bluuebunny/crossref_metadata_2025_split huggingface dataset:
pGlyco 2.0 enables precision N-glycoproteomics with comprehensive quality control and one-step mass spectrometry for intact glycopeptide identification
Authors: Liu Ming-Qi , Zeng Wen-Feng , Fang Pan , Cao Wei-Qian , Liu Chao , Yan Guo-Quan , Zhang Yang , Peng Chao , Wu Jian-Qiang , Zhang Xiao-Jin , Tu Hui-Jun , Chi Hao , Sun Rui-Xiang , Cao Yong , Dong Meng-Qiu , Jiang Bi-Yun , Huang Jiang-Ming , Shen Hua-Li , Wong Catherine C. L. , He Si-Min , Yang Peng-Yuan 
Published: August 2017

AbstractThe precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with 15N/13C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues.
Significance of penile hypersensitivity in premature ejaculation
Authors: Guo Liqiang , Liu Yuqiang , Wang Xuesheng , Yuan Mingzhen , Yu Yang , Zhang Xiulin , Zhao Shengtian 
Published: August 2017

AbstractTo assess the correlation between penile hypersensitivity and premature ejaculation (PE), a total of 420 consecutive subjects attending our andrologic clinic for suspected PE were enrolled. The entire cohort was asked to complete the self-report intravaginal ejaculation latency time (IELT) by stopwatch. According to the IELT, the subjects were classified into 3 groups. Vibratory thresholds were recorded at the glans penis and penile shaft using a biothesiometer. We found that vibratory thresholds in the glans penis and penile shaft were significantly lower in both mild and severe PE group than in the control group (3.81 ± 0.57 and 3.54 ± 0.43 vs 4.73 ± 0.77 for glans penis p = 0.000; 3.64 ± 0.52 and 3.37 ± 0.50 vs 4.62 ± 0.69 for penile shaft p = 0.002). The vibratory threshold decreased as the disease aggravated. In the mild and severe PE groups, a significant positive correlation was detected between the mean values of IELT and the vibratory thresholds. Furthermore, in the receiver operating characteristics curve analysis, the area under the curve of the glans penis and penile shaft vibratory thresholds predicting severe PE were 0.852 and 0.893 respectively. Our study established a dose-dependent association between penile vibratory threshold and PE. Therefore, the vibratory threshold can serve as a potential marker for predicting the severity of PE.
Comparison of musculoskeletal networks of the primate forelimb
Authors: Molnar Julia , Esteve-Altava Borja , Rolian Campbell , Diogo Rui 
Published: August 2017

AbstractAnatomical network analysis is a framework for quantitatively characterizing the topological organization of anatomical structures, thus providing a way to compare structural integration and modularity among species. Here we apply this approach to study the macroevolution of the forelimb in primates, a structure whose proportions and functions vary widely within this group. We analyzed musculoskeletal network models in 22 genera, including members of all major extant primate groups and three outgroup taxa, after an extensive literature survey and dissections. The modules of the proximal limb are largely similar among taxa, but those of the distal limb show substantial variation. Some network parameters are similar within phylogenetic groups (e.g., non-primates, strepsirrhines, New World monkeys, and hominoids). Reorganization of the modules in the hominoid hand compared to other primates may relate to functional changes such as coordination of individual digit movements, increased pronation/supination, and knuckle-walking. Surprisingly, humans are one of the few taxa we studied in which the thumb musculoskeletal structures do not form an independent anatomical module. This difference may be caused by the loss in humans of some intrinsic muscles associated with the digits or the acquisition of additional muscles that integrate the thumb more closely with surrounding structures.
Correcting for photodestruction in super-resolution optical fluctuation imaging
Authors: Peeters Yves , Vandenberg Wim , Duwé Sam , Bouwens Arno , Lukeš Tomáš , Ruckebusch Cyril , Lasser Theo , Dedecker Peter 
Published: August 2017

