bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxidation-specific epitopes restrain bone formation
Authors: Ambrogini Elena , Que Xuchu , Wang Shuling , Yamaguchi Fumihiro , Weinstein Robert S. , Tsimikas Sotirios , Manolagas Stavros C. , Witztum Joseph L. , Jilka Robert L. 
Published: May 2018

AbstractAtherosclerosis and osteoporosis are epidemiologically linked and oxidation specific epitopes (OSEs), such as phosphocholine (PC) of oxidized phospholipids (PC-OxPL) and malondialdehyde (MDA), are pathogenic in both. The proatherogenic effects of OSEs are opposed by innate immune antibodies. Here we show that high-fat diet (HFD)-induced bone loss is attenuated in mice expressing a single chain variable region fragment of the IgM E06 (E06-scFv) that neutralizes PC-OxPL, by increasing osteoblast number and stimulating bone formation. Similarly, HFD-induced bone loss is attenuated in mice expressing IK17-scFv, which neutralizes MDA. Notably, E06-scFv also increases bone mass in mice fed a normal diet. Moreover, the levels of anti-PC IgM decrease in aged mice. We conclude that OSEs, whether produced chronically or increased by HFD, restrain bone formation, and that diminished defense against OSEs may contribute to age-related bone loss. Anti-OSEs, therefore, may represent a novel therapeutic approach against osteoporosis and atherosclerosis simultaneously.
Energy-temperature uncertainty relation in quantum thermodynamics
Authors: Miller H. J. D. , Anders J. 
Published: May 2018

AbstractIt is known that temperature estimates of macroscopic systems in equilibrium are most precise when their energy fluctuations are large. However, for nanoscale systems deviations from standard thermodynamics arise due to their interactions with the environment. Here we include such interactions and, using quantum estimation theory, derive a generalised thermodynamic uncertainty relation valid for classical and quantum systems at all coupling strengths. We show that the non-commutativity between the system’s state and its effective energy operator gives rise to quantum fluctuations that increase the temperature uncertainty. Surprisingly, these additional fluctuations are described by the average Wigner-Yanase-Dyson skew information. We demonstrate that the temperature’s signal-to-noise ratio is constrained by the heat capacity plus a dissipative term arising from the non-negligible interactions. These findings shed light on the interplay between classical and non-classical fluctuations in quantum thermodynamics and will inform the design of optimal nanoscale thermometers.
CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing
Authors: Swings Toon , Marciano David C. , Atri Benu , Bosserman Rachel E. , Wang Chen , Leysen Marlies , Bonte Camille , Schalck Thomas , Furey Ian , Van den Bergh Bram , Verstraeten Natalie , Christie Peter J. , Herman Christophe , Lichtarge Olivier , Michiels Jan 
Published: June 2018

AbstractCRISPR advances genome engineering by directing endonuclease sequence specificity with a guide RNA molecule (gRNA). For precisely targeting a gene for modification, each genetic construct requires a unique gRNA. By generating a gRNA against the flippase recognition target (FRT) site, a common genetic element shared by multiple genetic collections, CRISPR-FRT circumvents this design constraint to provide a broad platform for fast, scarless, off-the-shelf genome engineering.
Double thermoelectric power factor of a 2D electron system
Authors: Zhang Yuqiao , Feng Bin , Hayashi Hiroyuki , Chang Cheng-Ping , Sheu Yu-Miin , Tanaka Isao , Ikuhara Yuichi , Ohta Hiromichi 
Published: June 2018

