bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing and phylogenetic analysis chloroplast genome of three Achyranthes species
Authors: Xu Jingya , Shen Xiaofeng , Liao Baosheng , Xu Jiang , Hou Dianyun
Published: July 2020

In this study, the chloroplast genome sequencing of the Achyranthes longifolia, Achyranthes bidentata and Achyranthes aspera were performed by Next-generation sequencing technology. The results revealed that there were a length of 151,520 bp (A. longifolia), 151,284 bp (A. bidentata), 151,486 bp (A. aspera), respectively. These chloroplast genome have a highly conserved structure with a pair of inverted repeat (IR) regions (25,150 bp; 25,145 bp; 25,150 bp), a large single copy (LSC) regions (83,732 bp; 83,933 bp; 83,966 bp) and a small single copy (SSC) regions (17,252 bp; 17,263 bp; 17,254 bp) in A. bidentate, A. aspera and A. longifolia. There were 127 genes were annotated, which including 8 rRNA genes, 37 tRNA genes and 82 functional genes. The phylogenetic analysis strongly revealed that Achyranthes is monophyletic, and A. bidentata was the closest relationship with A. aspera and A. longifolia. A. bidentata and A. longifolia were clustered together, the three Achyranthes species had the same origin, then the gunes of Achyranthes is the closest relative to Alternanthera, and that forms a group with Alternanthera philoxeroides. The research laid a foundation and provided relevant basis for the identification of germplasm resources in the future.
Geometric quantum discord of Heisenberg model with dissipative terms
Authors: Liang Jin , Zhang Chengwei
Published: July 2020

In this paper, we study a system with two interacting qubits described by the Heisenberg model with dissipative terms, and analyze decay dynamics and the steady-state of geometric quantum discords. Our results indicate that we can ignore the interaction force in the z-direction and adjust the parameters to change the loss of quantum correlation with time when the initial state satisfies some conditions. Moreover, we show that after a long enough period of time, unlike other parameters, the energy and the intensity of the non-uniform magnetic field do not affect the steady-state.
Wearable piezoelectric mass sensor based on pH sensitive hydrogels for sweat pH monitoring
Authors: Scarpa E. , Mastronardi V. M. , Guido F. , Algieri L. , Qualtieri A. , Fiammengo R. , Rizzi F. , De Vittorio M.
Published: July 2020

Colorimetric and electrochemical (bio)sensors are commonly employed in wearable platforms for sweat monitoring; nevertheless, they suffer from low stability of the sensitive element. In contrast, mass-(bio)sensors are commonly used for analyte detection at laboratory level only, due to their rigidity. To overcome these limitations, a flexible mass-(bio)sensor for sweat pH sensing is proposed. The device exploits the flexibility of piezoelectric AlN membranes fabricated on a polyimide substrate combined to the sensitive properties of a pH responsive hydrogel based on PEG-DA/CEA molecules. A resonant frequency shift is recorded due to the hydrogel swelling/shrinking at several pH. Our device shows a responsivity of about 12 kHz/pH unit when measured in artificial sweat formulation in the pH range 3–8. To the best of our knowledge, this is the first time that hydrogel mass variations are sensed by a flexible resonator, fostering the development of a new class of compliant and wearable devices.
Association between the neutrophil-to-lymphocyte ratio and obstructive sleep apnea: a meta-analysis
Authors: Rha Min-Seok , Kim Chang-Hoon , Yoon Joo-Heon , Cho Hyung-Ju
Published: July 2020

This meta-analysis is aimed to investigate the association between the neutrophil-to-lymphocyte ratio (NLR) and obstructive sleep apnea (OSA). The PubMed, Web of Science, Google Scholar, and Cochrane Library databases were searched to collect all relevant articles. The pooled standardized mean difference (SMD) with a 95% confidence interval (CI) was calculated using the random effects model. In addition, subgroup analysis and meta-regression analysis were performed. Eleven eligible articles containing 2,259 patients with OSA were included in this study. Pooled outcomes revealed that the NLR was significantly higher in patients with OSA than in controls (SMD 0.62, 95% CI 0.29–0.94, P = 0.002). In subgroup analyses, differences in the NLR between patients and controls increased with worsening OSA grades. Furthermore, meta-regression analysis showed that differences in mean BMI exerted a significant effect on differences in the NLR (P = 0.0003). In summary, our meta-analysis demonstrated that the NLR in OSA patients was significantly higher than that in controls, and the difference was larger in patients with severe OSA. These results indicate that the NLR may be a reliable marker for detecting systemic inflammation and predicting disease severity in patients with OSA.
Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritis
Authors: Chou Ching-Heng , Jain Vaibhav , Gibson Jason , Attarian David E. , Haraden Collin A. , Yohn Christopher B. , Laberge Remi-Martin , Gregory Simon , Kraus Virginia B.
Published: July 2020

