bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2
Authors: Israeli Ma’ayan , Finkel Yaara , Yahalom-Ronen Yfat , Paran Nir , Chitlaru Theodor , Israeli Ofir , Cohen-Gihon Inbar , Aftalion Moshe , Falach Reut , Rotem Shahar , Elia Uri , Nemet Ital , Kliker Limor , Mandelboim Michal , Beth-Din Adi , Israely Tomer , Cohen Ofer , Stern-Ginossar Noam , Bercovich-Kinori Adi 
Published: April 2022

AbstractThe global spread of SARS-CoV-2 led to major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SARS-CoV-2 can provide insights into the virus pathogenesis, and facilitate the development of novel therapeutics. Here, employing a genome-scale CRISPR screen, we provide a comprehensive data-set of cellular factors that are exploited by wild type SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. We identified several host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination, Heparan sulfate biogenesis and host phosphatidylglycerol biosynthesis. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential proviral gene for all variants inspected. We show that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals shows elevated levels of GATA6, suggesting a role in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and inhibition of viral infectivity. Overall, we show GATA6 may represent a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.
Modeling antiphase boundary energies of Ni3Al-based alloys using automated density functional theory and machine learning
Authors: Chen Enze , Tamm Artur , Wang Tao , Epler Mario E. , Asta Mark , Frolov Timofey 
Published: April 2022

AbstractAntiphase boundaries (APBs) are planar defects that play a critical role in strengthening Ni-based superalloys, and their sensitivity to alloy composition offers a flexible tuning parameter for alloy design. Here, we report a computational workflow to enable the development of sufficient data to train machine-learning (ML) models to automate the study of the effect of composition on the (111) APB energy in Ni3Al-based alloys. We employ ML to leverage this wealth of data and identify several physical properties that are used to build predictive models for the APB energy that achieve a cross-validation error of 0.033 J m−2. We demonstrate the transferability of these models by predicting APB energies in commercial superalloys. Moreover, our use of physically motivated features such as the ordering energy and stoichiometry-based features opens the way to using existing materials properties databases to guide superalloy design strategies to maximize the APB energy.
An extended computational approach for point-defect equilibria in semiconductor materials
Authors: Ogawa Takafumi , Taguchi Ayako , Kuwabara Akihide 
Published: April 2022

AbstractConcentrations of intrinsic and extrinsic point defects in crystalline materials with a bandgap are typically calculated in a constant-μ approach from defect formation energies based on density functional theory. In this work, calculations of thermal and charge equilibria among point defects are extended to a constant-N approach. The two approaches for point-defect equilibria are comparatively demonstrated in the application to Mg2Si doped with Li, Na, and Ag, which is a lightweight and environmentally friendly thermoelectric candidate material. Our results reveal the systematic behavior of defect and carrier concentrations. The dopant atoms form interstitial defects at similar concentrations to substitutional defects at the Mg sites, resulting in significantly reduced free-carrier concentrations compared to the expected values. The developed procedures could be utilized to find an optimal avenue for achieving higher carrier concentrations, e.g., with regard to annealing temperature and the concentration of dopant atoms, in various semiconductors and insulators.
Lipid level alteration in human and cellular models of alpha synuclein mutations
Authors: Avisar Hila , Guardia-Laguarta Cristina , Surface Matthew , Papagiannakis Nikos , Maniati Matina , Antonellou Roubina , Papadimitriou Dimitra , Koros Christos , Athanassiadou Aglaia , Przedborski Serge , Lerner Boaz , Stefanis Leonidas , Area-Gomez Estela , Alcalay Roy N. 
Published: April 2022

