bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying and validating subtypes within major psychiatric disorders based on frontal–posterior functional imbalance via deep learning
Authors: Chang Miao , Womer Fay Y. , Gong Xiaohong , Chen Xi , Tang Lili , Feng Ruiqi , Dong Shuai , Duan Jia , Chen Yifan , Zhang Ran , Wang Yang , Ren Sihua , Wang Yi , Kang Jujiao , Yin Zhiyang , Wei Yange , Wei Shengnan , Jiang Xiaowei , Xu Ke , Cao Bo , Zhang Yanbo , Zhang Weixiong , Tang Yanqing , Zhang Xizhe , Wang Fei
Published: October 2020

Converging evidence increasingly implicates shared etiologic and pathophysiological characteristics among major psychiatric disorders (MPDs), such as schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD). Examining the neurobiology of the psychotic-affective spectrum may greatly advance biological determination of psychiatric diagnosis, which is critical for the development of more effective treatments. In this study, ensemble clustering was developed to identify subtypes within a trans-diagnostic sample of MPDs. Whole brain amplitude of low-frequency fluctuations (ALFF) was used to extract the low-dimensional features for clustering in a total of 944 participants: 581 psychiatric patients (193 with SZ, 171 with BD, and 217 with MDD) and 363 healthy controls (HC). We identified two subtypes with differentiating patterns of functional imbalance between frontal and posterior brain regions, as compared to HC: (1) Archetypal MPDs (60% of MPDs) had increased frontal and decreased posterior ALFF, and decreased cortical thickness and white matter integrity in multiple brain regions that were associated with increased polygenic risk scores and enriched risk gene expression in brain tissues; (2) Atypical MPDs (40% of MPDs) had decreased frontal and increased posterior ALFF with no associated alterations in validity measures. Medicated Archetypal MPDs had lower symptom severity than their unmedicated counterparts; whereas medicated and unmedicated Atypical MPDs had no differences in symptom scores. Our findings suggest that frontal versus posterior functional imbalance as measured by ALFF is a novel putative trans-diagnostic biomarker differentiating subtypes of MPDs that could have implications for precision medicine.
Involvement of CsWRKY70 in salicylic acid-induced citrus fruit resistance against Penicillium digitatum
Authors: Deng Bing , Wang Wenjun , Ruan Changqing , Deng Lili , Yao Shixiang , Zeng Kaifang
Published: October 2020

Penicillium digitatum causes serious losses in postharvest citrus fruit. Exogenous salicylic acid (SA) can induce fruit resistance against various pathogens, but the mechanism remains unclear. Herein, a transcriptome-based approach was used to investigate the underlying mechanism of SA-induced citrus fruit resistance against P. digitatum. We found that CsWRKY70 and genes related to methyl salicylate (MeSA) biosynthesis (salicylate carboxymethyltransferase, SAMT) were induced by exogenous SA. Moreover, significant MeSA accumulation was detected in the SA-treated citrus fruit. The potential involvement of CsWRKY70 in regulating CsSAMT expression in citrus fruit was studied. Subcellular localization, dual luciferase, and electrophoretic mobility shift assays and an analysis of transient expression in fruit peel revealed that the nucleus‐localized transcriptional activator CsWRKY70 can activate the CsSAMT promoter by recognizing the W-box element. Taken together, the findings from this study offer new insights into the transcriptional regulatory mechanism of exogenous SA-induced disease resistance in Citrus sinensis fruit.
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species
Authors: Yi Xian-Gui , Yu Xia-Qing , Chen Jie , Zhang Min , Liu Shao-Wei , Zhu Hong , Li Meng , Duan Yi-Fan , Chen Lin , Wu Lei , Zhu Shun , Sun Zhong-Shuai , Liu Xin-Hong , Wang Xian-Rong
Published: October 2020

Cerasus serrulatais a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly ofC. serrulataby the use of Nanopore and Hi-C sequencing technologies. The assembledC. serrulatagenome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated thatC. serrulataandC. aviumhave 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 ofC. serrulataare distributed on all chromosomes ofC. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed thatC. serrulatahas 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The presentC. serrulataspecies diverged fromPrunus yedoensis~17.34 million years ago (Mya), while the divergence ofC. serrulataandC. aviumwas estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified inC. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies inC. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searchingC. serrulatawithin the PRGdb. This research provides high-quality genomic information aboutC. serrulataas well as insights into the evolutionary history ofCerasusspecies.
PpINH1, an invertase inhibitor, interacts with vacuolar invertase PpVIN2 in regulating the chilling tolerance of peach fruit
Authors: Wang Xingxing , Chen Yi , Jiang Shu , Xu Feng , Wang Hongfei , Wei Yingying , Shao Xingfeng
Published: October 2020

