bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-party quantum private computation of cardinalities of set intersection and union based on GHZ states
Authors: Zhang Cai , Long Yinxiang , Sun Zhiwei , Li Qin , Huang Qiong 
Published: December 2020

AbstractPrivate Set Intersection Cardinality (PSI-CA) and Private Set Union Cardinality (PSU-CA) are two cryptographic primitives whereby two or more parties are able to obtain the cardinalities of the intersection and the union of their respective private sets, and the privacy of their sets is preserved. In this paper, we propose a three-party protocol to finish these tasks by using quantum resources, where every two, as well as three, parties can obtain the cardinalities of the intersection and the union of their private sets with the help of a semi-honest third party (TP). In our protocol, GHZ states play a role in encoding private information that will be used by TP to compute the cardinalities. We show that the presented protocol is secure against well-known quantum attacks. In addition, we analyze the influence of six typical kinds of Markovian noise on our protocol.
A biomimetic engineered bone platform for advanced testing of prosthetic implants
Authors: Sladkova-Faure Martina , Pujari-Palmer Michael , Öhman-Mägi Caroline , López Alejandro , Wang Hanbin , Engqvist Håkan , de Peppo Giuseppe Maria 
Published: December 2020

AbstractExisting methods for testing prosthetic implants suffer from critical limitations, creating an urgent need for new strategies that facilitate research and development of implants with enhanced osseointegration potential. Herein, we describe a novel, biomimetic, human bone platform for advanced testing of implants in vitro, and demonstrate the scientific validity and predictive value of this approach using an assortment of complementary evaluation methods. We anchored titanium (Ti) and stainless steel (SS) implants into biomimetic scaffolds, seeded with human induced mesenchymal stem cells, to recapitulate the osseointegration process in vitro. We show distinct patterns of gene expression, matrix deposition, and mineralization in response to the two materials, with Ti implants ultimately resulting in stronger integration strength, as seen in other preclinical and clinical studies. Interestingly, RNAseq analysis reveals that the TGF-beta and the FGF2 pathways are overexpressed in response to Ti implants, while the Wnt, BMP, and IGF pathways are overexpressed in response to SS implants. High-resolution imaging shows significantly increased tissue mineralization and calcium deposition at the tissue-implant interface in response to Ti implants, contributing to a twofold increase in pullout strength compared to SS implants. Our technology creates unprecedented research opportunities towards the design of implants and biomaterials that can be personalized, and exhibit enhanced osseointegration potential, with reduced need for animal testing.
A Rab escort protein regulates the MAPK pathway that controls filamentous growth in yeast
Authors: Jamalzadeh Sheida , Pujari Atindra N. , Cullen Paul J. 
Published: December 2020

AbstractMAPK pathways regulate different responses yet can share common components. Although core regulators of MAPK pathways are well known, new pathway regulators continue to be identified. Overexpression screens can uncover new roles for genes in biological processes and are well suited to identify essential genes that cannot be evaluated by gene deletion analysis. In this study, a genome-wide screen was performed to identify genes that, when overexpressed, induce a reporter (FUS1-HIS3) that responds to ERK-type pathways (Mating and filamentous growth or fMAPK) but not p38-type pathways (HOG) in yeast. Approximately 4500 plasmids overexpressing individual yeast genes were introduced into strains containing the reporter by high-throughput transformation. Candidate genes were identified by measuring growth as a readout of reporter activity. Fourteen genes were identified and validated by re-testing: two were metabolic controls (HIS3, ATR1), five had established roles in regulating ERK-type pathways (STE4, STE7, BMH1, BMH2, MIG2) and seven represent potentially new regulators of MAPK signaling (RRN6, CIN5, MRS6, KAR2, TFA1, RSC3, RGT2). MRS6 encodes a Rab escort protein and effector of the TOR pathway that plays a role in nutrient signaling. MRS6 overexpression stimulated invasive growth and phosphorylation of the ERK-type fMAPK, Kss1. Overexpression of MRS6 reduced the osmotolerance of cells and phosphorylation of the p38/HOG MAPK, Hog1. Mrs6 interacted with the PAK kinase Ste20 and MAPKK Ste7 by two-hybrid analysis. Based on these results, Mrs6 may selectively propagate an ERK-dependent signal. Identifying new regulators of MAPK pathways may provide new insights into signal integration among core cellular processes and the execution of pathway-specific responses.
Risk stratification for early-onset fetal growth restriction in women with abnormal serum biomarkers: a retrospective cohort study
Authors: Ormesher L. , Warrander L. , Liu Y. , Thomas S. , Simcox L. , Smith G. C. S. , Myers J. E. , Johnstone E. D. 
Published: December 2020

