bluuebunny/crossref_metadata_2025_split huggingface dataset:
Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis
Authors: Wang Chunyan , Bae Jin H. , Zhang David Yu 
Published: January 2016

AbstractDNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C.
D25V apolipoprotein C-III variant causes dominant hereditary systemic amyloidosis and confers cardiovascular protective lipoprotein profile
Authors: Valleix Sophie , Verona Guglielmo , Jourde-Chiche Noémie , Nédelec Brigitte , Mangione P. Patrizia , Bridoux Frank , Mangé Alain , Dogan Ahmet , Goujon Jean-Michel , Lhomme Marie , Dauteuille Carolane , Chabert Michèle , Porcari Riccardo , Waudby Christopher A. , Relini Annalisa , Talmud Philippa J. , Kovrov Oleg , Olivecrona Gunilla , Stoppini Monica , Christodoulou John , Hawkins Philip N. , Grateau Gilles , Delpech Marc , Kontush Anatol , Gillmore Julian D. , Kalopissis Athina D. , Bellotti Vittorio 
Published: January 2016

AbstractApolipoprotein C-III deficiency provides cardiovascular protection, but apolipoprotein C-III is not known to be associated with human amyloidosis. Here we report a form of amyloidosis characterized by renal insufficiency caused by a new apolipoprotein C-III variant, D25V. Despite their uremic state, the D25V-carriers exhibit low triglyceride (TG) and apolipoprotein C-III levels, and low very-low-density lipoprotein (VLDL)/high high-density lipoprotein (HDL) profile. Amyloid fibrils comprise the D25V-variant only, showing that wild-type apolipoprotein C-III does not contribute to amyloid deposition in vivo. The mutation profoundly impacts helical structure stability of D25V-variant, which is remarkably fibrillogenic under physiological conditions in vitro producing typical amyloid fibrils in its lipid-free form. D25V apolipoprotein C-III is a new human amyloidogenic protein and the first conferring cardioprotection even in the unfavourable context of renal failure, extending the evidence for an important cardiovascular protective role of apolipoprotein C-III deficiency. Thus, fibrate therapy, which reduces hepatic APOC3 transcription, may delay amyloid deposition in affected patients.
Bioabsorbable polymer optical waveguides for deep-tissue photomedicine
Authors: Nizamoglu Sedat , Gather Malte C. , Humar Matjaž , Choi Myunghwan , Kim Seonghoon , Kim Ki Su , Hahn Sei Kwang , Scarcelli Giuliano , Randolph Mark , Redmond Robert W. , Yun Seok Hyun 
Published: January 2016

AbstractAdvances in photonics have stimulated significant progress in medicine, with many techniques now in routine clinical use. However, the finite depth of light penetration in tissue is a serious constraint to clinical utility. Here we show implantable light-delivery devices made of bio-derived or biocompatible, and biodegradable polymers. In contrast to conventional optical fibres, which must be removed from the body soon after use, the biodegradable and biocompatible waveguides may be used for long-term light delivery and need not be removed as they are gradually resorbed by the tissue. As proof of concept, we demonstrate this paradigm-shifting approach for photochemical tissue bonding (PTB). Using comb-shaped planar waveguides, we achieve a full thickness (>10 mm) wound closure of porcine skin, which represents ∼10-fold extension of the tissue area achieved with conventional PTB. The results point to a new direction in photomedicine for using light in deep tissues.
Evolution of the fish heart by sub/neofunctionalization of an elastin gene
Authors: Moriyama Yuuta , Ito Fumihiro , Takeda Hiroyuki , Yano Tohru , Okabe Masataka , Kuraku Shigehiro , Keeley Fred W. , Koshiba-Takeuchi Kazuko 
Published: January 2016

