bluuebunny/crossref_metadata_2025_split huggingface dataset:
Writing of strain-controlled multiferroic ribbons into MnWO4
Authors: Toyoda Shingo , Fiebig Manfred , Forster Lea , Arima Taka-hisa , Tokura Yoshinori , Ogawa Naoki 
Published: October 2021

AbstractLocal and low-dimensional structures, such as interfaces, domain walls and structural defects, may exhibit physical properties different from the bulk. Therein, a wide variety of local phases were discovered including conductive interfaces, sheet superconductivity, and magnetoelectric domain walls. The confinement of combined magnetic and electric orders to spatially selected regions may be particularly relevant for future technological applications because it may serve as basis of electrically controllable magnetic memory devices. However, direct observation of magnetoelectric low-dimensional structures cannot readily be done partly because of the lack of experimental techniques locally probing their physical nature. Here, we report an observation of multiferroic ribbon-like domains in a non-multiferroic environment in MnWO4. Using optical second harmonic generation imaging, we reveal that a multiferroic phase is stabilized by locally generated strain while the bulk magnetic structure is non-multiferroic. We further find that the confined multiferroic state retains domains with different directions of electric polarization and we demonstrate deterministic writing of a multiferroic state embedded in a non-multiferroic environment.
Breast cancer dormancy is associated with a 4NG1 state and not senescence
Authors: Prunier Chloé , Alay Ania , van Dijk Michiel , Ammerlaan Kelly L. , van Gelderen Sharon , Marvin Dieuwke L. , Teunisse Amina , Slieker Roderick C. , Szuhai Karoly , Jochemsen A. G. , Solé Xavier , ten Dijke Peter , Ritsma Laila 
Published: October 2021

AbstractReactivation of dormant cancer cells can lead to cancer relapse, metastasis, and patient death. Dormancy is a nonproliferative state and is linked to late relapse and death. No targeted therapy is currently available to eliminate dormant cells, highlighting the need for a deeper understanding and reliable models. Here, we thoroughly characterize the dormant D2.OR and ZR-75-1, and proliferative D2A1 breast cancer cell line models in vivo and/or in vitro, and assess if there is overlap between a dormant and a senescent phenotype. We show that D2.OR but not D2A1 cells become dormant in the liver of an immunocompetent model. In vitro, we show that D2.OR and ZR-75-1 cells in response to a 3D environment or serum-free conditions are growth-arrested in G1, of which a subpopulation resides in a 4NG1 state. The dormancy state is reversible and not associated with a senescence phenotype. This will aid future research on breast cancer dormancy.
Using predictive machine learning models for drug response simulation by calibrating patient-specific pathway signatures
Authors: Golriz Khatami Sepehr , Mubeen Sarah , Bharadhwaj Vinay Srinivas , Kodamullil Alpha Tom , Hofmann-Apitius Martin , Domingo-Fernández Daniel 
Published: October 2021

AbstractThe utility of pathway signatures lies in their capability to determine whether a specific pathway or biological process is dysregulated in a given patient. These signatures have been widely used in machine learning (ML) methods for a variety of applications including precision medicine, drug repurposing, and drug discovery. In this work, we leverage highly predictive ML models for drug response simulation in individual patients by calibrating the pathway activity scores of disease samples. Using these ML models and an intuitive scoring algorithm to modify the signatures of patients, we evaluate whether a given sample that was formerly classified as diseased, could be predicted as normal following drug treatment simulation. We then use this technique as a proxy for the identification of potential drug candidates. Furthermore, we demonstrate the ability of our methodology to successfully identify approved and clinically investigated drugs for four different cancers, outperforming six comparable state-of-the-art methods. We also show how this approach can deconvolute a drugs’ mechanism of action and propose combination therapies. Taken together, our methodology could be promising to support clinical decision-making in personalized medicine by simulating a drugs’ effect on a given patient.
Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes
Authors: Chen Jing , Guo Jun-tao 
Published: October 2021