AbstractAbnormal maternal serum biomarkers (AMSB), identified through the aneuploidy screening programme, are frequent incidental findings in pregnancy. They are associated with fetal growth restriction (FGR), but previous studies have not examined whether this association is with early-onset (< 34 weeks) or late-onset (> 34 weeks) FGR; as a result there is no consensus on management. The aims of this study were to determine the prevalence and phenotype of FGR in women with AMSB and test the predictive value of placental sonographic screening to predict early-onset FGR. 1196 pregnant women with AMSB underwent a 21–24 week “placental screen” comprising fetal and placental size, and uterine artery Doppler. Multivariable regression was used to calculate a predictive model for early-onset FGR (birthweight centile < 3rd/< 10th with absent umbilical end-diastolic flow, < 34 weeks). FGR prevalence was high (10.3%), however early-onset FGR was uncommon (2.3%). Placental screening effectively identified early-onset (area under the curve (AUC) 0.93, 95% confidence interval (CI) 0.87–1.00), but not late-onset FGR (AUC 0.70, 95% CI 0.64–0.75). Internal validation demonstrated robust performance for detection/exclusion of early-onset FGR. In this cohort, utilisation of our proposed algorithm with targeted fetal growth and Doppler surveillance, compared with universal comprehensive surveillance would have avoided 1044 scans, potentiating significant cost-saving for maternity services.
Heat stress elicits remodeling in the anther lipidome of peanut
Authors: Zoong Lwe Zolian S. , Welti Ruth , Anco Daniel , Naveed Salman , Rustgi Sachin , Narayanan Sruthi 
Published: December 2020

AbstractUnderstanding the changes in peanut (Arachis hypogaea L.) anther lipidome under heat stress (HT) will aid in understanding the mechanisms of heat tolerance. We profiled the anther lipidome of seven genotypes exposed to ambient temperature (AT) or HT during flowering. Under AT and HT, the lipidome was dominated by phosphatidylcholine (PC), phosphatidylethanolamine (PE), and triacylglycerol (TAG) species (> 50% of total lipids). Of 89 lipid analytes specified by total acyl carbons:total carbon–carbon double bonds, 36:6, 36:5, and 34:3 PC and 34:3 PE (all contain 18:3 fatty acid and decreased under HT) were the most important lipids that differentiated HT from AT. Heat stress caused decreases in unsaturation indices of membrane lipids, primarily due to decreases in highly-unsaturated lipid species that contained 18:3 fatty acids. In parallel, the expression of Fatty Acid Desaturase 3-2 (FAD3-2; converts 18:2 fatty acids to 18:3) decreased under HT for the heat-tolerant genotype SPT 06-07 but not for the susceptible genotype Bailey. Our results suggested that decreasing lipid unsaturation levels by lowering 18:3 fatty-acid amount through reducing FAD3 expression is likely an acclimation mechanism to heat stress in peanut. Thus, genotypes that are more efficient in doing so will be relatively more tolerant to HT.
Epigenetic differences at the HTR2A locus in progressive multiple sclerosis patients
Authors: Maltby Vicki E. , Lea Rodney A. , Burnard Sean , Xavier Alexandre , Van Cao Thao , White Nicole , Kennedy Daniel , Groen Kira , Sanders Katherine A. , Seeto Rebecca , Bray Samara , Gresle Melissa , Laverick Louise , Butzkueven Helmut , Scott Rodney J. , Lechner-Scott Jeannette 
Published: December 2020

AbstractThe pathology of progressive multiple sclerosis (MS) is poorly understood. We have previously assessed DNA methylation in the CD4+ T cells of relapsing–remitting (RR) MS patients compared to healthy controls and identified differentially methylated regions (DMRs) in HLA-DRB1 and RNF39. This study aimed to investigate the DNA methylation profiles of the CD4+ T cells of progressive MS patients. DNA methylation was measured in two separate case/control cohorts using the Illumina 450K/EPIC arrays and data was analysed with the Chip Analysis Methylation Pipeline (ChAMP). Single nucleotide polymorphisms (SNPs) were assessed using the Illumina Human OmniExpress24 arrays and analysed using PLINK. Expression was assessed using the Illumina HT12 array and analysed in R using a combination of Limma and Illuminaio. We identified three DMRs at HTR2A, SLC17A9 and HDAC4 that were consistent across both cohorts. The DMR at HTR2A is located within the bounds of a haplotype block; however, the DMR remained significant after accounting for SNPs in the region. No expression changes were detected in any DMRs. HTR2A is differentially methylated in progressive MS independent of genotype. This differential methylation is not evident in RRMS, making it a potential biomarker of progressive disease.
Multimodal fusion with deep neural networks for leveraging CT imaging and electronic health record: a case-study in pulmonary embolism detection
Authors: Huang Shih-Cheng , Pareek Anuj , Zamanian Roham , Banerjee Imon , Lungren Matthew P. 
Published: December 2020

