bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anthropogenic Nitrogen Deposition Increases Soil Carbon by Enhancing New Carbon of the Soil Aggregate Formation
Authors: Chang Ruiying , Zhou Wenjun , Fang Yunting , Bing Haijian , Sun Xiangyang , Wang Genxu 
Published: February 2019

AbstractAnthropogenic nitrogen (N) deposition can most likely increase temperate forest soil organic carbon (SOC) storage. Increased SOC is usually suggested to be associated with the suppression of SOC decomposition, which has been hypothesized to be due to the decrease in the activity of lignin‐degrading extracellular enzymes and/or the decrease in soil acidity under N addition. However, the potential mechanism of SOC protection derived from N addition is less understood. Here in a low‐deposition temperate montane forest, short‐term N addition could increase SOC storage in the aggregate fraction but not in the bulk soil. N‐induced SOC accumulation was partly associated with the suppressed SOC decomposition (indicated by lower soil respiration) that resulted from the reduced microbial biomass rather than from decreased lignin‐degrading enzyme activity or from reduced soil acidity. In addition, N addition promoted soil aggregate formation, which could partly suppress SOC decomposition by protecting new carbon that originated from plant litter residue to a greater degree, while dissolved organic carbon retention in the mineral soils played a limited role in the SOC sequestration derived from N addition, at least in the short term. A conceptual model was proposed and highlighted a new underlying mechanism of new carbon protection by enhanced aggregate formation, other than the role of microbial suppression, to explain the positive effect of anthropogenic N deposition on forest SOC.
KDEL receptor regulates secretion by lysosome relocation- and autophagy-dependent modulation of lipid-droplet turnover
Authors: Tapia Diego , Jiménez Tomás , Zamora Constanza , Espinoza Javier , Rizzo Riccardo , González-Cárdenas Alexis , Fuentes Danitza , Hernández Sergio , Cavieres Viviana A. , Soza Andrea , Guzmán Fanny , Arriagada Gloria , Yuseff María Isabel , Mardones Gonzalo A. , Burgos Patricia V. , Luini Alberto , González Alfonso , Cancino Jorge 
Published: February 2019

AbstractInter-organelle signalling has essential roles in cell physiology encompassing cell metabolism, aging and temporal adaptation to external and internal perturbations. How such signalling coordinates different organelle functions within adaptive responses remains unknown. Membrane traffic is a fundamental process in which membrane fluxes need to be sensed for the adjustment of cellular requirements and homeostasis. Studying endoplasmic reticulum-to-Golgi trafficking, we found that Golgi-based, KDEL receptor-dependent signalling promotes lysosome repositioning to the perinuclear area, involving a complex process intertwined to autophagy, lipid-droplet turnover and Golgi-mediated secretion that engages the microtubule motor protein dynein-LRB1 and the autophagy cargo receptor p62/SQSTM1. This process, here named ‘traffic-induced degradation response for secretion’ (TIDeRS) discloses a cellular mechanism by which nutrient and membrane sensing machineries cooperate to sustain Golgi-dependent protein secretion.
Redox gated polymer memristive processing memory unit
Authors: Zhang Bin , Fan Fei , Xue Wuhong , Liu Gang , Fu Yubin , Zhuang Xiaodong , Xu Xiao-Hong , Gu Junwei , Li Run-Wei , Chen Yu 
Published: February 2019

AbstractMemristors with enormous storage capacity and superior processing efficiency are of critical importance to overcome the Moore’s Law limitation and von Neumann bottleneck problems in the big data and artificial intelligence era. In particular, the integration of multifunctionalities into a single memristor promises an essential strategy of obtaining a high-performance electronic device that satisfies the nowadays increasing demands of data storage and processing. In this contribution, we report a proof-of-concept polymer memristive processing-memory unit that demonstrates programmable information storage and processing capabilities. By introducing redox active moieties of triphenylamine and ferrocene onto the pendants of fluorene skeletons, the conjugated polymer exhibits triple oxidation behavior and interesting memristive switching characteristics. Associated with the unique electrochemical and electrical behavior, the polymer device is capable of executing multilevel memory, decimal arithmetic operations of addition, subtraction, multiplication and division, as well as simple Boolean logic operations.
Improvement of antibody functionality by structure-guided paratope engraftment
Authors: Liu Qingbo , Lai Yen-Ting , Zhang Peng , Louder Mark K. , Pegu Amarendra , Rawi Reda , Asokan Mangaiarkarasi , Chen Xuejun , Shen Chen-Hsiang , Chuang Gwo-Yu , Yang Eun Sung , Miao Huiyi , Wang Yuge , Fauci Anthony S. , Kwong Peter D. , Mascola John R. , Lusso Paolo 
Published: February 2019

