bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upper Palaeolithic genomes reveal deep roots of modern Eurasians
Authors: Jones Eppie R. , Gonzalez-Fortes Gloria , Connell Sarah , Siska Veronika , Eriksson Anders , Martiniano Rui , McLaughlin Russell L. , Gallego Llorente Marcos , Cassidy Lara M. , Gamba Cristina , Meshveliani Tengiz , Bar-Yosef Ofer , Müller Werner , Belfer-Cohen Anna , Matskevich Zinovi , Jakeli Nino , Higham Thomas F. G. , Currat Mathias , Lordkipanidze David , Hofreiter Michael , Manica Andrea , Pinhasi Ron , Bradley Daniel G. 
Published: November 2015

AbstractWe extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.
Efficient near-infrared up-conversion photoluminescence in carbon nanotubes
Authors: Akizuki Naoto , Aota Shun , Mouri Shinichiro , Matsuda Kazunari , Miyauchi Yuhei 
Published: November 2015

AbstractPhotoluminescence phenomena normally obey Stokes’ law of luminescence according to which the emitted photon energy is typically lower than its excitation counterparts. Here we show that carbon nanotubes break this rule under one-photon excitation conditions. We found that the carbon nanotubes exhibit efficient near-infrared photoluminescence upon photoexcitation even at an energy lying >100–200 meV below that of the emission at room temperature. This apparently anomalous phenomenon is attributed to efficient one-phonon-assisted up-conversion processes resulting from unique excited-state dynamics emerging in an individual carbon nanotube with accidentally or intentionally embedded localized states. These findings may open new doors for energy harvesting, optoelectronics and deep-tissue photoluminescence imaging in the near-infrared optical range.
Charge density wave transition in single-layer titanium diselenide
Authors: Chen P , Chan Y. -H. , Fang X. -Y. , Zhang Y , Chou M Y , Mo S. -K. , Hussain Z , Fedorov A. -V. , Chiang T. -C. 
Published: November 2015

AbstractA single molecular layer of titanium diselenide (TiSe2) is a promising material for advanced electronics beyond graphene—a strong focus of current research. Such molecular layers are at the quantum limit of device miniaturization and can show enhanced electronic effects not realizable in thick films. We show that single-layer TiSe2 exhibits a charge density wave (CDW) transition at critical temperature TC=232±5 K, which is higher than the bulk TC=200±5 K. Angle-resolved photoemission spectroscopy measurements reveal a small absolute bandgap at room temperature, which grows wider with decreasing temperature T below TC in conjunction with the emergence of (2 × 2) ordering. The results are rationalized in terms of first-principles calculations, symmetry breaking and phonon entropy effects. The observed Bardeen-Cooper-Schrieffer (BCS) behaviour of the gap implies a mean-field CDW order in the single layer and an anisotropic CDW order in the bulk.
X-ray induced dimerization of cinnamic acid: Time-resolved inelastic X-ray scattering study
Authors: Inkinen Juho , Niskanen Johannes , Talka Tuomas , Sahle Christoph J. , Müller Harald , Khriachtchev Leonid , Hashemi Javad , Akbari Ali , Hakala Mikko , Huotari Simo 
Published: November 2015

AbstractA classic example of solid-state topochemical reactions is the ultraviolet-light induced photodimerization of α-trans-cinnamic acid (CA). Here, we report the first observation of an X-ray-induced dimerization of CA and monitor itin situusing nonresonant inelastic X-ray scattering spectroscopy (NRIXS). The time-evolution of the carbon core-electron excitation spectra shows the effects of two X-ray induced reactions: dimerization on a short time-scale and disintegration on a long time-scale. We used spectrum simulations of CA and its dimerization product, α-truxillic acid (TA), to gain insight into the dimerization effects. From the time-resolved spectra, we extracted component spectra and time-dependent weights corresponding to CA and TA. The results suggest that the X-ray induced dimerization proceeds homogeneously in contrast to the dimerization induced by ultraviolet light. We also utilized the ability of NRIXS for direct tomography with chemical-bond contrast to image the spatial progress of the reactions in the sample crystal. Our work paves the way for other time-resolved studies on chemical reactions using inelastic X-ray scattering.
Large-scale production of bioactive recombinant human acidic fibroblast growth factor in transgenic silkworm cocoons
Authors: Wang Feng , Wang Riyuan , Wang Yuancheng , Zhao Ping , Xia Qingyou 
Published: November 2015