Sucrose metabolism, particularly the decomposition of sucrose by invertase, plays a central role in plant responses to cold stress. Invertase inhibitors (INHs) evolved in higher plants as essential regulators of sucrose metabolism. By limiting invertase activity, INHs keep cellular sugar levels elevated, which provides enhanced protection to plants under stress. Our results showed that the expression of PpVIN2, the only vacuolar invertase (VIN) gene in peach fruit sensitive to chilling temperatures, increases significantly during cold storage, while VIN enzyme activity increases more modestly. We also found that peach fruit transiently overexpressing PpINH1 had decreased VIN activity. Interactions of PpINH1 and PpVIN2 with recombinant proteins were shown by yeast two-hybrid assays and bimolecular fluorescence complementation assays, as well as in vitro. During cold storage, trehalose-treated peach fruit had significantly increased PpINH1 expression, decreased VIN enzyme activity, and significantly higher sucrose content than did untreated fruit. As a result, the treated fruit had enhanced resistance to chilling injury. Collectively, our data show that the post-translational repression of VIN enzyme activity by PpINH1 helps maintain sucrose levels in peach fruit during cold storage, thereby improving resistance to chilling injury.
Self-compatibility in peach [Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles
Authors: Abdallah Donia , Baraket Ghada , Perez Veronica , Salhi Hannachi Amel , Hormaza Jose I.
Published: October 2020

Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.
Mechanism of self/nonself-discrimination in Brassica self-incompatibility
Authors: Murase Kohji , Moriwaki Yoshitaka , Mori Tomoyuki , Liu Xiao , Masaka Chiho , Takada Yoshinobu , Maesaki Ryoko , Mishima Masaki , Fujii Sota , Hirano Yoshinori , Kawabe Zen , Nagata Koji , Terada Tohru , Suzuki Go , Watanabe Masao , Shimizu Kentaro , Hakoshima Toshio , Takayama Seiji
Published: October 2020

Self-incompatibility (SI) is a breeding system that promotes cross-fertilization. In Brassica, pollen rejection is induced by a haplotype-specific interaction between pistil determinant SRK (S receptor kinase) and pollen determinant SP11 (S-locus Protein 11, also named SCR) from the S-locus. Although the structure of the B. rapa S9-SRK ectodomain (eSRK) and S9-SP11 complex has been determined, it remains unclear how SRK discriminates self- and nonself-SP11. Here, we uncover the detailed mechanism of self/nonself-discrimination in Brassica SI by determining the S8-eSRK–S8-SP11 crystal structure and performing molecular dynamics (MD) simulations. Comprehensive binding analysis of eSRK and SP11 structures reveals that the binding free energies are most stable for cognate eSRK–SP11 combinations. Residue-based contribution analysis suggests that the modes of eSRK–SP11 interactions differ between intra- and inter-subgroup (a group of phylogenetically neighboring haplotypes) combinations. Our data establish a model of self/nonself-discrimination in Brassica SI.
Publisher Correction: Converting microwave and telecom photons with a silicon photonic nanomechanical interface
Authors: Arnold G. , Wulf M. , Barzanjeh S. , Redchenko E. S. , Rueda A. , Hease W. J. , Hassani F. , Fink J. M.
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Strong enhancement of magnetic order from bulk to stretched monolayer FeSe as Hund’s metals
Authors: Moon Chang-Youn
Published: October 2020

Despite of the importance of magnetism in possible relation to other key properties in iron-based superconductors, its understanding is still far from complete especially for FeSe systems. On one hand, the origin of the absence of magnetic orders in bulk FeSe is yet to be clarified. On the other hand, it is still not clear how close monolayer FeSe on SrTiO3, with the highest transition temperature among iron-based superconductors, is to a magnetic instability. Here we investigate magnetic properties of bulk and monolayer FeSe using dynamical mean-field theory combined with density-functional theory. We find that suppressed magnetic order in bulk FeSe is associated with the reduction of interorbital charge fluctuations, an effect of Hund’s coupling, enhanced by a larger crystal-field splitting. Meanwhile, spatial isolation of Fe atoms in expanded monolayer FeSe leads into a strong magnetic order, which is completely destroyed by a small electron doping. Our work provides a comprehensive understanding of the magnetic order in iron-based superconductors and other general multi-orbital correlated systems as Hund’s metals.
Surface Josephson plasma waves in a high-temperature superconductor
Authors: Lu Qianbo , Bollinger Anthony T. , He Xi , Sundling Robert , Bozovic Ivan , Gozar Adrian
Published: October 2020