AbstractTwo-dimensional electron systems have attracted attention as thermoelectric materials, which can directly convert waste heat into electricity. It has been theoretically predicted that thermoelectric power factor can be largely enhanced when the two-dimensional electron layer is far narrower than the de Broglie wavelength. Although many studies have been made, the effectiveness has not been experimentally clarified thus far. Here we experimentally clarify that an enhanced two-dimensionality is efficient to enhance thermoelectric power factor. We fabricated superlattices of [N unit cell SrTi1−xNb
x
O3|11 unit cell SrTiO3]10—there are two different de Broglie wavelength in the SrTi1−xNb
x
O3 system. The maximum power factor of the superlattice composed of the longer de Broglie wavelength SrTi1−xNb
x
O3 exceeded ∼5 mW m−1 K−2, which doubles the value of optimized bulk SrTi1−xNb
x
O3. The present approach—use of longer de Broglie wavelength—is epoch-making and is fruitful to design good thermoelectric materials showing high power factor.
Ultrafast perturbation maps as a quantitative tool for testing of multi-port photonic devices
Authors: Vynck Kevin , Dinsdale Nicholas J. , Chen Bigeng , Bruck Roman , Khokhar Ali Z. , Reynolds Scott A. , Crudgington Lee , Thomson David J. , Reed Graham T. , Lalanne Philippe , Muskens Otto L. 
Published: June 2018

AbstractAdvanced photonic probing techniques are of great importance for the development of non-contact wafer-scale testing of photonic chips. Ultrafast photomodulation has been identified as a powerful new tool capable of remotely mapping photonic devices through a scanning perturbation. Here, we develop photomodulation maps into a quantitative technique through a general and rigorous method based on Lorentz reciprocity that allows the prediction of transmittance perturbation maps for arbitrary linear photonic systems with great accuracy and minimal computational cost. Excellent agreement is obtained between predicted and experimental maps of various optical multimode-interference devices, thereby allowing direct comparison of a device under test with a physical model of an ideal design structure. In addition to constituting a promising route for optical testing in photonics manufacturing, ultrafast perturbation mapping may be used for design optimization of photonic structures with reconfigurable functionalities.
Cyclophilin A enables specific HIV-1 Tat palmitoylation and accumulation in uninfected cells
Authors: Chopard Christophe , Tong Phuoc Bao Viet , Tóth Petra , Schatz Malvina , Yezid Hocine , Debaisieux Solène , Mettling Clément , Gross Antoine , Pugnière Martine , Tu Annie , Strub Jean-Marc , Mesnard Jean-Michel , Vitale Nicolas , Beaumelle Bruno 
Published: June 2018

AbstractMost HIV-1 Tat is unconventionally secreted by infected cells following Tat interaction with phosphatidylinositol (4,5) bisphosphate (PI(4,5)P2) at the plasma membrane. Extracellular Tat is endocytosed by uninfected cells before escaping from endosomes to reach the cytosol and bind PI(4,5)P2. It is not clear whether and how incoming Tat concentrates in uninfected cells. Here we show that, in uninfected cells, the S-acyl transferase DHHC-20 together with the prolylisomerases cyclophilin A (CypA) and FKBP12 palmitoylate Tat on Cys31 thereby increasing Tat affinity for PI(4,5)P2. In infected cells, CypA is bound by HIV-1 Gag, resulting in its encapsidation and CypA depletion from cells. Because of the lack of this essential cofactor, Tat is not palmitoylated in infected cells but strongly secreted. Hence, Tat palmitoylation specifically takes place in uninfected cells. Moreover, palmitoylation is required for Tat to accumulate at the plasma membrane and affect PI(4,5)P2-dependent membrane traffic such as phagocytosis and neurosecretion.
Emissions mitigation opportunities for savanna countries from early dry season fire management
Authors: Lipsett-Moore Geoffrey J. , Wolff Nicholas H. , Game Edward T. 
Published: June 2018