AbstractWith an increasing clinical demand for functional therapeutic proteins every year, there is an increasing requirement for the massive production of bioactive recombinant human acidic fibroblast growth factor (r-haFGF). In this present study, we delicately explore a strategy for the mass production of r-haFGF protein with biological activity in the transgenic silkworm cocoons. The sequence-optimized haFGF was inserted into an enhanced sericin-1 expression system to generate the original transgenic silkworm strain, which was then further crossed with a PIG jumpstarter strain to achieve the remobilization of the expression cassette to a “safe harbor” locus in the genome for the efficient expression of r-haFGF. In consequence, the expression of r-haFGF protein in the mutant line achieved a 5.6-fold increase compared to the original strain. The high content of r-haFGF facilitated its purification and large-scald yields. Furthermore, the r-haFGF protein bioactively promoted the growth, proliferation and migration of NIH/3T3 cells, suggesting the r-haFGF protein possessed native mitogenic activity and the potential for wound healing. These results show that the silk gland of silkworm could be an efficient bioreactor strategy for recombinant production of bioactive haFGF in silkworm cocoons.
Targeting inhibition of extracellular signal-regulated kinase kinase pathway with AZD6244 (ARRY-142886) suppresses growth and angiogenesis of gastric cancer
Authors: Gao Jin-Hang , Wang Chun-Hui , Tong Huan , Wen Shi-Lei , Huang Zhi-Yin , Tang Cheng-Wei 
Published: November 2015

AbstractAZD6244 (ARRY-142886), a highly selective MAPK-ERK kinase inhibitor, has shown excellent clinical efficacy in many tumors. However, the anti-tumor and anti-angiogenesis efficacy of AZD6244 on gastric cancer has not been well characterized. In this study, high p-ERK expression was associated with advanced TNM stage, increased lymphovascular invasion and poor survival. For absence of NRAS, KRAS and BRAF mutation, SGC7901 and BGC823 gastric cancer cells were relative resistance to AZD6244 in vitro. And such resistance was not attributed to the insufficient inhibition of ERK phosphorylation. However, tumor growth was significantly suppressed in SGC7901 xenografts by blockage of angiogenesis. This result was further supported by suppression of tube formation and migration in HUVEC cells after treatment with AZD6244. Moreover, the anti-angiogenesis effect of AZD6244 may predominantly attribute to its modulation on VEGF through p-ERK − c-Fos − HIF-1α integrated signal pathways. In conclusions, High p-ERK expression was associated with advanced TNM stage, increased lymphovascular invasion and poor survival. Targeting inhibition of p-ERK by AZD6244 suppress gastric cancer xenografts by blockage of angiogenesis without systemic toxicity. The anti-angiogenesis effect afford by AZD6244 may attribute to its modulation on p-ERK − c-Fos − HIF-1α − VEGF integrated signal pathways.
Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods
Authors: Hu Guodong , Cao Zanxia , Xu Shicai , Wang Wei , Wang Jihua 
Published: November 2015

AbstractThe 14-3-3σ proteins are a family of ubiquitous conserved eukaryotic regulatory molecules involved in the regulation of mitogenic signal transduction, apoptotic cell death and cell cycle control. A lot of small-molecule inhibitors have been identified for 14-3-3 protein-protein interactions (PPIs). In this work, we carried out molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method to study the binding mechanism between a 14-3-3σ protein and its eight inhibitors. The ranking order of our calculated binding free energies is in agreement with the experimental results. We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues. To improve the binding free energy of Rx group, we designed the inhibitor R9 with group R9 = 4-hydroxypheny. However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1. By further using the steer molecular dynamics (SMD) simulations, we identified a new hydrogen bond between the inhibitor R8 and residue Arg64 in the pulling paths. The information obtained from this study may be valuable for future rational design of novel inhibitors and provide better structural understanding of inhibitor binding to 14-3-3σ proteins.
Cardiac Optogenetics: Enhancement by All-trans-Retinal
Authors: Yu Jinzhu , Chen Kay , Lucero Rachel V. , Ambrosi Christina M. , Entcheva Emilia 
Published: November 2015