Electron density oscillations with acoustic dispersions and sustained at boundaries between different media provide information about surface and interface properties of heterostructures. In ultrathin metallic films these plasmonic excitations are heavily damped. Superconductivity is predicted to reduce dissipation allowing detection of these resonances. Emerging low-loss interface Cooper-pair waves have been studied before, however, the observation of surface-confined Josephson plasmons in highly anisotropic superconductors has remained elusive. Here, we report on generation and coupling to these excitations in an ultrathin single-crystal film of high-temperature superconductor La1.85Sr0.15CuO4. The film becomes brighter than Au below the critical temperature when probed with sub-gap THz photons. We show that the enhanced signal in the superconducting state, which can be visualized with a spatial resolution better than λ/3000, originates from near-field coupling of light to surface Josephson plasmons. Our results open a path towards non-invasive investigation of enhanced superconductivity in artificial multilayers, buried interface states in topological heterostructures, and non-linear phenomena in Josephson devices.
Transcriptional modulation of AREB-1 by CRISPRa improves plant physiological performance under severe water deficit
Authors: de Melo Bruno Paes , Lourenço-Tessutti Isabela Tristan , Paixão Joaquin Felipe Roca , Noriega Daniel David , Silva Maria Cristina Mattar , de Almeida-Engler Janice , Fontes Elizabeth Pacheco Batista , Grossi-de-Sa Maria Fatima
Published: October 2020

Plants are sessile organisms, which are vulnerable to environmental stresses. As such, plants have developed multiple molecular, physiological, and cellular mechanisms to cope with natural stressors. However, these environmental adversities, including drought, are sources of the main agribusiness problems since they interfere with plant growth and productivity. Particularly under water deprivation conditions, the abscisic acid-responsive element-binding protein AREB1/ABF2 plays an important role in drought stress response and physiological adaptation. In this investigation, we provide substantial confirmation for the role of AREB1/ABF2 in plant survival under severe water deficit using the CRISPR activation (CRISPRa) technique to enhance the AREB1 gene expression. In our strategy, the inactive nuclease dCas9 was fused with an Arabidopsis histone acetyltransferase 1, which improves gene expression by remodeling chromatin. The AREB1 overexpression promotes an improvement in the physiological performance of the transgenic homozygous plants under drought, which was associated with an increase in chlorophyll content, antioxidant enzyme activity, and soluble sugar accumulation, leading to lower reactive oxygen species accumulation. Finally, we found that the CRISPR-mediated up-regulation of AREB1 changes the abundance of several downstream ABA-inducible genes, allowing us to report that CRISPRa dCas9-HAT is a valuable biotechnological tool to improve drought stress tolerance through the positive regulation of AREB1.
RETRACTED ARTICLE: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family
Authors: Sarkar Indrani , Dey Prateek , Sharma Sanjeev Kumar , Ray Swapna Devi , Kochiganti Venkata Hanumat Sastry , Singh Renu , Pramod Padmanabhan , Singh Ram Pratap
Published: October 2020

Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents
Authors: Deichler Alfonso , Carrasco Denisse , Lopez-Jury Luciana , Vega-Zuniga Tomas , Márquez Natalia , Mpodozis Jorge , Marín Gonzalo J.
Published: October 2020

The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.
Thermal neutron transmutation doping of GaN semiconductors
Authors: Barber R. , Nguyen Q. , Brockman J. , Gahl J. , Kwon J.
Published: October 2020

High quality Ge doping of GaN is demonstrated using primarily thermal neutrons for the first time. In this study, GaN was doped with Ge to concentrations from 1016 Ge atoms/cm3 to 1018 Ge atoms/cm3. The doping concentrations were measured using gamma-ray spectroscopy and confirmed using SIMS analysis. The data from SIMS analysis also show consistent Ge doping concentration throughout the depth of the GaN wafers. After irradiation, the GaN was annealed in a nitrogen environment at 950 °C for 30 min. The neutron doping process turns out to produce spatially uniform doping throughout the whole volume of the GaN substrate.
Radionecrosis and cellular changes in small volume stereotactic brain radiosurgery in a porcine model
Authors: Zaer Hamed , Glud Andreas Nørgaard , Schneider Bret M. , Lukacova Slávka , Vang Hansen Kim , Adler John R. , Høyer Morten , Jensen Morten Bjørn , Hansen Rune , Hoffmann Lone , Worm Esben Schjødt , Sørensen Jens Chr. Hedemann , Orlowski Dariusz
Published: October 2020