AbstractRecent advancements in deep learning have led to a resurgence of medical imaging and Electronic Medical Record (EMR) models for a variety of applications, including clinical decision support, automated workflow triage, clinical prediction and more. However, very few models have been developed to integrate both clinical and imaging data, despite that in routine practice clinicians rely on EMR to provide context in medical imaging interpretation. In this study, we developed and compared different multimodal fusion model architectures that are capable of utilizing both pixel data from volumetric Computed Tomography Pulmonary Angiography scans and clinical patient data from the EMR to automatically classify Pulmonary Embolism (PE) cases. The best performing multimodality model is a late fusion model that achieves an AUROC of 0.947 [95% CI: 0.946–0.948] on the entire held-out test set, outperforming imaging-only and EMR-only single modality models.
Endophytic fungi protect tomato and nightshade plants against Tuta absoluta (Lepidoptera: Gelechiidae) through a hidden friendship and cryptic battle
Authors: Agbessenou Ayaovi , Akutse Komivi S. , Yusuf Abdullahi A. , Ekesi Sunday , Subramanian Sevgan , Khamis Fathiya M. 
Published: December 2020

AbstractEndophytic fungi live within plant tissues without causing any harm to the host, promote its growth, and induce systemic resistance against pests and diseases. To mitigate the challenging concealed feeding behavior of immature stages of Tuta absoluta in both tomato (Solanum lycopersicum) and nightshade (Solanum scabrum) host plants, 15 fungal isolates were assessed for their endophytic and insecticidal properties. Twelve isolates were endophytic to both host plants with varied colonization rates. Host plants endophytically-colonized by Trichoderma asperellum M2RT4, Beauveria bassiana ICIPE 706 and Hypocrea lixii F3ST1 outperformed all the other isolates in reducing significantly the number of eggs laid, mines developed, pupae formed and adults emerged. Furthermore, the survival of exposed adults and F1 progeny was significantly reduced by Trichoderma sp. F2L41 and B. bassiana isolates ICIPE 35(4) and ICIPE 35(15) compared to other isolates. The results indicate that T. asperellum M2RT4, B. bassiana ICIPE 706 and H. lixii F3ST1 have high potential to be developed as endophytic-fungal-based biopesticide for the management of T. absoluta.
Development of a pVEC peptide-based ribonucleoprotein (RNP) delivery system for genome editing using CRISPR/Cas9 in Chlamydomonas reinhardtii
Authors: Kang Seongsu , Jeon Seungjib , Kim Seungcheol , Chang Yong Keun , Kim Yeu-Chun 
Published: December 2020

AbstractRecent technical advances related to the CRISPR/Cas9-based genome editing system have enabled sophisticated genome editing in microalgae. Although the demand for research on genome editing in microalgae has increased over time, methodological research has not been established to date for the delivery of a ribonucleoprotein (Cas9/sgRNA complex) using a cell penetrating peptide into microalgal cell lines. Here, we present a ribonucleoprotein delivery system for Chlamydomonas reinhardtii mediated by the cell penetrating peptide pVEC (LLIILRRRIRKQAHAHSK) which is in a non-covalent form. Using this technically simple method, the ribonucleoprotein was successfully delivered into C. reinhardtii. Gene Maa7 and FKB12 were disrupted, and their distinguishing patterns of Indel mutations were analyzed with the observation of several insertions of sequences not originating from the genome DNA, such as chloroplast DNA, into the expected loci. In addition, the cytotoxicity of Cas9 and the ribonucleoprotein was investigated according to the concentration and time in the algal cells. It was observed that Cas9 alone without the sgRNA induces a more severe cytotoxicity compared to the ribonucleoprotein. Our study will not only contribute to algal cell biology and its genetic engineering for further applications involving various organisms but will also provide a deeper understating of the basic science of the CRISPR/Cas9 system.
Quantitative material analysis using secondary electron energy spectromicroscopy
Authors: Han W. , Zheng M. , Banerjee A. , Luo Y. Z. , Shen L. , Khursheed A. 
Published: December 2020