We elucidated the molecular cross-talk between cartilage and synovium in osteoarthritis, the most widespread arthritis in the world, using the powerful tool of single-cell RNA-sequencing. Multiple cell types were identified based on profiling of 10,640 synoviocytes and 26,192 chondrocytes: 12 distinct synovial cell types and 7 distinct articular chondrocyte phenotypes from matched tissues. Intact cartilage was enriched for homeostatic and hypertrophic chondrocytes, while damaged cartilage was enriched for prefibro- and fibro-, regulatory, reparative and prehypertrophic chondrocytes. A total of 61 cytokines and growth factors were predicted to regulate the 7 chondrocyte cell phenotypes. Based on production by > 1% of cells, 55% of the cytokines were produced by synovial cells (39% exclusive to synoviocytes and not expressed by chondrocytes) and their presence in osteoarthritic synovial fluid confirmed. The synoviocytes producing IL-1beta (a classic pathogenic cytokine in osteoarthritis), mainly inflammatory macrophages and dendritic cells, were characterized by co-expression of surface proteins corresponding to HLA-DQA1, HLA-DQA2, OLR1 or TLR2. Strategies to deplete these pathogenic intra-articular cell subpopulations could be a therapeutic option for human osteoarthritis.
A candidate multi-epitope vaccine against SARS-CoV-2
Authors: Kar Tamalika , Narsaria Utkarsh , Basak Srijita , Deb Debashrito , Castiglione Filippo , Mueller David M. , Srivastava Anurag P.
Published: July 2020

In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll-Like Receptors and MHC Receptors. The in silico cloning and codon optimization supported the proficient expression of the designed vaccine inE. coliexpression system. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.
Harmonization of postmortem donations for pediatric brain tumors and molecular characterization of diffuse midline gliomas
Authors: Kambhampati Madhuri , Panditharatna Eshini , Yadavilli Sridevi , Saoud Karim , Lee Sulgi , Eze Augustine , Almira-Suarez M. I. , Hancock Lauren , Bonner Erin R. , Gittens Jamila , Stampar Mojca , Gaonkar Krutika , Resnick Adam C. , Kline Cassie , Ho Cheng-Ying , Waanders Angela J. , Georgescu Maria-Magdalena , Rance Naomi E. , Kim Yong , Johnson Courtney , Rood Brian R. , Kilburn Lindsay B. , Hwang Eugene I. , Mueller Sabine , Packer Roger J. , Bornhorst Miriam , Nazarian Javad
Published: July 2020

Children diagnosed with brain tumors have the lowest overall survival of all pediatric cancers. Recent molecular studies have resulted in the discovery of recurrent driver mutations in many pediatric brain tumors. However, despite these molecular advances, the clinical outcomes of high grade tumors, including H3K27M diffuse midline glioma (H3K27M DMG), remain poor. To address the paucity of tissue for biological studies, we have established a comprehensive protocol for the coordination and processing of donated specimens at postmortem. Since 2010, 60 postmortem pediatric brain tumor donations from 26 institutions were coordinated and collected. Patient derived xenograft models and cell cultures were successfully created (76% and 44% of attempts respectively), irrespective of postmortem processing time. Histological analysis of mid-sagittal whole brain sections revealed evidence of treatment response, immune cell infiltration and the migratory path of infiltrating H3K27M DMG cells into other midline structures and cerebral lobes. Sequencing of primary and disseminated tumors confirmed the presence of oncogenic driver mutations and their obligate partners. Our findings highlight the importance of postmortem tissue donations as an invaluable resource to accelerate research, potentially leading to improved outcomes for children with aggressive brain tumors.
The anterior and medial thalamic nuclei and the human limbic system: tracing the structural connectivity using diffusion-weighted imaging
Authors: Grodd Wolfgang , Kumar Vinod Jangir , Schüz Almut , Lindig Tobias , Scheffler Klaus
Published: July 2020

The limbic system is a phylogenetically old, behaviorally defined system that serves as a center for emotions. It controls the expression of anger, fear, and joy and also influences sexual behavior, vegetative functions, and memory. The system comprises a collection of tel-, di-, and mesencephalic structures whose components have evolved and increased over time. Previous animal research indicates that the anterior nuclear group of the thalamus (ANT), as well as the habenula (Hb) and the adjacent mediodorsal nucleus (MD) each play a vital role in the limbic circuitry. Accordingly, diffusion imaging data of 730 subjects obtained from the Human Connectome Project and the masks of six nuclei (anterodorsal, anteromedial, anteroventral, lateral dorsal, Hb, and MD) served as seed regions for a direct probabilistic tracking to the rest of the brain using diffusion-weighted imaging. The results revealed that the ANT nuclei are part of the limbic and the memory system as they mainly connect via the mammillary tract, mammillary body, anterior commissure, fornix, and retrosplenial cortices to the hippocampus, amygdala, medio-temporal, orbito-frontal and occipital cortices. Furthermore, the ANT nuclei showed connections to the mesencephalon and brainstem to varying extents, a pattern rarely described in experimental findings. The habenula—usually defined as part of the epithalamus—was closely connected to the tectum opticum and seems to serve as a neuroanatomical hub between the visual and the limbic system, brainstem, and cerebellum. Finally, in contrast to experimental findings with tracer studies, directly determined connections of MD were mainly confined to the brainstem, while indirect MD fibers form a broad pathway connecting the hippocampus and medio-temporal areas with the mediofrontal cortex.
Clinical impact of irreversible electroporation ablation for unresectable hilar cholangiocarcinoma
Authors: Hsiao Chih-Yang , Yang Po-Chih , Li Xiaoyong , Huang Kai-Wen
Published: July 2020