Stereotactic radiosurgery (SRS) has proven an effective tool for the treatment of brain tumors, arteriovenous malformation, and functional conditions. However, radiation-induced therapeutic effect in viable cells in functional SRS is also suggested. Evaluation of the proposed modulatory effect of irradiation on neuronal activity without causing cellular death requires the knowledge of radiation dose tolerance at very small tissue volume. Therefore, we aimed to establish a porcine model to study the effects of ultra-high radiosurgical doses in small volumes of the brain. Five minipigs received focal stereotactic radiosurgery with single large doses of 40–100 Gy to 5–7.5 mm fields in the left primary motor cortex and the right subcortical white matter, and one animal remained as unirradiated control. The animals were followed-up with serial MRI,
PET scans, and histology 6 months post-radiation. We observed a dose-dependent relation of the histological and MRI changes at 6 months post-radiation. The necrotic lesions were seen in the grey matter at 100 Gy and in white matter at 60 Gy. Furthermore, small volume radiosurgery at different dose levels induced vascular, as well as neuronal cell changes and glial cell remodeling.
Short-term variability of the human serum metabolome depending on nutritional and metabolic health status
Authors: Agueusop Inoncent , Musholt Petra B. , Klaus Beate , Hightower Kendra , Kannt Aimo
Published: October 2020

The intra-individual variability of the human serum metabolome over a period of 4 weeks and its dependence on metabolic health and nutritional status was investigated in a single-center study under tightly controlled conditions in healthy controls, pre-diabetic individuals and patients with type-2 diabetes mellitus (T2DM, n = 10 each). Untargeted metabolomics in serum samples taken at three different days after overnight fasts and following intake of a standardized mixed meal showed that the human serum metabolome is remarkably stable: The median intra-class correlation coefficient (ICC) across all metabolites and all study participants was determined as 0.65. ICCs were similar for the three different health groups, before and after meal intake, and for different metabolic pathways. Only 147 out of 1438 metabolites (10%) had an ICC below 0.4 indicating poor stability over time. In addition, we confirmed previously identified metabolic signatures differentiating healthy, pre-diabetic and diabetic individuals. To our knowledge, this is the most comprehensive study investigating the temporal variability of the human serum metabolome under such tightly controlled conditions.
Author Correction: Cellulose Mediated Transferrin Nanocages for Enumeration of Circulating Tumor Cells for Head and Neck Cancer
Authors: Hazra Raj Shankar , Kale Narendra , Aland Gourishankar , Qayyumi Burhanuddin , Mitra Dipankar , Jiang Long , Bajwa Dilpreet , Khandare Jayant , Chaturvedi Pankaj , Quadir Mohiuddin
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases
Authors: Park Ji In , Kim Tae-Yoon , Oh Bumjo , Cho Hyunjeong , Kim Ji Eun , Yoo Seong Ho , Lee Jung Pyo , Kim Yon Su , Chun Jongsik , Kim Bong-Soo , Lee Hajeong
Published: October 2020

Immunoglobulin A nephropathy (IgAN) involves repeated events of gross haematuria with concurrent upper airway infections. The mucosal immune system, especially the tonsil, is considered the initial site of inflammation, although the role of the tonsillar microbiota has not been established in IgAN. In this study, we compared the tonsillar microbiota of patients with IgAN (n = 21) and other glomerular diseases (n = 36) as well as, healthy controls (n = 23) from three medical centres in Korea. The microbiota was analysed from tonsil swabs using the Illumina MiSeq system based on 16S rRNA gene. Tonsillar bacterial diversity was higher in IgAN than in other glomerular diseases, although it did not differ from that of healthy controls. Principal coordinates analysis revealed differences between the tonsillar microbiota of IgAN and both healthy and disease controls. The proportions of Rahnella, Ruminococcus_g2, and Clostridium_g21 were significantly higher in patients with IgAN than in healthy controls (corrected p < 0.05). The relative abundances of several taxa were correlated with the estimated glomerular filtration rate, blood urea nitrogen, haemoglobin, and serum albumin levels. Based on our findings, tonsillar microbiota may be associated with clinical features and possible immunologic pathogenesis of IgAN.
Measurement of the tilt of a moving domain wall shows precession-free dynamics in compensated ferrimagnets
Authors: Haltz E. , Sampaio J. , Krishnia S. , Berges L. , Weil R. , Mougin A.
Published: October 2020

One fundamental obstacle to efficient ferromagnetic spintronics is magnetic precession, which intrinsically limits the dynamics of magnetic textures. We experimentally demonstrate that this precession vanishes when the net angular momentum is compensated in domain walls driven by spin–orbit torque in a ferrimagnetic GdFeCo/Pt track. We use transverse in-plane fields to provide a robust and parameter-free measurement of the domain wall internal magnetisation angle, demonstrating that, at the angular compensation, the DW tilt is zero, and thus the magnetic precession that caused it is suppressed. Our results highlight the mechanism of faster and more efficient dynamics in materials with multiple spin lattices and vanishing net angular momentum, promising for high-speed, low-power spintronic applications.
Exploring food contents in scientific literature with FoodMine
Authors: Hooton Forrest , Menichetti Giulia , Barabási Albert-László
Published: October 2020