AbstractSavanna fires produce significant emissions globally, but if managed effectively could provide an important mitigation opportunity, particularly in African least developed countries. Here we show global opportunities for emissions reductions through early dry season burning for 37 countries including: 29 countries in Africa (69.1 MtCO2-e yr−1), six countries in South America (13.3 MtCO2-e yr−1), and Australia and Papua New Guinea (6.9 MtCO2-e yr−1). Emissions reduction estimates are based on the successful approach developed in Australia to reduce emissions from savanna fires using global-scale, remotely sensed estimates of monthly emissions. Importantly, 20 least developed countries in Africa account for 74% of the mitigation potential (60.2 MtCO2-e yr−1). More than 1.02 million km2 of savanna dominated protected areas within these countries could be used as pilot sites to test and advance a regional approach to mitigation efforts for savanna fires in Africa. Potential versus actual abatement opportunities are discussed.
Gene flow contributes to diversification of the major fungal pathogen Candida albicans
Authors: Ropars Jeanne , Maufrais Corinne , Diogo Dorothée , Marcet-Houben Marina , Perin Aurélie , Sertour Natacha , Mosca Kevin , Permal Emmanuelle , Laval Guillaume , Bouchier Christiane , Ma Laurence , Schwartz Katja , Voelz Kerstin , May Robin C. , Poulain Julie , Battail Christophe , Wincker Patrick , Borman Andrew M. , Chowdhary Anuradha , Fan Shangrong , Kim Soo Hyun , Le Pape Patrice , Romeo Orazio , Shin Jong Hee , Gabaldon Toni , Sherlock Gavin , Bougnoux Marie-Elisabeth , d’Enfert Christophe 
Published: June 2018

AbstractElucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species.Candida albicansis the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C.albicansisolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although,C.albicansshows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para)sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction.Candida albicansthus takes advantage of both clonality and gene flow to diversify.
Dissociating neural markers of stimulus memorability and subjective recognition during episodic retrieval
Authors: Bainbridge Wilma A. , Rissman Jesse 
Published: May 2018

AbstractWhile much of memory research takes an observer-centric focus looking at participant performance, recent work has pinpointed important item-centric effects on memory, or how intrinsically memorable a given stimulus is. However, little is known about the neural correlates of memorability during memory retrieval, or how such correlates relate to subjective memory behavior. Here, stimuli and blood-oxygen-level dependent data from a prior functional magnetic resonance imaging (fMRI) study were reanalyzed using a memorability-based framework. In that study, sixteen participants studied 200 novel face images and were scanned while making recognition memory judgments on those faces, interspersed with 200 unstudied faces. In the current investigation, memorability scores for those stimuli were obtained through an online crowd-sourced (N = 740) continuous recognition test that measured each image’s corrected recognition rate. Representational similarity analyses were conducted across the brain to identify regions wherein neural pattern similarity tracked item-specific effects (stimulus memorability) versus observer-specific effects (individual memory performance). We find two non-overlapping sets of regions, with memorability-related information predominantly represented within ventral and medial temporal regions and memory retrieval outcome-related information within fronto-parietal regions. These memorability-based effects persist regardless of image history, implying that coding of stimulus memorability may be a continuous and automatic perceptual process.
A novel dynamic multicellular co-culture system for studying individual blood-brain barrier cell types in brain diseases and cytotoxicity testing
Authors: Miranda-Azpiazu Patricia , Panagiotou Stavros , Jose Gin , Saha Sikha 
Published: June 2018

AbstractBlood brain barrier (BBB) cells play key roles in the physiology and pathology of the central nervous system (CNS). BBB dysfunction is implicated in many neurodegenerative diseases, including Alzheimer’s disease (AD). The BBB consists of capillary endothelial cells, pericytes encircling the endothelium and surrounding astrocytes extending their processes towards it. Although there have been many attempts to developin vitroBBB models, the complex interaction between these cell types makes it extremely difficult to determine their individual contribution to neurotoxicityin vivo. Thus, we developed and optimised anin vitromulticellular co-culture model within the Kirkstall Quasi Vivo System. The main aim was to determine the optimal environment to culture human brain primary endothelial cells, pericytes and astrocytes whilst maintaining cellular communication without formation of a barrier in order to assess the contribution of each cell type to the overall response. As a proof of concept for the present system, the effects of amyloid-beta 25-35 peptide (Aβ25-35), a hallmark of AD, were explored. This multicellular system will be a valuable tool for future studies on the specific roles of individual BBB cell type (while making connection with each other through medium) in CNS disorders as well as in cytotoxicity tests.
A Gold-Standard for Entity Resolution within Sexually Transmitted Infection Networks
Authors: Schneider John , Schumm L. Philip , Fraser Maya , Yeldandi Vijay , Liao Chuanhong 
Published: June 2018