AbstractAll-trans-Retinal (ATR) is a photosensitizer, serving as the chromophore for depolarizing and hyperpolarizing light-sensitive ion channels and pumps (opsins), recently employed as fast optical actuators. In mammalian optogenetic applications (in brain and heart), endogenous ATR availability is not considered a limiting factor, yet it is unclear how ATR modulation may affect the response to optical stimulation. We hypothesized that exogenous ATR may improve light responsiveness of cardiac cells modified by Channelrhodopsin2 (ChR2), hence lowering the optical pacing energy. In virally-transduced (Ad-ChR2(H134R)-eYFP) light-sensitive cardiac syncytium in vitro, ATR supplements ≤2 μM improved cardiomyocyte viability and augmented ChR2 membrane expression several-fold, while >4 μM was toxic. Employing integrated optical actuation (470 nm) and optical mapping, we found that 1–2 μM ATR dramatically reduced optical pacing energy (over 30 times) to several μW/mm2, lowest values reported to date, but also caused action potential prolongation, minor changes in calcium transients and no change in conduction. Theoretical analysis helped explain ATR-caused reduction of optical excitation threshold in cardiomyocytes. We conclude that cardiomyocytes operate at non-saturating retinal levels and carefully-dosed exogenous ATR can enhance the performance of ChR2 in cardiac cells and yield energy benefits over orders of magnitude for optogenetic stimulation.
IRE1α-XBP1 is a novel branch in the transcriptional regulation of Ucp1 in brown adipocytes
Authors: Asada Rie , Kanemoto Soshi , Matsuhisa Koji , Hino Kenta , Cui Min , Cui Xiang , Kaneko Masayuki , Imaizumi Kazunori 
Published: November 2015

AbstractThe unfolded protein response (UPR) not only resolves endoplasmic reticulum (ER) stress, but also regulates cellular physiological functions. In this study, we first linked the UPR to the physiological roles of brown adipose tissue (BAT). BAT is one of the tissues that control energy homeostasis in the body. Brown adipocytes are able to dissipate energy in the form of heat owing to their mitochondrial protein, uncoupling protein 1 (UCP1). We found that one of the UPR branches, the IRE1α-XBP1 pathway, was activated during the transcriptional induction of Ucp1. Inhibiting the IRE1α-XBP1 pathway reduced the induction of Ucp1 expression. However, the activation of the IRE1α-XBP1 pathway by ER stress never upregulated Ucp1. On the other hand, the activation of protein kinase A (PKA) induced Ucp1 transcription through the activation of IRE1α-XBP1. The inhibition of PKA abrogated the activation of IRE1α-XBP1 pathway, while the inhibition of a p38 mitogen activated protein kinase (p38 MAPK), which is one of the downstream molecules of PKA, never suppressed the activation of IRE1α-XBP1 pathway. These data indicate that PKA-dependent IRE1α-XBP1 activation is crucial for the transcriptional induction of Ucp1 in brown adipocytes and they demonstrate a novel, ER stress -independent role of the UPR during thermogenesis.
Structural, electronic and vibrational properties of few-layer 2H- and 1T-TaSe2
Authors: Yan Jia-An , Cruz Mack A. Dela , Cook Brandon , Varga Kalman 
Published: November 2015

AbstractTwo-dimensional metallic transition metal dichalcogenides (TMDs) are of interest for studying phenomena such as charge-density wave (CDW) and superconductivity. Few-layer tantalum diselenides (TaSe2) are typical metallic TMDs exhibiting rich CDW phase transitions. However, a description of the structural, electronic and vibrational properties for different crystal phases and stacking configurations, essential for interpretation of experiments, is lacking. We present first- principles calculations of structural phase energetics, band dispersion near the Fermi level, phonon properties and vibrational modes at the Brillouin zone center for different layer numbers, crystal phases and stacking geometries. Evolution of the Fermi surfaces as well as the phonon dispersions as a function of layer number reveals dramatic dimensionality effects in this CDW material. Our results indicate strong electronic interlayer coupling, detail energetically possible stacking geometries and provide a basis for interpretation of Raman spectra.
Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy: An analytical technique to understand therapeutic responses at the molecular level
Authors: Kalmodia Sushma , Parameswaran Sowmya , Yang Wenrong , Barrow Colin J. , Krishnakumar Subramanian 
Published: November 2015