Thanks to the many chemical and nutritional components it carries, diet critically affects human health. However, the currently available comprehensive databases on food composition cover only a tiny fraction of the total number of chemicals present in our food, focusing on the nutritional components essential for our health. Indeed, thousands of other molecules, many of which have well documented health implications, remain untracked. To explore the body of knowledge available on food composition, we built FoodMine, an algorithm that uses natural language processing to identify papers from PubMed that potentially report on the chemical composition of garlic and cocoa. After extracting from each paper information on the reported quantities of chemicals, we find that the scientific literature carries extensive information on the detailed chemical components of food that is currently not integrated in databases. Finally, we use unsupervised machine learning to create chemical embeddings, finding that the chemicals identified by FoodMine tend to have direct health relevance, reflecting the scientific community’s focus on health-related chemicals in our food.
Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference
Authors: Zerrouk Naouel , Miagoux Quentin , Dispot Aurelien , Elati Mohamed , Niarakis Anna
Published: October 2020

Rheumatoid arthritis (RA) is a systemic autoimmune disease that affects the synovial joints of the body. Rheumatoid arthritis fibroblast-like synoviocytes (RA FLS) are central players in the disease pathogenesis, as they are involved in the secretion of cytokines and proteolytic enzymes, exhibit invasive traits, high rate of self-proliferation and an apoptosis-resistant phenotype. We aim at characterizing transcription factors (TFs) that are master regulators in RA FLS and could potentially explain phenotypic traits. We make use of differentially expressed genes in synovial tissue from patients suffering from RA and osteoarthritis (OA) to infer a TF co-regulatory network, using dedicated software. The co-regulatory network serves as a reference to analyze microarray and single-cell RNA-seq data from isolated RA FLS. We identified five master regulators specific to RA FLS, namely BATF, POU2AF1, STAT1, LEF1 and IRF4. TF activity of the identified master regulators was also estimated with the use of two additional, independent software. The identified TFs contribute to the regulation of inflammation, proliferation and apoptosis, as indicated by the comparison of their differentially expressed target genes with hallmark molecular signatures derived from the Molecular Signatures Database (MSigDB). Our results show that TFs influence could be used to identify putative master regulators of phenotypic traits and suggest novel, druggable targets for experimental validation.
Mechanical behavior of frozen soil improved with sulphoaluminate cement and its microscopic mechanism
Authors: Yin Zhenhua , Zhang Hu , Zhang Jianming , Chai Mingtang
Published: October 2020

The foundation of constructions built in the permafrost areas undergo considerable creeping or thawing deformation because of the underlying ice-rich permafrost. Soil improvement may be of advantage in treating ice-rich permafrost at shallow depth. Sulphoaluminate cement was a potential material to improve frozen soil. Simultaneously, two other cements, ordinary Portland cement and Magnesium phosphate cement were selected as the comparison. The mechanical behavior of modified frozen soil was studied with thaw compression tests and unconfined compression strength tests. Meanwhile, the microscopic mechanism was explored by field emission scanning electron microscopy, particle size analysis and X-ray diffractometry. The results showed Sulphoaluminate cement was useful in reducing the thaw compression deformation and in enhancing the strength of the frozen soil. The improvement of the mechanical behavior depended mainly on two aspects: the formation of structural mineral crystals and the agglomeration of soil particles. The two main factors contributed to the improvement of mechanical properties simultaneously. The thicker AFt crystals result in a higher strength and AFt plays an important role in improving the mechanical properties of frozen soils.The study verified that Sulphoaluminate cement was an excellent stabilizer to improve ice-rich frozen soils.
Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm
Authors: Ting Ngoot-Chin , Sherbina Katrina , Khoo Jia-Shiun , Kamaruddin Katialisa , Chan Pek-Lan , Chan Kuang-Lim , Halim Mohd Amin Ab , Sritharan Kandha , Yaakub Zulkifli , Mayes Sean , Massawe Festo , Chang Peter L. , Nuzhdin Sergey V. , Sambanthamurthi Ravigadevi , Singh Rajinder
Published: October 2020

Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted fromE. oleifera×E. guineensisinterspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.
Renal fibrosis detected by diffusion-weighted magnetic resonance imaging remains unchanged despite treatment in subjects with renovascular disease
Authors: Ferguson Christopher M. , Eirin Alfonso , Abumoawad Abdelrhman , Saad Ahmed , Jiang Kai , Hedayat Ahmad F. , Misra Sanjay , Glockner James , Textor Stephen C. , Lerman Lilach O.
Published: October 2020

