bluuebunny/crossref_metadata_2025_split huggingface dataset:
An enrichment method based on synergistic and reversible covalent interactions for large-scale analysis of glycoproteins
Authors: Xiao Haopeng , Chen Weixuan , Smeekens Johanna M. , Wu Ronghu 
Published: April 2018

AbstractProtein glycosylation is ubiquitous in biological systems and essential for cell survival. However, the heterogeneity of glycans and the low abundance of many glycoproteins complicate their global analysis. Chemical methods based on reversible covalent interactions between boronic acid and glycans have great potential to enrich glycopeptides, but the binding affinity is typically not strong enough to capture low-abundance species. Here, we develop a strategy using dendrimer-conjugated benzoboroxole to enhance the glycopeptide enrichment. We test the performance of several boronic acid derivatives, showing that benzoboroxole markedly increases glycopeptide coverage from human cell lysates. The enrichment is further improved by conjugating benzoboroxole to a dendrimer, which enables synergistic benzoboroxole–glycan interactions. This robust and simple method is highly effective for sensitive glycoproteomics analysis, especially capturing low-abundance glycopeptides. Importantly, the enriched glycopeptides remain intact, making the current method compatible with mass-spectrometry-based approaches to identify glycosylation sites and glycan structures.
The genetic architecture of floral traits in the woody plant Prunus mume
Authors: Zhang Qixiang , Zhang He , Sun Lidan , Fan Guangyi , Ye Meixia , Jiang Libo , Liu Xin , Ma Kaifeng , Shi Chengcheng , Bao Fei , Guan Rui , Han Yu , Fu Yuanyuan , Pan Huitang , Chen Zhaozhe , Li Liangwei , Wang Jia , Lv Meiqi , Zheng Tangchun , Yuan Cunquan , Zhou Yuzhen , Lee Simon Ming-Yuen , Yan Xiaolan , Xu Xun , Wu Rongling , Chen Wenbin , Cheng Tangren 
Published: April 2018

AbstractMei (Prunus mume) is an ornamental woody plant that has been domesticated in East Asia for thousands of years. High diversity in floral traits, along with its recent genome sequence, makes mei an ideal model system for studying the evolution of woody plants. Here, we investigate the genetic architecture of floral traits in mei and its domestication history by sampling and resequencing a total of 351 samples including 348 mei accessions and three other Prunus species at an average sequencing depth of 19.3×. Highly-admixed population structure and introgression from Prunus species are identified in mei accessions. Through a genome-wide association study (GWAS), we identify significant quantitative traits locus (QTLs) and genomic regions where several genes, such as MYB108, are positively associated with petal color, stigma color, calyx color, and bud color. Results from this study shed light on the genetic basis of domestication in flowering plants, particularly woody plants.
Manipulation of insulin signaling phenocopies evolution of a host-associated polyphenism
Authors: Fawcett Meghan M. , Parks Mary C. , Tibbetts Alice E. , Swart Jane S. , Richards Elizabeth M. , Vanegas Juan Camilo , Cenzer Meredith , Crowley Laura , Simmons William R. , Hou Wenzhen Stacey , Angelini David R. 
Published: April 2018

AbstractPlasticity, the capacity of an organism to respond to its environment, is thought to evolve through changes in development altering the integration of environmental cues. In polyphenism, a discontinuous plastic response produces two or more phenotypic morphs. Here we describe evolutionary change in wing polyphenism and its underlying developmental regulation in natural populations of the red-shouldered soapberry bug, Jadera haematoloma (Insecta: Hemiptera: Rhopalidae) that have adapted to a novel host plant. We find differences in the fecundity of morphs in both sexes and in adult expression of insulin signaling components in the gonads. Further, the plastic response of ancestral-state bugs can be shifted to resemble the reaction norm of derived bugs by the introduction of exogenous insulin or RNA interference targeting the insulin signaling component encoded by FoxO. These results suggest that insulin signaling may be one pathway involved in the evolution of this polyphenism, allowing adaptation to a novel nutritional environment.
Non-contact identification and differentiation of illicit drugs using fluorescent films
Authors: Liu Ke , Shang Congdi , Wang Zhaolong , Qi Yanyu , Miao Rong , Liu Kaiqiang , Liu Taihong , Fang Yu 
Published: April 2018