AbstractThe evolution of phenotypic traits is a key process in diversification of life. However, the mechanisms underlying the emergence of such evolutionary novelties are largely unknown. Here we address the origin of bulbus arteriosus (BA), an organ of evolutionary novelty seen in the teleost heart outflow tract (OFT), which sophisticates their circulatory system. The BA is a unique organ that is composed of smooth muscle while the OFTs in other vertebrates are composed of cardiac muscle. Here we reveal that the teleost-specific extracellular matrix (ECM) gene,elastin b, was generated by the teleost-specific whole-genome duplication and neofunctionalized to contribute to acquisition of the BA by regulating cell fate determination of cardiac precursor cells into smooth muscle. Furthermore, we show that the mechanotransduceryapis involved in this cell fate determination. Our findings reveal a mechanism of generating evolutionary novelty through alteration of cell fate determination by the ECM.
Iron Age and Anglo-Saxon genomes from East England reveal British migration history
Authors: Schiffels Stephan , Haak Wolfgang , Paajanen Pirita , Llamas Bastien , Popescu Elizabeth , Loe Louise , Clarke Rachel , Lyons Alice , Mortimer Richard , Sayer Duncan , Tyler-Smith Chris , Cooper Alan , Durbin Richard 
Published: January 2016

AbstractBritish population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.
Substantial bulk photovoltaic effect enhancement via nanolayering
Authors: Wang Fenggong , Young Steve M. , Zheng Fan , Grinberg Ilya , Rappe Andrew M. 
Published: January 2016

AbstractSpontaneous polarization and inversion symmetry breaking in ferroelectric materials lead to their use as photovoltaic devices. However, further advancement of their applications are hindered by the paucity of ways of reducing bandgaps and enhancing photocurrent. By unravelling the correlation between ferroelectric materials’ responses to solar irradiation and their local structure and electric polarization landscapes, here we show from first principles that substantial bulk photovoltaic effect enhancement can be achieved by nanolayering PbTiO3 with nickel ions and oxygen vacancies ((PbNiO2)x(PbTiO3)1−x). The enhancement of the total photocurrent for different spacings between the Ni-containing layers can be as high as 43 times due to a smaller bandgap and photocurrent direction alignment for all absorption energies. This is due to the electrostatic effect that arises from nanolayering. This opens up the possibility for control of the bulk photovoltaic effect in ferroelectric materials by nanoscale engineering of their structure and composition.
TRAIP/RNF206 is required for recruitment of RAP80 to sites of DNA damage
Authors: Soo Lee Nam , Jin Chung Hee , Kim Hyoung-June , Yun Lee Seo , Ji Jae-Hoon , Seo Yoojeong , Hun Han Seung , Choi Minji , Yun Miyong , Lee Seok-Geun , Myung Kyungjae , Kim Yonghwan , Chul Kang Ho , Kim Hongtae 
Published: January 2016

AbstractRAP80 localizes to sites of DNA insults to enhance the DNA-damage responses. Here we identify TRAIP/RNF206 as a novel RAP80-interacting protein and find that TRAIP is necessary for translocation of RAP80 to DNA lesions. Depletion of TRAIP results in impaired accumulation of RAP80 and functional downstream partners, including BRCA1, at DNA lesions. Conversely, accumulation of TRAIP is normal in RAP80-depleted cells, implying that TRAIP acts upstream of RAP80 recruitment to DNA lesions. TRAIP localizes to sites of DNA damage and cells lacking TRAIP exhibit classical DNA-damage response-defect phenotypes. Biochemical analysis reveals that the N terminus of TRAIP is crucial for RAP80 interaction, while the C terminus of TRAIP is required for TRAIP localization to sites of DNA damage through a direct interaction with RNF20–RNF40. Taken together, our findings demonstrate that the novel RAP80-binding partner TRAIP regulates recruitment of the damage signalling machinery and promotes homologous recombination.
DSF Guided Refolding As A Novel Method Of Protein Production
Authors: Biter Amadeo B. , de la Peña Andres H. , Thapar Roopa , Lin Jean Z. , Phillips Kevin J. 
Published: January 2016

