bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host–symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress
Authors: Hoadley Kenneth D. , Lewis Allison M. , Wham Drew C. , Pettay D. Tye , Grasso Chris , Smith Robin , Kemp Dustin W. , LaJeunesse Todd C. , Warner Mark E. 
Published: July 2019

AbstractHigh sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment.
HIV-1 tropism prediction by the XGboost and HMM methods
Authors: Chen Xiang , Wang Zhi-Xin , Pan Xian-Ming 
Published: July 2019

AbstractHuman Immunodeficiency Virus 1 (HIV-1) co-receptor usage, called tropism, is associated with disease progression towards AIDS. Furthermore, the recently developed and developing drugs against co-receptors CCR5 or CXCR4 open a new thought for HIV-1 therapy. Thus, knowledge about tropism is critical for illness diagnosis and regimen prescription. To improve tropism prediction accuracy, we developed two novel methods, the extreme gradient boosting based XGBpred and the hidden Markov model based HMMpred. Both XGBpred and HMMpred achieved higher specificities (72.56% and 72.09%) than the state-of-the-art methods Geno2pheno (61.6%) and G2p_str (68.60%) in a 10-fold cross validation test at the same sensitivity of 93.73%. Moreover, XGBpred had more outstanding performances (with AUCs 0.9483, 0.9464) than HMMpred (0.8829, 0.8774) on the Hivcopred and Newdb (created in this work) datasets containing larger proportions of hard-to-predict dual tropic samples in the X4-using tropic samples. Therefore, we recommend the use of our novel method XGBpred to predict tropism. The two methods and datasets are available via http://spg.med.tsinghua.edu.cn:23334/XGBpred/. In addition, our models identified that positions 5, 11, 13, 18, 22, 24, and 25 were correlated with HIV-1 tropism.
A dual-model SERS and RRS analytical platform for Pb(II) based on Ag-doped carbon dot catalytic amplification and aptamer regulation
Authors: Wang Haidong , Huang Xiaowei , Wen Guiqing , Jiang Zhiliang 
Published: July 2019

AbstractSeveral carbon dots doping with diferent elements (Ca, Ag, Au) were fabricated and their catalytic properties had been investigated in this paper. It was found that the Ag-doped carbon dots (CDAg) had played a role of mimic enzyme on the reaction of HAuCl4-H2O2 and generated nanogold particles with surface enhanced Raman scattering (SERS) and resonance Rayleigh scattering (RRS) effects. The aptamer (Apt) can be adsorbed on the CDAg surface and cause the catalysis weakening. When the target Pb(II) was added, it would combine with the Apt to produce firm complexes Pb-Apt and desorb CDAg, which caused its catalytic effect restore. The formed nanogold had a strong RRS peak (at 375 nm) and a high SERS peak (at 1615 cm−1) in the presence of molecular probe (Victoria blue B, VBB). The dual-model signals of SERS and RRS increased linearly with Pb(II) concentration increase within the scope of 0.006–0.46 μmol/L and 0.01–0.46 μmol/L. And their detection limits respectively were 0.0032 μmol/L and 0.0048 μmol/L Pb(II).
Spatial variation of vector vortex beams with plasmonic metasurfaces
Authors: Zhang Yuchao , Gao Jie , Yang Xiaodong 
Published: July 2019

AbstractThe spatial variation of vector vortex beams with arbitrary polarization states and orbital angular momentum (OAM) values along the beam propagation is demonstrated by using plasmonic metasurfaces with the initial geometric phase profiles determined from the caustic theory. The vector vortex beam is produced by the superposition of deflected right- and left-handed circularly polarized component vortices with different helical phase charges, which are simultaneously generated off-axially by the single metasurface. Besides, the detailed evolution processes of intensity profile, polarization distribution and OAM value along the beam propagation distance is analyzed. The demonstrated arbitrary space-variant vector vortex beam will pave the way to many promising applications related to spin-to-orbital angular momentum conversion, spin-orbit hybrid entanglement, particle manipulation and transportation, and optical communication.
Disease-causing mutations in subunits of OXPHOS complex I affect certain physical interactions
Authors: Barshad Gilad , Zlotnikov-Poznianski Nicol , Gal Lihi , Schuldiner Maya , Mishmar Dan 
Published: July 2019