AbstractSensitive and rapid identification of illicit drugs in a non-contact mode remains a challenge for years. Here we report three film-based fluorescent sensors showing unprecedented sensitivity, selectivity, and response speed to the existence of six widely abused illicit drugs, including methamphetamine (MAPA), ecstasy, magu, caffeine, phenobarbital (PB), and ketamine in vapor phase. Importantly, for these drugs, the sensing can be successfully performed after 5.0 × 105, 4.0 × 105, 2.0 × 105, 1.0 × 105, 4.0 × 104, and 2.0 × 102 times dilution of their saturated vapor with air at room temperature, respectively. Also, presence of odorous substances (toiletries, fruits, dirty clothes, etc.), water, and amido-bond-containing organic compounds (typical organic amines, legal drugs, and different amino acids) shows little effect upon the sensing. More importantly, discrimination and identification of them can be realized by using the sensors in an array way. Based upon the discoveries, a conceptual, two-sensor based detector is developed, and non-contact detection of the drugs is realized.
The signalling game between plants and pollinators
Authors: Sun Shan , Leshowitz Michael I. , Rychtář Jan 
Published: April 2018

AbstractPlants can send floral signals to advertise their reward for pollinators. Based on the presence or absents of such signals, pollinators can determine whether to visit plants. Plants can send dishonest signals but foraging behaviours of pollinators can limit the cheating strategies of plants. We model the plant-pollinator interactions by the two-type Spence signalling game and investigate the conditions under which honest signalling can be established. In our model, plants either send costly signal or they do not. The cost of signal is dependent on the quality of plant. Pollinators can learn from the interactions with plants and can update their willingness to visit plants’ flowers to maximize their foraging efficiency. We find three general conditions that are required for the evolutionary stability of honest signaling. Those conditions are satisfied if there is (a) a high frequency of high-yield signalling plants in the population, (b) the balance between cost and benefit of signalling, and (c) high cost of dishonest signalling. Our model also predicts that other factors contributing to the establishment of honest signaling are the low abundance of pollinators, and the positive density-dependent and positive frequency-dependent relationship between plants and pollinators.
Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction
Authors: Zhong Liang , Mu Haiyuan , Wen Bingqiang , Zhang Wei , Wei Qingqing , Gao Ge , Han Jianyong , Cao Suying 
Published: April 2018

AbstractLong non-coding RNAs (lncRNA) play a key role in the orchestration of transcriptional regulation during development and many other cellular processes. The importance of the regulatory co-expression network was highlighted in the identification of the mechanism of these processes in humans and mice. However, elucidation of the properties of porcine lncRNAs involved in the regulatory network during pre-implantation embryonic development and fibroblast reprogramming to induced pluripotent stem cell (iPSC) has been limited to date. Using a weighted gene co-expression network analysis, we constructed the regulatory network and determined that the novel lncRNAs were functionally involved in key events of embryonic development during the pre-implantation period; moreover, reprogramming could be delineated by a small number of potentially functional modules of co-expressed genes. These findings indicate that lncRNAs may be involved in the transcriptional regulation of zygotic genome activation, first lineage segregation and somatic reprogramming to pluripotency. Furthermore, we performed a conservation and synteny analysis with the significant lncRNAs involved in these vital events and validated the results via experimental assays. In summary, the current findings provide a valuable resource to dissect the protein coding gene and lncRNA regulatory networks that underlie the progressive development of embryos and somatic reprogramming.
Prevalent metabolic derangement and severe thrombocytopenia in ABO-incompatible liver recipients with pre-transplant plasma exchange
Authors: Kwon Hye-Mee , Jun In-Gu , Lee JungBok , Moon Young-Jin , Jung Kyeo-Woon , Jeong Hye-Won , Park Yong-Seok , Song Jun-Gol , Hwang Gyu-Sam 
Published: April 2018