AbstractSuper-resolution optical fluctuation imaging overcomes the diffraction limit by analyzing fluctuations in the fluorophore emission. A key assumption of the imaging is that the fluorophores are independent, though this is invalidated in the presence of photodestruction. In this work, we evaluate the effect of photodestruction on SOFI imaging using theoretical considerations and computer simulations. We find that photodestruction gives rise to an additional signal that does not present an easily interpretable view of the sample structure. This additional signal is strong and the resulting images typically exhibit less noise. Accordingly, these images may be mis-interpreted as being more visually pleasing or more informative. To address this uncertainty, we develop a procedure that can robustly estimate to what extent any particular experiment is affected by photodestruction. We also develop a detailed assessment methodology and use it to evaluate the performance of several correction algorithms. We identify two approaches that can correct for the presence of even strong photodestruction, one of which can be implemented directly in the SOFI calculation software.
Linc-ing Circulating Long Non-coding RNAs to the Diagnosis and Malignant Prediction of Intraductal Papillary Mucinous Neoplasms of the Pancreas
Authors: Permuth Jennifer B. , Chen Dung-Tsa , Yoder Sean J. , Li Jiannong , Smith Andrew T. , Choi Jung W. , Kim Jongphil , Balagurunathan Yoganand , Jiang Kun , Coppola Domenico , Centeno Barbara A. , Klapman Jason , Hodul Pam , Karreth Florian A. , Trevino Jose G. , Merchant Nipun , Magliocco Anthony , Malafa Mokenge P. , Gillies Robert 
Published: August 2017

AbstractPancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective biomarkers for early detection. We hypothesized that circulating long non-coding RNAs (lncRNAs) may act as diagnostic markers of incidentally-detected cystic PDAC precursors known as intraductal papillary mucinous neoplasms (IPMNs) and predictors of their pathology/histological classification. Using NanoString nCounter® technology, we measured the abundance of 28 candidate lncRNAs in pre-operative plasma from a cohort of pathologically-confirmed IPMN cases of various grades of severity and non-diseased controls. Results showed that two lncRNAs (GAS5andSRA) aided in differentiating IPMNs from controls. An 8-lncRNA signature (includingADARB2-AS1,ANRIL,GLIS3-AS1,LINC00472,MEG3,PANDA,PVT1, andUCA1) had greater accuracy than standard clinical and radiologic features in distinguishing ‘aggressive/malignant’ IPMNs that warrant surgical removal from ‘indolent/benign’ IPMNs that can be observed. When the 8-lncRNA signature was combined with plasma miRNA data and quantitative ‘radiomic’ imaging features, the accuracy of predicting IPMN pathological classification improved. Our findings provide novel information on the ability to detect lncRNAs in plasma from patients with IPMNs and suggest that an lncRNA-based blood test may have utility as a diagnostic adjunct for identifying IPMNs and their pathology, especially when incorporated with biomarkers such as miRNAs, quantitative imaging features, and clinical data.
Prenatal noise stress impairs HPA axis and cognitive performance in mice
Authors: Jafari Zahra , Mehla Jogender , Kolb Bryan E. , Mohajerani Majid H. 
Published: August 2017

AbstractNoise stress is a common environmental pollutant whose adverse effect on offspring performance has been less studied. This study was novel in terms of using “noise” as a prenatal stress compared with physical stress to explore the effect of stress during gestation on HPA axis activation, cognitive performance, and motor coordination, as well as in investigating the effect of behavioral assessments on the corticosterone (CORT) levels. Three groups of C57BL/6 mice with a gestational history of either noise stress (NS), physical stress (PS), or no stress were examined in several behavioral tests. Plasma CORT level was significantly higher before starting the behavioral tests in NS group than the two other groups. It was significantly increased after the behavioral tests in both prenatal stressed groups relative to the controls. Stress caused anxiety-like behavior and reduced learning and memory performance in both stressed groups compared to the controls, as well as decreased motor coordination in the NS group relative to the other groups. The findings suggested that: prenatal NS severely changes the HPA axis; both prenatal stressors, and particularly NS, negatively impair the offspring’s cognitive and motor performance; and, they also cause a strong susceptibility to interpret environmental experiences as stressful conditions.
Cell based assay identifies TLR2 and TLR4 stimulating impurities in Interferon beta
Authors: Haile Lydia Asrat , Polumuri Swamy Kumar , Rao Roshni , Kelley-Baker Logan , Kryndushkin Dimitri , Rajaiah Rajesh , Israely Tomer , Rao V. Ashutosh , Verthelyi Daniela 
Published: August 2017