AbstractBroadly neutralizing antibodies (bNAbs) represent a promising alternative to antiretroviral drugs for HIV-1 prevention and treatment. Selected antibodies to the CD4-binding site bolster envelope trimer binding via quaternary contacts. Here, we rationally engraft a new paratope, i.e., the extended heavy-chain framework region 3 (FR3) loop of VRC03, which mediates quaternary interaction, onto several potent bNAbs, enabling them to reach an adjacent gp120 protomer. The interactive quaternary surface is delineated by solving the crystal structure of two FR3 loop-chimeric antibodies. Chimerization enhances the neutralizing activity of several potent bNAbs against a majority of global HIV-1 strains. Compared to unmodified antibodies, chimeric antibodies display lower autoreactivity and prolonged in vivo half-life in huFcRn mice and rhesus macaques. Thus, paratope engraftment may be used to expand the epitope repertory of natural antibodies, improving their functionality for disease prevention and treatment.
Whole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution
Authors: Stevens Marc J. A. , Tasara Taurai , Klumpp Jochen , Stephan Roger , Ehling-Schulz Monika , Johler Sophia 
Published: February 2019

AbstractBacillus cytotoxicus is a member of the Bacillus cereus group linked to fatal cases of diarrheal disease. Information on B. cytotoxicus is very limited; in particular comprehensive genomic data is lacking. Thus, we applied a genomic approach to characterize B. cytotoxicus and decipher its population structure. To this end, complete genomes of ten B. cytotoxicus were sequenced and compared to the four publicly available full B. cytotoxicus genomes and genomes of other B. cereus group members. Average nucleotide identity, core genome, and pan genome clustering resulted in clear distinction of B. cytotoxicus strains from other strains of the B. cereus group. Genomic content analyses showed that a hydroxyphenylalanine operon is present in B. cytotoxicus, but absent in all other members of the B. cereus group. It enables degradation of aromatic compounds to succinate and pyruvate and was likely acquired from another Bacillus species. It allows for utilization of tyrosine and might have given a B. cytotoxicus ancestor an evolutionary advantage resulting in species differentiation. Plasmid content showed that B. cytotoxicus is flexible in exchanging genes, allowing for quick adaptation to the environment. Genome-based phylogenetic analyses divided the B. cytotoxicus strains into four clades that also differed in virulence gene content.
Noise-induced vocal plasticity in urban white-crowned sparrows does not involve adjustment of trill performance components
Authors: Gentry Katherine E. , Luther David A. 
Published: February 2019

AbstractBackground noise can interfere with acoustic communication and subsequently influence signaling behavior. Immediate signaling flexibility (ISF) is a context-dependent form of behavioral plasticity that allows animals to temporarily change their acoustic behavior in response to noise fluctuations and potentially improve the chances of successful communication in noisy environments. The adaptive value of ISF is ultimately contingent on the response of the intended receiver, and there are differential effects on receiver response depending on which signal component is modified. However, there is scant research on whether ISF involves modification of a signal component specifically linked to mate attraction or territory defense. Our study addresses this knowledge gap and provides important insight into whether males employ short-term signal modification in a manner that could affect mate pairing success in birds. Specifically, we explore the maladaptive potential of ISF in the San Francisco, California population of Zonotrichia leucophrys nuttalli by testing for changes in trill bandwidth and rate—the specific trill structure components known to influence the receiver’s perception of vocal performance in this species—before and during noise broadcast experiments. Although Zonotrichia leucophrys nuttalli are capable of ISF, we found no evidence that noise induces temporary adjustment of the trill structure traits used by receivers to assess vocal performance.
Aberrant expression of a stabilized β-catenin mutant in keratocytes inhibits mouse corneal epithelial stratification
Authors: Zhang Lingling , Wang Yen-Chiao , Okada Yuka , Zhang Suohui , Anderson Matthew , Liu Chia-Yang , Zhang Yujin 
Published: February 2019

