bluuebunny/crossref_metadata_2025_split huggingface dataset:
High throughput barcoding method for genome-scale phasing
Authors: Redin David , Frick Tobias , Aghelpasand Hooman , Käller Max , Borgström Erik , Olsen Remi-Andre , Ahmadian Afshin 
Published: December 2019

AbstractThe future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.
Life-span extension by pigmented rice bran in the model yeast Saccharomyces cerevisiae
Authors: Sunthonkun Pitchapat , Palajai Rinsai , Somboon Pichayada , Suan Chua Lee , Ungsurangsri Malyn , Soontorngun Nitnipa 
Published: December 2019

AbstractBenefits of whole grains as dietary supplements and active ingredients in health products have been promoted. Despite being neglected as an agricultural byproduct of polished rice, pigmented rice bran has emerged as a promising source of natural anti-aging compounds. Indeed, the extract of red rice bran Hom Dang cultivar contained rich phenolic acids and flavonoids. It displayed high antioxidant activities in vitro and in vivo assays. Using yeast model, extract and bioactive compounds, quercetin and protocatechuic acid found in the rice bran pericarp, effectively reduced levels of intracellular reactive oxygen species (ROS), restored plasma membrane damages and prolonged life-span of pre-treated wild-yeast cells. Importantly, these molecules modulated life span-extension through a mechanism of ROS reduction that resembles to that operated under the highly conserved Tor1- and Sir2-dependent signaling pathways, with the human homologs TORC1 and SIRT1, respectively. The key longevity factors Sch9 and Rim15 kinases, Msn2/4 regulators and a novel transcription factor Asg1, the antioxidant enzymes superoxide dismutases and glutathione peroxidases played important role in mediating longevity. Yeast clearly provides an instrumental platform for rapid screening of compounds with anti-aging efficacies and advances knowledge in the molecular study of ageing.
An integrated screening system for the selection of exemplary substrates for natural and engineered cytochrome P450s
Authors: Kanoh Naoki , Kawamata-Asano Ayano , Suzuki Kana , Takahashi Yusuke , Miyazawa Takeshi , Nakamura Takemichi , Moriya Takashi , Hirano Hiroyuki , Osada Hiroyuki , Iwabuchi Yoshiharu , Takahashi Shunji 
Published: December 2019

AbstractInformation about substrate and product selectivity is critical for understanding the function of cytochrome P450 monooxygenases. In addition, comprehensive understanding of changes in substrate selectivity of P450 upon amino acid mutation would enable the design and creation of engineered P450s with desired selectivities. Therefore, systematic methods for obtaining such information are required. Herein, we developed an integrated P450 substrate screening system for the selection of “exemplary” substrates for a P450 of interest. The established screening system accurately selected the known exemplary substrates and also identified previously unknown exemplary substrates for microbial-derived P450s from a library containing sp3-rich synthetic small molecules. Synthetically potent transformations were also found by analyzing the reactions and oxidation products. The screening system was applied to analyze the substrate selectivity of the P450 BM3 mutants F87A and F87A/A330W, which acquired an ability to hydroxylate non-natural substrate steroids regio- and stereoselectively by two amino acid mutations. The distinct transition of exemplary substrates due to each single amino acid mutation was revealed, demonstrating the utility of the established system.
Tropical forest soil carbon stocks do not increase despite 15 years of doubled litter inputs
Authors: Sayer Emma J. , Lopez-Sangil Luis , Crawford John A. , Bréchet Laëtitia M. , Birkett Ali J. , Baxendale Catherine , Castro Biancolini , Rodtassana Chadtip , Garnett Mark H. , Weiss Lena , Schmidt Michael W. I. 
Published: December 2019