Irreversible electroporation (IRE) is a non-thermal ablation modality that has been shown to be safe and effective in its application to tumors that are close to risky areas. This study aims to assess the safety and efficacy of IRE for unresectable hilar cholangiocarcinoma. Nine patients from two medical centers in Asia received IRE treatment between June 2015 and July 2017. Before IRE treatment, percutaneous biliary decompressions had been performed on eight patients, and internal stenting had been performed on one patient. All patients tolerated the procedure well without high-grade complications. The ablated tumors had constant size without contrast enhancement for more than three months in eight patients and the level of CA19-9 decreased significantly in all patients. The percutaneous biliary drainage tube was removed from two patients with recanalization of the bile duct. The internal stent in one patient was removed without further stenting. The median overall survival period was 26 months, and the progression-free survival was 18 months. Bile ducts remained narrow in the majority (2/3) of the treated patients. Nevertheless, IRE ablation of unresectable hilar cholangiocarcinoma involving vital structures is a safe and feasible primary treatment for local tumor control and is effective in prolonging survival.
ULK1 and ULK2 are less redundant than previously thought: computational analysis uncovers distinct regulation and functions of these autophagy induction proteins
Authors: Demeter Amanda , Romero-Mulero Mari Carmen , Csabai Luca , Ölbei Márton , Sudhakar Padhmanand , Haerty Wilfried , Korcsmáros Tamás
Published: July 2020

Macroautophagy, the degradation of cytoplasmic content by lysosomal fusion, is an evolutionary conserved process promoting homeostasis and intracellular defence. Macroautophagy is initiated primarily by a complex containing ULK1 or ULK2 (two paralogs of the yeast Atg1 protein). To understand the differences between ULK1 and ULK2, we compared the human ULK1 and ULK2 proteins and their regulation. Despite the similarity in their enzymatic domain, we found that ULK1 and ULK2 have major differences in their autophagy-related interactors and their post-translational and transcriptional regulators. We identified 18 ULK1-specific and 7 ULK2-specific protein motifs serving as different interaction interfaces. We found that interactors of ULK1 and ULK2 all have different tissue-specific expressions partially contributing to diverse and ULK-specific interaction networks in various tissues. We identified three ULK1-specific and one ULK2-specific transcription factor binding sites, and eight sites shared by the regulatory region of both genes. Importantly, we found that both their post-translational and transcriptional regulators are involved in distinct biological processes—suggesting separate functions for ULK1 and ULK2. Unravelling differences between ULK1 and ULK2 could lead to a better understanding of how ULK-type specific dysregulation affects autophagy and other cellular processes that have been implicated in diseases such as inflammatory bowel disease and cancer.
Amelioration of oxidative stress-mediated apoptosis in copper oxide nanoparticles-induced liver injury in rats by potent antioxidants
Authors: Abdelazeim Samy A. , Shehata Nagwa Ibrahim , Aly Hanan Farouk , Shams Shams Gamal Eldin
Published: July 2020

The purpose of this study is to investigate the therapeutic efficacy of individual or combined doses of dehydro-epiandrosterone (DHEA) and quercetin in ameliorating some biochemical indices in liver of CuO-NPs intoxicated-rats. CuO-NPs (50 nm) was administered as a daily oral dose 100 mg/kg for 2 weeks to rats followed by the fore-mentioned antioxidants for 1 month. We highlighted the therapeutic effect of DHEA and quercetin against CuO-NPs toxicity through monitoring the alteration of liver enzyme activity, antioxidant defense mechanism, necrosis, apoptosis, histopathological alterations, and DNA damage. The rats given CuO-NPs only showed marked significant elevation in liver enzymes, alteration in oxidant-antioxidant balance and an elevation in the hepatic inflammatory marker; tumor necrosis factor-α. Additionally, over expression of both caspase-3 and Bax proteins were detected. Whereas, Bcl2 was down regulated and DNA fragmentation was elevated. Moreover, Histopathological examination of hepatic tissue reinforced the previous biochemical results. Co-treatment with either DHEA, quercetin alone or in combination ameliorated the deviated parameters with variable degrees against CuO-NPs toxicity in rat. In conclusion, our findings suggested that the aforementioned treatments exert therapeutic effect in CuO-NPs toxicity by diminishing oxidative stress, mRNA gene expression and hepatic tissues DNA damage.
Exercise intervention lowers aberrant serum WISP-1 levels with insulin resistance in breast cancer survivors: a randomized controlled trial
Authors: Chang Jae Seung , Kim Tae Ho , Kong In Deok
Published: July 2020

Insulin resistance is associated with increased risk for and recurrence of breast cancer. Recently, Wnt1-inducible signaling pathway protein-1 (WISP-1) was reported to impair glucose metabolism and insulin sensitivity. In various cancer tissues, Wnt signaling is upregulated and induces further oncogenic and metastatic activity. However, the effects of exercise on serum levels of WISP-1 and its upstream β-catenin have not been studied in cancer patients. We investigated the effects of exercise training on Wnt signaling and insulin sensitivity in breast cancer survivors (BCS). This single-center trial randomized 46 BCS into either 12-week exercise or control groups (1:1), and included an additional 12 age-matched healthy women. Kinanthropometric parameters, serum Wnt signaling markers, and gluco-lipid profiles were evaluated before and after the intervention. Serum β-catenin and WISP-1 concentrations were significantly higher in BCS than in healthy subjects. There was a positive correlation between β-catenin and WISP-1 levels.

