bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recharge and Nitrate Transport Through the Deep Vadose Zone of the Loess Plateau: A Regional‐Scale Model Investigation
Authors: Turkeltaub Tuvia , Jia Xiaoxu , Zhu Yuanjun , Shao Ming‐An , Binley Andrew 
Published: June 2018

AbstractThe Loess Plateau of China (LPC) is suffering from the impacts of overexploitation of groundwater, leading to a decline in the regional water table. This is compounded by relatively recent large‐scale transformation of land use, which may impact groundwater recharge and threaten future water quality from intensive nitrogen fertilizer application. Understanding the regional unsaturated water flow and nitrate travel time in the deep vadose zone is crucial for the sustainable management of the LPC groundwater system. We develop here a regional‐scale model that exploits an extensive database of soil properties derived from recent intensive soil profile sampling over the LPC, together with climate, vadose zone thickness, and land use data. The model solves the Richards equation and a conservative solute transport model using a multiple 1D column approach. A comparison between model simulations and observations at five sites reveals good model performance. Application over the LPC indicates that areas with dense irrigated agricultural land use contribute significantly to groundwater recharge. By using land use cover information from 1975 to 2008, simulations reveal that the transition from agriculture to forest and grassland accounts for a small reduction of the total annual recharge (6.1%). Modeled nitrate travel times through the deep unsaturated zone range between decades and centuries; however, recent loading of anthropogenic nitrate is expected to reach the aquifer in the near future under irrigated areas or where the vadose zone is relatively thin. The model simulations provide valuable information for assessing future vulnerability of groundwater resources over a regional scale.
Airborne Microbes Contribute to N2 Fixation in Surface Water of the Northern Red Sea
Authors: Rahav Eyal , Paytan Adina , Mescioglu Esra , Galletti Yuri , Rosenfeld Sahar , Raveh Ofrat , Santinelli Chiara , Ho Tung‐Yuan , Herut Barak 
Published: June 2018

AbstractDesert dust storms are frequent in the Northern Red Sea region, providing nutrients (i.e., PO4) and trace‐metals (i.e., Fe) that may stimulate dinitrogen (N2) fixation. Dust also carries a high diversity of airborne microbes (bacteria and archaea), including diazotrophs, that may remain viable during transport and upon deposition. Here we evaluate the impact of atmospheric deposition and its associated airborne diazotrophs on N2 fixation in the surface water of the low‐nutrient Northern Red Sea, using mesocosm bioassay experiments. We compared the chemical (nutritional) and sole airborne microbial impact of aerosol additions on N2 fixation using “live‐dust” (release nutrients/trace metals and viable airborne microorganisms) and “UV‐killed dust” (release only chemicals). Airborne diazotrophy accounted for about one third of the measured N2 fixation (0.35 ± 0.06 nmol N · L−1 · day−1 and 0.29 ± 0.06 nmol N · L−1 · day−1, for “February 2017” and “May 2017,” “live‐dust” additions, respectively). Two nifH sequences related to cluster III diazotrophs were amplified from the dust samples, consistent with the N2 fixation measurement results. We postulate that the deposition of viable airborne diazotrophs may enhance N2 fixation, especially in marine provinces subjected to high aerosol loads. We speculate that the relative contribution of airborne N2 fixation may increase in the future with the predicted increase in dust deposition.
Disconnection Between Trends of Atmospheric Drying and Continental Runoff
Authors: Yang Yuting , Zhang Shulei , McVicar Tim R. , Beck Hylke E. , Zhang Yongqiang , Liu Bing 
Published: June 2018

AbstractThe ratio of potential evapotranspiration (E0) over precipitation (P), known as the aridity index (AI), has been commonly used to stratify global aridity zones and widely adopted to assess changes in aridity globally. Anthropogenic climate change, in particular atmospheric warming, is projected to increase AI, which has in most cases been interpreted as increasing terrestrial aridity. In this study we demonstrate, for both past and future conditions, that such an interpretation requires reconsideration. Using catchment observations over the past 30 years and climate model projections for the 21st century, we show that increased AI does not ubiquitously lead to a decreased water availability over land, using surface runoff (Q) as an indicator. This is primarily caused by a higher Q sensitivity to changes in P (SP) and a lower Q sensitivity to changes in E0 (SE0), with the ratio of SP over SE0 being higher than the relative changes of E0 compared to P (i.e., |P × SP| > |E0 × SE0|). Assessment of Coupled Model Intercomparison Project Phase 5 model outputs indicates that both Q and AI change‐induced Q changes are increasing over the majority of the globe for the 21st century despite increasing AI (a drying atmosphere). Our findings demonstrate a disconnection between the atmospheric drying trends and surface runoff trends and call for caution when interpreting retrospective and future changes in terrestrial aridity based on AI and related measures.
High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize
Authors: Kianian Penny M. A. , Wang Minghui , Simons Kristin , Ghavami Farhad , He Yan , Dukowic-Schulze Stefanie , Sundararajan Anitha , Sun Qi , Pillardy Jaroslaw , Mudge Joann , Chen Changbin , Kianian Shahryar F. , Pawlowski Wojciech P. 
Published: June 2018

AbstractMeiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3). Our data suggest that sex-specific factors not only affect male–female CO number disparities but also cause fine differences in CO positions. Differences between male and female CO landscapes indicate that recombination has distinct implications for population structure and gene evolution in male and in female meioses.
Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing
Authors: Snoberger Aaron , Brettrager Evan J. , Smith David M. 
Published: June 2018

AbstractProtein degradation in all domains of life requires ATPases that unfold and inject proteins into compartmentalized proteolytic chambers. Proteasomal ATPases in eukaryotes and archaea contain poorly understood N-terminally conserved coiled-coil domains. In this study, we engineer disulfide crosslinks in the coiled-coils of the archaeal proteasomal ATPase (PAN) and report that its three identical coiled-coil domains can adopt three different conformations: (1) in-register and zipped, (2) in-register and partially unzipped, and (3) out-of-register. This conformational heterogeneity conflicts with PAN’s symmetrical OB-coiled-coil crystal structure but resembles the conformational heterogeneity of the 26S proteasomal ATPases’ coiled-coils. Furthermore, we find that one coiled-coil can be conformationally constrained even while unfolding substrates, and conformational changes in two of the coiled-coils regulate PAN switching between resting and active states. This switching functionally mimics similar states proposed for the 26S proteasome from cryo-EM. These findings thus build a mechanistic framework to understand regulation of proteasome activity.
Twinning in metastable high-entropy alloys
Authors: Huang Shuo , Huang He , Li Wei , Kim Dongyoo , Lu Song , Li Xiaoqing , Holmström Erik , Kwon Se Kyun , Vitos Levente 
Published: June 2018

AbstractTwinning is a fundamental mechanism behind the simultaneous increase of strength and ductility in medium- and high-entropy alloys, but its operation is not yet well understood, which limits their exploitation. Since many high-entropy alloys showing outstanding mechanical properties are actually thermodynamically unstable at ambient and cryogenic conditions, the observed twinning challenges the existing phenomenological and theoretical plasticity models. Here, we adopt a transparent approach based on effective energy barriers in combination with first-principle calculations to shed light on the origin of twinning in high-entropy alloys. We demonstrate that twinning can be the primary deformation mode in metastable face-centered cubic alloys with a fraction that surpasses the previously established upper limit. The present advance in plasticity of metals opens opportunities for tailoring the mechanical response in engineering materials by optimizing metastable twinning in high-entropy alloys.
Association between post-diagnostic use of cholera vaccine and risk of death in prostate cancer patients
Authors: Ji Jianguang , Sundquist Jan , Sundquist Kristina 
Published: June 2018

AbstractRecent evidence suggests that cholera toxin might have multiple functions regarding the ability to regulate the immune system. However, it is unknown whether subsequent administration of cholera vaccine might affect the mortality rate in patients with prostate cancer. Here we report that patients in Sweden, who were diagnosed with prostate cancer between July 2005 and December 2014 and used cholera vaccine, have a decreased risk of death from prostate cancer (HR, 0.57; 95% CI, 0.40–0.82) as compared to patients with prostate cancer but without cholera vaccine use, adjusted for a range of confounding factors. In addition, patients using cholera vaccine show a decreased risk of death overall (HR, 0.53; 95% CI, 0.41–0.69). The decreased mortality rate is largely consistent, irrespective of patients’ age or tumor stage at diagnosis. In this population-based study, we suggest that subsequent administration of cholera vaccine after prostate cancer diagnosis might reduce the mortality rate.
Crossmodal association of auditory and visual material properties in infants
Authors: Ujiie Yuta , Yamashita Wakayo , Fujisaki Waka , Kanazawa So , Yamaguchi Masami K. 
Published: June 2018

AbstractThe human perceptual system enables us to extract visual properties of an object’s material from auditory information. In monkeys, the neural basis underlying such multisensory association develops through experience of exposure to a material; material information could be processed in the posterior inferior temporal cortex, progressively from the high-order visual areas. In humans, however, the development of this neural representation remains poorly understood. Here, we demonstrated for the first time the presence of a mapping of the auditory material property with visual material (“Metal” and “Wood”) in the right temporal region in preverbal 4- to 8-month-old infants, using near-infrared spectroscopy (NIRS). Furthermore, we found that infants acquired the audio-visual mapping for a property of the “Metal” material later than for the “Wood” material, since infants form the visual property of “Metal” material after approximately 6 months of age. These findings indicate that multisensory processing of material information induces the activation of brain areas related to sound symbolism. Our findings also indicate that the material’s familiarity might facilitate the development of multisensory processing during the first year of life.
A distributed algorithm to maintain and repair the trail networks of arboreal ants
Authors: Chandrasekhar Arjun , Gordon Deborah M. , Navlakha Saket 
Published: June 2018