AbstractLipid profiles in biological fluids from patients with Parkinson’s disease (PD) are increasingly investigated in search of biomarkers. However, the lipid profiles in genetic PD remain to be determined, a gap of knowledge of particular interest in PD associated with mutant α-synuclein (SNCA), given the known relationship between this protein and lipids. The objective of this research is to identify serum lipid composition fromSNCAA53T mutation carriers and to compare these alterations to those found in cells and transgenic mice carrying the same genetic mutation. We conducted an unbiased lipidomic analysis of 530 lipid species from 34 lipid classes in serum of 30 participants withSNCAmutation with and without PD and 30 healthy controls. The primary analysis was done between 22 PD patients withSNCA+ (SNCA+/PD+) and 30 controls using machine-learning algorithms and traditional statistics. We also analyzed the lipid composition of human clonal-cell lines and tissue from transgenic mice overexpressing the sameSNCAmutation. We identified specific lipid classes that best discriminate betweenSNCA+/PD+ patients and healthy controls and found certain lipid species, mainly from the glycerophosphatidylcholine and triradylglycerol classes, that are most contributory to this discrimination. Most of these alterations were also present in human derived cells and transgenic mice carrying the same mutation. Our combination of lipidomic and machine learning analyses revealed alterations in glycerophosphatidylcholine and triradylglycerol in sera from PD patients as well as cells and tissues expressing mutant α-Syn. Further investigations are needed to establish the pathogenic significance of these α-Syn-associated lipid changes.
A highly photostable and bright green fluorescent protein
Authors: Hirano Masahiko , Ando Ryoko , Shimozono Satoshi , Sugiyama Mayu , Takeda Noriyo , Kurokawa Hiroshi , Deguchi Ryusaku , Endo Kazuki , Haga Kei , Takai-Todaka Reiko , Inaura Shunsuke , Matsumura Yuta , Hama Hiroshi , Okada Yasushi , Fujiwara Takahiro , Morimoto Takuya , Katayama Kazuhiko , Miyawaki Atsushi 
Published: April 2022

AbstractThe low photostability of fluorescent proteins is a limiting factor in many applications of fluorescence microscopy. Here we present StayGold, a green fluorescent protein (GFP) derived from the jellyfish Cytaeis uchidae. StayGold is over one order of magnitude more photostable than any currently available fluorescent protein and has a cellular brightness similar to mNeonGreen. We used StayGold to image the dynamics of the endoplasmic reticulum (ER) with high spatiotemporal resolution over several minutes using structured illumination microscopy (SIM) and observed substantially less photobleaching than with a GFP variant optimized for stability in the ER. Using StayGold fusions and SIM, we also imaged the dynamics of mitochondrial fusion and fission and mapped the viral spike proteins in fixed cells infected with severe acute respiratory syndrome coronavirus 2. As StayGold is a dimer, we created a tandem dimer version that allowed us to observe the dynamics of microtubules and the excitatory post-synaptic density in neurons. StayGold will substantially reduce the limitations imposed by photobleaching, especially in live cell or volumetric imaging.
Molecular spikes: a gold standard for single-cell RNA counting
Authors: Ziegenhain Christoph , Hendriks Gert-Jan , Hagemann-Jensen Michael , Sandberg Rickard 
Published: April 2022

AbstractSingle-cell sequencing methods rely on molecule-counting strategies to account for amplification biases, yet no experimental strategy to evaluate counting performance exists. Here, we introduce molecular spikes—RNA spike-ins containing built-in unique molecular identifiers (UMIs) that we use to identify critical experimental and computational conditions for accurate RNA counting in single-cell RNA-sequencing (scRNA-seq). Using molecular spikes, we uncovered impaired RNA counting in methods that were not informative for cellular RNA abundances due to inflated UMI counts. We further leverage molecular spikes to improve estimates of total endogenous RNA amounts in cells, and introduce a strategy to correct experiments with impaired RNA counting. The molecular spikes and the accompanying R package UMIcountR (https://github.com/cziegenhain/UMIcountR) will improve the validation of new methods, better estimate and adjust for cellular mRNA amounts and enable more indepth characterization of RNA counting in scRNA-seq.
Clinical target segmentation using a novel deep neural network: double attention Res-U-Net
Authors: Ashkani Chenarlogh Vahid , Shabanzadeh Ali , Ghelich Oghli Mostafa , Sirjani Nasim , Farzin Moghadam Sahar , Akhavan Ardavan , Arabi Hossein , Shiri Isaac , Shabanzadeh Zahra , Sanei Taheri Morteza , Kazem Tarzamni Mohammad 
Published: April 2022

