bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-source dataset of urban life in the city of Milan and the Province of Trentino
Authors: Barlacchi Gianni , De Nadai Marco , Larcher Roberto , Casella Antonio , Chitic Cristiana , Torrisi Giovanni , Antonelli Fabrizio , Vespignani Alessandro , Pentland Alex , Lepri Bruno 
Published: October 2015

AbstractThe study of socio-technical systems has been revolutionized by the unprecedented amount of digital records that are constantly being produced by human activities such as accessing Internet services, using mobile devices, and consuming energy and knowledge. In this paper, we describe the richest open multi-source dataset ever released on two geographical areas. The dataset is composed of telecommunications, weather, news, social networks and electricity data from the city of Milan and the Province of Trentino. The unique multi-source composition of the dataset makes it an ideal testbed for methodologies and approaches aimed at tackling a wide range of problems including energy consumption, mobility planning, tourist and migrant flows, urban structures and interactions, event detection, urban well-being and many others.
A connectivity-based test-retest dataset of multi-modal magnetic resonance imaging in young healthy adults
Authors: Lin Qixiang , Dai Zhengjia , Xia Mingrui , Han Zaizhu , Huang Ruiwang , Gong Gaolang , Liu Chao , Bi Yanchao , He Yong 
Published: October 2015

AbstractRecently, magnetic resonance imaging (MRI) has been widely used to investigate the structures and functions of the human brain in health and disease in vivo. However, there are growing concerns about the test-retest reliability of structural and functional measurements derived from MRI data. Here, we present a test-retest dataset of multi-modal MRI including structural MRI (S-MRI), diffusion MRI (D-MRI) and resting-state functional MRI (R-fMRI). Fifty-seven healthy young adults (age range: 19–30 years) were recruited and completed two multi-modal MRI scan sessions at an interval of approximately 6 weeks. Each scan session included R-fMRI, S-MRI and D-MRI data. Additionally, there were two separated R-fMRI scans at the beginning and at the end of the first session (approximately 20 min apart). This multi-modal MRI dataset not only provides excellent opportunities to investigate the short- and long-term test-retest reliability of the brain’s structural and functional measurements at the regional, connectional and network levels, but also allows probing the test-retest reliability of structural-functional couplings in the human brain.
Hirsutella sinensis mycelium attenuates bleomycin-induced pulmonary inflammation and fibrosis in vivo
Authors: Huang Tsung-Teng , Lai Hsin-Chih , Ko Yun-Fei , Ojcius David M. , Lan Ying-Wei , Martel Jan , Young John D. , Chong Kowit-Yu 
Published: October 2015

AbstractHirsutella sinensismycelium (HSM), the anamorph ofCordyceps sinensis, is a traditional Chinese medicine that has been shown to possess various pharmacological properties. We previously reported that this fungus suppresses interleukin-1β and IL-18 secretion by inhibiting both canonical and non-canonical inflammasomes in human macrophages. However, whether HSM may be used to prevent lung fibrosis and the mechanism underlying this activity remain unclear. Our results show that pretreatment with HSM inhibits TGF-β1–induced expression of fibronectin and α-SMA in lung fibroblasts. HSM also restores superoxide dismutase expression in TGF-β1–treated lung fibroblasts and inhibits reactive oxygen species production in lung epithelial cells. Furthermore, HSM pretreatment markedly reduces bleomycin–induced lung injury and fibrosis in mice. Accordingly, HSM reduces inflammatory cell accumulation in bronchoalveolar lavage fluid and proinflammatory cytokines levels in lung tissues. The HSM extract also significantly reduces TGF-β1 in lung tissues and this effect is accompanied by decreased collagen 3α1 and α-SMA levels. Moreover, HSM reduces expression of the NLRP3 inflammasome and P2X7R in lung tissues, whereas it enhances expression of superoxide dismutase. These findings suggest that HSM may be used for the treatment of pulmonary inflammation and fibrosis.
The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments
Authors: Granata Daniele , Baftizadeh Fahimeh , Habchi Johnny , Galvagnion Celine , De Simone Alfonso , Camilloni Carlo , Laio Alessandro , Vendruscolo Michele 
Published: October 2015