AbstractThis paper demonstrates how secondary electron energy spectroscopy (SEES) performed inside a scanning electron microscope (SEM) can be used to map sample atomic number and acquire bulk valence band density of states (DOS) information at low primary beam voltages. The technique uses an electron energy analyser attachment to detect small changes in the shape of the scattered secondary electron (SE) spectrum and extract out fine structure features from it. Close agreement between experimental and theoretical bulk valance band DOS distributions was obtained for six different test samples, where the normalised root mean square deviation ranged from 2.7 to 6.7%. High accuracy levels of this kind do not appear to have been reported before. The results presented in this paper point towards SEES becoming a quantitative material analysis companion tool for low voltage scanning electron microscopy (LVSEM) and providing new applications for Scanning Auger Microscopy (SAM) instruments.
Fabrication and characterization of mechanically competent 3D printed polycaprolactone-reduced graphene oxide scaffolds
Authors: Seyedsalehi Amir , Daneshmandi Leila , Barajaa Mohammed , Riordan John , Laurencin Cato T. 
Published: December 2020

AbstractThe ability to produce constructs with a high control over the bulk geometry and internal architecture has situated 3D printing as an attractive fabrication technique for scaffolds. Various designs and inks are actively investigated to prepare scaffolds for different tissues. In this work, we prepared 3D printed composite scaffolds comprising polycaprolactone (PCL) and various amounts of reduced graphene oxide (rGO) at 0.5, 1, and 3 wt.%. We employed a two-step fabrication process to ensure an even mixture and distribution of the rGO sheets within the PCL matrix. The inks were prepared by creating composite PCL-rGO films through solvent evaporation casting that were subsequently fed into the 3D printer for extrusion. The resultant scaffolds were seamlessly integrated, and 3D printed with high fidelity and consistency across all groups. This, together with the homogeneous dispersion of the rGO sheets within the polymer matrix, significantly improved the compressive strength and stiffness by 185% and 150%, respectively, at 0.5 wt.% rGO inclusion. The in vitro response of the scaffolds was assessed using human adipose-derived stem cells. All scaffolds were cytocompatible and supported cell growth and viability. These mechanically reinforced and biologically compatible 3D printed PCL-rGO scaffolds are a promising platform for regenerative engineering applications.
pH-controlled stacking direction of the β-strands in peptide fibrils
Authors: Tseng Wei-Hsuan , Chen Szu-Hua , Hiramatsu Hirotsugu 
Published: December 2020

AbstractPeptides provide a framework for generating functional biopolymers. In this study, the pH-dependent structural changes in the 21–29 fragment peptide of β2-microglobulin (β2m21–29) during self-aggregation, i.e., the formation of an amyloid fibril, were discussed. The β-sheet structures formed during parallel stacking under basic conditions (pH ≥ 7.7) adopted an anti-parallel stacking configuration under acidic conditions (pH ≤ 7.6). The parallel and anti-parallel β-sheets existed separately at the intermediate pH (pH = 7.6–7.7). These results were attributed to the rigidity of the β-sheets in the fibrils, which prevented the stable hydrogen bonding interactions between the parallel and anti-parallel β-sheet moieties. This observed pH dependence was ascribed to two phenomena: (i) the pH-dependent collapse of the β2m21–29 fibrils, which consisted of 16 ± 3 anti-parallel β-sheets containing a total of 2000 β-strands during the deprotonation of the NH3+ group (pKa = 8.0) of the β-strands that occurred within 0.7 ± 0.2 strands of each other and (ii) the subsequent formation of the parallel β-sheets. We propose a framework for a functional biopolymer that could alternate between the two β-sheet structures in response to pH changes.
Theoretical basis for the use of non-invasive thermal measurements to assess the brain injury in newborns undergoing therapeutic hypothermia
Authors: Walas Wojciech , Bandoła Dominika , Ostrowski Ziemowit , Rojczyk Marek , Mączko Anna , Halaba Zenon , Nowak Andrzej J. 
Published: December 2020

