Yongxian , Hou Qingfeng
Published: September 2020

CO2-Switchable surfactants have great potential in a wide range of industrial applications related to their ability to stabilize and destabilize emulsions upon command.
Molecular quaterpyridine-based metal complexes for small molecule activation: water splitting and CO2 reduction
Authors: Chen Lingjing , Chen Gui , Leung Chi-Fai , Cometto Claudio , Robert Marc , Lau Tai-Chu
Published: September 2020

This tutorial describes recent developments in the use of metal quaterpyridine complexes as electrocatalysts and photocatalysts for water splitting and CO2 reduction.
A historical overview of the activation and porosity of metal–organic frameworks
Authors: Zhang Xuan , Chen Zhijie , Liu Xinyao , Hanna Sylvia L. , Wang Xingjie , Taheri-Ledari Reza , Maleki Ali , Li Peng , Farha Omar K.
Published: September 2020

A historical overview of the activation and porosity of MOFs including strategies to design and preserve permanent porosity in MOFs.
POSS nanostructures in catalysis
Authors: Calabrese Carla , Aprile Carmela , Gruttadauria Michelangelo , Giacalone Francesco
Published: September 2020

In this review we highlight the use of appealing POSS-based nanostructures for both homogeneous and heterogeneous catalytic applications.
Impact of antimicrobial peptides on E. coli-mimicking lipid model membranes: correlating structural and dynamic effects using scattering methods
Authors: Nielsen Josefine Eilsø , Prévost Sylvain François , Jenssen Håvard , Lund Reidar
Published: September 2020

Using X-rays and neutrons we address the effect of AMPs on structure and dynamics of lipids in bacterial model membranes.
Membrane electrostatics sensed by tryptophan anchors in hydrophobic model peptides depends on non-aromatic interfacial amino acids: implications in hydrophobic mismatch
Authors: Pal Sreetama , Koeppe Roger E. , Chattopadhyay Amitabha
Published: September 2020

We investigate the contribution of membrane interfacial electrostatics in tryptophan-mediated responses of membrane proteins to hydrophobic mismatch.