AbstractInsertions and deletions (Indels) represent one of the major variation types in the human genome and have been implicated in diseases including cancer. To study the features of somatic indels in different cancer genomes, we investigated the indels from two large samples of cancer types: invasive breast carcinoma (BRCA) and lung adenocarcinoma (LUAD). Besides mapping somatic indels in both coding and untranslated regions (UTRs) from the cancer whole exome sequences, we investigated the overlap between these indels and transcription factor binding sites (TFBSs), the key elements for regulation of gene expression that have been found in both coding and non-coding sequences. Compared to the germline indels in healthy genomes, somatic indels contain more coding indels with higher than expected frame-shift (FS) indels in cancer genomes. LUAD has a higher ratio of deletions and higher coding and FS indel rates than BRCA. More importantly, these somatic indels in cancer genomes tend to locate in sequences with important functions, which can affect the core secondary structures of proteins and have a bigger overlap with predicted TFBSs in coding regions than the germline indels. The somatic CDS indels are also enriched in highly conserved nucleotides when compared with germline CDS indels.
Divergent leukaemia subclones as cellular models for testing vulnerabilities associated with gains in chromosomes 7, 8 or 18
Authors: Maher Michael , Diesch Jeannine , Le Pannérer Marguerite-Marie , Cabezón Marta , Mallo Mar , Vergara Sara , Méndez López Aleix , Mesa Tudel Alba , Solé Francesc , Sorigue Marc , Zamora Lurdes , Granada Isabel , Buschbeck Marcus 
Published: October 2021

AbstractHaematopoietic malignancies are frequently characterized by karyotypic abnormalities. The development of targeted drugs has been pioneered with compounds against gene products of fusion genes caused by chromosomal translocations. While polysomies are equally frequent as translocations, for many of them we are lacking therapeutic approaches aimed at synthetic lethality. Here, we report two new cell lines, named MBU-7 and MBU-8, that differ in complete trisomy of chromosome18, a partial trisomy of chromosome 7 and a tetrasomy of the p-arm of chromosome 8, but otherwise share the same mutational pattern and complex karyotype. Both cell lines are divergent clones of U-937 cells and have the morphology and immunoprofile of monocytic cells. The distinct karyotypic differences between MBU-7 and MBU-8 are associated with a difference in the specific response to nucleoside analogues. Taken together, we propose the MBU-7 and MBU-8 cell lines described here as suitable in vitro models for screening and testing vulnerabilities that are associated with the disease-relevant polysomies of chromosome 7, 8 and 18.
Predicting and comparing three corrective techniques for sagittal craniosynostosis
Authors: Cross Connor , Khonsari Roman H. , Larysz Dawid , Johnson David , Kölby Lars , Moazen Mehran 
Published: October 2021

AbstractSagittal synostosis is the most occurring form of craniosynostosis, resulting in calvarial deformation and possible long-term neurocognitive deficits. Several surgical techniques have been developed to correct these issues. Debates as to the most optimal approach are still ongoing. Finite element method is a computational tool that’s shown to assist with the management of craniosynostosis. The aim of this study was to compare and predict the outcomes of three reconstruction methods for sagittal craniosynostosis. Here, a generic finite element model was developed based on a patient at 4 months of age and was virtually reconstructed under all three different techniques. Calvarial growth was simulated to predict the skull morphology and the impact of different reconstruction techniques on the brain growth up to 60 months of age. Predicted morphology was then compared with in vivo and literature data. Our results show a promising resemblance to morphological outcomes at follow up. Morphological characteristics between considered techniques were also captured in our predictions. Pressure outcomes across the brain highlight the potential impact that different techniques have on growth. This study lays the foundation for further investigation into additional reconstructive techniques for sagittal synostosis with the long-term vision of optimizing the management of craniosynostosis.
Galvanic corrosion inhibition from aspect of bonding orbital theory in Cu/Ru barrier CMP
Authors: Lee Kangchun , Sun Seho , Lee Ganggyu , Yoon Gyeonghui , Kim Donghyeok , Hwang Junha , Jeong Hojin , Song Taeseup , Paik Ungyu 
Published: October 2021

