bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 Vaccine-elicited Antibodies Reverted to Their Inferred Naive Germline Reveal Associations between Binding Affinity and in vivo Activation
Authors: Dai Kaifan , Khan Salar N , Wang Yimeng , He Linling , Guenaga Javier , Ingale Jidnyasa , Sundling Christopher , O’Dell Sijy , McKee Krisha , Phad Ganesh , Corcoran Martin , Wilson Richard , Mascola John R , Zhu Jiang , Li Yuxing , Hedestam Gunilla B Karlsson , Wyatt Richard T 
Published: February 2016

AbstractThe elicitation of HIV-1 broadly neutralizing antibodies following envelope glycoprotein (Env) vaccination is exceedingly difficult. Suboptimal engagement of naïve B cells is suggested to limit these low frequency events, especially at the conserved CD4bs. Here, we analyzed CD4bs-directed monoclonal antibodies (mAbs) elicited by YU2 gp140-foldon trimers in a non-human primate by selective sorting using CD4bs “knock out” trimers. Following two inoculations, the CD4bs-directed mAbs efficiently recognized the eliciting immunogen in their affinity-maturing state but did not recognize CD4bs-defective probes. We reverted these mAbs to their most likely inferred germline (igL) state, leaving the HCDR3 unaltered, to establish correlates of in vitro affinity to in vivo activation. Most igL-reverted mAbs bound the eliciting gp140 immunogen, indicating that CD4bs-directed B cells possessing reasonable affinity existed in the naïve repertoire. We detected relatively high affinities for the majority of the igL mAbs to gp120 and of Fabs to gp140, which, as expected, increased when the antibodies ‘matured’ following vaccination. Affinity increases were associated with slower off-rates as well as with acquisition of neutralizing capacity. These data reveal in vitro binding properties associated with in vivo activation that result in functional archiving of antigen-specific B cells elicited by a complex glycoprotein antigen following immunization.
Amyloidβ Peptides in interaction with raft-mime model membranes: a neutron reflectivity insight
Authors: Rondelli Valeria , Brocca Paola , Motta Simona , Messa Massimo , Colombo Laura , Salmona Mario , Fragneto Giovanna , Cantù Laura , Del Favero Elena 
Published: February 2016

AbstractThe role of first-stage β–amyloid aggregation in the development of the Alzheimer disease, is widely accepted but still unclear. Intimate interaction with the cell membrane is invoked. We designed Neutron Reflectometry experiments to reveal the existence and extent of the interaction between β–amyloid (Aβ) peptides and a lone customized biomimetic membrane and their dependence on the aggregation state of the peptide. The membrane, asymmetrically containing phospholipids, GM1 and cholesterol in biosimilar proportion, is a model for a raft, a putative site for amyloid-cell membrane interaction. We found that the structured-oligomer of Aβ(1-42), its most acknowledged membrane-active state, is embedded as such into the external leaflet of the membrane. Conversely, the Aβ(1-42) unstructured early-oligomers deeply penetrate the membrane, likely mimicking the interaction at neuronal cell surfaces, when the Aβ(1-42) is cleaved from APP protein and the membrane constitutes a template for its further structural evolution. Moreover, the smaller Aβ(1-6) fragment, the N-terminal portion of Aβ, was also used. Aβ N-terminal is usually considered as involved in oligomer stabilization but not in the peptide-membrane interaction. Instead, it was seen to remove lipids from the bilayer, thus suggesting its role, once in the whole peptide, in membrane leakage, favouring peptide recruitment.
The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA
Authors: Zhao Zi-Hua , Cui Bing-Yi , Li Zhi-Hong , Jiang Fan , Yang Qian-Qian , Kučerová Zuzana , Stejskal Václav , Opit George , Cao Yang , Li Fu-Jun 
Published: February 2016

AbstractPsocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-productLiposcelisspp. psocids (L. bostrychophila,L. entomophila,L. decolor,L. paeta,L. brunnea,L. corrodens,L. mendax,L. rufa,L. pearmani, andL. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA.
A first-principles study on the phonon transport in layered BiCuOSe
Authors: Shao Hezhu , Tan Xiaojian , Liu Guo-Qiang , Jiang Jun , Jiang Haochuan 
Published: February 2016

AbstractFirst-principles calculations are employed to investigate the phonon transport of BiCuOSe. Our calculations reproduce the lattice thermal conductivity of BiCuOSe. The calculated grüneisen parameter is 2.4 ~ 2.6 at room temperature, a fairly large value indicating a strong anharmonicity in BiCuOSe, which leads to its ultralow lattice thermal conductivity. The contribution to total thermal conductivity from high-frequency optical phonons, which are mostly contributed by the vibrations of O atoms, is larger than 1/3, remarkably different from the usual picture with very little contribution from high-frequency optical phonons. Our calculations show that both the high group velocities and low scattering processes involved make the high-frequency optical modes contribute considerably to the total lattice thermal conductivity. In addition, we show that the sound velocity and bulk modulus along a and c axes exhibit strong anisotropy, which results in the anisotropic thermal conductivity in BiCuOSe.
Serum microRNA microarray analysis identifies miR-4429 and miR-4689 are potential diagnostic biomarkers for biliary atresia
Authors: Dong Rui , Shen Zhen , Zheng Chao , Chen Gong , Zheng Shan 
Published: February 2016

AbstractThis study aimed to investigate pathogenesis and novel diagnostic biomarkers of biliary atresia (BA). Serum samples from infants with BA and non-BA neonatal cholestasis (NC) were collected for miRNA microarray analysis and then differentially expressed miRNAs were screened. Differentially expressed miRNAs were validated by qRT-PCR using an independent serum samples from infants with BA and NC. Diagnostic utility of validated miRNAs was further analyzed using serum samples by receiver-operating characteristic curve analysis. Totally, 13 differentially expressed miRNAs were identified including 11 down-regulated and 2 up-regulated ones. Target genes of hsa-miR-4429 and hsa-miR-4689 were significantly involved in FoxO signaling pathway. Eight differentially expressed miRNAs were chosen for validation by qRT-PCR analysis and four miRNAs (hsa-miR-150-3p, hsa-miR-4429, hsa-miR-4689 and hsa-miR-92a-3p) were differentially expressed. The area under the curve of hsa-miR-4429 and hsa-miR-4689 was 0.789 (sensitivity = 83.33%, specificity = 80.00%) and 0.722 (sensitivity = 66.67%, specificity = 80.00%), respectively. Differentially expressed miRNAs including hsa-miR-4429 and hsa-miR-4689 might play critical roles in BA by regulating their target genes and these two miRNAs may have the potential to become diagnostic biomarkers.
Interface Structure of MoO3 on Organic Semiconductors
Authors: White Robin T. , Thibau Emmanuel S. , Lu Zheng-Hong 
Published: February 2016

AbstractWe have systematically studied interface structure formed by vapor-phase deposition of typical transition metal oxide MoO3on organic semiconductors. Eight organic hole transport materials have been used in this study. Ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy are used to measure the evolution of the physical, chemical and electronic structure of the interfaces at various stages of MoO3deposition on these organic semiconductor surfaces. For the interface physical structure, it is found that MoO3diffuses into the underlying organic layer, exhibiting a trend of increasing diffusion with decreasing molecular molar mass. For the interface chemical structure, new carbon and molybdenum core-level states are observed, as a result of interfacial electron transfer from organic semiconductor to MoO3. For the interface electronic structure, energy level alignment is observed in agreement with the universal energy level alignment rule of molecules on metal oxides, despite deposition order inversion.
Iron mitigates DMT1-mediated manganese cytotoxicity via the ASK1-JNK signaling axis: Implications of iron supplementation for manganese toxicity
Authors: Tai Yee Kit , Chew Katherine C. M. , Tan Bryce W. Q. , Lim Kah-Leong , Soong Tuck Wah 
Published: February 2016