AbstractWe previously reported that genetic deletion of β-catenin in mouse corneal keratocytes resulted in precocious corneal epithelial stratification. In this study, to strengthen the notion that corneal keratocyte-derived Wnt/β-catenin signaling regulates corneal epithelial stratification during mouse development, we examined the consequence of conditional overexpression of a stabilized β-catenin mutant (Ctnnb1ΔE3) in corneal keratocytes via a doxycycline (Dox)-inducible compound transgenic mouse strain. Histological analysis showed that conditional overexpression of Ctnnb1ΔE3 in keratocytes inhibited corneal epithelial stratification during postnatal development. Unlike the corneal epithelium of the littermate controls, which consisted of 5-6 cell layers at postnatal day 21 (P21), the mutant corneal epithelium contained 1-2 or 2-3 cell layers after Dox induction from embryonic day 0 (E0) to P21 and from E9 to P21, respectively. X-gal staining revealed that Wnt/β-catenin signaling activity was significantly elevated in the corneal keratocytes of the Dox-induced mutant mice, compared to the littermate controls. Furthermore, RT-qPCR and immunostaining data indicated that the expression of Bmp4 and ΔNp63 was downregulated in the mutant corneas, which was associated with reduced corneal epithelial proliferation in mutant epithelium, as revealed by immunofluorescent staining. However, the expression of Krt12, Krt14 and Pax6 in the mutant corneas was not altered after overexpression of Ctnnb1ΔE3 mutant protein in corneal keratocytes. Overall, mutant β-catenin accumulation in the corneal keratocytes inhibited corneal epithelial stratification probably through downregulation of Bmp4 and ΔNp63 in the corneal epithelium.
Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes
Authors: Rahman Anika T. , Arai Tatsuya , Yamauchi Akari , Miura Ai , Kondo Hidemasa , Ohyama Yasushi , Tsuda Sakae 
Published: February 2019

AbstractIce recrystallization is a phenomenon observed as the increase in ice crystal size within an already frozen material. Antifreeze proteins (AFPs), a class of proteins capable of arresting ice crystal growth, are known to inhibit this phenomenon even at sub milli-molar concentrations. A tremendous range in the possible applications of AFPs is hence expected in both medical and industrial fields, while a key determinant of the ice recrystallization inhibition (IRI) is hardly understood. Here, IRI efficiency and ice plane affinity were examined for the wild-type AFPI–III, a defective AFPIII isoform, and a fungal AFP isoform. To simplify the IRI analysis using the formal representation of Ostwald-ripening (r3 = r03 + kt), we monitored specific ice grains exhibiting only uniform growth, for which maximum Feret diameter was measured. The cube of an ice grain’s radius (r3) increased proportionately with time (t), and its slope gave the recrystallization rate (k). There was a significant difference in the IRI efficiency between the samples, and the fungal AFP possessing the activity with the smallest amount (0.27 μM) exhibited an affinity to multiple ice planes. These results suggest that the IRI efficiency is maximized when AFPs bind to a whole set of ice planes.
Highly Efficient Transgenesis in Ferrets Using CRISPR/Cas9-Mediated Homology-Independent Insertion at the ROSA26 Locus
Authors: Yu Miao , Sun Xingshen , Tyler Scott R. , Liang Bo , Swatek Anthony M. , Lynch Thomas J. , He Nan , Yuan Feng , Feng Zehua , Rotti Pavana G. , Choi Soon H. , Shahin Weam , Liu Xiaoming , Yan Ziying , Engelhardt John F. 
Published: February 2019