AbstractSoil organic carbon (SOC) dynamics represent a persisting uncertainty in our understanding of the global carbon cycle. SOC storage is strongly linked to plant inputs via the formation of soil organic matter, but soil geochemistry also plays a critical role. In tropical soils with rapid SOC turnover, the association of organic matter with soil minerals is particularly important for stabilising SOC but projected increases in tropical forest productivity could trigger feedbacks that stimulate the release of stored SOC. Here, we demonstrate limited additional SOC storage after 13–15 years of experimentally doubled aboveground litter inputs in a lowland tropical forest. We combined biological, physical, and chemical methods to characterise SOC along a gradient of bioavailability. After 13 years of monthly litter addition treatments, most of the additional SOC was readily bioavailable and we observed no increase in mineral-associated SOC. Importantly, SOC with weak association to soil minerals declined in response to long-term litter addition, suggesting that increased plant inputs could modify the formation of organo-mineral complexes in tropical soils. Hence, we demonstrate the limited capacity of tropical soils to sequester additional C inputs and provide insights into potential underlying mechanisms.
Landscape of heart proteome changes in a diet-induced obesity model
Authors: Vileigas Danielle F. , Harman Victoria M. , Freire Paula P. , Marciano Cecília L. C. , Sant’Ana Paula G. , de Souza Sérgio L. B. , Mota Gustavo A. F. , da Silva Vitor L. , Campos Dijon H. S. , Padovani Carlos R. , Okoshi Katashi , Beynon Robert J. , Santos Lucilene D. , Cicogna Antonio C. 
Published: December 2019

AbstractObesity is a pandemic associated with a high incidence of cardiovascular disease; however, the mechanisms are not fully elucidated. Proteomics may provide a more in-depth understanding of the pathophysiological mechanisms and contribute to the identification of potential therapeutic targets. Thus, our study evaluated myocardial protein expression in healthy and obese rats, employing two proteomic approaches. Male Wistar rats were established in two groups (n = 13/group): control diet and Western diet fed for 41 weeks. Obesity was determined by the adipose index, and cardiac function was evaluated in vivo by echocardiogram and in vitro by isolated papillary muscle analysis. Proteomics was based on two-dimensional gel electrophoresis (2-DE) along with mass spectrometry identification, and shotgun proteomics with label-free quantification. The Western diet was efficient in triggering obesity and impaired contractile function in vitro; however, no cardiac dysfunction was observed in vivo. The combination of two proteomic approaches was able to increase the cardiac proteomic map and to identify 82 differentially expressed proteins involved in different biological processes, mainly metabolism. Furthermore, the data also indicated a cardiac alteration in fatty acids transport, antioxidant defence, cytoskeleton, and proteasome complex, which have not previously been associated with obesity. Thus, we define a robust alteration in the myocardial proteome of diet-induced obese rats, even before functional impairment could be detected in vivo by echocardiogram.
Efficacy and safety of lavender essential oil (Silexan) capsules among patients suffering from anxiety disorders: A network meta-analysis
Authors: Yap Wuan Shuen , Dolzhenko Anton V. , Jalal Zahraa , Hadi Muhammad Abdul , Khan Tahir Mehmood 
Published: December 2019

AbstractA systematic review and network-meta analysis (NMA) were performed to estimate significance of the anxiolytic effect of lavender essential oil taken as silexan capsules versus other comparators (i.e., placebo/paroxetine/lorazepam). The outcome of interest was Hamilton Anxiety Scale (HAMA). Weighted mean differences (WMD) were calculated to estimate the treatment effect at the confidence interval of 95%. League tables were generated using treatment effect, for all pairwise comparisons, where WMD < 0 favors the column-defining treatment. Five studies were identified with a total of 524 participants receiving treatment with silexan 80 mg and 121 participants taking silexan 160 mg. The NMA results indicated that consumption of silexan 160 mg resulted in higher decline of HAMA score [WMD −1.14 (−1.10, 3.39)] in comparison to silexan 80 mg, placebo [−2.20 (−4.64, 0.24)] and paroxetine [−1.24 (−5.34, 2.85)]. The effect of silexan 80 mg was observed to be same as that of paroxetine. Overall, silexan 160 mg was noticed to be a more efficient treatment giving significant decline in HAMA score across other comparators. However, no improvements in HAMA score was observed for the group receiving lorazepam 0.5 mg when compared to silexan 160 mg, silexan 80 mg, paroxetine 20 mg, and placebo.
Spatial-sweep steady-state pattern electroretinography can detect subtle differences in visual function among healthy adults
Authors: Minami Sakiko , Nagai Norihiro , Suzuki Misa , Kurihara Toshihide , Sonobe Hideki , Watanabe Kazuhiro , Shinoda Hajime , Takagi Hitoshi , Tsubota Kazuo , Ozawa Yoko 
Published: December 2019