AbstractWe introduced Double Attention Res-U-Net architecture to address medical image segmentation problem in different medical imaging system. Accurate medical image segmentation suffers from some challenges including, difficulty of different interest object modeling, presence of noise, and signal dropout throughout the measurement. The base line image segmentation approaches are not sufficient for complex target segmentation throughout the various medical image types. To overcome the issues, a novel U-Net-based model proposed that consists of two consecutive networks with five and four encoding and decoding levels respectively. In each of networks, there are four residual blocks between the encoder-decoder path and skip connections that help the networks to tackle the vanishing gradient problem, followed by the multi-scale attention gates to generate richer contextual information. To evaluate our architecture, we investigated three distinct data-sets, (i.e., CVC-ClinicDB dataset, Multi-site MRI dataset, and a collected ultrasound dataset). The proposed algorithm achieved Dice and Jaccard coefficients of 95.79%, 91.62%, respectively for CRL, and 93.84% and 89.08% for fetal foot segmentation. Moreover, the proposed model outperformed the state-of-the-art U-Net based model on the external CVC-ClinicDB, and multi-site MRI datasets with Dice and Jaccard coefficients of 83%, 75.31% for CVC-ClinicDB, and 92.07% and 87.14% for multi-site MRI dataset, respectively.
Characterization of host factors associated with the internal ribosomal entry sites of foot-and-mouth disease and classical swine fever viruses
Authors: Ide Yutaro , Kitab Bouchra , Ito Nobumasa , Okamoto Riai , Tamura Yui , Matsui Takafumi , Sakoda Yoshihiro , Tsukiyama-Kohara Kyoko 
Published: April 2022

AbstractFoot-and-mouth disease virus (FMDV) and classical swine fever virus (CSFV) possess positive-sense single-stranded RNA genomes and an internal ribosomal entry site (IRES) element within their 5′-untranslated regions. To investigate the common host factors associated with these IRESs, we established cell lines expressing a bicistronic luciferase reporter plasmid containing an FMDV-IRES or CSFV-IRES element between theRenillaand firefly luciferase genes. First, we treated FMDV-IRES cells with the French maritime pine extract, Pycnogenol (PYC), and examined its suppressive effect on FMDV-IRES activity, as PYC has been reported to have antiviral properties. Next, we performed microarray analysis to identify the host factors that modified their expression upon treatment with PYC, and confirmed their function using specific siRNAs. We found that polycystic kidney disease 1-like 3 (PKD1L3) and ubiquitin-specific peptidase 31 (USP31) were associated with FMDV-IRES activity. Moreover, silencing of these factors significantly suppressed CSFV-IRES activity. Thus, PKD1L3 and USP31 are host factors associated with the functions of FMDV- and CSFV-IRES elements.
Investigation of optical and electrical properties of novel 4T all perovskite tandem solar cell
Authors: Moradbeigi Mahsa , Razaghi Mohammad 
Published: April 2022

AbstractIn this paper, a combined three-dimensional (3D) optical-electrical simulation of non-pb and flexible four-terminal (4T) all perovskite tandem solar cell (APTSC) is presented. In this structure, polyethylene terephthalate (PET) is used as substrates, while the top sub cell has a $$MAGeI_{3}$$

M
A
G
e

I
3

absorber layer and the bottom sub cell has a $$MASnI_{3}$$

M
A
S
n

I
3

absorber layer. This structure is used as a reference in this paper and the optical and electrical properties of it are investigated using the finite element method (FEM). It is shown that this structure has a total power conversion efficiency (PCE) of $$24.65\%$$

24.65
%

. Then, the elimination of the buffer layer and the addition of antireflection layer (ARL) strategies, as well as the use of periodic nano-texture patterns, are used to increase the reference structure’s total PCE. A free-buffer layer tandem device is presented to minimize the parasitic absorption. While the total PCE is improved by $$1.14\%$$

1.14
%

in this case, one of the fabrication steps is also eliminated. A plasma-polymer-fluorocarbon (PPFC) coating layer is suggested as ARL on the substrates of both sub cells to reduce reflection loss. With optimized these layers thickness, total PCE is increased by $$12.76\%$$

12.76
%

. Because the PPFC layer is hydrophobic, the top surface of two sub cells in this structure has self-cleaning characteristic. As a result, this device offers long-term moisture resistance. Finally, the best structure in terms of the maximum total PCE is presented by increasing optical path-length utilizing nano-photonic and nano-plasmonic structures. The final structure is offered as a 4T tandem solar cell (TSC) that is environmentally friendly, extremely flexible, and has self-cleaning capability, with a total PCE of $$30.14\%$$

