bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oat evolution revealed in the maternal lineages of 25 Avena species
Authors: Fu Yong-Bi 
Published: March 2018

AbstractCultivated hexaploid oat has three different sets of nuclear genomes (A, C, D), but its evolutionary history remains elusive. A multiplexed shotgun sequencing procedure was explored to acquire maternal phylogenetic signals from chloroplast and mitochondria genomes of 25 Avena species. Phylogenetic analyses of the acquired organelle SNP data revealed a new maternal pathway towards hexaploids of oat genome evolution involving three diploid species (A. ventricosa, A. canariensis and A. longiglumis) and two tetraploid species (A. insularis and A. agadiriana). Cultivated hexaploid A. sativa acquired its maternal genome from an AC genome tetraploid close to A. insularis. Both AC genome A. insularis and AB genome A. agadiriana obtained a maternal genome from an ancient A, not C, genome diploid close to A. longiglumis. Divergence dating showed the major divergences of C genome species 19.9–21.2 million years ago (Mya), of the oldest A genome A. canariensis 13–15 Mya, and of the clade with hexaploids 8.5–9.5 Mya. These findings not only advance our knowledge on oat genome evolution, but also have implications for oat germplasm conservation and utilization in breeding.
Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities
Authors: Ahmad Rafidah , Sahidin I. , Taher Muhammad , Low ChenFei , Noor Normah Mohd , Sillapachaiyaporn Chanin , Chuchawankul Siriporn , Sarachana Tewarit , Tencomnao Tewin , Iskandar Faizah , Rajab Nor Fadilah , Baharum Syarul Nataqain 
Published: March 2018

AbstractPolygonumins A, a new compound, was isolated from the stem of Polygonum minus. Based on NMR results, the compound’s structure is identical to that of vanicoside A, comprising four phenylpropanoid ester units and a sucrose unit. The structure differences were located at C-3″″′. The cytotoxic activity of polygonumins A was evaluated on several cancer cell lines by a cell viability assay using tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The compound showed the highest antiproliferative (p < 0.05) activities against K562 (Human Leukaemia Cell Line), MCF7 (Human breast adenocarcinoma cell line), and HCT116 (Colorectal cancer cells) cells. Cytotoxic studies against V79–4 cells were carried out and showed that polygonumins A was toxic at 50 µg/ml, suggesting that this compound may be used as an anticancer drug without affecting normal cells. Polygonumins A also showed promising activity as an HIV-1 protease inhibitor with 56% relative inhibition. Molecular docking results indicated that the compound possesses high binding affinity towards the HIV protease over the low binding free energy range of -10.5 to -11.3 kcal/mol. P. minus is used in Malaysian traditional medicine for the treatment of tumour cells. This is the first report on the use of P. minus as an HIV-1 protease inhibitor.
Mechanisms by which Bisphenol A affect the photosynthetic apparatus in cucumber (Cucumis sativus L.) leaves
Authors: Li Yu-Ting , Liang Ying , Li Yue-Nan , Che Xing-Kai , Zhao Shi-Jie , Zhang Zi-Shan , Gao Hui-Yuan 
Published: March 2018

AbstractBisphenol A (BPA), a widely distributed pollutant, suppresses photosynthesis in leaves. In previous studies on higher plants, the plants were treated by BPA through irrigation to root. This method cannot distinguish whether the BPA directly suppresses photosynthesis in leaves, or indirectly influences photosynthesis through affecting the function of root. Here, only the leaves but not the roots of cucumber were infiltrated with BPA solution. The photosystem II and I (PSII, PSI) were insensitive to BPA under darkness. BPA aggravated the PSII but not the PSI photoinhibition under light. BPA also inhibited CO2 assimilation, and the effect of BPA on PSII photoinhibition disappeared when the CO2 assimilation was blocked. The H2O2 accumulated in BPA-treated leaves under light. And the BPA-caused PSII photoinhibition was prevented under low (2%) O2. We also proved that the BPA-caused PSII photoinhibition depend on the turnover of D1 protein. In conclusion, this study proved that BPA could directly suppress photosynthesis in leaves, however, BPA does not damage PSII directly, but inhibits CO2 assimilation and over-reduces the electron transport chain under light, which increases the production of reactive oxygen species (H2O2), the over-accumulated ROS inhibits the turnover of D1 protein and consequently aggravates PSII photoinhibition.
Factors associated with negative T-SPOT.TB results among smear-negative tuberculosis patients in China
Authors: Kang Wanli , Wu Meiying , Yang Kunyun , Ertai A. , Wu Shucai , Geng Shujun , Li Zhihui , Li Mingwu , Pang Yu , Tang Shenjie 
Published: March 2018