AbstractWe aimed to establish a highly sensitive method for measuring visual function using spatial-sweep steady-state pattern electroretinography (swpPERG). Overall, 35 eyes of 35 healthy adults (18 men; mean age, 32.3 years) were examined using swpPERG, and the data were recorded using spatial-patterned and contrast-reversed stimuli of size 1 (thickest) to 6. Data were converted into frequency-domain using a Fourier transform and expressed by signal-to-noise ratio (SNR). The number of participants who showed SNR ≥ 1 was significantly lesser at stimulus sizes 5 and 6 compared with those at greater stimulus sizes. Among the data with SNR ≥ 1, SNRs were negatively correlated with age at stimulus size 5 (r = −0.500, P = 0.029), and positively correlated with macular volume evaluated by optical coherence tomography (OCT) within a 6-mm circle diameter from the fovea of the retinal nerve fibre layer at size 4 (r = 0.409, P = 0.025) and of the ganglion cell layer at size 5 (r = 0.567, P = 0.011). We found that SNRs of swpPERG, recorded using the EvokeDx system, were correlated with age and macular morphology in participants without diagnosed eye diseases. The system detected subtle differences in retinal function, which may help in early disease diagnosis and visual evaluation in neuroprotective interventions in the future.
Nucleic acids enrichment of fungal pathogens to study host-pathogen interactions
Authors: Rodríguez Antonio , Guillemyn Brecht , Coucke Paul , Vaneechoutte Mario 
Published: December 2019

AbstractFungal infections, ranging from superficial to life-threatening infections, represent a major public health problem that affects 25% of the worldwide population. In this context, the study of host-pathogen interactions within the host is crucial to advance antifungal therapy. However, since fungal cells are usually outnumbered by host cells, the fungal transcriptome frequently remains uncovered. We compared three different methods to selectively lyse human cells from in vitro mixes, composed of Candida cells and peripheral blood mononuclear cells. In order to prevent transcriptional modification, the mixes were stored in RNAlater. We evaluated the enrichment of fungal cells through cell counting using microscopy and aimed to further enrich fungal nucleic acids by centrifugation and by reducing contaminant nucleic acids from the host. We verified the enrichment of fungal DNA and RNA through qPCR and RT-qPCR respectively and confirmed that the resulting RNA has high integrity scores, suitable for downstream applications. The enrichment method provided here, i.e., lysis with Buffer RLT followed by centrifugation, may contribute to increase the proportion of nucleic acids from fungi in clinical samples, thus promoting more comprehensive analysis of fungal transcriptional profiles. Although we focused on C. albicans, the enrichment may be applicable to other fungal pathogens.
Cytokines Levels and Salivary Microbiome Play A Potential Role in Oral Lichen Planus Diagnosis
Authors: Carvalho Maria Fernanda Marques Silva de , Cavalieri Denise , Do Nascimento Sabrina , Lourenço Talita Gomes Baeta , Ramos Danielle Viana Ribeiro , Pasqualin Denise da Cunha , Martins Leandro Aurélio Liporoni , Rocha Fernanda Agostini , Heller Débora , Marti Luciana 
Published: December 2019