AbstractManganese (Mn2+) neurotoxicity from occupational exposure is well documented to result in a Parkinson-like syndrome. Although the understanding of Mn2+ cytotoxicity is still incomplete, both Mn2+ and Fe2+ can be transported via the divalent metal transporter 1 (DMT1), suggesting that competitive uptake might disrupt Fe2+ homeostasis. Here, we found that DMT1 overexpression significantly enhanced Mn2+ cytoplasmic accumulation and JNK phosphorylation, leading to a reduction in cell viability. Although a robust activation of autophagy was observed alongside these changes, it did not trigger autophagic cell death, but was instead shown to be essential for the degradation of ferritin, which normally sequesters labile Fe2+. Inhibition of ferritin degradation through the neutralization of lysosomal pH resulted in increased ferritin and enhanced cytoplasmic Fe2+ depletion. Similarly, direct Fe2+ chelation also resulted in aggravated Mn2+-mediated JNK phosphorylation, while Fe2+ repletion protected cells and this occurs via the ASK1-thioredoxin pathway. Taken together, our study presents the novel findings that Mn2+ cytotoxicity involves the depletion of the cytoplasmic Fe2+ pool and the increase in autophagy-lysosome activity is important to maintain Fe2+ homeostasis. Thus, Fe2+ supplementation could have potential applications in the prevention and treatment of Mn2+-mediated toxicity.
Competition in the presence of aging: dominance, coexistence, and alternation between states
Authors: Pérez Toni , Klemm Konstantin , Eguíluz Víctor M. 
Published: February 2016

AbstractWe study the stochastic dynamics of coupled states with transition probabilities depending on local persistence, this is, the time since a state has changed. When the system has a preference to adopt older states the system orders quickly due to the dominance of old states. When preference for new states prevails, the system can show coexistence of states or synchronized collective behavior resulting in long ordering times. In this case, the magnetization of the system oscillates around zero. Finally we discuss a potential application in social systems.
Spectroscopic Study of Terahertz Generation in Mid-Infrared Quantum Cascade Lasers
Authors: Jiang Yifan , Vijayraghavan Karun , Jung Seungyong , Jiang Aiting , Kim Jae Hyun , Demmerle Frederic , Boehm Gerhard , Amann Markus C. , Belkin Mikhail A. 
Published: February 2016

AbstractTerahertz quantum cascade laser sources based on intra-cavity difference-frequency generation are currently the only room-temperature mass-producible diode-laser-like emitters of coherent 1–6 THz radiation. Device performance has improved dramatically over the past few years to reach milliwatt-level power output and broad tuning from 1.2 to 5.9 THz, all at room-temperature. Terahertz output in these sources originates from intersubband optical nonlinearity in the laser active region. Here we report the first comprehensive spectroscopic study of the optical nonlinearity and investigate its dependence on the mid-infrared pump frequencies. Our work shows that the terahertz generation efficiency can vary by a factor of 2 or greater depending on the spectral position of the mid-infrared pumps for a fixed THz difference-frequency. We have also measured for the first time the linewidth for transitions between the lower quantum cascade laser states, which is critical for determining terahertz nonlinearity and predicting optical loss in quantum cascade laser waveguides.
Hierarchically structured activated carbon for ultracapacitors
Authors: Kim Mok-Hwa , Kim Kwang-Bum , Park Sun-Min , Roh Kwang Chul 
Published: February 2016