AbstractWe compared the positive rates of T-SPOT.TB and bacterial culture in the smear-negative PTB, and analyzed the factors affecting the results of negative T-SPOT.TB and bacterial culture. Retrospective evaluation of data from smear-negative PTB patients who underwent T-SPOT.TB and bacterial culture were done. The agreement and concordance were analyzed between T-SPOT.TB and bacterial culture. Multivariable logistic regression analysis was used to explore the factors associated with positive results of T-SPOT.TB and bacterial culture in smear-negative PTB. 858 eligible smear-negative PTB patients were included in the study. The agreement rate was 25.6% (22.7~28.5%) between T-SPOT.TB and bacterial culture in smear- negative PTB patients. The positive rate of T-SPOT.TB was higher than that of bacterial culture in smear-negative PTB patients (p < 0.001). There were nearly no concordance between T-SPOT.TB and bacterial culture (p > 0.05). Using multivariable logistic regression analysis we found that older age ≥ 60 years (OR = 0.469, 95% CI: 0.287–0.768) and decreased albumin (OR = 0.614, 95% CI: 0.380–0.992) were associated with negative diagnostic results of T-SPOT.TB in smear-negative PTB patients. Female (OR = 0.654, 95% CI: 0.431–0.992) were associated with negative diagnostic results of bacteria culture in smear-negative PTB patients. Our results indicated that the older age and decreased albumin were independently associated with negative T-SPOT.TB responses.
Systematic Evaluation of Non-Uniform Sampling Parameters in the Targeted Analysis of Urine Metabolites by 1H,1H 2D NMR Spectroscopy
Authors: Schlippenbach Trixi von , Oefner Peter J. , Gronwald Wolfram 
Published: March 2018

AbstractNon-uniform sampling (NUS) allows the accelerated acquisition of multidimensional NMR spectra. The aim of this contribution was the systematic evaluation of the impact of various quantitative NUS parameters on the accuracy and precision of 2D NMR measurements of urinary metabolites. Urine aliquots spiked with varying concentrations (15.6–500.0 µM) of tryptophan, tyrosine, glutamine, glutamic acid, lactic acid, and threonine, which can only be resolved fully by 2D NMR, were used to assess the influence of the sampling scheme, reconstruction algorithm, amount of omitted data points, and seed value on the quantitative performance of NUS in 1H,1H-TOCSY and 1H,1H-COSY45 NMR spectroscopy. Sinusoidal Poisson-gap sampling and a compressed sensing approach employing the iterative re-weighted least squares method for spectral reconstruction allowed a 50% reduction in measurement time while maintaining sufficient quantitative accuracy and precision for both types of homonuclear 2D NMR spectroscopy. Together with other advances in instrument design, such as state-of-the-art cryogenic probes, use of 2D NMR spectroscopy in large biomedical cohort studies seems feasible.
Effects of In vivo Emergent Tigecycline Resistance on the Pathogenic Potential of Acinetobacter baumannii
Authors: Hornsey Michael , Wareham David W. 
Published: March 2018

AbstractMultidrug-resistant lineages of Acinetobacter baumannii (MDRAB) are important nosocomial pathogens. As tigecycline remains active against most MDRAB we sought to investigate whether tigecycline resistance impacts biological fitness. The effects of treatment-emergent tigecycline resistance were investigated in vitro and in vivo using two pre- (AB210; W6976) and post-therapy (AB211; W7282) clinical pairs, recovered from individual patients, where tigecycline resistance was associated with up-regulated efflux activity. All isolates belonged to the same epidemic UK lineage. Significant differences were observed in end-point survival proportions between AB210 and AB211, but not between W6976 and W7282, using the Galleria mellonella infection model. Isolate AB211 outcompeted AB210 in vivo, in contrast to isolate W7282, which was outcompeted by its pre-therapy counterpart, W6972. Whole-genome sequencing of isolates W6976 and W7282 revealed a mutation in the adeABC regulatory gene, adeS in W7282; resulting in a Ser-8 → Arg substitution. Previous whole-genome comparison of AB210 and AB211 also identified a non-synonymous mutation in adeS, among several other lesions in genes involved in biofilm formation and DNA mismatch repair; consistent with the phenotypic differences described here. In conclusion, the differing effects on the wider phenotype were not predictable from the antibiograms or clonal lineage, despite a common mechanism of tigecycline resistance.
Interferon-β deficiency at asthma exacerbation promotes MLKL mediated necroptosis
Authors: Cerps Samuel C. , Menzel Mandy , Mahmutovic Persson Irma , Bjermer Leif , Akbarshahi Hamid , Uller Lena 
Published: March 2018

