bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the use of sensory information to detect and track prey by the Sunda pangolin (Manis javanica) with conservation in mind
Authors: DiPaola Joshua D. , Yindee Marnoch , Plotnik Joshua M. 
Published: June 2020

AbstractPangolins are of conservation concern as one of the most heavily poached, yet least understood mammals. The Sunda pangolin (Manis javanica) in particular is a critically endangered species. Here, we investigate the behaviour of these pangolins, for the first time, using a battery of cognitive tasks based on a manipulation of available sensory information. In an object-choice task in which only one of two containers was baited with food, the pangolins were able to find the food with olfactory information alone (N = 2), but not with visual or acoustic information alone (N = 1). The single subject tested on all three domains was further tested on how he used smell to find food by providing him with an opportunity to find it from a controlled distance or by using scent trails as a guide. The results suggest that our subject may have the capacity to exploit scent trails left by prey which can be tracked to a final source, though we found no evidence to suggest that he had the ability to initiate hunts based on distant prey odors. Despite the small sample size, this is the first controlled experiment to investigate pangolin foraging behaviour and cognition, which may have implications for the future protection of pangolin habitat based on the location of prey species.
Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks
Authors: Sheykhali Somaye , Fernández-Gracia Juan , Traveset Anna , Ziegler Maren , Voolstra Christian R. , Duarte Carlos M. , Eguíluz Víctor M. 
Published: June 2020

AbstractUnderstanding the response of ecological networks to perturbations and disruptive events is needed to anticipate the biodiversity loss and extinction cascades. Here, we study how network plasticity reshapes the topology of mutualistic networks in response to species loss. We analyze more than one hundred empirical mutualistic networks and considered random and targeted removal as mechanisms of species extinction. Network plasticity is modeled as either random rewiring, as the most parsimonious approach, or resource affinity-driven rewiring, as a proxy for encoding the phylogenetic similarity and functional redundancy among species. This redundancy should be positively correlated with the robustness of an ecosystem, as functions can be taken by other species once one of them is extinct. We show that effective modularity,i.e. the ability of an ecosystem to adapt or restructure, increases with increasing numbers of extinctions, and with decreasing the replacement probability. Importantly, modularity is mostly affected by the extinction rather than by rewiring mechanisms. These changes in community structure are reflected in the robustness and stability due to their positive correlation with modularity. Resource affinity-driven rewiring offers an increase of modularity, robustness, and stability which could be an evolutionary favored mechanism to prevent a cascade of co-extinctions.
Using eye movements to detect visual field loss: a pragmatic assessment using simulated scotoma
Authors: Asfaw Daniel S. , Jones Pete R. , Edwards Laura A. , Smith Nicholas D. , Crabb David P. 
Published: June 2020

AbstractGlaucoma is a leading cause of irreversible sight-loss and has been shown to affect natural eye-movements. These changes may provide a cheap and easy-to-obtain biomarker for improving disease detection. Here, we investigated whether these changes are large enough to be clinically useful. We used a gaze-contingent simulated visual field (VF) loss paradigm, in which participants experienced a variable magnitude of simulated VF loss based on longitudinal data from a real glaucoma patient (thereby controlling for other variables, such as age and general health). Fifty-five young participants with healthy vision were asked to view two short videos and three pictures, either with: (1) no VF loss, (2) moderate VF loss, or (3) advanced VF loss. Eye-movements were recorded using a remote eye tracker. Key eye-movement parameters were computed, including saccade amplitude, the spread of saccade endpoints (bivariate contour ellipse area), location of saccade landing positions, and similarity of fixations locations among participants (quantified using kernel density estimation). The simulated VF loss caused some statistically significant effects in the eye movement parameters. Yet, these effects were not capable of consistently identifying simulated VF loss, despite it being of a magnitude likely easily detectable by standard automated perimetry.
Spatial pattern of Bois noir: case study of a delicate balance between disease progression and recovery
Authors: Murolo Sergio , Garbarino Matteo , Mancini Valeria , Romanazzi Gianfranco 
Published: June 2020