AbstractRapid monitoring of the response to treatment in cancer patients is essential to predict the outcome of the therapeutic regimen early in the course of the treatment. The conventional methods are laborious, time-consuming, subjective and lack the ability to study different biomolecules and their interactions, simultaneously. Since; mechanisms of cancer and its response to therapy is dependent on molecular interactions and not on single biomolecules, an assay capable of studying molecular interactions as a whole, is preferred. Fourier Transform Infrared (FTIR) spectroscopy has become a popular technique in the field of cancer therapy with an ability to elucidate molecular interactions. The aim of this study, was to explore the utility of the FTIR technique along with multivariate analysis to understand whether the method has the resolution to identify the differences in the mechanism of therapeutic response. Towards achieving the aim, we utilized the mouse xenograft model of retinoblastoma and nanoparticle mediated targeted therapy. The results indicate that the mechanism underlying the response differed between the treated and untreated group which can be elucidated by unique spectral signatures generated by each group. The study establishes the efficiency of non-invasive, label-free and rapid FTIR method in assessing the interactions of nanoparticles with cellular macromolecules towards monitoring the response to cancer therapeutics.
The Shiga toxin 2 production level in enterohemorrhagic Escherichia coli O157:H7 is correlated with the subtypes of toxin-encoding phage
Authors: Ogura Yoshitoshi , Mondal Shakhinur Islam , Islam Md Rakibul , Mako Toshihiro , Arisawa Kokichi , Katsura Keisuke , Ooka Tadasuke , Gotoh Yasuhiro , Murase Kazunori , Ohnishi Makoto , Hayashi Tetsuya 
Published: November 2015

AbstractEnterohemorrhagic E. coli (EHEC) causes diarrhea and hemorrhagic colitis with life-threatening complications, such as hemolytic uremic syndrome. Their major virulence factor is Shiga toxin (Stx), which is encoded by bacteriophages. Of the two types of Stx, the production of Stx2, particularly that of Stx2a (a subtype of Stx2), is a major risk factor for severe EHEC infections, but the Stx2 production level is highly variable between strains. Here, we define four major and two minor subtypes of Stx2a-encoding phages according to their replication proteins. The subtypes are correlated with Stx2a titers produced by the host O157 strains, suggesting a critical role of the phage subtype in determining the Stx2a production level. We further show that one of the two subclades in the clade 8, a proposed hyper-virulent lineage of O157, carries the Stx2 phage subtype that confers the highest Stx2 production to the host strain. The presence of this subclade may explain the proposed high virulence potential of clade 8. These results provide novel insights into the variation in virulence among O157 strains and highlight the role of phage variation in determining the production level of the virulence factors that phages encode.
Osteogenesis of peripheral blood mesenchymal stem cells in self assembling peptide nanofiber for healing critical size calvarial bony defect
Authors: Wu Guofeng , Pan Mengjie , Wang Xianghai , Wen Jinkun , Cao Shangtao , Li Zhenlin , Li Yuanyuan , Qian Changhui , Liu Zhongying , Wu Wutian , Zhu Lixin , Guo Jiasong 
Published: November 2015

AbstractPeripheral blood mesenchymal stem cells (PBMSCs) may be easily harvested from patients, permitting autologous grafts for bone tissue engineering in the future. However, the PBMSC’s capabilities of survival, osteogenesis and production of new bone matrix in the defect area are still unclear. Herein, PBMSCs were seeded into a nanofiber scaffold of self-assembling peptide (SAP) and cultured in osteogenic medium. The results indicated SAP can serve as a promising scaffold for PBMSCs survival and osteogenic differentiation in 3D conditions. Furthermore, the SAP seeded with the induced PBMSCs was splinted by two membranes of poly(lactic)-glycolic acid (PLGA) to fabricate a composited scaffold which was then used to repair a critical-size calvarial bone defect model in rat. Twelve weeks later the defect healing and mineralization were assessed by H&E staining and microcomputerized tomography (micro-CT). The osteogenesis and new bone formation of grafted cells in the scaffold were evaluated by immunohistochemistry. To our knowledge this is the first report with solid evidence demonstrating PBMSCs can survive in the bone defect area and directly contribute to new bone formation. Moreover, the present data also indicated the tissue engineering with PBMSCs/SAP/PLGA scaffold can serve as a novel prospective strategy for healing large size cranial defects.
Dietary fat intake and endometrial cancer risk: dose-response meta-analysis of epidemiological studies
Authors: Jiang Luo , Hou Rui , Gong Ting-Ting , Wu Qi-Jun 
Published: November 2015