Tissue fibrosis is an important index of renal disease progression. Diffusion-weighted magnetic resonance imaging’s (DWI-MRI) apparent diffusion coefficient (ADC) reveals water diffusion is unobstructed by microstructural alterations like fibrosis. We hypothesized that ADC may indicate renal injury and response to therapy in patients with renovascular disease (RVD). RVD patients were treated with medical therapy (MT) and percutaneous transluminal renal angioplasty (MT + PTRA) (n = 11, 3 bilaterally, n = 14 kidneys) or MT (n = 9). ADC and renal hypoxia (R2*) by blood-oxygen-level-dependent MRI were studied before (n = 27) and 3 months after (n = 20) treatment. Twelve patients underwent renal biopsies. Baseline ADC values were correlated with changes in eGFR, serum creatinine (SCr), systolic blood pressure (SBP), renal hypoxia, and renal vein levels of pro-inflammatory marker tumor necrosis-factor (TNF)-α. Renal oxygenation, eGFR, and SCr improved after MT + PTRA. ADC inversely correlated with the histological degree of renal fibrosis, but remained unchanged after MT or MT + PTRA. Basal ADC values correlated modestly with change in SBP, but not in renal hypoxia, TNF-α levels, or renal function. Lower ADC potentially reflects renal injury in RVD patients, but does not change in response to medical or interventional therapy over 3 months. Future studies need to pinpoint indices of kidney recovery potential.
Computational analysis of eugenol inhibitory activity in lipoxygenase and cyclooxygenase pathways
Authors: das Chagas Pereira de Andrade Francisco , Mendes Anderson Nogueira
Published: October 2020

Chronic inflammation is triggered by numerous diseases such as osteoarthritis, Crohn's disease and cancer. The control of the pro-inflammatory process can prevent, mitigate and/or inhibit the evolution of these diseases. Therefore, anti-inflammatory drugs have been studied as possible compounds to act in these diseases. This paper proposes a computational analysis of eugenol in relation to aspirin and diclofenac and analyzing the ADMET profile and interactions with COX-2 and 5-LOX enzymes, important enzymes in the signaling pathway of pro-inflammatory processes. Through the analysis of ADMET in silico, it was found that the pharmacokinetic results of eugenol are similar to NSAIDs, such as diclofenac and aspirin. Bioinformatics analysis using coupling tests showed that eugenol can bind to COX-2 and 5-LOX. These results corroborate with different findings in the literature that demonstrate anti-inflammatory activity with less gastric irritation, bleeding and ulcerogenic side effects of eugenol. The results of bioinformatics reinforce studies that try to propose eugenol as an anti-inflammatory compound that can act in the COX-2/5-LOX pathways, replacing some NSAIDs in different diseases.
Efficacy of fungicides in controlling rice blast and dirty panicle diseases in Thailand
Authors: Kongcharoen Nattapatphon , Kaewsalong Nipon , Dethoup Tida
Published: October 2020

In this study, the fungicidal activities of the fungicides azoxystrobin, difenoconazole + propiconazole, carbendazim, flutriafol, fluopyram + tebuconazole, mancozeb and thiophanate-methyl against rice blast and dirty panicle pathogens were evaluated under laboratory and field conditions. Mancozeb exhibited the highest level of fungicidal activity against the blast pathogenPyricularia oryzae, with an EC50value of 0.25 parts per million (ppm). The combination of two fungicides, fluopyram + tebuconazole, showed the strongest fungicidal effect againstBipolaris oryzaeandCurvularia lunata, with EC50values of 0.587 ppm and 0.435 ppm,respectively. Meanwhile, carbendazim and flutriafol demonstrated the best level of fungicidal activity againstFusarium incarnatum, with the lowest EC50values of 0.211 ppm and 0.214 ppm,respectively. The results showed that the fungicides, triazole and strobilurin, had significant effects against rice blast and dirty panicle diseases. The combination of fluopyram + tebuconazole, when applied twice, was the most effective in reducing dirty panicle disease by up to 60% and increasing rice yield by 29% more than the untreated control. Fluopyram + tebuconazole, difenoconazole + propiconazole, flutriafol and azoxystrobin achieved stronger fungicidal activity against rice blast disease, reducing its severity by 32–33% when applied twice by foliar spraying. However, carbendazim, mancozeb and thiophanate-methyl had low to moderate fungicidal activity against both rice diseases in this study.
Habitat preferences of Southern Ground-hornbills in the Kruger National Park: implications for future conservation measures
Authors: Combrink Leigh , Combrink Hendrik J. , Botha André J. , Downs Colleen T.
Published: October 2020