AbstractTo resolve the pore-associated bottleneck problem observed in the electrode materials used for ultracapacitors, which inhibits the transport of the electrolyte ions, we designed hierarchically structured activated carbon (HAC) by synthesizing a mesoporous silica template/carbon composite and chemically activating it to simultaneously remove the silica template and increase the pore volume. The resulting HAC had a well-designed, unique porous structure, which allowed for large interfaces for efficient electric double-layer formation. Given the unique characteristics of the HAC, we believe that the developed synthesis strategy provides important insights into the design and fabrication of hierarchical carbon nanostructures. The HAC, which had a specific surface area of 1,957 m2 g−1, exhibited an extremely high specific capacitance of 157 F g−1 (95 F cc−1), as well as a high rate capability. This indicated that it had superior energy storage capability and was thus suitable for use in advanced ultracapacitors.
Detecting signatures of positive selection associated with musical aptitude in the human genome
Authors: Liu Xuanyao , Kanduri Chakravarthi , Oikkonen Jaana , Karma Kai , Raijas Pirre , Ukkola-Vuoti Liisa , Teo Yik-Ying , Järvelä Irma 
Published: February 2016

AbstractAbilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude.
Niclosamide inhibits leaf blight caused by Xanthomonas oryzae in rice
Authors: Kim Sung-Il , Song Jong Tae , Jeong Jin-Yong , Seo Hak Soo 
Published: February 2016

AbstractRice leaf blight, which is caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), results in huge losses in grain yield. Here, we show that Xoo-induced rice leaf blight is effectively controlled by niclosamide, an oral antihelminthic drug and molluscicide, which also functions as an anti-tumor agent. Niclosamide directly inhibited the growth of the three Xoo strains PXO99, 10208 and K3a. Niclosamide moved long distances from the site of local application to distant rice tissues. Niclosamide also increased the levels of salicylate and induced the expression of defense-related genes such as OsPR1 and OsWRKY45, which suppressed Xoo-induced leaf wilting. Niclosamide had no detrimental effects on vegetative/reproductive growth and yield. These combined results indicate that niclosamide can be used to block bacterial leaf blight in rice with no negative side effects.
Mitigation of Coral Reef Warming Across the Central Pacific by the Equatorial Undercurrent: A Past and Future Divide
Authors: Karnauskas Kristopher B. , Cohen Anne L. , Gove Jamison M. 
Published: February 2016

AbstractGlobal climate models (GCMs) predict enhanced warming and nutrient decline across the central tropical Pacific as trade winds weaken with global warming. Concurrent changes in circulation, however, have potential to mitigate these effects for equatorial islands. The implications for densely populated island nations, whose livelihoods depend on ecosystem services, are significant. A unique suite of in situ measurements coupled with state-of-the-art GCM simulations enables us to quantify the mitigation potential of the projected circulation change for three coral reef ecosystems under two future scenarios. Estimated historical trends indicate that over 100% of the large-scale warming to date has been offset locally by changes in circulation, while future simulations predict a warming mitigation effect of only 5–10% depending on the island. The pace and extent to which GCM projections overwhelm historical trends will play a key role in defining the fate of marine ecosystems and island communities across the tropical Pacific.
Quantitative molecular phenotyping with topically applied SERS nanoparticles for intraoperative guidance of breast cancer lumpectomy
Authors: Wang Yu , Kang Soyoung , Khan Altaz , Ruttner Gabriel , Leigh Steven Y. , Murray Melissa , Abeytunge Sanjee , Peterson Gary , Rajadhyaksha Milind , Dintzis Suzanne , Javid Sara , Liu Jonathan T.C. 
Published: February 2016