Exercise training in BCS significantly reduced body fat and waist circumference and enhanced aerobic and muscular fitness. Exercise decreased β-catenin and WISP-1 levels and improved gluco-lipid profiles. There was a notable correlation between changes in HOMA-IR indexes and serum WISP-1, but not with β-catenin during the exercise intervention. In conclusion, a 12-week community-based exercise intervention resulted in significant reductions in serum β-catenin and WISP-1 levels, accompanied by favorable improvements in body composition, physical fitness, and biochemical parameters in BCS.
We also highlight that this is the first report concerning effects of exercise on circulating β-catenin and WISP-1 levels and correlations between WISP-1 and insulin sensitivity, which could be important for determining prognoses for BCS.
Ophidiomycosis surveillance of snakes in Georgia, USA reveals new host species and taxonomic associations with disease
Authors: Haynes Ellen , Chandler Houston C. , Stegenga Benjamin S. , Adamovicz Laura , Ospina Emilie , Zerpa-Catanho Dessireé , Stevenson Dirk J. , Allender Matthew C.
Published: July 2020

Ophidiomycosis (snake fungal disease) is caused by the fungusOphidiomyces ophiodiicolaand threatens snake health worldwide. It has been documented throughout the eastern United States and severe cases have recently been reported in Georgia, USA. To evaluate disease distribution and prevalence in this state, 786 free-ranging snakes were examined for skin lesions consistent with ophidiomycosis and swabbed to detectO. ophiodiicolaDNA using qPCR. Sampled snakes represented 34 species and 4 families; 27.5% had skin lesions, 13.3% were positive forO. ophiodiicolaDNA, and 77.8% of the qPCR positive individuals had skin lesions. This is the first report ofO. ophiodiicolain five of the 22 species that were qPCR positive. Multinomial logistic regression modeling indicated thatDrymarchon couperihad a higher relative risk of apparent ophidiomycosis (lesions present and qPCR positive), and the best models predicting qPCR result and ophidiomycosis category included individual factors and excluded temporal and spatial factors. Phylogeny-based bipartite network analysis showed thatNerodia erythrogaster,Nerodia taxispilota, andD. couperihad the highest prevalence of apparent ophidiomycosis; this category was more prevalent in the subfamily Colubrinae and less prevalent in Natricinae. These results provide important information about ophidiomycosis epidemiology, which has implications for snake conservation.
Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes
Authors: Hyde Josephine , Correa Maria A. , Hughes Grant L. , Steven Blaire , Brackney Doug E.
Published: July 2020

The microbiome is an assemblage of microorganisms living in association with a multicellular host. Numerous studies have identified a role for the microbiome in host physiology, development, immunity, and behaviour. The generation of axenic (germ-free) and gnotobiotic model systems has been vital to dissecting the role of the microbiome in host biology. We have previously reported the generation of axenic Aedes aegypti mosquitoes, the primary vector of several human pathogenic viruses, including dengue virus and Zika virus. In order to better understand the influence of the microbiome on mosquitoes, we examined the transcriptomes of axenic and conventionally reared Ae. aegypti before and after a blood meal. Our results suggest that the microbiome has a much lower effect on the mosquito’s gene expression than previously thought with only 170 genes influenced by the axenic state, while in contrast, blood meal status influenced 809 genes. The pattern of expression influenced by the microbiome is consistent with transient changes similar to infection rather than sweeping physiological changes. While the microbiome does seem to affect some pathways such as immune function and metabolism, our data suggest the microbiome is primarily serving a nutritional role in development with only minor effects in the adult.
PCDH7 interacts with GluN1 and regulates dendritic spine morphology and synaptic function
Authors: Wang Yuanyuan , Kerrisk Campbell Meghan , Tom Irene , Foreman Oded , Hanson Jesse E. , Sheng Morgan
Published: July 2020

The N-terminal domain (NTD) of the GluN1 subunit (GluN1-NTD) is important for NMDA receptor structure and function, but the interacting proteins of the GluN1-NTD are not well understood. Starting with an unbiased screen of ~ 1,500 transmembrane proteins using the purified GluN1-NTD protein as a bait, we identify Protocadherin 7 (PCDH7) as a potential interacting protein. PCDH7 is highly expressed in the brain and has been linked to CNS disorders, including epilepsy. Using primary neurons and brain slice cultures, we find that overexpression and knockdown of PCDH7 induce opposing morphological changes of dendritic structures. We also find that PCDH7 overexpression reduces synaptic NMDA receptor currents. These data show that PCDH7 can regulate dendritic spine morphology and synaptic function, possibly via interaction with the GluN1 subunit.
The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage
Authors: Allers Kristina , Stahl-Hennig Christiane , Fiedler Tomas , Wibberg Daniel , Hofmann Jörg , Kunkel Désirée , Moos Verena , Kreikemeyer Bernd , Kalinowski Jörn , Schneider Thomas
Published: July 2020

The intesinal microbiome is considered important in human immunodeficiency virus (HIV) pathogenesis and therefore represents a potential therapeutic target to improve the patients’ health status. Longitudinal alterations in the colonic mucosa-associated microbiome during simian immunodeficiency virus (SIV) infection were investigated using a 16S rRNA amplicon approach on the Illumina sequencing platform and bioinformatics analyses. Following SIV infection of six animals, no alterations in microbial composition were observed before the viral load peaked in the colon. At the time of acute mucosal SIV replication, the phylum Bacteroidetes including the Bacteroidia class as well as the phylum Firmicutes and its families Ruminococcaceae and Eubacteriaceae became more abundant. Enrichment of Bacteroidetes was maintained until the chronic phase of SIV infection. The shift towards Bacteroidetes in the mucosa-associated microbiome was associated with the extent of SIV infection-induced mucosal CD4+ T cell depletion and correlated with increasing rates of enterocyte damage. These observations suggest that Bacteroidetes strains increase during virus-induced mucosal immune destruction. As Bacteroidetes belong to the lipopolysaccharide- and short chain fatty acids-producing bacteria, their rapid enrichment may contribute to inflammatory tissue damage and metabolic alterations in SIV/HIV infection. These aspects should be considered in future studies on therapeutic interventions.
Build-up of serial dependence in color working memory
Authors: Barbosa Joao , Compte Albert
Published: July 2020