Understanding how a species utilises its habitat, and the processes that give rise to its movements and patterns of space use, is critical for its conservation. Southern Ground-hornbills Bucorvus leadbeateri are listed as Endangered in South Africa, as a result of habitat loss and persecution. The National Species Recovery Plan lists reintroductions as a suitable conservation action, but highlights “understanding the exact habitat requirements of Southern Ground-hornbills” as a knowledge gap. In this study, we used tracking data from six Southern Ground-hornbill groups (a total of 37,060 GPS locations) in the Kruger National Park to investigate their seasonal home range differences and habitat preferences. We used first-passage time analysis to determine the scale at which Southern Ground-hornbills concentrate their foraging efforts and whether specific movement behaviours were linked to habitat types. We found marked differences in seasonal home ranges, with all groups showing a range contraction during the breeding season. Grassland and open woodland habitat types were used throughout the year in accordance with their availability within the territory, with grassland, open woodland and dense thicket being favoured habitats for foraging. Our habitat preference results, based on longitudinal GPS data, allowed us to determine ideal habitat ratios (grassland:open woodland:low shrubland of 1.00:6.10:0.09 ha) to assist with the selection of suitable reintroduction sites for Southern Ground-hornbills. With an increasing number of species being threatened with extinction, reintroductions into suitable habitats may be a useful conservation mitigation measure. However, our findings highlight the importance of a thorough understanding of a species’ movement and space use prior to the selection of areas for reintroduction to ensure the establishment and sustainability of these species at these sites.
Molecular targets for diagnostic and intraoperative imaging of pancreatic ductal adenocarcinoma after neoadjuvant FOLFIRINOX treatment
Authors: Vuijk F. A. , de Muynck L. D. A. N. , Franken L. C. , Busch O. R. , Wilmink J. W. , Besselink M. G. , Bonsing B. A. , Bhairosingh S. S. , Kuppen P. J. K. , Mieog J. S. D. , Sier C. F. M. , Vahrmeijer A. L. , Verheij J. , Fariňa-Sarasqueta A. , Swijnenburg R. J.
Published: October 2020

Neoadjuvant systemic treatment is increasingly being integrated in the standard treatment of pancreatic ductal adenocarcinoma (PDAC) patients to improve oncological outcomes. Current available imaging techniques remain unreliable in assessing response to therapies, as they cannot distinguish between (vital) tumor tissue and therapy induced fibrosis (TIF). Consequently, resections with tumor positive margins and subsequent early post-operative recurrences occur and patients eligible for potential radical resection could be missed. To optimize patient selection and monitor results of neoadjuvant treatment, PDAC-specific diagnostic and intraoperative molecular imaging methods are required. This study aims to evaluate molecular imaging targets for PDAC after neoadjuvant FOLFIRINOX treatment. Expression of integrin αvβ6, carcinoembryonic antigen cell adhesion molecule 5 (CEACAM5), mesothelin, prostate-specific membrane antigen (PSMA), urokinase-type plasminogen activator receptor, fibroblast activating receptor, integrin α5 subunit and epidermal growth factor receptor was evaluated using immunohistochemistry. Immunoreactivity was determined using the semiquantitative H-score. Resection specimens from patients after neoadjuvant FOLFIRINOX treatment containing PDAC (n = 32), tumor associated pancreatitis (TAP) and TIF (n = 15), normal pancreas parenchyma (NPP) (n = 32) and tumor positive (n = 24) and negative (n = 56) lymph nodes were included. Integrin αvβ6, CEACAM5, mesothelin and PSMA stainings showed significantly higher expression in PDAC compared to TAP and NPP. No expression of αvβ6, CEACAM5 and mesothelin was observed in TIF. Integrin αvβ6 and CEACAM5 allow for accurate metastatic lymph node detection. Targeting integrin αvβ6, CEA, mesothelin and PSMA has the potential to distinguish vital PDAC from fibrotic tissue after neoadjuvant FOLFIRINOX treatment. Integrin αvβ6 and CEACAM5 detect primary tumors and tumor positive lymph nodes.
Electrode-free visual prosthesis/exoskeleton control using augmented reality glasses in a first proof-of-technical-concept study
Authors: Hazubski Simon , Hoppe Harald , Otte Andreas
Published: October 2020

In the field of neuroprosthetics, the current state-of-the-art method involves controlling the prosthesis with electromyography (EMG) or electrooculography/electroencephalography (EOG/EEG). However, these systems are both expensive and time consuming to calibrate, susceptible to interference, and require a lengthy learning phase by the patient. Therefore, it is an open challenge to design more robust systems that are suitable for everyday use and meet the needs of patients. In this paper, we present a new concept of complete visual control for a prosthesis, an exoskeleton or another end effector using augmented reality (AR) glasses presented for the first time in a proof-of-concept study. By using AR glasses equipped with a monocular camera, a marker attached to the prosthesis is tracked. Minimal relative movements of the head with respect to the prosthesis are registered by tracking and used for control. Two possible control mechanisms including visual feedback are presented and implemented for both a motorized hand orthosis and a motorized hand prosthesis. Since the grasping process is mainly controlled by vision, the proposed approach appears to be natural and intuitive.
Fabrication of piezoelectric poly(l-lactic acid)/BaTiO3 fibre by the melt-spinning process
Authors: Oh Hyun Ju , Kim Do-Kun , Choi Young Chan , Lim Seung-Ju , Jeong Jae Bum , Ko Jae Hoon , Hahm Wan-Gyu , Kim Sang-Woo , Lee Yongju , Kim Hyeok , Yeang Byeong Jin
Published: October 2020