AbstractDefective production of antiviral interferon (IFN)-β is thought to contribute to rhinovirus-induced asthma exacerbations. These exacerbations are associated with elevated lung levels of lactate dehydrogenase (LDH), indicating occurrence of cell necrosis. We thus hypothesized that reduced lung IFN-β could contribute to necrotic cell death in a model of asthma exacerbations. Wild-type and IFN-β−/− mice were given saline or house dust mite (HDM) intranasally for 3 weeks to induce inflammation. Double-stranded RNA (dsRNA) was then given for additional 3 days to induce exacerbation. HDM induced an eosinophilic inflammation, which was not associated with increased expression of cleaved caspase-3, cleaved PARP or elevated bronchoalveolar lavage fluid (BALF) LDH levels in wild-type. However, exacerbation evoked by HDM + dsRNA challenges increased BALF levels of LDH, apoptotic markers and the necroptotic markers receptor-interacting protein (RIP)-3 and phosphorylation of mixed linage kinase domain-like protein (pMLKL), compared to HDM + saline. Absence of IFN-β at exacerbation further increased BALF LDH and protein expression of pMLKL compared to wild-type. We demonstrate that cell death markers are increased at viral stimulus-induced exacerbation in mouse lungs, and that absence of IFN-β augments markers of necroptotic cell death at exacerbation. Our data thus suggest a novel role of deficient IFN-β production at viral-induced exacerbation.
Phagocytosis depends on TRPV2-mediated calcium influx and requires TRPV2 in lipids rafts: alteration in macrophages from patients with cystic fibrosis
Authors: Lévêque Manuella , Penna Aubin , Le Trionnaire Sophie , Belleguic Chantal , Desrues Benoît , Brinchault Graziella , Jouneau Stéphane , Lagadic-Gossmann Dominique , Martin-Chouly Corinne 
Published: March 2018

AbstractWhereas many phagocytosis steps involve ionic fluxes, the underlying ion channels remain poorly defined. As reported in mice, the calcium conducting TRPV2 channel impacts the phagocytic process. Macrophage phagocytosis is critical for defense against pathogens. In cystic fibrosis (CF), macrophages have lost their capacity to act as suppressor cells and thus play a significant role in the initiating stages leading to chronic inflammation/infection. In a previous study, we demonstrated that impaired function of CF macrophages is due to a deficient phagocytosis. The aim of the present study was to investigate TRPV2 role in the phagocytosis capacity of healthy primary human macrophage by studying its activity, its membrane localization and its recruitment in lipid rafts. In primary human macrophages, we showed that P. aeruginosa recruits TRPV2 channels at the cell surface and induced a calcium influx required for bacterial phagocytosis. We presently demonstrate that to be functional and play a role in phagocytosis, TRPV2 might require a preferential localization in lipid rafts. Furthermore, CF macrophage displays a perturbed calcium homeostasis due to a defect in TRPV2. In this context, deregulated TRPV2-signaling in CF macrophages could explain their defective phagocytosis capacity that contribute to the maintenance of chronic infection.
Nutritional status and gait speed in a nationwide population-based sample of older adults
Authors: Mendes Joana , Borges Nuno , Santos Alejandro , Padrão Patrícia , Moreira Pedro , Afonso Cláudia , Negrão Rita , Amaral Teresa F. 
Published: March 2018

AbstractThe association between nutritional status and gait speed remains unclear. This study described gait speed in older adults and quantified the association between overweight, obesity, undernutrition risk and gait speed. Gait speed as potential indicator of nutritional outcomes was also explored. A cross-sectional analysis was conducted in a population-based sample of 1,500 older adults ≥65 years old. Compared to “normal body mass index” women, odds ratio for a slow gait speed was approximately 2-fold higher in“overweight”, 4-fold higher in “obese” and 6-fold higher in women at “undernutrition risk”. “Undernutrition risk” category resulted from joining “undernutrition risk/undernutrition”. For men, these associations were in the same direction, but the odds ratio estimates halved. In women, identified gait speed cut-offs were 0.87 m/s for “obesity” and 0.79 m/s for “undernutrition risk”. In men, 0.94 m/s is the cut-off in which most older adults were correctly classified relative to “undernutrition risk”. About half of Portuguese older adults presented a gait speed ≤0.8 m/s. Overweight, obesity and undernutrition risk were directly and increasingly associated with slow gait speed, but approximately twice as high in women compared to men. Gait speed revealed potential utility in marking nutritional problems, but further investigation is recommended.
Hsp90 interacts with multiple dengue virus 2 proteins
Authors: Srisutthisamphan Kanjana , Jirakanwisal Krit , Ramphan Suwipa , Tongluan Natthida , Kuadkitkan Atichat , Smith Duncan R. 
Published: March 2018