AbstractIn this report, the galvanic corrosion inhibition between Cu and Ru metal films is studied, based on bonding orbital theory, using pyridinecarboxylic acid groups which show different affinities depending on the electron configuration of each metal resulting from a π-backbonding. The sp2 carbon atoms adjacent to nitrogen in the pyridine ring provide π-acceptor which forms a complex with filled d-orbital of native oxides on Cu and Ru metal film. The difference in the d-orbital electron density of each metal oxide leads to different π-backbonding strength, resulting in dense or sparse adsorption on native metal oxides. The dense adsorption layer is formed on native Cu oxide film due to the full-filled d-orbital electrons, which effectively suppresses anodic reaction in Cu film. On the other hand, only a sparse adsorption layer is formed on native Ru oxide due to its relatively weak affinity between partially filled d-orbital and pyridine groups. The adsorption behaviour is investigated through interfacial interaction analysis and electrochemical interaction evaluation. Based on this finding, the galvanic corrosion behaviour between Cu and Ru during chemical mechanical planarization (CMP) processing has been controlled.
Biomarkers of persistent renal vulnerability after acute kidney injury recovery
Authors: Fuentes-Calvo Isabel , Cuesta Cristina , Sancho-Martínez Sandra M. , Hidalgo-Thomas Omar A. , Paniagua-Sancho María , López-Hernández Francisco J. , Martínez-Salgado Carlos 
Published: October 2021

AbstractAcute kidney injury (AKI) is a risk factor for new AKI episodes, chronic kidney disease, cardiovascular events and death, as renal repair may be deficient and maladaptive, and activate proinflammatory and profibrotic signals. AKI and AKI recovery definitions are based on changes in plasma creatinine, a parameter mostly associated to glomerular filtration, but largely uncoupled from renal tissue damage. The evolution of structural and functional repair has been incompletely described. We thus aimed at identifying subclinical sequelae persisting after recovery from cisplatin-induced AKI in rats. Compared to controls, after plasma creatinine recovery, post-AKI kidneys showed histological alterations and attendant susceptibility to new AKI episodes. Tubular function (assessed by the furosemide stress test, FST) also remained affected. Lingering parenchymal and functional subclinical alterations were paralleled by tapering, but abnormally high levels of urinary albumin, transferrin, insulin-like growth factor-binding protein 7 (IGFBP7), tissue inhibitor of metalloproteinases-2 (TIMP-2) and, especially, the [TIMP-2]*[IGFBP7] product. As subclinical surrogates of incomplete renal recovery, the FST and the urinary [TIMP-2]*[IGFBP7] product provide two potential diagnostic tools to monitor the sequelae and kidney vulnerability after the apparent recovery from AKI.
Effectiveness and antimicrobial susceptibility profiles during primary antimicrobial prophylaxis for pediatric acute myeloid leukemia
Authors: Yeh Ting-Chi , Hou Jen-Yin , Huang Ting-Huan , Lu Chien-Hung , Sun Fang-Ju , Huang Hsiu-Mei , Liu Hsi-Che 
Published: October 2021

AbstractLimited data are available on antimicrobials exposure and microbiology evolution in pediatric acute myeloid leukemia (AML) patients underwent antimicrobials prophylaxis. To assess the effectiveness of antimicrobials prophylaxis, antibiotic susceptibilities of bacteria, and exposure of antimicrobials during intensive chemotherapy for AML patients, 90 consecutive de novo AML patients aged 0–18 years between January 1, 1997 and March 31, 2018 were enrolled. Vancomycin, ciprofloxacin and voriconazole prophylaxis was administered from January 1, 2010. During the preprophylaxis period, January 1997 to December 2009, 62 patients experienced a total of 87 episodes of bloodstream infection (BSI) and 17 episodes of invasive fungal infection (IFI) among 502 courses of chemotherapy. In contrast, 16 episodes of BSI occurred and no IFIs were reported to occur in 28 patients who received 247 courses of chemotherapy in the prophylaxis period. Patients who received antimicrobial prophylaxis had a significant reduction of BSI, IFI, and febrile neutropenia in comparison with patients without prophylaxis. Exposure to amikacin, carbapenem, amphotericin B was reduced in the prophylaxis period. Imipenem susceptibility of Enterobacter cloacae as well as vancomycin susceptibility of Enterococcus species were reduced in the prophylaxis period. At the time of the last follow up, patients with prophylaxis had a better subsequent 5-year overall survival rate than those without prophylaxis. Prophylactic antimicrobials administration in children with AML who undergo chemotherapy can significantly reduce the rates of life-threatening infection, exposure to antimicrobials, and might result in a better outcome.
Population genomics and evidence of clonal replacement of Plasmodium falciparum in the Peruvian Amazon
Authors: Villena Fredy E. , Lizewski Stephen E. , Joya Christie A. , Valdivia Hugo O. 
Published: October 2021