AbstractOral lichen planus (OLP) is a chronic Th1-mediated inflammatory mucocutaneous disease of the skin and oral mucosa that can have various clinical presentations. Lesions are usually bilateral and often painful. While cutaneous Lichen Planus (LP) lesions are self-limiting, the oral lesions are chronic and rarely remissive. The diagnosis of oral lichen planus (OLP) is often challenging, and confirmation by histopathological criterion is generally advised. The aim of our study was to identify the cytokines present in OLP-suggestive lesions and in non-specific inflammatory lesions (NSIL) used as controls. Moreover, assess cytokines protein levels and oral microbiota composition in whole saliva samples. Histopathological analysis, immunohistochemistry and gene expression were used as techniques to analyze the oral mucosal tissue samples. ELISA was conducted to analyze salivary cytokine levels and 16S rRNA sequencing was used to determine the salivary microbiome. As a result we observed larger number of infiltrated lymphocytes (p = 0.025), as well, more T CD4 lymphocytes in the epithelial tissue (p = 0.006) in OLP samples compared to NSIL. In addition, the OLP samples displayed more apoptotic cells compared to NSIL (p = 0.047). Regarding the cytokine analysis, IFN-γ and IL-33 were more expressed in OLP lesions than in NSIL samples (p < 0.001; p = 0.026). Furthermore, our results demonstrated higher levels of IFN-γ protein expression in the saliva of OLP group compared to controls (p = 0.0156). We also observed noted differences in the oral microbiota composition between OLP and NSIL saliva samples. In conclusion, OLP lesions presented larger numbers of apoptotic and inflammatory cells, higher levels of IFN-γ and IL-33 compared to NSIL, and these lesions also differ regarding oral microbiota composition. These results are consistent with the Th-1-mediated chronic inflammation nature of oral lichen planus investigated lesions and displayed unique features that could be used as a diagnostic tool.
DPP8 is a novel therapeutic target for multiple myeloma
Authors: Sato Tsutomu , Tatekoshi Ayumi , Takada Kohichi , Iyama Satoshi , Kamihara Yusuke , Jawaid Paras , Rehman Mati Ur , Noguchi Kyo , Kondo Takashi , Kajikawa Sayaka , Arita Kotaro , Wada Akinori , Murakami Jun , Arai Miho , Yasuda Ichiro , Dang Nam H. , Hatano Ryo , Iwao Noriaki , Ohnuma Kei , Morimoto Chikao 
Published: December 2019

AbstractDipeptidyl peptidases (DPPs) are proteolytic enzymes that are ideal therapeutic targets in human diseases. Indeed, DPP4 inhibitors are widely used in clinical practice as anti-diabetic agents. In this paper, we show that DPP4 inhibitors also induced cell death in multiple human myeloma cells. Among five DPP4 inhibitors, only two of them, vildagliptin and saxagliptin, exhibited apparent cytotoxic effects on myeloma cell lines, without any difference in suppression of DPP4 activity. As these two DPP4 inhibitors are known to have off-target effects against DPP8/9, we employed the specific DPP8/9 inhibitor 1G244. 1G244 demonstrated anti-myeloma effects on several cell lines and CD138+ cells from patients as well as in murine xenograft model. Through siRNA silencing approach, we further confirmed that DPP8 but not DPP9 is a key molecule in inducing cell death induced by DPP8/9 inhibition. In fact, the expression of DPP8 in CD38+ cells from myeloma patients was higher than that of healthy volunteers. DPP8/9 inhibition induced apoptosis, as evidenced by activated form of PARP, caspases-3 and was suppressed by the pan-caspase inhibitor Z-VAD-FMK. Taken together, these results indicate that DPP8 is a novel therapeutic target for myeloma treatment.
Protective effects of Salidroside on cardiac function in mice with myocardial infarction
Authors: Chen Pengsheng , Liu Jia , Ruan Hongyun , Zhang Miaomiao , Wu Peng , Yimei Du , Han Bing 
Published: December 2019

AbstractSalidroside (SAL) is the major ingredient of Rhodiola rosea, and has been traditionally used in Chinese medicine for decades. Numerous studies have demonstrated the protective effects of SAL for myocardial ischemia. However, it is yet to be deciphered whether SAL has cardioprotective effects after myocardial infarction (MI) in vivo. In the present study, we established a mouse MI model via coronary artery ligation. The aim was to investigate whether SAL treatment could reduce mortality, improve cardiac function and attenuate myocardial remodeling in MI mice. Post-surgery, mice were randomly administered SAL or normal saline. After 21 days, SAL was found to significantly reduce mortality, improve cardiac function, reduce fibrosis and infarct size compared to normal saline. In addition, oral administration of SAL could attenuate myocardial inflammation and apoptosis and promote angiogenesis. SAL down-regulated the expression levels of TNF-α, TGF-β1, IL-1β, Bax and up-regulate the expression of Bcl-2, VEGF, Akt and eNOS. These results indicated that SAL could alleviate the pathological processes of myocardial remodeling in MI mice, and may be a potentially effective therapeutic approach for the management of clinical ischemic cardiovascular diseases.
Effects of temperature and superparasitism on quality and characteristics of thelytokous Wolbachia-infected Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae) during mass rearing
Authors: Zhou Jin-Cheng , Li Yuan-Yuan , Liu Quan-Quan , Ning Su-Fang , Che Wu-Nan , Cong Bin , Dong Hui 
Published: December 2019