AbstractThe free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures and we show that this is the case through a series of biophysical measurements.
Grain Boundary Plane Orientation Fundamental Zones and Structure-Property Relationships
Authors: Homer Eric R. , Patala Srikanth , Priedeman Jonathan L. 
Published: October 2015

AbstractGrain boundary plane orientation is a profoundly important determinant of character in polycrystalline materials that is not well understood. This work demonstrates how boundary plane orientation fundamental zones, which capture the natural crystallographic symmetries of a grain boundary, can be used to establish structure-property relationships. Using the fundamental zone representation, trends in computed energy, excess volume at the grain boundary and temperature-dependent mobility naturally emerge and show a strong dependence on the boundary plane orientation. Analysis of common misorientation axes even suggests broader trends of grain boundary energy as a function of misorientation angle and plane orientation. Due to the strong structure-property relationships that naturally emerge from this work, boundary plane fundamental zones are expected to simplify analysis of both computational and experimental data. This standardized representation has the potential to significantly accelerate research in the topologically complex and vast five-dimensional phase space of grain boundaries.
Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX
Authors: Dong Lili , Tan Qiwen , Ye Wei , Liu Dongli , Chen Haifeng , Hu Hongwei , Wen Duo , Liu Yang , Cao Ya , Kang Jingwu , Fan Jia , Guo Wei , Wu Weizhong 
Published: October 2015

AbstractAlpha-fetoprotein (AFP) is a liver cancer associated protein and has long been utilized as a serum tumor biomarker of disease progression. AFP is usually detected in HCC patients by an antibody based system. Recently, however, aptamers generated from systematic evolution of ligands by exponential enrichment (SELEX) were reported to have an alternative potential in targeted imaging, diagnosis and therapy. In this study, AFP-bound ssDNA aptamers were screened and identified using capillary electrophoresis (CE) SELEX technology. After cloning, sequencing and motif analysis, we successfully confirmed an aptamer, named AP273, specifically targeting AFP. The aptamer could be used as a probe in AFP immunofluorescence imaging in HepG2, one AFP positive cancer cell line, but not in A549, an AFP negative cancer cell line. More interesting, the aptamer efficiently inhibited the migration and invasion of HCC cells after in vivo transfection. Motif analysis revealed that AP273 had several stable secondary motifs in its structure. Our results indicate that CE-SELEX technology is an efficient method to screen specific protein-bound ssDNA and AP273 could be used as an agent in AFP-based staining, diagnosis and therapy, although more works are still needed.
Trypsin- and low pH-mediated fusogenicity of avian metapneumovirus fusion proteins is determined by residues at positions 100, 101 and 294
Authors: Yun Bingling , Guan Xiaolu , Liu Yongzhen , Gao Yanni , Wang Yongqiang , Qi Xiaole , Cui Hongyu , Liu Changjun , Zhang Yanping , Gao Li , Li Kai , Gao Honglei , Gao Yulong , Wang Xiaomei 
Published: October 2015

AbstractAvian metapneumovirus (aMPV) and human metapneumovirus (hMPV) are members of the genus Metapneumovirus in the subfamily Pneumovirinae. Metapneumovirus fusion (F) protein mediates the fusion of host cells with the virus membrane for infection. Trypsin- and/or low pH-induced membrane fusion is a strain-dependent phenomenon for hMPV. Here, we demonstrated that three subtypes of aMPV (aMPV/A, aMPV/B and aMPV/C) F proteins promoted cell-cell fusion in the absence of trypsin. Indeed, in the presence of trypsin, only aMPV/C F protein fusogenicity was enhanced. Mutagenesis of the amino acids at position 100 and/or 101, located at a putative cleavage region in aMPV F proteins, revealed that the trypsin-mediated fusogenicity of aMPV F proteins is regulated by the residues at positions 100 and 101. Moreover, we demonstrated that aMPV/A and aMPV/B F proteins mediated cell-cell fusion independent of low pH, whereas the aMPV/C F protein did not. Mutagenesis of the residue at position 294 in the aMPV/A, aMPV/B and aMPV/C F proteins showed that 294G played a critical role in F protein-mediated fusion under low pH conditions. These findings on aMPV F protein-induced cell-cell fusion provide new insights into the molecular mechanisms underlying membrane fusion and pathogenesis of aMPV.
Noninvasive imaging of radiolabeled exosome-mimetic nanovesicle using 99mTc-HMPAO
Authors: Hwang Do Won , Choi Hongyoon , Jang Su Chul , Yoo Min Young , Park Ji Yong , Choi Na Eun , Oh Hyun Jeong , Ha Seunggyun , Lee Yun-Sang , Jeong Jae Min , Gho Yong Song , Lee Dong Soo 
Published: October 2015