Serial dependence, how immediately preceding experiences bias our current estimations, has been described experimentally during delayed-estimation of many different visual features, with subjects tending to make estimates biased towards previous ones. It has been proposed that these attractive biases help perception stabilization in the face of correlated natural scene statistics, although this remains mostly theoretical. Color, which is strongly correlated in natural scenes, has never been studied with regard to its serial dependencies. Here, we found significant serial dependence in 7 out of 8 datasets with behavioral data of humans (total n = 760) performing delayed-estimation of color with uncorrelated sequential stimuli. Moreover, serial dependence strength built up through the experimental session, suggesting metaplastic mechanisms operating at a slower time scale than previously proposed (e.g. short-term synaptic facilitation). Because, in contrast with natural scenes, stimuli were temporally uncorrelated, this build-up casts doubt on serial dependencies being an ongoing adaptation to the stable statistics of the environment.
Genome-wide mapping and allelic fingerprinting provide insights into the genetics of resistance to wheat stripe rust in India, Kenya and Mexico
Authors: Juliana Philomin , Singh Ravi Prakash , Huerta-Espino Julio , Bhavani Sridhar , Randhawa Mandeep S. , Kumar Uttam , Joshi Arun Kumar , Bhati Pradeep Kumar , Mir Hector Eduardo Villasenor , Mishra Chandra Nath , Singh Gyanendra Pratap
Published: July 2020

Stripe or yellow rust (YR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss. is a persistent biotic-stress threatening global wheat production. To broaden our understanding of the shared genetic basis of YR resistance across multi-site and multi-year evaluations, we performed a large genome-wide association study using 43,706 YR observations on 23,346 wheat lines from the International Maize and Wheat Improvement Center evaluated between 2013 and 2019 at sites in India, Kenya and Mexico, against predominant races prevalent in the countries.
We identified 114 repeatable markers tagging 20 quantitative trait loci (QTL) associated with YR on ten chromosomes including 1D, 2A, 2B, 2D, 3A, 4A, 4D, 5A, 5B and 6B, among which four QTL, QYr.cim-2DL.2, QYr.cim-2AS.1, QYr.cim-2BS.2 and QYr.cim-2BS.3 were significant in more than ten datasets.
Furthermore, we report YR-associated allelic fingerprints for the largest panel of wheat breeding lines (52,067 lines) till date, creating substantial opportunities for YR favorable allele enrichment using molecular markers. Overall, the markers and fingerprints reported in this study provide excellent insights into the genetic architecture of YR resistance in different geographical regions, time-periods and wheat germplasm and are a huge resource to the global wheat breeding community for accelerating YR resistance breeding efforts.
Influenza virus infection affects insulin signaling, fatty acid-metabolizing enzyme expressions, and the tricarboxylic acid cycle in mice
Authors: Ohno Marumi , Sekiya Toshiki , Nomura Naoki , Daito Taku ji , Shingai Masashi , Kida Hiroshi
Published: July 2020

Although the severity of influenza virus infections has been associated with host energy metabolism, the related mechanisms have not yet been clarified. Here we examined the effects of influenza virus infection on host energy metabolism in mice. After infecting mice with intranasal applications of 500 plaque-forming units of A/Puerto Rico/8/34 (H1N1; PR8) virus, the serum levels of most intermediates in the tricarboxylic acid (TCA) cycle and related metabolic pathways were significantly reduced. These data suggest that substrate supply to the TCA cycle is reduced under these conditions, rather than specific metabolic reactions being inhibited. Then, we focused on glucose and fatty acid metabolism that supply substrates to the TCA cycle. Akt phosphorylation following insulin injections was attenuated in the livers of PR8 virus-infected mice. Furthermore, glucose tolerance tests revealed that the PR8 virus-infected mice showed higher blood glucose levels than the vehicle-inoculated control mice. These results suggest that influenza virus infection impairs insulin signaling, which regulates glucose uptake. However, increases in the hepatic expressions of fatty acid-metabolizing enzymes suggest that fatty acids accumulate in liver cells of infected mice. Collectively, our data indicate that influenza virus infection dysregulates host energy metabolism. This line of investigation provides novel insights into the pathogenesis of influenza.
Effect of echinalkamide identified from Echinacea purpurea (L.) Moench on the inhibition of osteoclastogenesis and bone resorption
Authors: Chang Bo Yoon , Lee Seul Ki , Kim Da Eun , Bae Jin Hye , Ho Thanh Tam , Park So-Young , Lee Mi Kyeong , Kim Sung Yeon
Published: July 2020

Plant cell cultures have been exploited to provide stable production and new secondary metabolites for better pharmacological activity. Fractionation of adventitious root cultures of Echinacea purpurea resulted in the isolation of eleven constituents, including three new compounds. The structures of the three new compounds were determined to be an alkylamide (1), a polyacetylene (2) and a lignan (3) on the basis of combined spectroscopic analysis. To discover new types of antiresorptive agents, we screened for new compounds that regulate osteoclast differentiation, and survival. Among three new compounds, echinalkamide (compound 1) had considerably inhibitory effects on RANKL-induced osteoclast differentiation, and on proliferation of osteoclasts and efficiently attenuated osteoclastic bone resorption without toxicity. In addition, echinalamide treatment inhibited the osteoclast—specific gene expression level. Echinalkamide achieved this inhibitory effect by disturbing phosphorylation of MAPK and activation of osteoclast transcription factors c-Fos and NFATc1. Conclusionally, our study investigated that echinalkamide remarkably inhibited osteoclast differentiation and osteoclast specific gene expression through repression of the MAPK–c-Fos–NFATC1 cascade.
Effects of effortful swallowing on cardiac autonomic control in individuals with neurogenic dysphagia: a prospective observational analytical study
Authors: Gomes Livia M. S. , da Silva Roberta G. , Pedroni Cristiane R. , Garner David M. , Raimundo Rodrigo D. , Valenti Vitor E.
Published: July 2020