AbstractThelytokousWolbachia-infectedTrichogrammaspp. are widely used egg parasitoids against lepidopteran pests in biological control programs.Wolbachiamay manipulate host wasps for superparasitism and is sensitive to temperature. To explore effects of temperature and superparasitism, we compared fitness parameters andWolbachia-mediated phenotype of thelytokousWolbachia-infectedTrichogramma dendrolimibetween those emerging from superparasitised or single-parasitised hosts at 17, 21, 25, or 29 °C. Infected mothers ofT. dendrolimishowed reduced superparasitism and parasitism increased with temperature.Wolbachiatitre decreased with temperature when females emerged from singly-parasitised hosts, but there was no correlation in superparasitised hosts. Females showed higherWolbachiatitres at 21, 25, or 29 °C when developing from superparasitised hosts. The daily male ratio of offspring increased with temperature, and the day-age threshold for 5%, 50%, or 95% daily male ratio decreased with temperature in both parasitism forms. Females that emerged from superparasitised hosts had a shorter life span and reduced fecundity. These results indicate thatWolbachiamay affect host behaviour by increasing superparasitism to enhance its spread, but this has negative effects on thelytokousWolbachia-infectedT. dendrolimi.
Fabrication of porous NiMn2O4 nanosheet arrays on nickel foam as an advanced sensor material for non-enzymatic glucose detection
Authors: Zhang Jie , Sun Yudong , Li Xianchun , Xu Jiasheng 
Published: December 2019

AbstractIn this work, porous NiMn2O4 nanosheet arrays on nickel foam (NiMn2O4 NSs@NF) was successfully fabricated by a simple hydrothermal step followed by a heat treatment. Porous NiMn2O4 NSs@NF is directly used as a sensor electrode for electrochemical detecting glucose. The NiMn2O4 nanosheet arrays are uniformly grown and packed on nickel foam to forming sensor electrode. The porous NiMn2O4 NSs@NF electrode not only provides the abundant accessible active sites and the effective ion-transport pathways, but also offers the efficient electron transport pathways for the electrochemical catalytic reaction by the high conductive nickel foam. This synergy effect endows porous NiMn2O4 NSs@NF with excellent electrochemical behaviors for glucose detection. The electrochemical measurements are used to investigate the performances of glucose detection. Porous NiMn2O4 NSs@NF for detecting glucose exhibits the high sensitivity of 12.2 mA mM−1 cm−2 at the window concentrations of 0.99–67.30 μM (correlation coefficient = 0.9982) and 12.3 mA mM−1 cm−2 at the window concentrations of 0.115–0.661 mM (correlation coefficient = 0.9908). In addition, porous NiMn2O4 NSs@NF also exhibits a fast response of 2 s and a low LOD of 0.24 µM. The combination of porous NiMn2O4 nanosheet arrays and nickel foam is a meaningful strategy to fabricate high performance non-enzymatic glucose sensor. These excellent properties reveal its potential application in the clinical detection of glucose.
Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors
Authors: Golonka David , Fischbach Patrick , Jena Siddhartha G. , Kleeberg Julius R. W. , Essen Lars-Oliver , Toettcher Jared E. , Zurbriggen Matias D. , Möglich Andreas 
Published: December 2019

AbstractPhytochrome photoreceptors mediate adaptive responses of plants to red and far-red light. These responses generally entail light-regulated association between phytochromes and other proteins, among them the phytochrome-interacting factors (PIF). The interaction with Arabidopsis thaliana phytochrome B (AtPhyB) localizes to the bipartite APB motif of the A. thaliana PIFs (AtPIF). To address a dearth of quantitative interaction data, we construct and analyze numerous AtPIF3/6 variants. Red-light-activated binding is predominantly mediated by the APB N-terminus, whereas the C-terminus modulates binding and underlies the differential affinity of AtPIF3 and AtPIF6. We identify AtPIF variants of reduced size, monomeric or homodimeric state, and with AtPhyB affinities between 10 and 700 nM. Optogenetically deployed in mammalian cells, the AtPIF variants drive light-regulated gene expression and membrane recruitment, in certain cases reducing basal activity and enhancing regulatory response. Moreover, our results provide hitherto unavailable quantitative insight into the AtPhyB:AtPIF interaction underpinning vital light-dependent responses in plants.