AbstractMitochondrial complex I (CI) is the largest multi-subunit oxidative phosphorylation (OXPHOS) protein complex. Recent availability of a high-resolution human CI structure, and from two non-human mammals, enabled predicting the impact of mutations on interactions involving each of the 44 CI subunits. However, experimentally assessing the impact of the predicted interactions requires an easy and high-throughput method. Here, we created such a platform by cloning all 37 nuclear DNA (nDNA) and 7 mitochondrial DNA (mtDNA)-encoded human CI subunits into yeast expression vectors to serve as both ‘prey’ and ‘bait’ in the split murine dihydrofolate reductase (mDHFR) protein complementation assay (PCA). We first demonstrated the capacity of this approach and then used it to examine reported pathological OXPHOS CI mutations that occur at subunit interaction interfaces. Our results indicate that a pathological frame-shift mutation in the MT-ND2 gene, causing the replacement of 126 C-terminal residues by a stretch of only 30 amino acids, resulted in loss of specificity in ND2-based interactions involving these residues. Hence, the split mDHFR PCA is a powerful assay for assessing the impact of disease-causing mutations on pairwise protein-protein interactions in the context of a large protein complex, thus offering a possible mechanistic explanation for the underlying pathogenicity.
Phosphoproteomics analysis of male and female Schistosoma mekongi adult worms
Authors: Simanon Nattapon , Adisakwattana Poom , Thiangtrongjit Tipparat , Limpanont Yanin , Chusongsang Phiraphol , Chusongsang Yupa , Anuntakarun Songtham , Payungporn Sunchai , Ampawong Sumate , Reamtong Onrapak 
Published: July 2019

AbstractSchistosoma mekongi is one of the major causative agents of human schistosomiasis in Southeast Asia. Praziquantel is now the only drug available for treatment and there are serious concerns about parasite resistance to it. Therefore, a dataset of schistosome targets is necessary for drug development. Phosphorylation regulates signalling pathways to control cellular processes that are important for the parasite’s growth and reproduction. Inhibition of key phosphoproteins may reduce the severity of schistosomiasis. In this research, we studied the phosphoproteomes of S. mekongi male and female adult worms by using computational and experimental approaches. Using a phosphoproteomics approach, we determined that 88 and 44 phosphoproteins were male- and female-biased, respectively. Immunohistochemistry using anti-phosphoserine antibodies demonstrated phosphorylation on the tegument and muscle of male S. mekongi worms and on the vitelline gland and gastrointestinal tract of female worms. This research revealed S. mekongi sex-dependent phosphoproteins. Our findings provide a better understanding of the role of phosphorylation in S. mekongi and could be integrated with information from other Schistosoma species to facilitate drug and vaccine development.
Differential expression of individual transcript variants of PD-1 and PD-L2 genes on Th-1/Th-2 status is guaranteed for prognosis prediction in PCNSL
Authors: Takashima Yasuo , Kawaguchi Atsushi , Sato Ryuichi , Yoshida Kenichi , Hayano Azusa , Homma Jumpei , Fukai Junya , Iwadate Yasuo , Kajiwara Koji , Ishizawa Shin , Hondoh Hiroaki , Nakano Masakazu , Ogawa Seishi , Tashiro Kei , Yamanaka Ryuya 
Published: July 2019