AbstractBois noir (BN) is the most important phytoplasma disease of Euro-Mediterranean area and induces severe loss of production and even the death of vines. Understanding the delicate balance between disease progression and recovery of BN infected plants over space and time is crucial to set up management tools. The data collected and analysed allowed to provide insights into dispersal pattern of the disease, caused by’Candidatus Phytoplasma solani’. Point pattern analysis (PPA) was applied to assess the spatial arrangement of symptomatic plants and the spatial correlation of disease levels in four vineyards. For spatio-temporal patterns of BN, a mark-correlation function was applied. Space-time PPA over multiple years (2011–2015) provided graphical visualisation of grapevines more severely affected by BN along the borders of the vineyards, mainly in 2011 when disease incidence was high. PPA across the symptomatic plants in the four vineyards confirmed this visual trend: an overall aggregated pattern at small (<10 m) spatial scales (2013) that were more evident later at all spatial scales (0–15 m). Application of this innovative spatial approach based on point and surface pattern analyses allowed the spread and severity of BN to be monitored, to define the dispersal routes of the pathogen. Such data will contribute to better understand the distribution of symptomatic plants over space and time and to define a model for preventive strategies to reduce future infections.
Paroxysmal eruptions tracked by variations of helium isotopes: inferences from Piton de la Fournaise (La Réunion island)
Authors: Boudoire G. , Rizzo A. L. , Arienzo I. , Di Muro A. 
Published: June 2020

AbstractHelium (He) with its isotopes (3He,4He) is a key tracer enabling the Earth’s mantle and dynamics to be characterized. Enrichment in primordial helium (3He) has been detected in volcanic gases of numerous magmatic systems in different geodynamic settings. Despite past use to monitor volcano-tectonic unrest, temporal3He/4He variability in volcanic emissions is still poorly constrained. Here, we investigate noble gas chemistry of Piton de la Fournaise hotspot volcano, where temporal fluctuations of3He/4He in response to the eruptive activity have never been studied. We compare the3He/4He signature of volcanic gases and fluid inclusions and we highlight analogous evolution of the3He/4He signature in both during the last decades of eruptive activity (1990–2017), even during the same eruption. We show that the maximum enrichment in3He is found in magmatic fluids that fed the most voluminous eruptions which culminated in caldera collapse events. We argue that this enrichment in3He mostly reflects a greater contribution of magmatic fluids from a primitive component of the mantle plume. These results emphasize that He isotopes may provide warnings of increases in deep magmatic contributions that potentially herald paroxysmal eruptions, as documented here at Piton de la Fournaise (2007) and also at Kilauea (2018).
Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex
Authors: Shah Sarah , Chen Yibi , Bhattacharya Debashish , Chan Cheong Xin 
Published: June 2020

AbstractDinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.
Hierarchical multi-shell hollow micro–meso–macroporous silica for Cr(VI) adsorption
Authors: Soltani Roozbeh , Marjani Azam , Soltani Reza , Shirazian Saeed 
Published: June 2020

AbstractThe development of easier, cheaper, and more effective synthetic strategies for hierarchical multimodal porous materials and multi-shell hollow spheres remains a challenging topic to utilize them as adsorbents in environmental applications. Here, the hierarchical architecture of multi-shell hollow micro–meso–macroporous silica with pollen-like morphology (MS-HMS-PL) has been successfully synthesized via a facile soft-templating approach and characterized for the first time. MS-HMS-PL sub-microspheres showed a trimodal hierarchical pore architecture with a high surface area of 414.5 m2 g−1, surpassing most of the previously reported multishelled hollow nanomaterials. Due to its facile preparation route and good physicochemical properties, MS-HMS-PL could be a potential candidate material in water purification, catalysis, and drug delivery. To investigate the applicability of MS-HMS-PL as an adsorbent, its adsorption performance for Cr(VI) in water was evaluated. Important adsorption factors affecting the adsorption capacity of adsorbent were systematically studied and Kinetics, isotherms, and thermodynamics parameters were computed via the non-linear fitting technique. The maximum capacity of adsorption computed from the Langmuir isotherm equation for Cr(VI) on MS-HMS-PL was 257.67 mg g−1 at 293 K and optimum conditions (pH 4.0, adsorbent dosage 5.0 mg, and contact time 90 min).
The clinical treatment and outcome of cerebellopontine angle medulloblastoma: a retrospective study of 15 cases
Authors: Wu Tao , Qu Pei-ran , Zhang Shun , Li Shi-wei , Zhang Jing , Wang Bo , Liu Pinan , Li Chun-de , Zhao Fu 
Published: June 2020