AbstractInfections with the mosquito-borne dengue virus (DENV) remain a significant public health challenge. In the absence of a commercial therapeutic to treat DENV infection, a greater understanding of the processes of cellular replication is required. The abundant cellular chaperone protein heat shock protein 90 (Hsp90) has been shown to play a proviral role in the replication cycle of several viruses, predominantly through the stabilization of specific viral proteins. To investigate any potential role of Hsp90 in DENV infection the interaction between Hsp90 and DENV proteins was determined through co-immunoprecipitation experiments. Six DENV proteins namely envelope (E) and nonstructural (NS) proteins NS1, NS2B, NS3, NS4B and NS5 were shown to interact with Hsp90, and four of these proteins (E, NS1, NS3 and NS5) were shown to colocalize to a variable extent with Hsp90. Despite the extensive interactions between Hsp90 and DENV proteins, inhibition of the activity of Hsp90 had a relatively minor effect on DENV replication, with inhibition of Hsp90 resulting in a decrease of cellular E protein (but not nonstructural proteins) coupled with an increase of E protein in the medium and an increased virus titer. Collectively these results indicate that Hsp90 has a slight anti-viral effect in DENV infection.
Cisplatin generates oxidative stress which is accompanied by rapid shifts in central carbon metabolism
Authors: Yu Wangie , Chen Yunyun , Dubrulle Julien , Stossi Fabio , Putluri Vasanta , Sreekumar Arun , Putluri Nagireddy , Baluya Dodge , Lai Stephen Y. , Sandulache Vlad C. 
Published: March 2018

AbstractCisplatin is commonly utilized in the treatment of solid tumors. Its mechanism of action is complex and multiple mechanisms of resistance have been described. We sought to determine the impact of cisplatin-generated oxidative stress on head and neck squamous cell carcinoma (HNSCC) proliferation, survival and metabolic activity in order to identify a potential metabolic signature associated with cisplatin response. DNA-bound cisplatin represents a small fraction of total intra-cellular cisplatin but generates a robust oxidative stress response. Neutralization of oxidative stress reverses cisplatin toxicity independent of the mechanism of cell death and TP53 mutational status. Cisplatin-induced oxidative stress triggers rapid shifts in carbon flux in 3 commonly utilized catabolic pathways: glycolysis, pentose phosphate pathway and citric acid cycle. Among these metabolic shifts, decreased flux from pyruvate into lactate is the only metabolic effect consistently observed across multiple HNSCC cell lines of varying genomic backgrounds and may reflect differential cisplatin sensitivity. Oxidative stress is a critical component of cisplatin cytotoxicity in HNSCC and is reflected in acute changes in carbon flux from pyruvate into lactate. This suggests that lactate may contribute to a metabolic signature of acute cisplatin toxicity, and could prove useful in optimizing cisplatin-based treatment regimens in HNSCC.
Oxic Fe(III) reduction could have generated Fe(II) in the photic zone of Precambrian seawater
Authors: Swanner Elizabeth D. , Maisch Markus , Wu Wenfang , Kappler Andreas 
Published: March 2018

AbstractMany marine Precambrian iron formations (IF) record deep anoxic seawater enriched in Fe(II) (i.e. ferruginous) overlain by mildly oxygenated surface water. This is reflected by iron-rich sediments forming in deep basins, and relatively iron-poor sediments forming in shallow, sunlit waters. Such an iron gradient is often interpreted as a redox interface where dissolved Fe(II) was oxidized and precipitated as Fe(III)-bearing minerals. As such, sedimentary iron enrichments are proxy to the progressive oxidation of the oceans through geological time. However, this interpretation is founded on the assumption that Fe(II) could not persist within an oxygenated water column. Here, we cultivated cyanobacteria in an illuminated column supplied with Fe(II)-rich seawater medium in a laboratory-scale analog of a continental margin supporting IF deposition. We first observed Fe(II) oxidation with oxygen, then biologically-mediated reduction of Fe(III) (oxyhydr)oxides, which maintained a pool of Fe(II) in the presence of oxygen. Such steady-state iron redox cycling may have maintained dissolved, and hence mobile Fe(II) in oxygenated seawater above ferruginous deep basins such as those inferred for many Precambrian IF.
Genetic diversity of the enterohaemolysin gene (ehxA) in non-O157 Shiga toxin-producing Escherichia coli strains in China
Authors: Fu Shanshan , Bai Xiangning , Fan Ruyue , Sun Hui , Xu Yanmei , Xiong Yanwen 
Published: March 2018