Considering that neurogenic oropharyngeal dysphagia is a prevalent condition with or without cardiac disease we should contemplate issues surrounding cardiovascular difficulties during rehabilitation. This study aims to evaluate the effects of effortful swallowing maneuver (ESM) on heart rate variability (HRV) in subjects with neurogenic oropharyngeal dysphagia. We studied 22 individuals [8 Stroke and 14 Parkinson Disease (PD) subjects aged between 41 and 75 years old] with neurogenic oropharyngeal dysphagia regardless of gender. HRV was assessed under two circumstances: spontaneous swallowing versus ESM. Surface electromyography of the suprahyoid muscles was undertaken to measure the swallowing muscle excitation, which then confirmed higher muscle activity during ESM. We attained no changes in HRV between the two swallowing events [HR: spontaneous swallowing 78.68 ± 13.91 bpm vs. ESM 102.57 ± 107.81 bpm, p = 0.201; RMSSD (root-mean square of differences between adjacent normal RR intervals in a time interval): spontaneous swallowing 16.99 ± 15.65 ms vs. ESM 44.74 ± 138.85 ms, p = 0.312; HF (high frequency): spontaneous swallowing 119.35 ± 273 ms2 vs. ESM 99.83 ± 194.58 ms2, p = 0.301; SD1 (standard deviation of the instantaneous variability of the beat-to-beat heart rate): spontaneous swallowing 12.02 ± 1.07 ms vs. ESM 31.66 ± 98.25 ms, p = 0.301]. The effortful swallowing maneuver did not cause clinically significant changes in autonomic control of HR in this group of subjects with oropharyngeal dysphagia.
Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12
Authors: Cheng Wenwen , Yan Xuanyu , Xiao Jiali , Chen Yunyun , Chen Minghui , Jin Jiayi , Bai Yu , Wang Qi , Liao Zhiyong , Chen Qiongzhen
Published: July 2020

Alginate-degrading bacteria or alginate lyases can be used to oligomerize alginate. In this study, an alginate-degrading bacterium with high alginolytic activity was successfully screened by using Sargassum fusiforme sludge. When the strain was grown on a plate containing sodium alginate, the transparent ring diameter (D) was 2.2 cm and the ratio (D/d) of transparent ring diameter to colony diameter (d) was 8.8. After 36 h in culture at a temperature of 28 °C shaken at 150 r/min, the enzymatic activity of the fermentation supernatant reached 160 U/mL, and the enzymatic activity of the bacterial precipitate harvested was 2,645 U/mL. The strain was named Cobetia sp. cqz5-12. Its genome is circular in shape, 4,209,007 bp in size, with a 62.36% GC content. It contains 3,498 predicted coding genes, 72 tRNA genes, and 21 rRNA genes. The functional annotations for the coding genes demonstrated that there were 181 coding genes in the genome related to carbohydrate transport and metabolism and 699 coding genes with unknown functions. Three putative coding genes, alg2107, alg2108 and alg2112, related to alginate degradation were identified by analyzing the carbohydrate active enzyme (CAZy) database. Moreover, proteins Alg2107 and Alg2112 were successfully expressed and exhibited alginate lyase activity.
Fragmentation of plastic objects in a laboratory seawater microcosm
Authors: Gerritse Jan , Leslie Heather A. , de Tender Caroline A. , Devriese Lisa I. , Vethaak A. Dick
Published: July 2020

We studied the fragmentation of conventional thermoplastic and compostable plastic items in a laboratory seawater microcosm. In the microcosm, polyurethane foams, cellulose acetate cigarette filters, and compostable polyester and polylactic acid items readily sank, whereas polyethylene air pouches, latex balloons, polystyrene foams and polypropylene cups remained afloat. Microbial biofilms dominated by Cyanobacteria, Proteobacteria, Planctomycetes and Bacteriodetes grew on the plastics, and caused some of the polyethylene items to sink to the bottom. Electrical resistances (ER) of plastic items decreased as function of time, an indication that seawater had penetrated into microscopic crevices in the plastic that had developed over time. Rate constants for ER decrease in polyethylene items in the microcosm were similar to tensile elongation decrease of polyethylene sheets floating in sea, measured previously by others. Weight loss of plastic items was ≤ 1% per year for polyethylene, polystyrene and polypropylene, 3–5% for latex, polyethylene terephthalate and polyurethane, 15% for cellulose acetate, and 7–27% for polyester and polylactic acid compostable bags. The formation of microplastics observed in the microcosm was responsible for at least part of the weight loss. This study emphasizes the need to obtain experimental data on plastic litter degradation under conditions that are realistic for marine environments.
Tofacitinib treatment aggravates Staphylococcus aureus septic arthritis, but attenuates sepsis and enterotoxin induced shock in mice
Authors: Jarneborn Anders , Mohammad Majd , Engdahl Cecilia , Hu Zhicheng , Na Manli , Ali Abukar , Jin Tao
Published: July 2020