AbstractMedulloblastoma (MB) is the most common malignant pediatric brain tumor arising in the cerebellum or the 4th ventricle. Cerebellopontine angle (CPA) MBs are extremely rare tumors, with few cases previously described. In this study, we sought to describe the clinical characteristics, molecular features and outcomes of CPA MB. We retrospectively reviewed a total of 968 patients who had a histopathological diagnosis of MB at the Beijing Neurosurgical Institute between 2002 and 2016. The demographic characteristics, clinical manifestations and radiological features were retrospectively analyzed. Molecular subgroup was evaluated by the expression profiling array or immunohistochemistry. Overall survival (OS) and progression-free survival (PFS) were calculated using Kaplan-Meier analysis. In this study, 15 patients (12 adults and 3 children) with a mean age at diagnosis of 25.1 years (range 4–45 years) were included. CPA MBs represented 1.5% of the total cases of MB (15/968). Two molecular subgroups were identified in CPA MBs: 5 WNT-MBs (33%) and 10 SHH-MBs (67%). CPA WNT-MBs had the extracerebellar growth with the involvement of brainstem (P = 0.002), whereas CPA SHH-MBs predominantly located within the cerebellar hemispheres (P = 0.004). The 5-year OS and PFS rates for CPA MB were 80.0% ± 10.3% and 66.7% ± 12.2%, respectively. Pediatric patients with CPA MBs had worse outcomes than adult patients (OS: P = 0.019, PFS: P = 0.078). In conclusion, CPA MB is extremely rare and consists of two subgroups. Adult patients with CPA MB had a good prognosis. Maximum safe surgical resection combined with adjuvant radiotherapy and chemotherapy can be an effective treatment strategy for this rare tumor.
Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession
Authors: Krishna Mayank , Gupta Shruti , Delgado – Baquerizo Manuel , Morriën Elly , Garkoti Satish Chandra , Chaturvedi Rupesh , Ahmad Shandar 
Published: June 2020

AbstractThis study investigated the potential role of a nitrogen-fixing early-coloniserAlnus NepalensisD. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth.Janthinobacterium lividum,Candidatus XiphinematobacterandRhodoplaneswere indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successionalQuercus leucotrichophora(Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.
Feedback between high-pressure genesis of abiotic methane and strain localization in subducted carbonate rocks
Authors: Giuntoli Francesco , Vitale Brovarone Alberto , Menegon Luca 
Published: June 2020

AbstractFluid-rock interactions exert key control over rock rheology and strain localization. Redox may significantly affect the reaction pathways and, thereby, the mechanical properties of the rock. This effect may become critical in volatile-rich, redox sensitive rocks such as carbonate-rich lithologies, the breakdown of which can significantly modify the net volume change of fluid-mediated reactions. Subduction focus the largest recycling of crustal carbonates and the most intense seismic activity on Earth. Nevertheless, the feedbacks between deep carbon mobilization and deformation remain poorly investigated. We present quantitative microstructural results from natural samples and thermodynamic modeling indicating that percolation of reducing fluids exerts strong control on the mobilization of carbon and on strain localization in subducted carbonate rocks. Fluid-mediated carbonate reduction progressed from discrete domains unaffected by ductile deformation into localized shear zones deforming via diffusion creep, dissolution-precipitation creep and grain boundary sliding. Grain-size reduction and creep cavitation along localized shear zones enhanced fluid-carbonate interactions and fluid channelization. These results indicate that reduction of carbonate rocks can exert an important positive feedback on strain localization and fluid channelization, with potential implications on seismic activity and transport of deep hydrocarbon-bearing fluids.
High frequency of intermediary alleles in the HTT gene in Northern Sweden - The Swedish Huntingtin Alleles and Phenotype (SHAPE) study
Authors: Sundblom Jimmy , Niemelä Valter , Ghazarian Maria , Strand Ann-Sofi , Bergdahl Ingvar A. , Jansson Jan-Håkan , Söderberg Stefan , Stattin Eva-Lena 
Published: June 2020