AbstractNon-O157 Shiga toxin-producing Escherichia coli (STEC) is increasingly recognized as an important enteric foodborne pathogen. The hallmark of the disease is the production of Shiga toxins; however, there are other virulence factors that contribute to the pathogenesis of STEC. This study aimed to investigate the prevalence and genetic diversity of the enterohaemolysin gene, ehxA, among non-O157 STEC strains from human, animal, and food sources. The ehxA gene was amplified from 138 (31.8%) of 434 non-O157 STEC strains, among which 36 unique ehxA sequences were identified. Based on ehxA sequence analysis, three phylogenetic ehxA groups (I II, and III) were determined. Correlations between ehxA groups and sources, serotypes, and virulent gene profiles were observed. The ehxA group II strains were mostly diarrhoeal patient-derived and may demonstrate higher pathogenic potential compared with the ehxA group I and group III strains. Five types of replicons (I1-Ig, FIB, K, F, and B/O) were identified in the 138 ehxA-positive strains, and 3.6%, 5.8%, and 52.2% of the strains harboured toxB, katP and espP genes, respectively, implying marked genetic diversity of ehxA containing plasmids in non-O157 STEC strains. Sequence-based ehxA genotyping might be important in modern strain typing and in epidemiological surveillance of non-O157 STEC infections.
Quantum man-in-the-middle attack on the calibration process of quantum key distribution
Authors: Fei Yang-Yang , Meng Xiang-Dong , Gao Ming , Wang Hong , Ma Zhi 
Published: March 2018

AbstractQuantum key distribution (QKD) protocol has been proved to provide unconditionally secure key between two remote legitimate users in theory. Key distribution signals are transmitted in a quantum channel which is established by the calibration process to meet the requirement of high count rate and low error rate. All QKD security proofs implicitly assume that the quantum channel has been established securely. However, the eavesdropper may attack the calibration process to break the security assumption of QKD and provide precondition to steal information about the final key successfully. In this paper, we reveal the security risk of the calibration process of a passive-basis-choice BB84 QKD system by launching a quantum man-in-the-middle attack which intercepts all calibration signals and resends faked ones. Large temporal bit-dependent or basis-dependent detector efficiency mismatch can be induced. Then we propose a basis-dependent detector efficiency mismatch (BEM) based faked states attack on a single photon BB84 QKD to stress the threat of BEM. Moreover, the security of single photon QKD systems with BEM is studied simply and intuitively. Two effective countermeasures are suggested to remove the general security risk of the calibration process.
Whole transcriptome profiling of Late-Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease
Authors: Annese Anita , Manzari Caterina , Lionetti Claudia , Picardi Ernesto , Horner David S. , Chiara Matteo , Caratozzolo Mariano Francesco , Tullo Apollonia , Fosso Bruno , Pesole Graziano , D’Erchia Anna Maria 
Published: March 2018

AbstractAlzheimer’s Disease (AD) is the most common cause of dementia affecting the elderly population worldwide. We have performed a comprehensive transcriptome profiling of Late-Onset AD (LOAD) patients using second generation sequencing technologies, identifying 2,064 genes, 47 lncRNAs and 4 miRNAs whose expression is specifically deregulated in the hippocampal region of LOAD patients. Moreover, analyzing the hippocampal, temporal and frontal regions from the same LOAD patients, we identify specific sets of deregulated miRNAs for each region, and we confirm that the miR-132/212 cluster is deregulated in each of these regions in LOAD patients, consistent with these miRNAs playing a role in AD pathogenesis. Notably, a luciferase assay indicates that miR-184 is able to target the 3’UTR NR4A2 - which is known to be involved in cognitive functions and long-term memory and whose expression levels are inversely correlated with those of miR-184 in the hippocampus. Finally, RNA editing analysis reveals a general RNA editing decrease in LOAD hippocampus, with 14 recoding sites significantly and differentially edited in 11 genes. Our data underline specific transcriptional changes in LOAD brain and provide an important source of information for understanding the molecular changes characterizing LOAD progression.