AbstractIn current molecular medicine, next-generation sequencing (NGS) for transcript variant detection and multivariable analyses are valid methods for evaluating gene expression, cancer mechanisms, and prognoses of patients. We conducted RNA-sequencing on samples from patients with primary central nervous system lymphoma (PCNSL) using NGS and performed multivariable analysis on gene expression data and correlations focused on Th-1/Th-2 helper T cell balance and immune checkpoint to identify diagnosis/prognosis markers and cancer immune pathways in PCNSL. We selected 84 transcript variants to limit the analysis range for Th-1/Th-2 balance and stimulatory and inhibitory checkpoints in 31 PCNSLs. Of these, 21 highly-expressed transcript variants were composed of the formulas for prognoses based on Th-1/Th-2 status and checkpoint activities. Using formulas, Th-1low, Th-2high, and stimulatory checkpointhigh resulted in poor prognoses. Further, Th-1highTh-2low was associated with good prognoses. On the other hand, CD40-001high and CD70-001high as stimulatory genes, and LAG3-001high, PDCD1 (PD-1)-001/002/003high, and PDCD1LG2 (PD-L2)-201low as inhibitory genes were associated with poor prognoses. Interestingly, Th-1highTh-2low and Th-1lowTh-2high were correlated with stimulatory checkpointlow as CD70-001low and inhibitory checkpointlow as HAVCR2 (TIM-3)-001low and PDCD1LG2-001/201low, respectively. Focused on the inhibitory checkpoint, specific variants of CD274 (PD-L1)-001 and PDCD1-002 served severe hazard ratios. In particular, PDCD1-002high by a cut off score was associated with poor prognoses, in addition to PDCD1-001/003high, PDCD1LG2-201low, and LAG3-001high. These results mainly suggest that expression of transcript variants of PDCD1 and PDCD1LG2 on the Th-1/Th-2 balance enable prognostic prediction in PCNSL. This study provides insights for development of molecular target therapies and identification of diagnosis/prognosis markers in PCNSL.
Human DC-SIGN and CD23 do not interact with human IgG
Authors: Temming A. Robin , Dekkers Gillian , van de Bovenkamp Fleur S. , Plomp H. Rosina , Bentlage Arthur E. H. , Szittner Zoltán , Derksen Ninotska I. L. , Wuhrer Manfred , Rispens Theo , Vidarsson Gestur 
Published: July 2019

AbstractThe precise mechanisms underlying anti-inflammatory effects of intravenous immunoglobulin (IVIg) therapies remain elusive. The sialylated IgG fraction within IVIg has been shown to be therapeutically more active in mouse models. Functionally, it has been suggested that IgG undergoes conformational changes upon Fc-sialylation which sterically impede binding to conventional FcγRs, but simultaneously allow binding to human DC-SIGN (SIGN-R1 in mice) and also CD23. These latter C-type lectins have been proposed responsible for the immunomodulatory effects in mouse models. However, there is conflicting evidence supporting direct interactions between sialylated human IgG and CD23/DC-SIGN. While cells expressing human CD23 and DC-SIGN in their native configuration bound their natural ligands IgE and ICAM-3, respectively, no IgG binding was observed, regardless of Fc-glycan sialylation in any context (with or without bisection and/or fucosylation) or presence of sialylated Fab-glycans. This was tested by both by FACS and a novel cellular Surface Plasmon Resonance imaging (cSPRi) approach allowing for monitoring low-affinity but high-avidity interactions. In summary, we find no evidence for human CD23 or DC-SIGN being bona fide receptors to human IgG, regardless of IgG Fc- or Fab-glycosylation status. However, these results do not exclude the possibility that either IgG glycosylation or C-type lectins affect IVIg therapies.
Generation and characterization of a stable cell line persistently replicating and secreting the human hepatitis delta virus
Authors: Ni Yi , Zhang Zhenfeng , Engelskircher Lisa , Verch Georg , Tu Thomas , Lempp Florian A. , Urban Stephan 
Published: July 2019

AbstractHuman hepatitis delta virus (HDV) causes the most severe form of viral hepatitis. Approximately 15–25 million people are chronically infected with HDV. As a satellite virus of the human hepatitis B virus (HBV), HDV uses the HBV-encoded envelope proteins for egress from and de novo entry into hepatocytes. So far, in vitro production of HDV particles is restricted to co-transfection of cells with HDV/HBV encoding cDNAs. This approach has several limitations. In this study, we established HuH7-END cells, which continuously secrete infectious HDV virions. The cell line was generated through stepwise stable integration of the cDNA of the HDV antigenome, the genes for the HBV envelope proteins and the HBV/HDV receptor NTCP. We found that HuH7-END cells release infectious HDV particles up to 400 million copies/milliliter and support virus spread to co-cultured cells. Due to the expression of NTCP, HuH7-END cells are also susceptible to de novo HDV entry. Virus production is stable for >16 passages and can be scaled up for preparation of large HDV virus stocks. Finally, HuH7-END cells are suitable for screening of antiviral drugs targeting HDV replication. In summary, the HuH7-END cell line provides a novel tool to study HDV replication in vitro.
Label propagation method based on bi-objective optimization for ambiguous community detection in large networks
Authors: Luo Junhai , Ye Lei 
Published: July 2019