AbstractDesensitisation with therapeutic plasma exchange (TPE) is essential for ABO-incompatible (ABO-I) liver transplants (LTs). However, excessive citrate load and coagulation disturbances after TPE have been poorly studied, in particular in cirrhotic patients with hypocapnic alkalosis, metabolic compensation and electrolyte imbalances. We retrospectively evaluated 1123 consecutive LT recipients (923 ABO-compatible [ABO-C], 200 ABO-I) from November 2008 to May 2015. TPE was generally performed a day before LT and blood sampling was performed before anaesthesia induction. We performed propensity score matching (PSM) and inverse probability treatment weighting (IPTW) analyses. In 199 PSM pairs, metabolic alkalosis was prevalent in ABO-I LT recipients (expectedly due to citrate conversion) with higher pH ≥ 7.50 (IPTW-adjusted odds ratio [aOR] = 2.23) than in ABO-C LT recipients. With increasing cirrhosis severity, the arterial pH and bicarbonate levels showed dose-dependent relationships, whereas mild hypoxaemia was more prevalent in ABO-I LT recipients. ABO-I LT recipients exhibited worsened hypokalaemia ≤3.0 mmol/l (17.6%, aOR = 1.44), hypomagnesaemia ≤1.7 mg/dl (27.6%, aOR = 3.43) and thrombocytopenia <30,000/µl (19.1%, aOR = 2.26) confirmed by lower maximal clot firmness (P = 0.001) in rotational thromboelastometry (EXTEM), which necessitated platelet transfusions. Preoperative identification of these change may prevent worsening of severe electrolyte disturbances and thrombocytopenia for optimal LT anaesthesia.
MicroRNA 199a-5p induces apoptosis by targeting JunB
Authors: Yan Mengjie , Yang Sibao , Meng Fanbo , Zhao Zhihui , Tian Zhisen , Yang Ping 
Published: April 2018

AbstractMicroRNAs participate in a variety of physiological and pathophysiological processes in various organs including the heart. Our previous work revealed that the level of miR-199a-5p was significantly higher in failing hearts than in control hearts. However, whether it is associated with the progression of heart failure (HF) and mediates cardiomyocyte apoptosis remained unclear. In the present study, we used various biochemical and molecular biological approaches to investigate the changes in miR-199a-5p levels in failing hearts in a rat model induced by acute myocardial infarction. We found that miR-199a-5p levels in the heart increased with the progression of HF, and overexpression of miR-199a-5p significantly increased apoptosis in untreated H9C2 cells and potentiated angiotensin II-induced apoptosis. Thus, our results indicate that miR-199a-5p is involved in the progression of HF and mediates cardiomyocyte apoptosis. We also confirmed that JunB, a member of the activator protein-1 transcription factor family, is one of direct targets of miR-199a-5p via a dual-luciferase reporter assay and mutagenesis on the 3′ untranslated region of the JunB gene. Consistent with the above findings, overexpression of JunB in H9c2 cells suppressed cell apoptosis. Based on our findings, miR-199a-5p induces apoptosis by targeting JunB.
Application of droplet digital PCR in the analysis of genome integration and organization of the transgene in BAC transgenic mice
Authors: Nakagaki Ayumi , Urakawa Asuka , Hirano Shiori , Anami Takeru , Kishino Tatsuya 
Published: April 2018

AbstractTransgenic (Tg) mice containing bacterial artificial chromosome (BAC) DNA are widely used for gene expression analysis and gene therapy models because BAC transgenes provide gene expression at physiological levels with the same developmental timing as endogenous genes. To ensure correct interpretation of transgene functions, investigation of the genomic organisation and integration of the BAC transgene is required. Here, we describe a reliable method based on droplet digital PCR (ddPCR) and inverse PCR to estimate copy number, genomic organisation and insertion sites of BAC transgenes in the mouse genome. We generated BAC Tg mice containing fragments of BAC clone RP23-59P20. ddPCR and iPCR analysis showed that the transgene consisted of five fragments of the BAC clone containing the Mkrn3 gene region, and that the transgene was inserted into Bckdhb, homozygous deletion of which causes the maple syrup urine disease phenotype. The ddPCR method described here should prove useful for analysis of genomic organisation and integration of BAC transgenes.
Structural defects in a nanomesh of bulk MoS2 using an anodic aluminum oxide template for photoluminescence efficiency enhancement
Authors: Kim TaeWan , Kim DongHwan , Choi Chan Ho , Joung DaeHwa , Park JongHoo , Shin Jae Cheol , Kang Sang-Woo 
Published: April 2018