AbstractExosomes known as nano-sized extracellular vesicles attracted recent interests due to their potential usefulness in drug delivery. Amid remarkable advances in biomedical applications of exosomes, it is crucial to understand in vivo distribution and behavior of exosomes. Here, we developed a simple method for radiolabeling of macrophage-derived exosome-mimetic nanovesicles (ENVs) with 99mTc-HMPAO under physiologic conditions and monitored in vivo distribution of 99mTc-HMPAO-ENVs using SPECT/CT in living mice. ENVs were produced from the mouse RAW264.7 macrophage cell line and labeled with 99mTc-HMPAO for 1 hr incubation, followed by removal of free 99mTc-HMPAO. SPECT/CT images were serially acquired after intravenous injection to BALB/c mouse. When ENVs were labeled with 99mTc-HMPAO, the radiochemical purity of 99mTc-HMPAO-ENVs was higher than 90% and the expression of exosome specific protein (CD63) did not change in 99mTc-HMPAO-ENVs. 99mTc-HMPAO-ENVs showed high serum stability (90%) which was similar to that in phosphate buffered saline until 5 hr. SPECT/CT images of the mice injected with 99mTc-HMPAO-ENVs exhibited higher uptake in liver and no uptake in brain, whereas mice injected with 99mTc-HMPAO showed high brain uptake until 5 hr. Our noninvasive imaging of radiolabeled-ENVs promises better understanding of the in vivo behavior of exosomes for upcoming biomedical application.
Tumor-induced lymph node alterations detected by MRI lymphography using gadolinium nanoparticles
Authors: Partridge S. C. , Kurland B. F. , Liu C.-L. , Ho R. J. Y. , Ruddell A. 
Published: October 2015

AbstractContrast-enhanced MRI lymphography shows potential to identify alterations in lymph drainage through lymph nodes (LNs) in cancer and other diseases. MRI studies have typically used low molecular weight gadolinium contrast agents, however larger gadolinium-loaded nanoparticles possess characteristics that could improve the specificity and sensitivity of lymphography. The performance of three gadolinium contrast agents with different sizes and properties was compared by 3T MRI after subcutaneous injection. Mice bearing B16-F10 melanoma footpad tumors were imaged to assess tumor-induced alterations in lymph drainage through tumor-draining popliteal and inguinal LNs versus contralateral uninvolved drainage. Gadolinium lipid nanoparticles were able to identify tumor-induced alterations in contrast agent drainage into the popliteal LN, while lower molecular weight or albumin-binding gadolinium agents were less effective. All of the contrast agents distributed in foci around the cortex and medulla of tumor-draining popliteal LNs, while they were restricted to the cortex of non-draining LNs. Surprisingly, second-tier tumor-draining inguinal LNs exhibited reduced uptake, indicating that tumors can also divert LN drainage. These characteristics of tumor-induced lymph drainage could be useful for diagnosis of LN pathology in cancer and other diseases. The preferential uptake of nanoparticle contrasts into tumor-draining LNs could also allow selective targeting of therapies to tumor-draining LNs.
The roles of lithium-philic giant nitrogen-doped graphene in protecting micron-sized silicon anode from fading
Authors: Liu Xiaoxu , Chao Dongliang , Zhang Qiang , Liu Hai , Hu Hailong , Zhao Jiupeng , Li Yao , Huang Yizhong , Lin Jianyi , Shen Ze Xiang 
Published: October 2015