AbstractThe Anfinsen hypothesis, the demonstration of which led to the Nobel prize in Chemistry, posits that all information required to determine a proteins’ three dimensional structure is contained within its amino acid sequence. This suggests that it should be possible, in theory, to fold any protein in vitro. In practice, however, protein production by refolding is challenging because suitable refolding conditions must be empirically determined for each protein and can be painstaking. Here we demonstrate, using a variety of proteins, that differential scanning fluorimetry (DSF) can be used to determine and optimize conditions that favor proper protein folding in a rapid and high-throughput fashion. The resulting method, which we deem DSF guided refolding (DGR), thus enables the production of aggregation-prone and disulfide-containing proteins by refolding from E. coli inclusion bodies, which would not normally be amenable to production in bacteria.
Semi-coke briquettes: towards reducing emissions of primary PM2.5, particulate carbon and carbon monoxide from household coal combustion in China
Authors: Li Qing , Li Xinghua , Jiang Jingkun , Duan Lei , Ge Su , Zhang Qi , Deng Jianguo , Wang Shuxiao , Hao Jiming 
Published: January 2016

AbstractDirect household use of unprocessed raw coals for cooking and heating without any air pollution control device has caused serious indoor and outdoor environment problems by emitting particulate matter (PM) and gaseous pollutants. This study examined household emission reduction by switching from unprocessed bituminous and anthracite coals to processed semi-coke briquettes. Two typical stoves were used to test emission characteristics when burning 20 raw coal samples commonly used in residential heating activities and 15 semi-coke briquette samples which were made from bituminous coals by industrial carbonization treatment. The carbonization treatment removes volatile compounds from raw coals which are the major precursors for PM formation and carbon emission. The average emission factors of primary PM2.5, elemental carbon, organic carbon and carbon monoxide for the tested semi-coke briquettes are much lower than those of the tested raw coals. Based on the current coal consumption data in China, switching to semi-coke briquettes can reduce average emission factors of these species by about 92%, 98%, 91% and 34%, respectively. Additionally, semi-coke briquette has relatively lower price and higher burnout ratio. The replacement of raw coals with semi-coke briquettes is a feasible path to reduce pollution emissions from household activities.
Preservation of carbon dioxide clathrate hydrate in the presence of trehalose under freezer conditions
Authors: Nagashima Hironori D. , Takeya Satoshi , Uchida Tsutomu , Ohmura Ryo 
Published: January 2016

AbstractTo investigate the preservation of CO2 clathrate hydrate in the presence of sugar for the novel frozen dessert, mass fractions of CO2 clathrate hydrate in CO2 clathrate hydrate samples coexisting with trehalose were intermittently measured. The samples were prepared from trehalose aqueous solution with trehalose mass fractions of 0.05 and 0.10 at 3.0 MPa and 276.2 K. The samples having particle sizes of 1.0 mm and 5.6–8.0 mm were stored at 243.2 K and 253.2 K for three weeks under atmospheric pressure. The mass fractions of CO2 clathrate hydrate in the samples were 0.87–0.97 before the preservation and CO2 clathrate hydrate still remained 0.56–0.76 in the mass fractions for 5.6–8.0 mm samples and 0.37–0.55 for 1.0 mm samples after the preservation. The preservation in the trehalose system was better than in the sucrose system and comparable to that in the pure CO2 clathrate hydrate system. This comparison indicates that trehalose is a more suitable sugar for the novel frozen carbonated dessert using CO2 clathrate hydrate than sucrose in terms of CO2 concentration in the dessert. It is inferred that existence of aqueous solution in the samples is a significant factor of the preservation of CO2 clathrate hydrate in the presence of sugar.
Renormalization-group approach to quantum Fisher information in an XY model with staggered Dzyaloshinskii-Moriya interaction
Authors: Liu X. M. , Cheng W. W. , Liu J. -M. 
Published: January 2016

AbstractWe investigate the quantum Fisher information and quantum phase transitions of an XY spin chain with staggered Dzyaloshinskii-Moriya interaction using the quantum renormalization-group method. The quantum Fisher information, its first-derivatives and the finite-size scaling behaviors are rigorously calculated respectively. The singularity of the derivatives at the phase transition point as a function of lattice size is carefully discussed and it is revealed that the scaling exponent for quantum Fisher information at the critical point can be used to describe the correlation length of this model, addressing the substantial role of staggered Dzyaloshinskii-Moriya interaction in modulating quantum phase transitions.
Suicide Risk Associated with Experience of Violence and Impulsivity in Alcohol Dependent Patients
Authors: Khemiri Lotfi , Jokinen Jussi , Runeson Bo , Jayaram-Lindström Nitya 
Published: January 2016