AbstractContact tracing for venereal disease control has been widespread since 1936 and relies on reported information about contacts’ attributes to determine whether two contacts may represent the same individual. We developed and implemented a gold-standard for determining overlap between contacts reported by different individuals using cell phone numbers as unique identifiers. This method was then used to evaluate the performance of using reported names and demographic characteristics to infer overlap. Cell-phone numbers, names and demographic data for a sample of high-risk men in India and their contacts were collected using a novel, hybrid instrument involving both cell-phone data extraction and Computer-Assisted Personal Interviewing (CAPI). Logistic regression was used to model the probability that a pair of contacts reported by different respondents were identical, based on the correspondence between their reported names and attributes. A discrete mixture model is proposed which provides predictions nearly as good as the logistic model but may be used in a new population without re-calibration. Despite achieving AUCs of 0.83–0.86, the low rate of true overlap among a very large number of contact pairs still results in a high rate of false positives. Next generation contact tracing calls for more archived or digital matching processes.
Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches
Authors: Mir Daiana , Gräf Tiago , Esteves de Matos Almeida Sabrina , Pinto Aguinaldo Roberto , Delatorre Edson , Bello Gonzalo 
Published: June 2018

AbstractThe subtype C Eastern Africa clade (CEA), a particularly successful HIV-1 subtype C lineage, has seeded several sub-epidemics in Eastern African countries and Southern Brazil during the 1960s and 1970s. Here, we characterized the past population dynamics of the major CEAsub-epidemics in Eastern Africa and Brazil by using Bayesian phylodynamic approaches based on coalescent and birth-death models. All phylodynamic models support similar epidemic dynamics and exponential growth rates until roughly the mid-1980s for all the CEAsub-epidemics. Divergent growth patterns, however, were supported afterwards. The Bayesian skygrid coalescent model (BSKG) and the birth-death skyline model (BDSKY) supported longer exponential growth phases than the Bayesian skyline coalescent model (BSKL). The BDSKY model uncovers patterns of a recent decline for the CEAsub-epidemics in Burundi/Rwanda and Tanzania (Re < 1) and a recent growth for Southern Brazil (Re > 1); whereas coalescent models infer an epidemic stabilization. To the contrary, the BSKG model captured a decline of Ethiopian CEAsub-epidemic between the mid-1990s and mid-2000s that was not uncovered by the BDSKY model. These results underscore that the joint use of different phylodynamic approaches may yield complementary insights into the past HIV population dynamics.
The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal
Authors: Kuippers Gina , Boothman Christopher , Bagshaw Heath , Ward Michael , Beard Rebecca , Bryan Nicholas , Lloyd Jonathan R. 
Published: June 2018

AbstractIntermediate level radioactive waste (ILW) generally contains a heterogeneous range of organic and inorganic materials, of which some are encapsulated in cement. Of particular concern are cellulosic waste items, which will chemically degrade under the conditions predicted during waste disposal, forming significant quantities of isosaccharinic acid (ISA), a strongly chelating ligand. ISA therefore has the potential to increase the mobility of a wide range of radionuclides via complex formation, including Ni-63 and Ni-59. Although ISA is known to be metabolized by anaerobic microorganisms, the biodegradation of metal-ISA complexes remains unexplored. This study investigates the fate of a Ni-ISA complex in Fe(III)-reducing enrichment cultures at neutral pH, representative of a microbial community in the subsurface. After initial sorption of Ni onto Fe(III)oxyhydroxides, microbial ISA biodegradation resulted in >90% removal of the remaining Ni from solution when present at 0.1 mM, whereas higher concentrations of Ni proved toxic. The microbial consortium associated with ISA degradation was dominated by close relatives to Clostridia and Geobacter species. Nickel was preferentially immobilized with trace amounts of biogenic amorphous iron sulfides. This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from the groundwater in the subsurface geosphere surrounding a geodisposal facility.
mTORC1 controls long-term memory retrieval
Authors: Pereyra Magdalena , Katche Cynthia , de Landeta Ana Belén , Medina Jorge H. 
Published: June 2018