AbstractA stable Si-based anode with a high initial coulombic efficiency (ICE) for lithium-ion batteries (LIB) is critical for energy storage. In the present paper, a new scalable method is adopted in combination with giant nitrogen-doped graphene and micron-size electrode materials. We first synthesize a new type of freestanding LIB anode composed of micron-sized Si (mSi) particles wrapped by giant nitrogen-doped graphene (mSi@GNG) film. High ICE (>85%) and long cycle life (more than 80 cycles) are obtained. In the mSi@GNG composite, preferential formation of a stable solid electrolyte interphase (SEI) on the surface of graphene sheets is achieved. The formation and components of SEI are identified for the first time by using UV-resonance Raman spectroscopy and Raman mapping, which will revive the study of formation and evolution of SEI by Raman. New mechanism is proposed that the giant graphene sheets protect the mSi particles from over-lithiation and fracture. Such a simple and scalable method may also be applied to other anode systems to boost their energy and power densities for LIB.
Intraspecific diversity among partners drives functional variation in coral symbioses
Authors: Parkinson John Everett , Banaszak Anastazia T. , Altman Naomi S. , LaJeunesse Todd C. , Baums Iliana B. 
Published: October 2015

AbstractThe capacity of coral-dinoflagellate mutualisms to adapt to a changing climate relies in part on standing variation in host and symbiont populations, but rarely have the interactions between symbiotic partners been considered at the level of individuals. Here, we tested the importance of inter-individual variation with respect to the physiology of coral holobionts. We identified six genetically distinct Acropora palmata coral colonies that all shared the same isoclonal Symbiodinium ‘fitti’ dinoflagellate strain. No other Symbiodinium could be detected in host tissues. We exposed fragments of each colony to extreme cold and found that the stress-induced change in symbiont photochemical efficiency varied up to 3.6-fold depending on host genetic background. The S. ‘fitti’ strain was least stressed when associating with hosts that significantly altered the expression of 184 genes under cold shock; it was most stressed in hosts that only adjusted 14 genes. Key expression differences among hosts were related to redox signaling and iron availability pathways. Fine-scale interactions among unique host colonies and symbiont strains provide an underappreciated source of raw material for natural selection in coral symbioses.
Clinical significance of Anoctamin-1 gene at 11q13 in the development and progression of head and neck squamous cell carcinomas
Authors: Rodrigo Juan P. , Menéndez Sofía Tirados , Hermida-Prado Francisco , Álvarez-Teijeiro Saúl , Villaronga M. Ángeles , Alonso-Durán Laura , Vallina Aitana , Martínez-Camblor Pablo , Astudillo Aurora , Suárez Carlos , María García-Pedrero Juana 
Published: October 2015

AbstractThis study investigates the clinical significance of Anoctamin-1 gene mapping at 11q13 amplicon in both the development and progression of head and neck squamous cell carcinomas (HNSCC). ANO1 protein expression was evaluated by immunohistochemistry in a cohort of 372 surgically treated HNSCC patients and also in 35 laryngeal precancerous lesions. ANO1 gene amplification was determined by real-time PCR in all the laryngeal premalignancies and 60 of the HNSCCs and molecular data correlated with clinical outcome. ANO1 gene amplification was frequently detected in both premalignant lesions (63%) and HNSCC tumours (58%), whereas concomitant ANO1 expression occurred at a much lower frequency (20 and 22%). Interestingly, laryngeal dysplasias harbouring ANO1 gene amplification showed a higher risk of malignant transformation (HR = 3.62; 95% CI 0.79–16.57; P = 0.097; Cox regression). ANO1 expression and gene amplification showed no significant associations with clinicopathological parameters in HNSCC. However, remarkably ANO1 expression differentially influenced patient survival depending on the tumour site. Collectively, this study provides original evidence demonstrating the distinctive impact of ANO1 expression on HNSCC prognosis depending on the tumour site.
Rational regional distribution of sugarcane cultivars in China
Authors: Luo Jun , Pan Yong-Bao , Xu Liping , Grisham Michael Paul , Zhang Hua , Que Youxiong 
Published: October 2015

AbstractKnowing yield potential and yield stability of sugarcane cultivars is of significance in guiding sugarcane breeding and rationalising regional distribution of sugarcane cultivars. In the present study, a heritability-adjusted genotype main effect plus genotype × environment (HA-GGE) biplot program was used to analyze the cane and sucrose yields of 44 newly released sugarcane cultivars at eight pilot test sites. The cane and sucrose yields of nine cultivars were higher than those of the control cultivar ROC22. From the perspective of cane yield, cultivars FN 40 and YZ 06–407 were well adapted to a wider range of conditions and produced relatively high cane yields in several pilot sites. From the perspective of sucrose yield, cultivars LC 03–1137, FN 38, FN 41, MT 01–77 and LC 05–136 were well adapted to a wide range of conditions and produced relatively high sucrose yields. Based on these results, three high yielding and widely adapted cultivars, namely, FN 39, LC 05–136 and YZ 05–51 were recommended for production in three major Chinese sugarcane planting areas. The results will provide a theoretical basis for recommending the effective use and rational regional distribution of sugarcane cultivars in China.
Trans-presentation of IL-15 modulates STAT5 activation and Bcl-6 expression in TH1 cells
Authors: Cooley Ian D. , Read Kaitlin A. , Oestreich Kenneth J. 
Published: October 2015