AbstractCommunity detection is of great significance because it serves as a basis for network research and has been widely applied in real-world scenarios. It has been proven that label propagation is a successful strategy for community detection in large-scale networks and local clustering coefficient can measure the degree to which the local nodes tend to cluster together. In this paper, we try to optimize two objects about the local clustering coefficient to detect community structure. To avoid the trend that merges too many nodes into a large community, we add some constraints on the objectives. Through the experiments and comparison, we select a suitable strength for one constraint. Last, we merge two objectives with linear weighting into a hybrid objective and use the hybrid objective to guide the label update in our proposed label propagation algorithm. We perform amounts of experiments on both artificial and real-world networks. Experimental results demonstrate the superiority of our algorithm in both modularity and speed, especially when the community structure is ambiguous.
A ubiquitin-like domain is required for stabilizing the N-terminal ATPase module of human SMCHD1
Authors: Pedersen Lars C. , Inoue Kaoru , Kim Susan , Perera Lalith , Shaw Natalie D. 
Published: July 2019

AbstractVariants in the gene SMCHD1, which encodes an epigenetic repressor, have been linked to both congenital arhinia and a late-onset form of muscular dystrophy called facioscapulohumeral muscular dystrophy type 2 (FSHD2). This suggests that SMCHD1 has a diversity of functions in both developmental time and space. The C-terminal end of SMCHD1 contains an SMC-hinge domain which mediates homodimerization and chromatin association, whereas the molecular architecture of the N-terminal region, which harbors the GHKL-ATPase domain, is not well understood. We present the crystal structure of the human SMCHD1 N-terminal ATPase module bound to ATP as a functional dimer. The dimer is stabilized by a novel N-terminal ubiquitin-like fold and by a downstream transducer domain. While disease variants map to what appear to be critical interdomain/intermolecular interfaces, only the FSHD2-specific mutant constructs we tested consistently abolish ATPase activity and/or dimerization. These data suggest that the full functional profile of SMCHD1 has yet to be determined.
High-Throughput Yeast Aging Analysis for Cryptococcus (HYAAC) microfluidic device streamlines aging studies in Cryptococcus neoformans
Authors: Orner Erika P. , Zhang Pengchao , Jo Myeong C. , Bhattacharya Somanon , Qin Lidong , Fries Bettina C. 
Published: July 2019

AbstractCryptococcus neoformans (Cn) is a deadly fungal pathogen responsible for ~ 180,000 deaths per year and despite effective antifungals, treatment failure and resistance to antifungals are increasingly problematic. Aging and age-related phenotypes are prominent virulence traits that contribute to the resilience of Cn to host responses and antifungals. Traditional methods to study aging in Cn are expensive, inefficient and in need of improvement. Here, we demonstrate the development and use of a High-Throughput Yeast Aging Analysis for Cryptococcus (HYAAC) microfluidic device to better study aging and age-associated genes in Cn. Compared to traditional methods, the HYAAC is superior in its efficiency to isolate, manipulate and observe old cells for analysis. It allows for the trapping and tracking of individual cells over the course of their lifespan, allowing for more precise measurements of lifespan, tracking of age-related phenotypes with age, and a more high-throughput ability to investigate genes associated with aging.
MiRNA-144-3p inhibits high glucose induced cell proliferation through suppressing FGF16
Authors: Chen Cuimin , Zhao Chunyan , Gu Cao , Cui Xiao , Wu Jinhui 
Published: July 2019