AbstractTwo-dimensional (2D) materials beyond graphene have attracted considerable interest because of the zero bandgap drawbacks of graphene. Transition metal dichalcogenides (TMDs), such as MoS2 and WSe2, are the potential candidates for next 2D materials because atomically thin layers of TMDs exhibit unique and versatile electrical and optical properties. Although bulk TMDs materials have an indirect bandgap, an indirect-to-direct bandgap transition is observed in monolayers of TMDs (MoS2, WSe2, and MoSe2). Optical properties of TMD films can be improved by the introduction of structural defects. For example, large-area spatial tuning of the optical transition of bulk MoS2 films is achieved by using an anodic aluminum oxide (AAO) template to induce structural defects such as edge- and terrace-terminated defects in a nanomesh structure. Strong photoluminescence emission peaks with a band gap of 1.81 eV are observed, possibly because of radiative transition at the defect sites. This work shows that the AAO template lithography method has potential for the production of homogenous large-scale nanomesh structures for practical semiconductor processing applications in future MoS2-based electronic and optical devices.
Skillful prediction of hot temperature extremes over the source region of ancient Silk Road
Authors: Zhang Jingyong , Yang Zhanmei , Wu Lingyun 
Published: April 2018

AbstractThe source region of ancient Silk Road (SRASR) in China, a region of around 150 million people, faces a rapidly increased risk of extreme heat in summer. In this study, we develop statistical models to predict summer hot temperature extremes over the SRASR based on a timescale decomposition approach. Results show that after removing the linear trends, the inter-annual components of summer hot days and heatwaves over the SRASR are significantly related with those of spring soil temperature over Central Asia and sea surface temperature over Northwest Atlantic while their inter-decadal components are closely linked to those of spring East Pacific/North Pacific pattern and Atlantic Multidecadal Oscillation for 1979–2016. The physical processes involved are also discussed. Leave-one-out cross-validation for detrended 1979–2016 time series indicates that the statistical models based on identified spring predictors can predict 47% and 57% of the total variances of summer hot days and heatwaves averaged over the SRASR, respectively. When the linear trends are put back, the prediction skills increase substantially to 64% and 70%. Hindcast experiments for 2012–2016 show high skills in predicting spatial patterns of hot temperature extremes over the SRASR. The statistical models proposed herein can be easily applied to operational seasonal forecasting.
The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA
Authors: Mäkelä Miia R. , Aguilar-Pontes María Victoria , van Rossen-Uffink Diana , Peng Mao , de Vries Ronald P. 
Published: April 2018

AbstractIn nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.
Topical pharyngeal anesthesia provides no additional benefit to propofol sedation for esophagogastroduodenoscopy: a randomized controlled double-blinded clinical trial
Authors: Sun Xiaotian , Xu Yang , Zhang Xueting , Li Aitong , Zhang Hanqing , Yang Teng , Liu Yan 
Published: April 2018

AbstractPropofol sedation has been applied during esophagogastroduodenoscopy procedures, but whether topical pharyngeal anesthesia should be administered at the same time has rarely been reported. Our study examined the role of topical pharyngeal anesthesia in sedated endoscopies in a randomized controlled double-blinded clinical trial. A total of 626 patients who underwent sedated esophagogastroduodenoscopy were randomized into the experimental group (n = 313) or the control group (n = 313). The discomfort score, immediately and one day after the procedure, was not statistically significant [7.2 (5–9) vs. 7.5 (6–9), P = 0.210; 2.3 (0–3) vs. 2.6 (0–4), P = 0.095, respectively]. Two patients in the experimental group and three patients in the control group needed oral medication for pharyngeal discomfort (P = 0.354). The satisfaction score was 9.2 (8–10) in the experimental group and 8.9 (7–10) in the control group (P = 0.778). Lidocaine topical pharyngeal anesthesia in propofol-sedated esophagogastroduodenoscopy did not further reduce the pharyngeal discomfort or improve the satisfaction. This clinical trial was registered at ClinicalTrials.gov (ClinicalTrials.gov ID: NCT03070379).
Anisotropic diamond etching through thermochemical reaction between Ni and diamond in high-temperature water vapour
Authors: Nagai Masatsugu , Nakanishi Kazuhiro , Takahashi Hiraku , Kato Hiromitsu , Makino Toshiharu , Yamasaki Satoshi , Matsumoto Tsubasa , Inokuma Takao , Tokuda Norio 
Published: April 2018