AbstractEpidemiological studies have provided controversial evidence of the association between dietary fat intake and endometrial cancer (EC) risk. To address this inconsistency, we conducted this dose-response meta-analysis by total dietary fat intake, based on epidemiological studies published up to the end of June 2015 identified from PubMed, EMBASE and Web of Science. Two authors (RH and Q-JW) independently performed the eligibility evaluation and data extraction. All differences were resolved by discussion with the third investigator (LJ). Random-effects models were used to estimate summary relative risks (RRs) and 95% confidence intervals (CIs). Overall, the search yielded 16 studies (6 cohort and 10 case-control studies) that involved a total of 7556 EC cases and 563,781 non-cases. The summary RR for EC for each 30g/day increment intake was 0.98 (95%CI = 0.95–1.001; I2 = 0%; n = 11) for total dietary fat. Non-significant results were observed in plant-based fat (summary RR = 1.05, 95%CI = 0.94–1.18; I2 = 0%; n = 5) and animal-based fat (summary RR = 1.17, 95%CI = 0.92–1.36; I2 = 85.0%; n = 6). Additionally, the null associations were observed in almost all the subgroup and sensitivity analyses. In conclusion, findings of the present meta-analysis suggested a lack of association between total dietary fat intake and EC risk. Further studies, especially prospective designed studies are warranted to confirm our findings.
Influence of copper content on the electrocatalytic activity toward methanol oxidation of CoχCuy alloy nanoparticles-decorated CNFs
Authors: Ghouri Zafar Khan , Barakat Nasser A. M. , Kim Hak Yong 
Published: November 2015

AbstractIn this study, CoCu alloy nanoparticles-incorporated carbon nanofibers are introduced as effective non precious electrocatalyst for methanol oxidation in alkaline medium. The introduced electrocatalyst has been synthesized by simple and effective process; electrospinning. Typically, calcination, in nitrogen atmosphere, of electrospun nanofibers composed of cobalt acetate, copper acetate and poly (vinyl alcohol) leads to form carbon nanofibers decorated by CoCu nanoparticles. The nanofibrous morphology and alloy structure have been confirmed by SEM, TEM and XRD analyses. Investigation of the electrocatalytic activity indicates that copper content has strong influence, the alloy nanoparticles having the composition Cu5%Co95%showed distinct high performance; 100 times higher than other formulations. Overall, the introduced study revealed the veil about the distinct role of copper in enhancing the electrocatalytic activity of cobalt-based materials.
Supranormal orientation selectivity of visual neurons in orientation-restricted animals
Authors: Sasaki Kota S. , Kimura Rui , Ninomiya Taihei , Tabuchi Yuka , Tanaka Hiroki , Fukui Masayuki , Asada Yusuke C. , Arai Toshiya , Inagaki Mikio , Nakazono Takayuki , Baba Mika , Kato Daisuke , Nishimoto Shinji , Sanada Takahisa M. , Tani Toshiki , Imamura Kazuyuki , Tanaka Shigeru , Ohzawa Izumi 
Published: November 2015

AbstractAltered sensory experience in early life often leads to remarkable adaptations so that humans and animals can make the best use of the available information in a particular environment. By restricting visual input to a limited range of orientations in young animals, this investigation shows that stimulus selectivity, e.g., the sharpness of tuning of single neurons in the primary visual cortex, is modified to match a particular environment. Specifically, neurons tuned to an experienced orientation in orientation-restricted animals show sharper orientation tuning than neurons in normal animals, whereas the opposite was true for neurons tuned to non-experienced orientations. This sharpened tuning appears to be due to elongated receptive fields. Our results demonstrate that restricted sensory experiences can sculpt the supranormal functions of single neurons tailored for a particular environment. The above findings, in addition to the minimal population response to orientations close to the experienced one, agree with the predictions of a sparse coding hypothesis in which information is represented efficiently by a small number of activated neurons. This suggests that early brain areas adopt an efficient strategy for coding information even when animals are raised in a severely limited visual environment where sensory inputs have an unnatural statistical structure.