Poly(l-lactic acid) (PLLA) based piezoelectric polymers are gradually becoming the substitute for the conventional piezoelectric ceramic and polymeric materials due to their low cost and biodegradable, non-toxic, piezoelectric and non-pyroelectric nature. To improve the piezoelectric properties of melt-spun poly(l-lactic acid) (PLLA)/BaTiO3, we optimized the post-processing conditions to increase the proportion of the β crystalline phase. The α → β phase transition behaviour was determined by two-dimensional wide-angle x-ray diffraction and differential scanning calorimetry. The piezoelectric properties of PLLA/BaTiO3 fibres were characterised in their yarn and textile form through a tapping method. From these results, we confirmed that the crystalline phase transition of PLLA/BaTiO3 fibres was significantly enhanced under the optimised post-processing conditions at a draw ratio of 3 and temperature of 120 °C during the melt-spinning process. The results indicated that PLLA/BaTiO3 fibres could be a one of the material for organic-based piezoelectric sensors for application in textile-based wearable piezoelectric devices.
Eruptive Spitz nevus, a striking example of benign metastasis
Authors: Raghavan Shyam S. , Kapler Elisa S. , Dinges Martin M. , Bastian Boris C. , Yeh Iwei
Published: October 2020

Metastasis is generally considered a characteristic of malignant tumors. Herein, we describe a patient with more than one hundred discrete Spitz nevi scattered all over her skin. Molecular analysis from three of the lesions identified a ROS1 fusion oncogene with identical genomic breakpoints, indicating that the nevi arose from a single transformed melanocyte and then disseminated throughout the integument. The demonstration of widespread distribution of a benign tumor with limited proliferative capability indicates that metastatic dissemination is not contingent on full malignant transformation. Thus, eruptive Spitz nevus is a striking example of benign metastasis, demonstrating that metastasis can occur before malignant transformation.
Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace
Authors: Brander Søren , Horvath Istvan , Ipsen Johan Ø. , Peciulyte Ausra , Olsson Lisbeth , Hernández-Rollán Cristina , Nørholm Morten H. H. , Mossin Susanne , Leggio Leila Lo , Probst Corinna , Thiele Dennis J. , Johansen Katja S.
Published: October 2020

Lytic polysaccharide monooxygenase (LPMO) and copper binding protein CopC share a similar mononuclear copper site. This site is defined by an N-terminal histidine and a second internal histidine side chain in a configuration called the histidine brace. To understand better the determinants of reactivity, the biochemical and structural properties of a well-described cellulose-specific LPMO from Thermoascus aurantiacus (TaAA9A) is compared with that of CopC from Pseudomonas fluorescens (PfCopC) and with the LPMO-like protein Bim1 from Cryptococcus neoformans. PfCopC is not reduced by ascorbate but is a very strong Cu(II) chelator due to residues that interacts with the N-terminus. This first biochemical characterization of Bim1 shows that it is not redox active, but very sensitive to H2O2, which accelerates the release of Cu ions from the protein. TaAA9A oxidizes ascorbate at a rate similar to free copper but through a mechanism that produce fewer reactive oxygen species. These three biologically relevant examples emphasize the diversity in how the proteinaceous environment control reactivity of Cu with O2.
Analysis of a multiple-quantum-dots embedded ring structure for potential optically-controlled quantum switch or spin filter
Authors: He Zelong , Zhao Xinwei , Chen Kongfa , Bai Jiyuan , Guo Yong
Published: October 2020

We theoretically study the average current through a ring embedded with multiple quantum dots in each arm subjected to a time-dependent external field. A current resonance band can be observed in a six-quantum-dot system. In the presence of a time-dependent external field, mutual transformation occurs between the resonance band and antiresonance band, indicating an effective optically-controlled quantum switch can be realized in a wider quantum dot’s energy regime. As the Zeeman effect is introduced, the conversion between 100 and − 100% for spin polarization $$p$$
p
can be realized by adjusting the frequency of time-dependent external field, suggesting a physical scheme of an optically-controlled spin filter. The present work sheds lights onto the design and quantum computation of future nano-devices.