30.14
%

, which is greater than the total PCE of the reference structure by $$22.27\%$$

22.27
%

.
Magnetic chitosan stabilized Cu(II)-tetrazole complex: an effective nanocatalyst for the synthesis of 3-imino-2-phenylisoindolin-1-one derivatives under ultrasound irradiation
Authors: Nasrollahzadeh Mahmoud , Shafiei Nasrin , Orooji Yasin 
Published: April 2022

AbstractIn the present research, a recyclable catalyst has been prepared via a simple approach using chitosan as a linear polysaccharide. This paper reports the synthesis of novel copper(II) complex of 5-phenyl-1H-tetrazole immobilized on magnetic chitosan (MCS@PhTet@Cu(II)) as an effective catalyst. Transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM), vibrating sample magnetometer (VSM), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDS), and inductively coupled plasma mass spectrometry (ICP-MS) techniques were applied for the characterization of the catalyst. The catalytic activity of MCS@PhTet@Cu(II) was evaluated in the ultrasound-assisted synthesis of 3-imino-2-phenylisoindolin-1-one derivatives via the reaction between benzoyl chloride and arylcyanamides in ethanol at ambient temperature. Utilizing a wide variety of arylcyanamides under mild conditions, no use of toxic organic solvents, moderate reaction time, high yields along with catalyst excellent reusability and easy separation of the products without any tedious separation techniques, made this method a novel and simple process. The resulting heterogeneous catalyst showed valuable advantages such as easier work-up, better stability, and greater separation ability using an external magnet. The catalyst showed high efficacy and recyclability even after five cycles with no significant loss of its efficacy. The present methodology provides a path for the preparation of structurally diverse heterocyclic compounds, which may exhibit important biological activity.
Combined effects of handgrip strength and sensory impairment on the prevalence of cognitive impairment among older adults in Korea
Authors: Lee JuHee , Suh Yujin , Park Jungah , Kim Go-Un , Lee Sumi 
Published: April 2022

AbstractOlder adults commonly experience concurrent lower handgrip strength and sensory impairment. However, previous studies have analyzed the individual effects of either handgrip strength or sensory impairment on cognitive impairment. To address this gap, this study investigated the combined effects of handgrip strength and sensory impairment on cognitive impairment among older adults. In total, 2930 participants aged 65 and older were analyzed using 2014–2018 data from the Korean Longitudinal Study of Aging. Participants underwent assessments of handgrip strength (grip dynamometer), sensory impairment (self-reported responses), and cognitive impairment (Korean version of the Mini-Mental State Examination). Low handgrip strength, compared to normal handgrip strength, was associated with cognitive impairment. In participants with low handgrip strength, vision and hearing impairment were associated with cognitive impairment (odds ratio [OR] 1.36, 95% confidence interval [CI] 1.06–1.75; OR 2.58, 95% CI 1.77–3.78, respectively) compared to those with normal handgrip strength. Participants with low handgrip strength and dual sensory impairment had the highest OR for cognitive impairment (OR 3.73, 95% CI 2.65–5.25). Due to the strong association of low handgrip strength and dual sensory impairment with cognitive impairment, people living with low handgrip strength and dual sensory impairment should be classified as a high-risk group for cognitive impairment and should be prioritized for interventions.
A hybrid machine learning approach for estimating the water-use efficiency and yield in agriculture
Authors: Dehghanisanij Hossein , Emami Hojjat , Emami Somayeh , Rezaverdinejad Vahid 
Published: April 2022