AbstractDiamond possesses excellent physical and electronic properties, and thus various applications that use diamond are under development. Additionally, the control of diamond geometry by etching technique is essential for such applications. However, conventional wet processes used for etching other materials are ineffective for diamond. Moreover, plasma processes currently employed for diamond etching are not selective, and plasma-induced damage to diamond deteriorates the device-performances. Here, we report a non-plasma etching process for single crystal diamond using thermochemical reaction between Ni and diamond in high-temperature water vapour. Diamond under Ni films was selectively etched, with no etching at other locations. A diamond-etching rate of approximately 8.7 μm/min (1000 °C) was successfully achieved. To the best of our knowledge, this rate is considerably greater than those reported so far for other diamond-etching processes, including plasma processes. The anisotropy observed for this diamond etching was considerably similar to that observed for Si etching using KOH.
Personality traits affecting judgement bias task performance in dogs (Canis familiaris)
Authors: Barnard Shanis , Wells Deborah L. , Milligan Adam D. S. , Arnott Gareth , Hepper Peter G. 
Published: April 2018

AbstractCertain personality traits (e.g. anxiousness, fearfulness), are known to affect the cognitive processing of environmental stimuli, such as the judgement of ambiguous stimuli (judgement bias). Our aim was to assess if personality traits are predictive of a more or less ‘pessimistic’ or ‘optimistic’ judgement bias in the domestic dog. We assessed dog personality (N = 31) using two validated protocols: the Dog Mentality Assessment (standardised battery test) and the CBARQ (owner-based survey). We used a common task based on the animals’ latency to approach a bowl placed in one of three ambiguous positions (Near Positive, Middle, Near Negative) between a baited (Positive) and a non-baited food bowl (Negative) to assess judgement bias. Linear Mixed Model analyses revealed that dogs scoring higher on sociability, excitability and non-social-fear had shorter response latencies to bowls in an ambiguous location, indicating a more ‘optimistic’ bias. In contrast, dogs scoring higher on separation-related-behaviour and dog-directed-fear/aggression traits were more likely to judge an ambiguous stimulus as leading to a negative outcome, indicating a more ‘pessimistic’ bias. Results, partially consistent with previous findings in humans, indicate that personality plays a role in the cognitive processing of environmental stimuli in the domestic dog.
Intracellular glycolysis in brown adipose tissue is essential for optogenetically induced nonshivering thermogenesis in mice
Authors: Jeong Jae Hoon , Chang Ji Suk , Jo Young-Hwan 
Published: April 2018

AbstractRelease of fatty acids from lipid droplets upon activation of the sympathetic nervous system (SNS) is a key step in nonshivering thermogenesis in brown adipose tissue (BAT). However, intracellular lipolysis appears not to be critical for cold-induced thermogenesis. As activation of the SNS increases glucose uptake, we studied whether intracellular glycolysis plays a role in BAT thermogenesis. To stimulate BAT-innervating sympathetic nerves in vivo, we expressed channelrhodopsin-2 (ChR2) in catecholaminergic fibers by crossbreeding tyrosine hydroxylase-Cre mice with floxed-stop ChR2 mice. Acute optogenetic stimulation of sympathetic efferent fibers of BAT increased body temperature and lowered blood glucose levels that were completely abolished by the β-adrenergic receptor antagonist. Knockdown of the Ucp1 gene in BAT blocked the effects of optogenetic stimulation on body temperature and glucose uptake. Inhibition of glucose uptake in BAT and glycolysis abolished optogenetically induced thermogenesis. Stimulation of sympathetic nerves upregulated expression of the lactate dehydrogenase-A and -B genes in BAT. Optogenetic stimulation failed to induce thermogenesis following treatment with the LDH inhibitor. Pharmacological blockade and genetic deletion of the monocarboxylate transporter 1 completely abolished the effects of sympathetic activation. Our results suggest that intracellular glycolysis and lactate shuttle play an important role in regulating acute thermogenesis in BAT.