AbstractImmunogenicity can have devastating consequences on the safety and efficacy of therapeutic proteins. Therefore, evaluating and mitigating the risk of product immunogenicity is critical for the development these products. This study, showed that Betaseron and Extavia, which are reported to be more immunogenic among IFNβ products in clinical usage, contain residual innate immune response modulating impurities (IIRMIs) capable of activating NF-κB and induced expression of inflammatory mediators. These IIRMIs were undetectable in Rebif or Avonex. The stimulatory effect was attributed solely to IIRMIs because it was evident in murine cells lacking the interferon receptor (IFNAR). The IIRMIs in Betaseron and Extavia triggered NF-κB activation in HEK-293 cells bearing TLR2 and TLR4 in MyD88 dependent manner. Importantly, the IIRMIs in Betaseron induced up-regulation of IL-6, IL-1β, and ccl5 in the skin of IFNAR knock out mice following subcutaneous administration. This indicates that trace level IIRMIs in Betaseron could contribute to the higher immunogenicity rates seen in clinics. Together these data suggest that cell based assays can reveal subtle but clinically relevant differences in IIRMIs following manufacturing changes or between products with the same active ingredients but different manufacturing processes. Appreciating these differences may inform immunogenicity risk assessments.
Intermittence and connectivity of interactions in pigeon flock flights
Authors: Chen Duxin , Liu Xiaolu , Xu Bowen , Zhang Hai-Tao 
Published: August 2017

AbstractCollective circular motion is a common yet spectacular behavior of pigeon flocks. Efficient and robust inter-individual communication is required for flock coordination during this widely-spreaded movement pattern. When a flock hovers near the home loft, the rotational direction undergoes regular spontaneous variations. Based on intensive analyses of high spatial-temporal resolution GPS data, we quantified the intensity of velocity alignment among different individuals in terms of their velocity fluctuations. It is found that pigeon flocks employ an intermittent interaction (alignment) mechanism, where intra-group information transmission is not required at every instant. However, the union of the topologies of several consecutive interaction networks always keeps connected. This biological observation strongly suggests the presence of a jointly connected topology in pigeon flocks, which helps substantially reduce the communication and/or information processing requirements while retaining the agility and stability of the group. Finally, we conducted extensive investigation on the interaction mechanism as well as the spontaneous changes in rotational direction of pigeon flocks. These results shed some light onto the coordination mechanism exploration of bird flocks’ collective motions.
Hydrogen peroxide dynamics in subcellular compartments of malaria parasites using genetically encoded redox probes
Authors: Rahbari Mahsa , Rahlfs Stefan , Przyborski Jude M. , Schuh Anna Katharina , Hunt Nicholas H. , Fidock David A. , Grau Georges E. , Becker Katja 
Published: August 2017

AbstractRedox balance is essential for the survival, growth and multiplication of malaria parasites and oxidative stress is involved in the mechanism of action of many antimalarial drugs. Hydrogen peroxide (H2O2) plays an important role in redox signalling and pathogen-host cell interactions. For monitoring intra- and subcellular redox events, highly sensitive and specific probes are required. Here, we stably expressed the ratiometric H2O2redox sensor roGFP2-Orp1 in the cytosol and the mitochondria ofPlasmodium falciparum (P. falciparum)NF54-attBblood-stage parasites and evaluated its sensitivity towards oxidative stress, selected antimalarial drugs, and novel lead compounds. In both compartments, the sensor showed reproducible sensitivity towards H2O2in the low micromolar range and towards antimalarial compounds at pharmacologically relevant concentrations. Upon short-term exposure (4 h), artemisinin derivatives, quinine and mefloquine impacted H2O2levels in mitochondria, whereas chloroquine and a glucose-6-phosphate dehydrogenase (G6PD) inhibitor affected the cytosol; 24 h exposure to arylmethylamino steroids and G6PD inhibitors revealed oxidation of mitochondria and cytosol, respectively. Genomic integration of an H2O2sensor expressed in subcellular compartments ofP. falciparumprovides the basis for studying complex parasite-host cell interactions or drug effects with spatio-temporal resolution while preserving cell integrity, and sets the stage for high-throughput approaches to identify antimalarial agents perturbing redox equilibrium.
Comprehensive transcriptome profiling of Salvia miltiorrhiza for discovery of genes associated with the biosynthesis of tanshinones and phenolic acids
Authors: Zhou Wei , Huang Qiang , Wu Xiao , Zhou Zewen , Ding Mingquan , Shi Min , Huang Fenfen , Li Shen , Wang Yao , Kai Guoyin 
Published: August 2017