AbstractPrevious studies have shown that P. falciparum parasites in South America have undergone population bottlenecks resulting in clonal lineages that are differentially distributed and that have been responsible for several outbreaks different endemic regions. In this study, we explored the genomic profile of 18 P. falciparum samples collected in the Peruvian Amazon Basin (Loreto) and 6 from the Peruvian North Coast (Tumbes). Our results showed the presence of three subpopulations that matched previously typed lineages in Peru: Bv1 (n = 17), Clonet D (n = 4) and Acre-Loreto type (n = 3). Gene coverage analysis showed that none of the Bv1 samples presented coverage for pfhrp2 and pfhrp3. Genotyping of drug resistance markers showed a high prevalence of Chloroquine resistance mutations S1034C/N1042D/D1246Y in pfmdr1 (62.5%) and K45T in pfcrt (87.5%). Mutations associated with sulfadoxine and pyrimethamine treatment failure were found on 88.8% of the Bv1 samples which were triple mutants for pfdhfr (50R/51I/108N) and pfdhps (437G/540E/581G). Analysis of the pfS47 gene that allows P. falciparum to evade mosquito immune responses showed that the Bv1 lineage presented one pfS47 haplotype exclusive to Loreto and another haplotype that was present in both Loreto and Tumbes. Furthermore, a possible expansion of Bv1 was detected since 2011 in Loreto. This replacement could be a result of the high prevalence of CQ resistance polymorphisms in Bv1, which could have provided a selective advantage to the indirect selection pressures driven by the use of CQ for P. vivax treatment.
It’s complicated: characterizing the time-varying relationship between cell phone mobility and COVID-19 spread in the US
Authors: Jewell Sean , Futoma Joseph , Hannah Lauren , Miller Andrew C. , Foti Nicholas J. , Fox Emily B. 
Published: October 2021

AbstractRestricting in-person interactions is an important technique for limiting the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Although early research found strong associations between cell phone mobility and infection spread during the initial outbreaks in the United States, it is unclear whether this relationship persists across locations and time. We propose an interpretable statistical model to identify spatiotemporal variation in the association between mobility and infection rates. Using 1 year of US county-level data, we found that sharp drops in mobility often coincided with declining infection rates in the most populous counties in spring 2020. However, the association varied considerably in other locations and across time. Our findings are sensitive to model flexibility, as more restrictive models average over local effects and mask much of the spatiotemporal variation. We conclude that mobility does not appear to be a reliable leading indicator of infection rates, which may have important policy implications.
Structure dynamics of HIV-1 Env trimers on native virions engaged with living T cells
Authors: Carlon-Andres Irene , Malinauskas Tomas , Padilla-Parra Sergi 
Published: October 2021

AbstractThe HIV-1 envelope glycoprotein (Env) mediates viral entry into the host cell. Although the highly dynamic nature of Env intramolecular conformations has been shown with single molecule spectroscopy in vitro, the bona fide Env intra- and intermolecular mechanics when engaged with live T cells remains unknown. We used two photon fast fluorescence lifetime imaging detection of single-molecule Förster Resonance Energy Transfer occurring between fluorescent labels on HIV-1 Env on native virions. Our observations reveal Env dynamics at two levels: transitions between different intramolecular conformations and intermolecular interactions between Env within the viral membrane. Furthermore, we show that three broad neutralizing anti-Env antibodies directed to different epitopes restrict Env intramolecular dynamics and interactions between adjacent Env molecules when engaged with living T cells. Importantly, our results show that Env-Env interactions depend on efficient virus maturation, and that is disrupted upon binding of Env to CD4 or by neutralizing antibodies. Thus, this study illuminates how different intramolecular conformations and distribution of Env molecules mediate HIV-1 Env–T cell interactions in real time and therefore might control immune evasion.
Research on efficiency optimal torque distribution of stator module combined permanent magnet synchronous machine
Authors: Xu Yingying , Zhang Bingyi , Feng Guihong 
Published: October 2021