AbstractAlcohol dependence (AD) and aggression-impulsivity are both associated with increased suicide risk. There is a need to evaluate clinical tools in order to improve suicide risk assessment of AD patients. The present study consisted of 95 individuals with a diagnosis of AD, consecutively admitted for addiction treatment, compared with 95 healthy controls. Suicidal risk was assessed together with exposure of violence and impulsivity. AD patients reported significantly higher rates of exposure to violence in childhood, as measured by the Karolinska Interpersonal Violence Scale (KIVS), compared to HC. Within the AD group, individuals with history of suicidal ideation and suicidal behavior reported higher levels of violence experience compared to AD individuals without such history. AD patients with previous suicidal ideation scored higher on self-reported impulsivity as assessed by the Barratt Impulsivity Scale (BIS). Our main finding was that experience of trauma and expression of violent behavior, coupled with increased impulsivity are associated with an elevated suicide risk in AD patients. Future longitudinal studies assessing these traits are needed to evaluate their potential role in identifying AD patients at risk of future suicide.
Machine learning bandgaps of double perovskites
Authors: Pilania G. , Mannodi-Kanakkithodi A. , Uberuaga B. P. , Ramprasad R. , Gubernatis J. E. , Lookman T. 
Published: January 2016

AbstractThe ability to make rapid and accurate predictions on bandgaps of double perovskites is of much practical interest for a range of applications. While quantum mechanical computations for high-fidelity bandgaps are enormously computation-time intensive and thus impractical in high throughput studies, informatics-based statistical learning approaches can be a promising alternative. Here we demonstrate a systematic feature-engineering approach and a robust learning framework for efficient and accurate predictions of electronic bandgaps of double perovskites. After evaluating a set of more than 1.2 million features, we identify lowest occupied Kohn-Sham levels and elemental electronegativities of the constituent atomic species as the most crucial and relevant predictors. The developed models are validated and tested using the best practices of data science and further analyzed to rationalize their prediction performance.
Silver Nanoparticle-Deposited Boron Nitride Nanosheets as Fillers for Polymeric Composites with High Thermal Conductivity
Authors: Wang Fangfang , Zeng Xiaoliang , Yao Yimin , Sun Rong , Xu Jianbin , Wong Ching-Ping 
Published: January 2016

AbstractPolymer composites with high thermal conductivity have recently attracted much attention, along with the rapid development of the electronic devices toward higher speed and performance. However, a common method to enhance polymer thermal conductivity through an addition of high thermally conductive fillers usually cannot provide an expected value, especially for composites requiring electrical insulation. Here, we show that polymeric composites with silver nanoparticle-deposited boron nitride nanosheets as fillers could effectively enhance the thermal conductivity of polymer, thanks to the bridging connections of silver nanoparticles among boron nitride nanosheets. The thermal conductivity of the composite is significantly increased from 1.63 W/m-K for the composite filled with the silver nanoparticle-deposited boron nitride nanosheets to 3.06 W/m-K at the boron nitride nanosheets loading of 25.1 vol %. In addition, the electrically insulating properties of the composite are well preserved. Fitting the measured thermal conductivity of epoxy composite with one physical model indicates that the composite with silver nanoparticle-deposited boron nitride nanosheets outperforms the one with boron nitride nanosheets, owning to the lower thermal contact resistance among boron nitride nanosheets’ interfaces. The finding sheds new light on enhancement of thermal conductivity of the polymeric composites which concurrently require the electrical insulation.
Determination of Interleukin 27-Producing CD4+ and CD8+ T Cells for The Differentiation Between Tuberculous and Malignant Pleural Effusions
Authors: Liu Ya-Lan , Wu Yan-Bing , Zhai Kan , Wang Xiao-Juan , Shi Huan-Zhong 
Published: January 2016