AbstractTanshinones and phenolic acids are crucial bioactive compounds biosynthesized in Salvia miltiorrhiza. Methyl jasmonate (MeJA) is an effective elicitor to enhance the production of phenolic acids and tanshinones simultaneously, while yeast extract (YE) is used as a biotic elicitor that only induce tanshinones accumulation. However, little was known about the different molecular mechanism. To identify the downstream and regulatory genes involved in tanshinone and phenolic acid biosynthesis, we conducted comprehensive transcriptome profiling of S. miltiorrhiza hairy roots treated with either MeJA or YE. Total 55588 unigenes were assembled from about 1.72 billion clean reads, of which 42458 unigenes (76.4%) were successfully annotated. The expression patterns of 19 selected genes in the significantly upregulated unigenes were verified by quantitative real-time PCR. The candidate downstream genes and other cytochrome P450s involved in the late steps of tanshinone and phenolic acid biosynthesis pathways were screened from the RNA-seq dataset based on co-expression pattern analysis with specific biosynthetic genes. Additionally, 375 transcription factors were identified to exhibit a significant up-regulated expression pattern in response to induction. This study can provide us a valuable gene resource for elucidating the molecular mechanism of tanshinones and phenolic acids biosynthesis in hairy roots of S. miltiorrhiza.
Blue Laser Diode Based Free-space Optical Data Transmission elevated to 18 Gbps over 16 m
Authors: Huang Yu-Fang , Chi Yu-Chieh , Kao Hsuan-Yun , Tsai Chen-Ting , Wang Huai-Yung , Kuo Hao-Chung , Nakamura Shuji , Huang Ding-Wei , Lin Gong-Ru 
Published: August 2017

AbstractUp to 18-Gbps direct encoding of blue laser diode (BLD) is demonstrated for free-space data transmission. By reshaping the orthogonal frequency multiplexed (16-QAM OFDM) stream with sidelobe filtering, the raw data rate expedites from 17.2 to 18.4 Gbps. Employing an ultrafast p-i-n photodiode with smaller active area diameter and lower noise equivalent power significantly enlarges the data rate by 1.6 Gbps or upgrades the signal-to-noise ratio (SNR) by 0.2 dB. Replacing the 80-mW BLD with the 120-mW one essentially increases the received SNR by 0.4 dB under enhanced modulation throughput. Reinforcing the beam collimation and collection by increasing the numerical aperture with a plano-convex hyper-hemispherical lens further improves the SNR by 0.6 dB. After optimization, the 16-QAM OFDM data with and without sidelobe filtering are respectively delivered at raw data rates of 16.4 and 18 Gbps with spectral-density usage efficiency as high as 4 bit/s/Hz over 16 m in free space, wherein the BLD carried QAM-OFDM data stream remains its capacity after reformation with sidelobe filtering as the superior inter-carrier-interference immunity reinforces.
Identification of neuromedin U precursor-related peptide and its possible role in the regulation of prolactin release
Authors: Mori Kenji , Ida Takanori , Fudetani Mami , Mori Miwa , Kaiya Hiroyuki , Hino Jun , Nakahara Keiko , Murakami Noboru , Miyazato Mikiya , Kangawa Kenji 
Published: August 2017