AbstractUnderstanding how stored information emerges is a main question in the neurobiology of memory that is now increasingly gaining attention. However, molecular events underlying this memory stage, including involvement of protein synthesis, are not well defined. Mammalian target of rapamycin complex 1 (mTORC1), a central regulator of protein synthesis, has been implicated in synaptic plasticity and is required for memory formation. Using inhibitory avoidance (IA), we evaluated the role of mTORC1 in memory retrieval. Infusion of a selective mTORC1 inhibitor, rapamycin, into the dorsal hippocampus 15 or 40 min but not 3 h before testing at 24 h reversibly disrupted memory expression even in animals that had already expressed IA memory. Emetine, a general protein synthesis inhibitor, provoked a similar impairment. mTORC1 inhibition did not interfere with short-term memory retrieval. When infused before test at 7 or 14 but not at 28 days after training, rapamycin impaired memory expression. mTORC1 blockade in retrosplenial cortex, another structure required for IA memory, also impaired memory retention. In addition, pretest intrahippocampal rapamycin infusion impaired object location memory retrieval. Our results support the idea that ongoing protein synthesis mediated by activation of mTORC1 pathway is necessary for long but not for short term memory.
Climatic niche divergence drives patterns of diversification and richness among mammal families
Authors: Castro-Insua Adrián , Gómez-Rodríguez Carola , Wiens John J. , Baselga Andrés 
Published: June 2018

AbstractA major goal of evolutionary biology is to understand why clades differ dramatically in species richness. A key to this challenge is to uncover the correlates of variation in diversification rate (speciation – extinction) among clades. Here, we explore the relationship between diversification rates and the climatic niches of species and clades among 92 families of terrestrial mammals. We use a time-calibrated molecular phylogeny of mammals and climatic data from 3335 species. We show that considerable variation in net diversification rates among mammal families is explained by niche divergence (59%) and rates of niche change (51%). Diversification rates in turn explain most variation in species richness among families (79%). Contrary to expectations, patterns of diversification are not explained by differences in geographic range areas of clades, nor by their climatic niche position (i.e. whether they are primarily tropical or temperate). Overall, these results suggest that speciation through climatic niche divergence may help drive large-scale patterns of diversification and richness. Our results help explain diversification patterns in a major clade of vertebrates, and suggest that similar underlying principles may explain the diversification of many terrestrial clades.
Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil
Authors: Silva Paulo E. S. , Reis Mariana P. , Ávila Marcelo P. , Dias Marcela F. , Costa Patrícia S. , Suhadolnik Maria L. S. , Kunzmann Bárbara G. , Carmo Anderson O. , Kalapotakis Evanguedes , Chartone-Souza Edmar , Nascimento Andréa M. A. 
Published: June 2018

AbstractLeprosy is a chronic infectious peripheral neuropathy that is caused by Mycobacterium leprae, and the skin is one of its preferred target sites. However, the effects of this infection on the skin microbiome remain largely unexplored. Here, we characterize and compare the lesional and non-lesional skin microbiomes of leprosy patients and healthy individuals through the deep sequencing of 16 S rRNA genes. Additionally, a subset of patients was monitored throughout the multi-drug therapy to investigate its effect on the leprous skin microbiome. Firmicutes-associated OTUs (primarily Staphylococcus) prevailed in healthy individuals. By contrast, Firmicutes was underrepresented and Proteobacteria was enriched in the patients’ skin, although a single dominant taxon has not been observed at a finer taxonomic resolution. These differences can be explained by the significant decrease in Staphylococcus and Streptococcus as well as the enrichment in Brevundimonas. The overrepresentation of Micrococcus in patients is also remarkable. Genus-level compositional profiles revealed no significant intrapersonal difference between lesional and non-lesional sites. Treatment-associated changes indicated a loss of diversity and a shift in the community composition, with stronger impacts on the OTUs that are considered indigenous bacteria. Therefore, the molecular signatures associated with leprosy identified herein might be of importance for early diagnostics.