AbstractThe aim of this paper is to propose a new non-invasive methodology to estimate thermogenesis in newborns with perinatal asphyxia (PA) undergoing therapeutic hypothermia (TH). Metabolic heat production (with respect to either a neonate’s body mass or its body surface) is calculated from the newborn’s heat balance, estimating all remaining terms of this heat balance utilising results of only non-invasive thermal measurements. The measurement devices work with standard equipment used for therapeutic hypothermia and are equipped with the Global System for Mobile Communications (GSM), which allows one to record and monitor the course of the therapy remotely (using an internet browser) without disturbing the medical personnel. This methodology allows one to estimate thermogenesis in newborns with perinatal asphyxia undergoing therapeutic hypothermia. It also offers information about instantaneous values of the rate of cooling together with values of remaining rates of heat transfer. It also shows the trend of any changes, which are recorded during treatment. Having information about all components of the heat balance one is able to facilitate comparison of results obtained for different patients, in whom these components may differ. The proposed method can be a new tool for measuring heat balance with the possibility of offering better predictions regarding short-term neurologic outcomes and tailored management in newborns treated by TH.
Probing of heavy metals in the feathers of shorebirds of Central Asian Flyway wintering grounds
Authors: Pandiyan Jeganathan , Jagadheesan Rajendran , Karthikeyan Ganesan , Mahboob Shahid , Al-Ghanim Khalid A. , Al-Misned Fahad , Ahmed Zubair , Krishnappa Kaliyamoorthy , Elumalai Kuppusamy , Govindarajan Marimuthu 
Published: December 2020

AbstractThe study is intended to deliver the incidence of heavy metals in the feathers of shorebirds from two important Central Asian Flyway (CAF) migratory shorebirds wintering sites such as the Point Calimere Wildlife Sanctuary (PWLS) and Pichavaram Mangrove Forest (PMF), India. Feathers of fifteen species of shorebirds and seven different metals viz., Cu, Cr, Co, Pb, Hg, Ni and Zn were analyzed. Zn was highest in Dunlin, Little-ringed Plover, Marsh Sandpiper, and Common sandpiper, Ni showed highest in Little ringed plover, and Common sandpiper, Co, Cr, and Cu were maximum in Little stint, Marsh sandpiper, and Dunlin, respectively. The Hg was higher in Black-winged stilt, Common redshank, Curlew Sandpiper, Eurasian curlew, Lesser Sand-plover, Temminck’s stint, Kentish plover, Spotted redshank, and Wood sandpiper, the Pb found highest in Kentish plover, Painted stork, Spotted redshank, Wood sandpiper, Eurasian Curlew, and Lesser sand-plover. The concentration of metals showed significant variations among the species of shorebirds studied (P < 0.001). The mercury negatively correlated with the other metals than the other six metals studied in both the wetlands. The order of metal concentration in the feathers of shorebirds was Zn > Ni > Co > Cr > Cu > Pb > Hg. Nevertheless, the current study revealed that the level of metals in the shorebirds is alarming; since the PWLS and PMF are located along the CAF routes, it needs intensive studies on various pollutions to manage both the resident as well as migratory shorebirds.
Reference gene selection for transcriptional profiling in Cryptocercus punctulatus, an evolutionary link between Isoptera and Blattodea
Authors: Li Zhen , Li Xiangrui , Zhang Qingwen , Yuan Ling , Zhou Xuguo 
Published: December 2020

AbstractThe subsocial life style and wood-feeding capability of Cryptocercus gives us an evolutionary key to unlock some outstanding questions in biology. With the advent of the Genomics Era, there is an unprecedented opportunity to address the evolution of eusociality and the acquisition of lignocellulases at the genetic level. However, to quantify gene expression, an appropriate normalization strategy is warranted to control for the non-specific variations among samples across different experimental conditions. To search for the internal references, 10 housekeeping genes from a gut transcriptome of a wood-feeding cockroach, Cryptocercus punctulatus, were selected as the candidates for the RT-qPCR analysis. The expression profiles of these candidates, including ACT, EF1α, GAPDH, HSP60, HSP70, αTUB, UBC, RPS18, ATPase and GST, were analyzed using a panel of analytical tools, including geNorm, NormFinder, BestKeeper, and comparative ΔCT method. RefFinder, a comprehensive ranking system integrating all four above-mentioned algorithms, rated ACT as the most stable reference gene for different developmental stages and tissues. Expression analysis of the target genes, Hex-1 and Cell-1, using the most or the least appropriate reference genes and a single or multiple normalizers signified this research. Our finding is the first step toward establishing a standardized RT-qPCR analysis in Cryptocercus.