AbstractThere is a need to image excised tissues during tumor-resection procedures in order to identify residual tumors at the margins and to guide their complete removal. The imaging of dysregulated cell-surface receptors is a potential means of identifying the presence of diseases with high sensitivity and specificity. However, due to heterogeneities in the expression of protein biomarkers in tumors, molecular-imaging technologies should ideally be capable of visualizing a multiplexed panel of cancer biomarkers. Here, we demonstrate that the topical application and quantification of a multiplexed cocktail of receptor-targeted surface-enhanced Raman scattering (SERS) nanoparticles (NPs) enables rapid quantitative molecular phenotyping (QMP) of the surface of freshly excised tissues to determine the presence of disease. In order to mitigate the ambiguity due to nonspecific sources of contrast such as off-target binding or uneven delivery, a ratiometric method is employed to quantify the specific vs. nonspecific binding of the multiplexed NPs. Validation experiments with human tumor cell lines, fresh human tumor xenografts in mice and fresh human breast specimens demonstrate that QMP imaging of excised tissues agrees with flow cytometry and immunohistochemistry and that this technique may be achieved in less than 15 minutes for potential intraoperative use in guiding breast-conserving surgeries.
Nocturnally migrating songbirds drift when they can and compensate when they must
Authors: Horton Kyle G. , Van Doren Benjamin M. , Stepanian Phillip M. , Hochachka Wesley M. , Farnsworth Andrew , Kelly Jeffrey F. 
Published: February 2016

AbstractThe shortest possible migratory route for birds is not always the best route to travel. Substantial research effort has established that birds in captivity are capable of orienting toward the direction of an intended goal, but efforts to examine how free-living birds use navigational information under conditions that potentially make direct flight toward that goal inefficient have been limited in spatiotemporal scales and in the number of individuals observed because of logistical and technological limitations. Using novel and recently developed techniques for analysis of Doppler polarimetric weather surveillance radar data, we examined two impediments for nocturnally migrating songbirds in eastern North America following shortest-distance routes: crosswinds and oceans. We found that migrants in flight often drifted sideways on crosswinds, but most strongly compensated for drift when near the Atlantic coast. Coastal migrants’ tendency to compensate for wind drift also increased through the night, while no strong temporal differences were observed at inland sites. Such behaviors suggest that birds migrate in an adaptive way to conserve energy by assessing while airborne the degree to which they must compensate for wind drift.
Enhancing performance and uniformity of CH3NH3PbI3−xClx perovskite solar cells by air-heated-oven assisted annealing under various humidities
Authors: Zhou Qing , Jin Zhiwen , Li Hui , Wang Jizheng 
Published: February 2016

AbstractTo fabricate high-performance metal-halide perovskite solar cells, a thermal annealing process is indispensable in preparing high quality perovskite film. And usually such annealing is performed on hot plate. However hot-plate annealing could cause problems such as inhomogeneous heating (induced by non-tight contact between the sample and the plate), it is also not fit for large scale manufactory. In this paper, we conduct the annealing process in air-heated oven under various humidity environments, and compared the resulted films (CH3NH3PbI3−xClx) and devices (Al/PC61BM/CH3NH3PbI3−xClx/PEDOT:PSS/ITO/glass) with that obtained via hot-plate annealing. It is found that the air-heated-oven annealing is superior to the hot-plate annealing: the annealing time is shorter, the films are more uniform, and the devices exhibit higher power conversion efficiency and better uniformity. The highest efficiencies achieved for the oven and hot-plate annealing processes are 14.9% and 13.5%, and the corresponding standard deviations are 0.5% and 0.8%, respectively. Our work here indicates that air-heated-oven annealing could be a more reliable and more efficient way for both lab research and large-scale production.
Facile synthesis of flexible macroporous polypropylene sponges for separation of oil and water
Authors: Wang Guowei , Uyama Hiroshi 
Published: February 2016

AbstractOil spill disasters always occur accidentally, accompanied by the release of plenty of crude oil that could spread quickly over a wide area, creating enormous damage to the fragile marine ecological system. Therefore, the facile large-scale synthesis of hydrophobic three-dimensional (3-D) porous sorbents from low cost raw materials is in urgent demand. In this study, we report the facile template-free synthesis of polypropylene (PP) sponge by using a thermally-induced phase separation (TIPS) technique. The obtained sponge showed macroporous structure, excellent mechanical property, high hydrophobicity and superoleophilicity. Oil could be separated from an oil/water mixture by simple immersing the sponge into the mixture and subsequent squeezing the sponge. All of these features make this sponge the most promising oil sorbent that will replace commercial non-woven PP fabrics.