AbstractThe large permanent magnet synchronous machine (PMSM) usually adopts a modular technique to facilitate manufacture and maintenance. The rated power of large mechanical equipment is selected according to the limit capacity, and the motor efficiency is low at a low load. A kind of unwinding stator module combined permanent magnet synchronous machine (SMCPMSM) is proposed. Each module is mechanically and electrically decoupled. It can operate independently. The number of input modules can be flexibly selected according to the torque requirements in direct drive SMCPMSM to realise the optimum efficiency control of the ball mill. The work presents the loss model of the SMCPMSM and analyzes the torque distribution ratio of the modules. The mathematical model of torque distribution with optimum efficiency is established by using the genetic algorithm. The optimum efficiency control under different loads is determined. The motor performance of four operation modes is simulated by the finite element. An 80 kW prototype is developed, and its experiments are carried out. The experimental results verify the validity of the proposed method.
Model predictive current control with lower switching frequency for permanent magnet synchronous motor drives
Authors: Wang Shuang , Zhang Yuanyuan , Wu Deliang , Zhao Jianfei , Hu Yayuan 
Published: October 2021

AbstractThe model predictive current control (MPCC) technique has been an effective alternative for motor drive applications requiring fast dynamic response. However, the conventional MPCC suffers from high switching losses due to high switching frequency of the inverter. This study proposes a low average switching frequency MPCC method based on boundary‐constrained quadratically extrapolated current trajectory for a permanent magnet synchronous motor drive. First, a quadratic function‐based current prediction model is constructed to obtain the current trajectory in the long‐term future. Second, the boundary constraint is designed to obtain the prediction horizon which is changing in real‐time in order to ensure the validity of the predicted current trajectory. Finally, the cost function established according to the value of the prediction horizon is used to reduce the average switching frequency. In comparison with the conventional MPCC method, the proposed method can significantly reduce the switching frequency of the inverter. In the meantime, fast dynamic response and high steady‐state performance of the conventional MPCC method are preserved. Both simulation and experimental results of the proposed method and the conventional MPCC method are presented to verify the feasibility and advantages of the proposed method.
Tracing the large-scale magnetic field morphology in protoplanetary disks using molecular line polarization
Authors: Lankhaar Boy , Vlemmings Wouter , Bjerkeli Per 
Published: October 2021

Context. Magnetic fields are fundamental to the accretion dynamics of protoplanetary disks and they likely affect planet formation. Typical methods to study the magnetic field morphology observe the polarization of dust or spectral lines. However, it has recently become clear that dust-polarization in ALMA’s (Atacama Large (sub)Millimeter Array) spectral regime does not always faithfully trace the magnetic field structure of protoplanetary disks, which leaves spectral line polarization as a promising method for mapping the magnetic field morphologies of such sources.
Aims. We aim to model the emergent polarization of different molecular lines in the ALMA wavelength regime that are excited in protoplanetary disks. We explore a variety of disk models and molecules to identify those properties that are conducive to the emergence of polarization in spectral lines and may therefore be viably used for magnetic field measurements in protoplanetary disks.
Methods. We used POlarized Radiative Transfer Adapted to Lines in conjunction with the Line Emission Modeling Engine. Together, they allowed us to treat the polarized line radiative transfer of complex three-dimensional physical and magnetic field structures.
Results. We present simulations of the emergence of spectral line polarization of different molecules and molecular transitions in the ALMA wavelength regime. We find that molecules that thermalize at high densities, such as HCN, are also the most susceptible to polarization. We find that such molecules are expected to be significantly polarized in protoplanetary disks, while molecules that thermalize at low densities, such as CO, are only significantly polarized in the outer disk regions. We present the simulated polarization maps at a range of inclinations and magnetic field morphologies, and we comment on the observational feasibility of ALMA linear polarization observations of protoplanetary disks.
Conclusions. We conclude that those molecules with strong dipole moments and relatively low collision rates are most useful for magnetic field observations through line polarization measurements in high density regions such as protoplanetary disks.