AbstractThis paper introduces the narrow strip irrigation (NSI) method and aims to estimate water-use efficiency (WUE) and yield in apple orchards under NSI in the Miandoab region located southeast of Lake Urmia using a machine learning approach. To perform the estimation, a hybrid method based on an adaptive neuro-fuzzy inference system (ANFIS) and seasons optimization (SO) algorithm was proposed. According to the irrigation and climate factors, six different models have been proposed to combine the parameters in the SO-ANFIS. The proposed method is evaluated on a test data set that contains information about apple orchards in Miandoab city from 2019 to 2021. The NSI model was compared with two popular irrigation methods including two-sided furrow irrigation (TSFI) and basin irrigation (BI) on benchmark scenarios. The results justified that the NSI model increased WUE by 1.90 kg/m3 and 3.13 kg/m3, and yield by 8.57% and 14.30% compared to TSFI and BI methods, respectively. The experimental results show that the proposed SO-ANFIS has achieved the performance of 0.989 and 0.988 in terms of R2 criterion in estimating WUE and yield of NSI irrigation method, respectively. The results confirmed that the SO-ANFIS outperformed the counterpart methods in terms of performance measures.
Drivers of genomic loss of heterozygosity in leiomyosarcoma are distinct from carcinomas
Authors: Seligson Nathan D. , Tang Joy , Jin Dexter X. , Bennett Monica P. , Elvin Julia A. , Graim Kiley , Hays John L. , Millis Sherri Z. , Miles Wayne O. , Chen James L. 
Published: April 2022

AbstractLeiomyosarcoma (LMS) is a rare, aggressive, mesenchymal tumor. Subsets of LMS have been identified to harbor genomic alterations associated with homologous recombination deficiency (HRD); particularly alterations in BRCA2. Whereas genomic loss of heterozygosity (gLOH) has been used as a surrogate marker of HRD in other solid tumors, the prognostic or clinical value of gLOH in LMS (gLOH-LMS) remains poorly defined. We explore the genomic drivers associated with gLOH-LMS and their clinical import. Although the distribution of gLOH-LMS scores are similar to that of carcinomas, outside of BRCA2, there was no overlap with previously published gLOH-associated genes from studies in carcinomas. We note that early stage tumors with elevated gLOH demonstrated a longer disease-free interval following resection in LMS patients. Taken together, and despite similarities to carcinomas in gLOH distribution and clinical import, gLOH-LMS are driven by different genomic signals. Additional studies will be required to isolate and confirm the unique differences in biological factors driving these differences.
Wearable fitness tracker use in federally qualified health center patients: strategies to improve the health of all of us using digital health devices
Authors: Holko Michelle , Litwin Tamara R. , Munoz Fatima , Theisz Katrina I. , Salgin Linda , Jenks Nancy Piper , Holmes Beverly W. , Watson-McGee Pamelia , Winford Eboni , Sharma Yashoda 
Published: April 2022

AbstractAs the use of connected devices rises, an understanding of how digital health technologies can be used for equitable healthcare across diverse communities is needed. We surveyed 1007 adult patients at six Federally Qualified Health Centers regarding wearable fitness trackers. Findings indicate the majority interest in having fitness trackers. Barriers included cost and lack of information, revealing that broad digital health device adoption requires education, investment, and high-touch methods.
Development of broadly neutralizing antibodies targeting the cytomegalovirus subdominant antigen gH
Authors: Parsons Andrea J. , Ophir Sabrina I. , Duty J. Andrew , Kraus Thomas A. , Stein Kathryn R. , Moran Thomas M. , Tortorella Domenico 
Published: April 2022

AbstractHuman cytomegalovirus (HCMV) is a β-herpesvirus that increases morbidity and mortality in immunocompromised individuals including transplant recipients and newborns. New anti-HCMV therapies are an urgent medical need for diverse patient populations. HCMV infection of a broad range of host tissues is dependent on the gH/gL/gO trimer and gH/gL/UL28/UL130/UL131A pentamer complexes on the viral envelope. We sought to develop safe and effective therapeutics against HCMV by generating broadly-neutralizing, human monoclonal antibodies (mAbs) from VelocImmune® mice immunized with gH/gL cDNA. Following high-throughput binding and neutralization screening assays, 11 neutralizing antibodies were identified with unique CDR3 regions and a high-affinity (KD 1.4-65 nM) to the pentamer complex. The antibodies bound to distinct regions within Domains 1 and 2 of gH and effectively neutralized diverse clinical strains in physiologically relevant cell types including epithelial cells, trophoblasts, and monocytes. Importantly, combined adminstration of mAbs with ganciclovir, an FDA approved antiviral, greatly limited virus dissemination. Our work identifies several anti-gH/gL mAbs and sheds light on gH neutralizing epitopes that can guide future vaccine strategies.