AbstractWe study how the arboreal turtle ant (Cephalotes goniodontus) solves a fundamental computing problem: maintaining a trail network and finding alternative paths to route around broken links in the network. Turtle ants form a routing backbone of foraging trails linking several nests and temporary food sources. This species travels only in the trees, so their foraging trails are constrained to lie on a natural graph formed by overlapping branches and vines in the tangled canopy. Links between branches, however, can be ephemeral, easily destroyed by wind, rain, or animal movements. Here we report a biologically feasible distributed algorithm, parameterized using field data, that can plausibly describe how turtle ants maintain the routing backbone and find alternative paths to circumvent broken links in the backbone. We validate the ability of this probabilistic algorithm to circumvent simulated breaks in synthetic and real-world networks, and we derive an analytic explanation for why certain features are crucial to improve the algorithm’s success. Our proposed algorithm uses fewer computational resources than common distributed graph search algorithms, and thus may be useful in other domains, such as for swarm computing or for coordinating molecular robots.
Simulating polaron biophysics with Rydberg atoms
Authors: Płodzień Marcin , Sowiński Tomasz , Kokkelmans Servaas 
Published: June 2018

AbstractTransport of excitations along proteins can be formulated in a quantum physics context, based on the periodicity and vibrational modes of the structures. Numerically exact solutions of the corresponding equations are very challenging to obtain on classical computers. Approximate solutions based on the Davydov ansatz have demonstrated the possibility of stabilized solitonic excitations along the protein, however, experimentally these solutions have never been directly observed. Here we propose an alternative study of biophysical transport phenomena based on a quantum simulator composed of a chain of ultracold dressed Rydberg atoms, which allows for a direct observation of the Davydov phenomena. We show that there is an experimentally accessible range of parameters where the system directly mimics the Davydov equations and their solutions. Moreover, we show that such a quantum simulator has access to the regime in between the small and large polaron regimes, which cannot be described perturbatively.
Expression of human mutant cyclin dependent kinase 4, Cyclin D and telomerase extends the life span but does not immortalize fibroblasts derived from loggerhead sea turtle (Caretta caretta)
Authors: Fukuda Tomokazu , Eitsuka Takahiro , Donai Kenichiro , Kurita Masanori , Saito Tomomi , Okamoto Hitoshi , Kinoshita Kodzue , Katayama Masafumi , Nitto Hiroshi , Uchida Takafumi , Onuma Manabu , Sone Hideko , Inoue-Murayama Miho , Kiyono Tohru 
Published: June 2018

AbstractConservation of the genetic resources of endangered animals is crucial for future generations. The loggerhead sea turtle (Caretta caretta) is a critically endangered species, because of human hunting, hybridisation with other sea turtle species, and infectious diseases. In the present study, we established primary fibroblast cell lines from the loggerhead sea turtle, and showed its species specific chromosome number is 2n = 56, which is identical to that of the hawksbill and olive ridley sea turtles. We first showed that intensive hybridization among multiple sea turtle species caused due to the identical chromosome number, which allows existence of stable hybridization among the multiple sea turtle species. Expressions of human-derived mutant Cyclin-dependent kinase 4 (CDK4) and Cyclin D dramatically extended the cell culture period, when it was compared with the cell culture period of wild type cells. The recombinant fibroblast cell lines maintained the normal chromosome condition and morphology, indicating that, at the G1/S phase, the machinery to control the cellular proliferation is evolutionally conserved among various vertebrates. To our knowledge, this study is the first to demonstrate the functional conservation to overcome the negative feedback system to limit the turn over of the cell cycle between mammalian and reptiles. Our cell culture method will enable the sharing of cells from critically endangered animals as research materials.
Heroin Abuse Results in Shifted RNA Expression to Neurodegenerative Diseases and Attenuation of TNFα Signaling Pathway
Authors: Zhu Mei , Xu Yu , Wang Huawei , Shen Zongwen , Xie Zhenrong , Chen Fengrong , Gao Yunhong , Chen Xin , Zhang Ying , Wu Qiang , Li Xuejun , Yu Juehua , Luo Huayou , Wang Kunhua 
Published: June 2018