AbstractThe numbers of IL-27+CD4+and IL-27+CD8+T cells have been found to be increased in tuberculous pleural effusion (TPE) as compared with malignant pleural effusion (MPE). The objective of the present study was to investigate whether pleural IL-27+CD4+and IL-27+CD8+T cells can distinguish patients with TPE from those with MPE. Paired specimen of pleural fluid and peripheral blood were collected from 35 patients with TPE and 46 MPE. The numbers of IL-27+CD4+and IL-27+CD8+T cells were simultaneously determined by flow cytometry. Receiver operating characteristic curve analysis was used to evaluate the capacity of IL-27+CD4+and IL-27+CD8+T cells to differentiate TPE from MPE. The sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), positive predictive value (PPV) and negative predictive value (NPV) of IL-27+CD4+T cells were 94.3%, 93.5%, 14.46, 0.06, 91.7% and 95.6%, respectively. The sensitivity, specificity, PLR, NLR, PPV and NPV of IL-27+CD8+T cells were 80.0%, 93.5%, 12.27, 0.21, 90.3% and 86.0%, respectively. The number of IL-27+CD4+in pleural fluid is a helpful diagnostic biomarker for the diagnosis of TPE, which performs better than that of IL-27+CD8+T cells.
Synthesis of two-dimensional TlxBi1−x compounds and Archimedean encoding of their atomic structure
Authors: Gruznev Dimitry V. , Bondarenko Leonid V. , Matetskiy Andrey V. , Mihalyuk Alexey N. , Tupchaya Alexandra Y. , Utas Oleg A. , Eremeev Sergey V. , Hsing Cheng-Rong , Chou Jyh-Pin , Wei Ching-Ming , Zotov Andrey V. , Saranin Alexander A. 
Published: January 2016

AbstractCrystalline atomic layers on solid surfaces are composed of a single building block, unit cell, that is copied and stacked together to form the entire two-dimensional crystal structure. However, it appears that this is not an unique possibility. We report here on synthesis and characterization of the one-atomic-layer-thick TlxBi1−x compounds which display quite a different arrangement. It represents a quasi-periodic tiling structures that are built by a set of tiling elements as building blocks. Though the layer is lacking strict periodicity, it shows up as an ideally-packed tiling of basic elements without any skips or halting. The two-dimensional TlxBi1−x compounds were formed by depositing Bi onto the Tl-covered Si(111) surface where Bi atoms substitute appropriate amount of Tl atoms. Atomic structure of each tiling element as well as arrangement of TlxBi1−x compounds were established in a detail. Electronic properties and spin texture of the selected compounds having periodic structures were characterized. The shown example demonstrates possibility for the formation of the exotic low-dimensional materials via unusual growth mechanisms.
miRNA-378 reverses chemoresistance to cisplatin in lung adenocarcinoma cells by targeting secreted clusterin
Authors: Chen Xuesong , Jiang Ying , Huang Zheping , Li Dandan , Chen Xiaodi , Cao Mengru , Meng Qingwei , Pang Hui , Sun Lichun , Zhao Yanbin , Cai Li 
Published: January 2016

AbstractCisplatin resistance is a major obstacle in the treatment of NSCLC and its mechanism has not been fully elucidated. The objectives of the study were to determine the role of miR-378 in the sensitivity of lung adenocarcinoma cells to cisplatin (cDDP) and its working mechanism. With TargetScan and luciferase assay, miR-378 was found to directly target sCLU. miR-378 and sCLU were regulated in A549/cDDP and Anip973/cDDP cells to investigate the effect of miR-378 on the sensitivity and apoptotic effects of cDDP. The effect of miR-378 upregulation on tumor growth was analyzed in a nude mouse xenograft model. The correlation between miR-378 and chemoresistance was tested in patient samples. We found that upregulation of miR-378 in A549/cDDP and Anip973/cDDP cells significantly down-regulated sCLU expression and sensitized these cells to cDDP. miR-378 overexpression inhibited tumor growth and sCLU expression in a xenograft animal model. Analysis of human lung adenocarcinoma tissues revealed that the cDDP sensitive group expressed higher levels of miR-378 and lower levels of sCLU. miR-378 and sCLU were negatively correlated. To conclude, we identified sCLU as a novel miR-378 target and we showed that targeting sCLU via miR-378 may help disable the chemoresistance against cisplatin in lung adenocarcinoma cells.