AbstractThe discovery of neuropeptides provides insights into the regulation of physiological processes. The precursor for the neuropeptide neuromedin U contains multiple consensus sequences for proteolytic processing, suggesting that this precursor might generate additional peptides. We performed immunoaffinity chromatography of rat brain extracts and consequently identified such a product, which we designated neuromedin U precursor-related peptide (NURP). In rat brain, NURP was present as two mature peptides of 33 and 36 residues. Radioimmunoassays revealed NURP immunoreactivity in the pituitary, small intestine, and brain of rats, with the most intense reactivity in the pituitary. Intracerebroventricular administration of NURP to both male and female rats robustly increased plasma concentrations of prolactin but not of other anterior pituitary hormones. In contrast, NURP failed to stimulate prolactin release from dispersed anterior pituitary cells. Pretreatment of rats with bromocriptine, a dopamine receptor agonist, blocked the prolactin-releasing activity of NURP. In rats pretreated with the antagonist sulpiride, intracerebroventricular administration of NURP did not increase plasma prolactin concentrations more than administration of saline. These data suggest that NURP induces prolactin release by acting indirectly on the pituitary; dopamine from the hypothalamus, which inhibits prolactin release, may be involved in this activity of NURP.
Hyperactive TGF-β Signaling in Smooth Muscle Cells Exposed to HIV-protein(s) and Cocaine: Role in Pulmonary Vasculopathy
Authors: Dalvi Pranjali , Sharma Himanshu , Konstantinova Tomara , Sanderson Miles , Brien-Ladner Amy O’ , Dhillon Navneet K. 
Published: August 2017

AbstractWe earlier demonstrated synergistic increase in the proliferation of pulmonary smooth muscle cells on exposure to HIV-proteins and/or cocaine due to severe down-modulation of bone morphogenetic protein receptor (BMPR) axis: the anti-proliferative arm of TGF-β super family of receptors. Here, now we demonstrate the effect of HIV-Tat and cocaine on the proliferative TGF-β signaling cascade. We observed a significant increase in the secretion of TGF-β1 ligand along with enhanced protein expression of TGFβ Receptor (TGFβR)-1, TGFβR-2 and phosphorylated SMAD2/3 in human pulmonary arterial smooth muscle cells on treatment with cocaine and Tat. Further, we noticed an increase in the levels of p-TAK1 complexed with TGFβR-2. Concomitant to this a significant increase in the activation of TAK1-mediated, SMAD-independent downstream signaling molecules: p-MKK4 and p-JNK was observed. However, activation of MKK3/6-p38MAPK, another axis downstream of TAK1 was found to be reduced due to attenuation in the protein levels of BMPR2. Both SMAD and non-SMAD dependent TGFβR cascades were found to contribute to hyper-proliferation. Finally the increase in the levels of phosphorylated TGFβR1 and TGFβR2 on exposure to HIV-proteins and cocaine was confirmed in pulmonary smooth muscle cells from cocaine injected HIV-transgenic rats and in total lung extracts from HIV infected cocaine and/or opioid users.
Restless legs syndrome in Parkinson disease: Clinical characteristics, abnormal iron metabolism and altered neurotransmitters
Authors: Piao Ying-Shan , Lian Teng-Hong , Hu Yang , Zuo Li-Jun , Guo Peng , Yu Shu-Yang , Liu Li , Jin Zhao , Zhao Hui , Li Li-Xia , yu Qiu-Jin , Wang Rui-Dan , Chen Sheng-Di , Chan Piu , Wang Xiao-Min , Zhang Wei 
Published: August 2017

AbstractRelationships among clinical characteristics, iron metabolism and neurotransmitters in Parkinson disease (PD) patients with restless legs syndrome (RLS) remains unclear. We divided 218 patients into PD with and with no RLS (PD-RLS and PD-NRLS) groups by RLS-rating scale (RLS-RS) score. Motor and non-motor symptoms were rated by related scales. Iron and related proteins, and neurotransmitters in cerebrospinal fluid (CSF) and serum were measured. PD-RLS frequency was 40.37%. PD-RLS group had longer duration, higher stage and scores of motor symptoms, depression, anxiety, sleep disorders, fatigue and apathy, and increased transferrin and decreased iron, ferritin, dopamine (DA) and 5-hydroxytryptamine (5-HT) in CSF. In CSF of PD-RLS group, RLS-RS score was positively correlated with transferrin level and negatively correlated with iron and ferritin levels; RLS-RS score was negatively correlated with DA and 5-HT levels; transferrin level was negatively correlated with DA and 5-HT levels, and ferritin level was positively correlated with DA level. In serum, PD-RLS group had decreased iron and transferrin levels, which were negatively correlated with RLS-RS score. PD-RLS was common and severer in motor and some non-motor symptoms. Iron deficiency induced by its metabolism dysfunctions in peripheral and central systems might cause PD-RLS through decreasing brain DA and 5-HT.