AbstractDuring infection, naïve CD4+ T helper cells differentiate into specialized effector subsets based upon environmental signals propagated by the cytokine milieu. Recently, this paradigm has been complicated by the demonstration that alterations in the cytokine environment can result in varying degrees of plasticity between effector T helper cell populations. Therefore, elucidation of the mechanisms by which cytokines regulate T helper cell differentiation decisions is increasingly important. The gamma common cytokine IL-15 is currently undergoing clinical trials for the treatment of malignancies, due to its well-established role in the regulation of natural killer and CD8+ T cell immune responses. However, the effect of IL-15 signaling on CD4+ T cell activity is incompletely understood. One mechanism by which IL-15 activity is conferred is through trans-presentation via the IL-15 receptor alpha subunit. Here, we demonstrate that differentiated TH1 cells are responsive to trans-presented IL-15. Importantly, while trans-presentation of IL-15 results in STAT5 activation and maintenance of the TH1 gene program, IL-15 treatment alone allows for increased Bcl-6 expression and the upregulation of a TFH-like profile. Collectively, these findings describe a novel role for IL-15 in the modulation of CD4+ T cell responses and provide valuable insight for the use of IL-15 in immunotherapeutic approaches.
First Principles Study on the Electronic Structure and Interface Stability of Hybrid Silicene/Fluorosilicene Nanoribbons
Authors: Jiang Q. G. , Zhang J. F. , Ao Z. M. , Wu Y. P. 
Published: October 2015

AbstractThe interface stability of hybrid silicene/fluorosilicene nanoribbons (SFNRs) has been investigated by using density functional theory calculations, where fluorosilicene is the fully fluorinated silicene. It is found that the diffusion of F atoms at the zigzag and armchair interfaces of SFNRs is endothermic and the corresponding minimum energy barriers are respectively 1.66 and 1.56 eV, which are remarkably higher than the minimum diffusion energy barrier of one F atom and two F atoms on pristine silicene 1.00 and 1.29 eV, respectively. Therefore, the thermal stability of SFNRs can be significantly enhanced by increasing the F diffusion barriers through silicene/fluorosilicene interface engineering. In addition, the electronic and magnetic properties of SFNRs are also investigated. It is found that the armchair SFNRs are nonmagnetic semiconductors and the band gap of armchair SFNRs presents oscillatory behavior when the width of silicene part changing. For the zigzag SFNRs, the antiferromagnetic semiconducting state is the most stable one. This work provides fundamental insights for the applications of SFNRs in electronic devices.
Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome
Authors: Åqvist Johan , Kamerlin Shina C.L. 
Published: October 2015

AbstractProtein synthesis on the ribosome involves hydrolysis of GTP in several key steps of the mRNA translation cycle. These steps are catalyzed by the translational GTPases of which elongation factor Tu (EF-Tu) is the fastest GTPase known. Here, we use extensive computer simulations to explore the origin of its remarkably high catalytic rate on the ribosome and show that it is made possible by a very large positive activation entropy. This entropy term (TΔS‡) amounts to more than 7 kcal/mol at 25 °C. It is further found to be characteristic of the reaction mechanism utilized by the translational, but not other, GTPases and it enables these enzymes to attain hydrolysis rates exceeding 500 s−1. This entropy driven mechanism likely reflects the very high selection pressure on the speed of protein synthesis, which drives the rate of each individual GTPase towards maximal turnover rate of the whole translation cycle.
2.6.1 Trifluoromethylation
Authors: Lishchynskyi A. , Novak P. , Grushin V. V. 
Published: October 2015

AbstractMetal-catalyzed/-promoted trifluoromethylation reactions represent a powerful tool for the synthesis of a broad variety of organic compounds bearing a CF3 group on sp3-, sp2-, or sp-hybridized carbon atoms.