Abstract
As a major cause of blindness, diabetic retinopathy (DR) is often found in the developed countries. Our previous study identified a down-regulated miRNA: miR-144-3p in response to hyperglycemia. The present study aims to investigate the role of miR-144-3p in proliferation of microvascular epithelial cells. Endothelial cells were treated with different concentrations of glucose, after which miR-144-3p were detected with real-time PCR assay. MiR-144-3p mimics or inhibitors were used to increase or knockdown the level of this miRNA. Western blotting assay and ELISA assay were used to measure the expression and concentration of VEGF protein. 5-Bromo-2-deoxyUridine (BrdU) labeled cell cycle assay was used to detect cells in S phase. MiRNA targets were predicted by using a TargetScan tool, and were further verified by luciferase reporter assay. In the present study, we focussed on a significantly down-regulated miRNA, miR-144-3p, and investigated its role in high glucose (HG) induced cell proliferation. Our data showed that miR-144-3p mimics significantly inhibited HG induced cell proliferation and reduced the percentage of cells in S phase. HG induced up-regulation of VEGF was also prohibited by miR-144-3p mimics. Through wound-healing assay, we found that miR-144-3p suppressed cell migration after HG treatments. Moreover, we predicted and proved that fibroblast growth factor (FGF)16 is a direct target of miR-144-3p. Finally, miR-144-3p attenuated HG induced MAPK activation. In conclusion, we demonstrated that miR-144-3p inhibited high glucose-induced cell proliferation through suppressing FGF16 and MAPK signaling pathway, suggesting a possible role of miR-144-FGF16 in the development of DR.
Effective low‐cost solution using cascaded connection of two modified notch filters to mitigate the second and third harmonic currents in single‐phase dual‐stage half‐bridge microinverter
Authors: Vongkoon Pokkrong , Liutanakul Pisit , Wiwatcharagoses Nophadon 
Published: July 2019

On the grid side, the half‐bridge topology of the microinverter is of interest for solar rooftop applications because of its high efficiency, low component count, and cost‐effectiveness. However, it has an inherent double‐line frequency ripple voltage on the dc‐link, which causes the injection of a third‐order harmonic current when the voltage control loop is closed. Furthermore, in practice, different average voltages or different capacitances of the two capacitors at the dc‐link produce a second‐order harmonic current that flows into the grid. In this paper, the analytical details of these harmonics are comprehensively described, and a simple and effective low‐cost technique using the cascaded connection of two modified notch filters is proposed in the voltage control loop to mitigate their effects. The simulation and experimental results of a 300 W microinverter indicate that the proposed filters represent an effective low‐cost solution and perform well in accordance with the IEEE 1547 standard, even if the capacitances at the dc‐link are mismatched by 20%. Besides, the prototype is tested when occurring of the changing +1% of the line frequency, or appearing of the distorted waveform of grid voltage with the composition of 6% of fifth‐order harmonic.
Functionalised polymer brushes grafted onto nanosiliceous support for removal of cadmium (II) in environmental and biological samples
Authors: Ghoroghi Atefeh , Ahmad Panahi Homayon , Arjmandpour Saba , Moniri Elham 
Published: July 2019

The experiments in this work were based on the use of grafted polymers on glass nanoparticles for eliminating cadmium ions from environmental and biological samples. Glass nanoparticles (NPs) were modified with (3‐mercaptopropyl) trimetoxisilane followed by the graft polymerisation of N,N‐dimethylacrylamide and allylamine and then with bromoacetic acid. The grafted polymers on the glass NPs were characterised by Fourier transform infra‐red spectroscopy, scanning electron microscopy, and elemental analysis. Surface morphology was investigated via transmission electron microscopy. The optimum pH for cadmium adsorption and the adsorption capacity of the nanoadsorbent were 6.5 and 46.70 mg g−1, respectively. The Langmuir, Freundlich and Redlich‐Peterson models were employed to analyse the equilibrium adsorption data of Cd (II) on the grafted glass NPs. Finally, the grafted glass NPs were utilised for Cd (II) elimination from the biological and environmental samples.