AbstractThe domestic ferret (Mustela putorius furo) has proven to be a useful species for modeling human genetic and infectious diseases of the lung and brain. However, biomedical research in ferrets has been hindered by the lack of rapid and cost-effective methods for genome engineering. Here, we utilized CRISPR/Cas9-mediated, homology-independent insertion at the ROSA26 “safe harbor” locus in ferret zygotes and created transgenic animals expressing a dual-fluorescent Cre-reporter system flanked by PhiC31 and Bxb1 integrase attP sites. Out of 151 zygotes injected with circular transgene-containing plasmid and Cas9 protein loaded with the ROSA26 intron-1 sgRNA, there were 23 births of which 5 had targeted integration events (22% efficiency). The encoded tdTomato transgene was highly expressed in all tissues evaluated. Targeted integration was verified by PCR analyses, Southern blot, and germ-line transmission. Function of the ROSA26-CAG-LoxPtdTomatoStopLoxPEGFP (ROSA-TG) Cre-reporter was confirmed in primary cells following Cre expression. The Phi31 and Bxb1 integrase attP sites flanking the transgene will also enable rapid directional insertion of any transgene without a size limitation at the ROSA26 locus. These methods and the model generated will greatly enhance biomedical research involving lineage tracing, the evaluation of stem cell therapy, and transgenesis in ferret models of human disease.
Reverse immunodynamics: a new method for identifying targets of protective immunity
Authors: Spensley Katrina J. , Wikramaratna Paul S. , Penman Bridget S. , Walker Andrew , Smith Adrian L. , Pybus Oliver G. , Jean Létitia , Gupta Sunetra , Lourenço José 
Published: February 2019

AbstractDespite a dramatic increase in our ability to catalogue variation among pathogen genomes, we have made far fewer advances in using this information to identify targets of protective immunity. Epidemiological models predict that strong immune selection can cause antigenic variants to structure into genetically discordant sets of antigenic types (e.g. serotypes). A corollary of this theory is that targets of immunity may be identified by searching for non-overlapping associations of amino acids among co-circulating antigenic variants. We propose a novel population genetics methodology that combines such predictions with phylogenetic analyses to identify genetic loci (epitopes) under strong immune selection. We apply this concept to the AMA-1 protein of the malaria parasite Plasmodium falciparum and find evidence of epitopes among certain regions of low variability which could render them ideal vaccine candidates. The proposed method can be applied to a myriad of multi-strain pathogens for which vast amounts of genetic data has been collected in recent years.
A mechanical method of cerebral cortical folding development based on thermal expansion
Authors: Wang Linlin , Yao Jianyao , Hu Ning 
Published: February 2019

AbstractCortical folding malformations are associated with several severe neurological disorders, including epilepsy, schizophrenia and autism. However, the mechanism behind cerebral cortical folding development is not yet clear. In this paper, we propose a mechanical method based on thermal expansion to simulate the development of human cerebral cortical folding. The influences of stiffness ratio, growth rate ratio, and initial cortical plate thickness on cortical folding are discussed. The results of our thermal expansion model are consistent with previous studies, indicating that abnormal values of the aforementioned three factors could directly lead to cortical folding malformation in a generally fixed pattern.
Disappearance of white sharks leads to the novel emergence of an allopatric apex predator, the sevengill shark
Authors: Hammerschlag Neil , Williams Lacey , Fallows Monique , Fallows Chris 
Published: February 2019

AbstractDespite global declines of apex predatory sharks, evidence for ecosystem consequences remains limited and debated. This is likely a result of both the logistical difficulties of measuring such processes in marine systems and also due to shifting baselines, whereby the ecosystem changes have occurred prior to monitoring. Between 2000–2018, we conducted standardized monitoring of white shark (Carcharodon carcharias) abundance patterns (N = 6,333 shark sightings) and predatory activity (N = 8,076 attacks on seals) at Seal Island, a Cape fur seal (Arctocephalus pusillus pusillus) colony in False Bay, South Africa. Over the 18-year study, declines in white shark abundance and attack rates were documented between 2015–2018, with anomalous lows occurring in 2017 and 2018. This included prolonged periods of complete white shark absence from Seal Island. The disappearance of white sharks from Seal Island coincided with the unprecedented appearance of sevengill sharks (Notorynchus cepedianus; N = 120 sightings), an otherwise allopatric kelp-associated apex predator in False Bay. We also recorded a sevengill shark attacking a live seal in the absence of white sharks. These data provide empirical evidence for behavioral shifts in an allopatric marine predator following the decline and disappearance of white sharks from a foraging site. This study demonstrates the importance of historical data and long-term monitoring for disentangling ecological consequences of apex predator declines.
Impact of diverse chemotherapeutic agents and external factors on activation of brown adipose tissue in a large patient collective
Authors: Brendle Cornelia , Stefan Norbert , Stef Irina , Ripkens Sabine , Soekler Martin , la Fougère Christian , Nikolaou Konstantin , Pfannenberg Christina 
Published: February 2019