Tofacitinib, a janus kinase inhibitor, is a novel immunosuppressive drug for treatment of rheumatoid arthritis (RA). Septic arthritis (SA) and sepsis caused byStaphylococcus aureus(S. aureus), for which RA patients are at risk, are infections with high mortality. The aim of this study was to investigate the effect of tofacitinib onS. aureusinfections using mouse models. In vitro tofacitinib treated mouse splenocytes were stimulated withS. aureusderived stimuli. Mice pre-treated with tofacitinib were inoculated intravenously with either arthritogenic- or septic doses ofS. aureus. Arthritis severity and mortality were compared between groups. Additionally, pre-treated mice were challenged with staphylococcal toxin TSST-1 to induce shock. Tofacitinib inhibited splenocyte proliferation and IFN-γ production in response to TSST-1 and deadS. aureus. In SA, tofacitinib treatment aggravated arthritis with more severe bone erosions. However, in sepsis, treated mice displayed significantly prolonged survival compared to controls. Similarly, in staphylococcal enterotoxin-induced shock tofacitinib pre-treatment, but not late treatment dramatically reduced mortality, which was accompanied by decreased levels of TNF-α and IFN-γ. Our findings show that tofacitinib treatment increase susceptibility of SA in mice, but has a positive effect on survival inS. aureus-induced sepsis and a strong protective effect in toxin-induced shock.
Rearing enhancement of Ovalipes trimaculatus (Crustacea: Portunidae) zoea I by feeding on Artemia persimilis nauplii enriched with alternative microalgal diets
Authors: Martelli Antonela , Barbieri Elena S. , Dima Jimena B. , Barón Pedro J.
Published: July 2020

The southern surf crab Ovalipes trimaculatus (de Haan, 1833) presents a high potential for aquaculture. In this study, we analyze the benefits of different dietary treatments on its molt success and fitness of larval stages. Artemia persimilis nauplii were enriched with monospecific (Nannochloropsis oculata, Tetraselmis suecica, Dunaliella salina, Isochrysis galbana and Chaetoceros gracilis) and multispecific (Mix) microalgal diets twice a day over a 48-h period. Mean total length (TL), growth instar number (I) and gut fullness rate (GFR) of nauplii showed significant differences between dietary treatments at several sampling times, optimal results being observed in those providing Mix. Artemia nauplii grown under most experimental dietary treatments reached the capture size limit for Ovalipes trimaculatus zoea I (700 µm) within 24 h. After that time interval, Mix-enriched nauplii were amongst those with higher protein contents. Ovalipes trimaculatus zoea I fed on Artemia nauplii enriched during 24 h under different dietary treatments showed significant differences in survival, inter-molt duration, molting success to zoea II and motility. Optimal results were observed in zoea I fed on Mix-enriched Artemia nauplii. This work not only represents a first step towards the dietary optimization for O. trimaculatus zoeae rearing but also provides the first results on the use of enriched A. persimilis.
Inter-laboratory reproducibility of an untargeted metabolomics GC–MS assay for analysis of human plasma
Authors: Lin Yanping , Caldwell Gary W. , Li Ying , Lang Wensheng , Masucci John
Published: July 2020

There is a long-standing concern for the lack of reproducibility of the untargeted metabolomic approaches used in pharmaceutical research. Two types of human plasma samples were split into two batches and analyzed in two individual labs for untargeted GC–MS metabolomic profiling. The two labs used the same silylation sample preparation protocols but different instrumentation, data processing software, and database. There were 55 metabolites annotated reproducibly, independent of the labs. The median coefficient variations (CV%) of absolute spectra ion intensities in both labs were less than 30%. However, the comparison of normalized ion intensity among biological groups, were inconsistent across labs. Predicted power based on annotated metabolites was evaluated post various normalization, data transformation and scaling. For the first time our study reveals the numerical details about the variations in metabolomic annotation and relative quantification using plain inter-laboratory GC–MS untargeted metabolomic approaches. Especially we compare several commonly used post-acquisition strategies and found normalization could not strengthen the annotation accuracy or relative quantification precision of untargeted approach, instead it will impact future experimental design. Standardization of untargeted metabolomics protocols, including sample preparation, instrumentation, data processing, etc., is critical for comparison of untargeted data across labs.
Abrogation of Marek’s disease virus replication using CRISPR/Cas9
Authors: Hagag Ibrahim T. , Wight Darren J. , Bartsch Denise , Sid Hicham , Jordan Ingo , Bertzbach Luca D. , Schusser Benjamin , Kaufer Benedikt B.
Published: July 2020

Marek’s disease virus (MDV) is a highly cell-associated alphaherpesvirus that causes deadly lymphomas in chickens. While vaccination protects against clinical symptoms, MDV field strains can still circulate in vaccinated flocks and continuously evolve towards greater virulence. MDV vaccines do not provide sterilizing immunity, allowing the virus to overcome vaccine protection, and has increased the need for more potent vaccines or alternative interventions. In this study, we addressed if the CRISPR/Cas9 system can protect cells from MDV replication. We first screened a number of guide RNAs (gRNAs) targeting essential MDV genes for their ability to prevent virus replication. Single gRNAs significantly inhibited virus replication, but could result in the emergence of escape mutants. Strikingly, combining two or more gRNAs completely abrogated virus replication and no escape mutants were observed upon serial passaging. Our study provides the first proof-of-concept, demonstrating that the CRISPR/Cas9 system can be efficiently used to block MDV replication. The presented findings lay the foundation for future research to completely protect chickens from this deadly pathogen.
Photoluminescence of InAs/GaAs quantum dots under direct two-photon excitation
Authors: Hu Xian , Zhang Yang , Guzun Dorel , Ware Morgan E. , Mazur Yuriy I. , Lienau Christoph , Salamo Gregory J.
Published: July 2020