AbstractRepeated administration of heroin results in the induction of physical dependence, which is characterized as a behavioral state of compulsive drug seeking and a high rate of relapse even after periods of abstinence. However, few studies have been dedicated to characterization of the long-term alterations in heroin-dependent patients (HDPs). Herein, we examined the peripheral blood from 810 HDPs versus 500 healthy controls (HCs) according to the inclusion criteria. Compared with the control group, significant decreases of albumin, triglyceride, and total cholesterol levels were identified in HDPs (P < 0.001) versus HCs coupled with an insignificant decrease in BMI. Meanwhile, RNA-sequencing analyses were performed on blood of 16 long-term HDPs and 25 HCs. The results showed that the TNFα signaling pathway and hematopoiesis related genes were inhibited in HDPs. We further compared the transcriptome data to those of SCA2 and posttraumatic stress disorder patients, identified neurodegenerative diseases related genes were commonly up-regulated in coupled with biological processes “vesicle transport”, “mitochondria” and “splicing”. Genes in the categories of “protein ubiquitination” were down-regulated indicating potential biochemical alterations shared by all three comparative to their controls. In summary, this is a leading study performing a series of through investigations and using delicate approaches. Results from this study would benefit the study of drug addiction overall and link long-term heroin abuse to neurodegenerative diseases.
A new quantitative 3D approach to imaging of structural joint disease
Authors: Turmezei T. D. , Treece G. M. , Gee A. H. , Houlden R. , Poole K. E. S. 
Published: June 2018

AbstractImaging of joints with 2D radiography has not been able to detect therapeutic success in research trials while 3D imaging, used regularly in the clinic, has not been approved for this purpose. We present a new 3D approach to this challenge called joint space mapping (JSM) that measures joint space width in 3D from standard clinical computed tomography (CT) data, demonstrating its analysis steps, technical validation, and reproducibility. Using high resolution peripheral quantitative CT as gold standard, we show a marginal over-estimation in accuracy of +0.13 mm and precision of ±0.32 mm. Inter-operator reproducibility bias was near-zero at −0.03 mm with limits of agreement ±0.29 mm and a root mean square coefficient of variation 7.5%. In a technical advance, we present results from across the hip joint in 3D with optimum validation and reproducibility metrics shown at inner joint regions. We also show JSM versatility using different imaging data sets and discuss potential applications. This 3D mapping approach provides information with greater sensitivity than reported for current radiographic methods that could result in improved patient stratification and treatment monitoring.
The joint influence of competition and mutualism on the biodiversity of mutualistic ecosystems
Authors: Gracia-Lázaro Carlos , Hernández Laura , Borge-Holthoefer Javier , Moreno Yamir 
Published: June 2018

AbstractIn the past years, there have been many advances –but also many debates– around mutualistic communities, whose structural features appear to facilitate mutually beneficial interactions and increase biodiversity, under some given population dynamics. However, most approaches neglect the structure of inter-species competition by adopting a mean-field perspective that does not deal with competitive interactions properly. Here, we build up a multilayer network that naturally accounts for mutualism and competition and show, through a dynamical population model and numerical simulations, that there is an intricate relation between competition and mutualism. Specifically, the multilayer structure is coupled to a dynamical model in which the intra-guild competitive terms are weighted by the abundance of shared mutualistic relations. We find that mutualism does not have the same consequences on the evolution of specialist and generalist species, and that there is a non-trivial profile of biodiversity in the parameter space of competition and mutualism. Our findings emphasize how the simultaneous consideration of positive and negative interactions derived from the real networks is key to understand the delicate trade-off between topology and biodiversity in ecosystems and call for the need to incorporate more realistic interaction patterns when modeling the structural and dynamical stability of mutualistic systems.
Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015
Authors: Thépault Amandine , Rose Valérie , Quesne Ségolène , Poezevara Typhaine , Béven Véronique , Hirchaud Edouard , Touzain Fabrice , Lucas Pierrick , Méric Guillaume , Mageiros Leonardos , Sheppard Samuel K. , Chemaly Marianne , Rivoal Katell 
Published: June 2018

AbstractPathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C. jejuni isolates from France using three types of genotype data: comparative genomic fingerprints; MLST genes; 15 host segregating genes previously identified by whole genome sequencing. Consistent with previous studies, chicken was an important source of campylobacteriosis in France (31–63% of clinical isolates assigned). There was also evidence that ruminants are a source (22–55% of clinical isolates assigned), suggesting that further investigation of potential transmission routes from ruminants to human would be useful. Additionally, we found evidence of environmental and pet sources. However, the relative importance as sources varied according to the year of isolation and the genotyping technique used. Annual variations in attribution emphasize the dynamic nature of zoonotic transmission and the need to perform source attribution regularly.