AbstractIncreased activity of brown adipose tissue (BAT) activity in adults is thought to prevent obesity. Therefore, regulators of BAT activity might serve as anti-obesity therapy in future, but are not investigated thoroughly up to now. In our study, we assessed retrospectively the association of BAT activity with several external factors and diverse chemotherapeutic and immunosuppressive agents in a collective of 702 patients. The patients underwent at least two clinically indicated PET/CT examinations in the course of different oncological and inflammatory diseases. BAT activity was identified according to predefined PET/CT criteria in all examinations. In multivariate analysis, the type of disease, the disease activity and the therapeutic regimen did not influence BAT activity. In contrast, sex and age were confirmed as independent factors for BAT activity. For the association of therapeutic agents with BAT activity, we examined 53 different disease-related agents, which were applied to patients without initial BAT activity between their PET/CT examinations. Out of these, cytarabine therapy was significantly associated with increased new onset of BAT activity. Cytarabine is a therapeutic agent for lymphoma patients. Further targeted studies might investigate the usefulness of Cytarabine serving as possible therapeutic approach against obesity via BAT regulation.
Artificial neural networks for density-functional optimizations in fermionic systems
Authors: Custódio Caio A. , Filletti Érica R. , França Vivian V. 
Published: February 2019

AbstractIn this work we propose an artificial neural network functional to the ground-state energy of fermionic interacting particles in homogeneous chains described by the Hubbard model. Our neural network functional was proven to have an excellent performance: it deviates from numerically exact calculations by less than 0.15% for a vast regime of interactions and for all the regimes of filling factors and magnetizations. When compared to analytical functionals, the neural functional was found to be more precise for all the regimes of parameters, being particularly superior at the weakly interacting regime: where the analytical parametrization fails the most, ~7%, against only ~0.1% for the neural network. We have also applied our homogeneous functional to finite, localized impurities and harmonically confined systems within density-functional theory (DFT) methods. The results show that while our artificial neural network approach is substantially more accurate than other equivalently simple and fast DFT treatments, it has similar performance than more costly DFT calculations and other independent many-body calculations, at a fraction of the computational cost.
Global Disease Outbreaks Associated with the 2015–2016 El Niño Event
Authors: Anyamba Assaf , Chretien Jean-Paul , Britch Seth C. , Soebiyanto Radina P. , Small Jennifer L. , Jepsen Rikke , Forshey Brett M. , Sanchez Jose L. , Smith Ryan D. , Harris Ryan , Tucker Compton J. , Karesh William B. , Linthicum Kenneth J. 
Published: February 2019

AbstractInterannual climate variability patterns associated with the El Niño-Southern Oscillation phenomenon result in climate and environmental anomaly conditions in specific regions worldwide that directly favor outbreaks and/or amplification of variety of diseases of public health concern including chikungunya, hantavirus, Rift Valley fever, cholera, plague, and Zika. We analyzed patterns of some disease outbreaks during the strong 2015–2016 El Niño event in relation to climate anomalies derived from satellite measurements. Disease outbreaks in multiple El Niño-connected regions worldwide (including Southeast Asia, Tanzania, western US, and Brazil) followed shifts in rainfall, temperature, and vegetation in which both drought and flooding occurred in excess (14–81% precipitation departures from normal). These shifts favored ecological conditions appropriate for pathogens and their vectors to emerge and propagate clusters of diseases activity in these regions. Our analysis indicates that intensity of disease activity in some ENSO-teleconnected regions were approximately 2.5–28% higher during years with El Niño events than those without. Plague in Colorado and New Mexico as well as cholera in Tanzania were significantly associated with above normal rainfall (p < 0.05); while dengue in Brazil and southeast Asia were significantly associated with above normal land surface temperature (p < 0.05). Routine and ongoing global satellite monitoring of key climate variable anomalies calibrated to specific regions could identify regions at risk for emergence and propagation of disease vectors. Such information can provide sufficient lead-time for outbreak prevention and potentially reduce the burden and spread of ecologically coupled diseases.