Self-assembled quantum dots grown by molecular beam epitaxy have been a hotbed for various fundamental research and device applications over the past decades. Among them, InAs/GaAs quantum dots have shown great potential for applications in quantum information, quantum computing, infrared photodetection, etc. Though intensively studied, some of the optical nonlinear properties of InAs/GaAs quantum dots, specifically the associated two-photon absorption of the wetting and barrier layers, have not been investigated yet. Here we report a study of the photoluminescence of these dots by using direct two-photon excitation. The quadratic power law dependence of the photoluminescence intensity, together with the ground-state resonant peak of quantum dots appearing in the photoluminescence excitation spectrum, unambiguously confirms the occurrence of the direct two-photon absorption in the dots. A three-level rate equation model is proposed to describe the photogenerated carrier dynamics in the quantum dot-wetting layer-GaAs system. Moreover, higher-order power law dependence of photoluminescence intensity is observed on both the GaAs substrate and the wetting layer by two-photon excitation, which is accounted for by a model involving the third-harmonic generation at the sample interface. Our results open a door for understanding the optical nonlinear effects associated with this fundamentally and technologically important platform.
Plasma phenylalanine and glutamine concentrations correlate with subsequent hepatocellular carcinoma occurrence in liver cirrhosis patients: an exploratory study
Authors: Liang Kung-Hao , Cheng Mei-Ling , Lo Chi-Jen , Lin Yang-Hsiang , Lai Ming-Wei , Lin Wey-Ran , Yeh Chau-Ting
Published: July 2020

Aberrant metabolisms have been hypothesized to precede the occurrence of hepatocellular carcinoma (HCC), therefore, we investigated biomarkers associated with subsequent HCC in peripheral bloods using metabolomic technologies. A cohort of 475 HCC-naïve liver cirrhotic patients were recruited and prospectively followed. A total of 39 patients developed HCC in the follow-up period. Baseline plasma metabolites were explored using untargeted nuclear magnetic resonance. Candidates were then quantified by ultra-performance liquid chromatography. A series of univairiate and multivariate analysis showed that Phenylalanine (Phe) and Glutamine (Gln) levels are associated with time to HCC, independent of viological etiologies and age. A HCC risk score R was then constructed using the polynomial combination of age, Phe and Gln in the units of micromolar (μM):$$\begin{aligned} {\text{R }} & = {\text{ Age }}* \, \left( {0.0694} \right) + {\text{ Phe }}* \, \left( {0.3399} \right) + {\text{ Phe }^{2}}* \, \left( { - 0.00188154} \right) \hfill \\ & \quad + {\text{ Gln }}* \, \left( { - 0.0133} \right) + {\text{ Gln }^{2}}* \, \left( { \, 0.00002244} \right) \hfill \\ \end{aligned}$$

R

=

Age

∗

0.0694

+

Phe

∗

0.3399

+

Phe

2

∗

-
0.00188154

+

Gln

∗

-
0.0133

+

Gln

2

∗

0.00002244

R correlates with the time to HCC significantly (Hazard ratio [HR] = 2.368, 95% confidence interval [CI] 1.760–3.187, P < 0.001). An additional cross-sectional analysis showed that Phe and Gln concentrations both correlates with HCC occurrence in the next 3 years (area under the receiver operating characteristic curve [AUC] = 0.607 and 0.629, P = 0.033 and 0.010 respectively). In conclusion, phenylalanine and glutamine concentrations in the peripheral blood correlate with subsequent HCC.
In situ based surface-enhanced Raman spectroscopy (SERS) for the fast and reproducible identification of PHB producers in cyanobacterial cultures
Authors: Hermann Daniel-Ralph , Lilek David , Daffert Christina , Fritz Ines , Weinberger Simone , Rumpler Vanessa , Herbinger Birgit , Prohaska Katerina
Published: July 2020

Reproducible in situ SERS delivers a significantly reduced analysis time compared to HPLC, allowing timely decisions regarding Synechocystis PHB production.
Rapid DNA detection and one-step RNA detection catalyzed by Bst DNA polymerase and narrow-thermal-cycling
Authors: Li Mengzhe , Liu Mengmeng , Ma Cuiping , Shi Chao
Published: July 2020

We reported a novel and rapid DNA and one-step RNA detection platform based on Bst DNA polymerase and narrow-thermal-cycling for the first time.
A QCM-based rupture event scanning technique as a simple and reliable approach to study the kinetics of DNA duplex dissociation
Authors: Kurus N. N. , Dultsev F. N. , Golyshev V. M. , Nekrasov D. V. , Pyshnyi D. V. , Lomzov A. A.
Published: July 2020

Rupture event scanning (REVS) is applied for the first time within an approach based on dynamic force spectroscopy.
Using hyperspectral imaging automatic classification of gastric cancer grading with a shallow residual network
Authors: Liu Song , Wang Quan , Zhang Geng , Du Jian , Hu Bingliang , Zhang Zhoufeng
Published: July 2020

This paper proposed the use of hyperspectral data to classify gastric cancer grading and design of a classifier with a low computational cost.
Novel copper-based and pH-sensitive nanomedicine for enhanced chemodynamic therapy
Authors: Wang Li , Zhang Zhicheng , Ding Yawen , Wu Jinhui , Hu Yiqiao , Yuan Ahu
Published: July 2020

We utilized albumin as reducing agent to establish a novel pH-sensitive nanocarrier with abundant Cu+, which can encapsulate HDAC inhibitor vorinostat to form uniform V-CuNPs for synergistic chromatin remodelling and chemodynamic therapy.