AbstractTrinucleotide (CAG) repeat expansions longer than 39 in the huntingtin (HTT) gene cause Huntington’s disease (HD). The frequency of intermediate alleles (IA) with a length of 27–35 in the general population is not fully known, but studied in specific materials connected to the incidence of HD. The Swedish Huntingtin Alleles and Phenotype (SHAPE) study aims to assess the frequency of trinucleotide repeat expansions in the HTT gene in north Sweden. 8260 individuals unselected for HD from the counties of Norr- and Västerbotten in the north of Sweden were included. DNA samples were obtained and analysis of the HTT gene was performed, yielding data on HTT gene expansion length in 7379 individuals. A high frequency of intermediate alleles, 6.8%, was seen. Also, individuals with repeat numbers lower than ever previously reported (<5) were found. These results suggest a high frequency of HD in the norther parts of Sweden. Subsequent analyses may elucidate the influence of IA:s on traits other than HD.
Use of Surface Corrugations for Energy-Efficient Chaotic Stirring in Low Reynolds Number Flows
Authors: Gepner S. W. , Floryan J. M. 
Published: June 2020

AbstractWe demonstrate that an intensive stirring can be achieved in laminar channel flows in a passive manner by utilizing the recently discovered instability waves which lead to chaotic particle movements. The stirring is suitable for mixtures made of delicate constituents prone to mechanical damage, such as bacteria and DNA samples, as collisions between the stream and both the bounding walls as well as mechanical mixing devices are avoided. Debris accumulation is prevented as no stagnant fluid zones are formed. Groove symmetries can be used to limit stirring to selected parts of the flow domain. The energy cost of flows with such stirring is either smaller or marginally larger than the energy cost of flows through smooth channels.
CRISPR/Cas9 knockout of human arylamine N-acetyltransferase 1 in MDA-MB-231 breast cancer cells suggests a role in cellular metabolism
Authors: Carlisle Samantha M. , Trainor Patrick J. , Hong Kyung U. , Doll Mark A. , Hein David W. 
Published: June 2020

AbstractHuman arylamine N-acetyltransferase 1 (NAT1), present in all tissues, is classically described as a phase-II xenobiotic metabolizing enzyme but can also catalyze the hydrolysis of acetyl-Coenzyme A (acetyl-CoA) in the absence of an arylamine substrate using folate as a cofactor. NAT1 activity varies inter-individually and has been shown to be overexpressed in estrogen receptor-positive (ER+) breast cancers. NAT1 has also been implicated in breast cancer progression however the exact role of NAT1 remains unknown. The objective of this study was to evaluate the effect of varying levels of NAT1 N-acetylation activity in MDA-MB-231 breast cancer cells on global cellular metabolism and to probe for unknown endogenous NAT1 substrates. Global, untargeted metabolomics was conducted via ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) on MDA-MB-231 breast cancer cell lines constructed with siRNA and CRISPR/Cas9 technologies to vary only in NAT1 N-acetylation activity. Many metabolites were differentially abundant in NAT1-modified cell lines compared to the Scrambled parental cell line. N-acetylasparagine and N-acetylputrescine abundances were strongly positively correlated (r = 0.986 and r = 0.944, respectively) with NAT1 N-acetylation activity whereas saccharopine abundance was strongly inversely correlated (r = −0.876). Two of the most striking observations were a reduction in de novo pyrimidine biosynthesis and defective β-oxidation of fatty acids in the absence of NAT1. We have shown that NAT1 expression differentially affects cellular metabolism dependent on the level of expression. Our results support the hypothesis that NAT1 is not just a xenobiotic metabolizing enzyme and may have a role in endogenous cellular metabolism.
Soil bacterial communities in three rice-based cropping systems differing in productivity
Authors: Huang Min , Tian Alin , Chen Jiana , Cao Fangbo , Chen Yumei , Liu Longsheng 
Published: June 2020

AbstractSoil microorganisms play an important role in determining productivity of agro-ecosystems. This study was conducted to compare diversity, richness, and structure (relative abundance at the phylum level) of soil bacterial communities among three rice-based cropping systems, namely, a winter fallow-rice-rice (FRR), green manure (Chinese milk vetch)-rice-rice (MRR), and oilseed rape-rice-rice (ORR), in which MRR and ORR had significantly higher productivity than FRR. A 16S rRNA gene sequence analysis showed that no significant differences were observed in diversity and richness indices (observed species, Shannon, Simpson, Chao1, abundance-based coverage estimators, and phylogeny-based metrics) of soil bacterial communities among the three cropping systems. However, relative abundances of dominant phyla in soil bacterial communities, including Proteobacteria, Acidobacteria, Nitrospirae, Gemmatimonadetes, and Verrucomicrobia, were significantly different among the three cropping systems. In particular, a significant reduction in the relative abundance of Nitrospirae was observed in both MRR and ORR compared with FRR. These results indicate that bacterial community structure was affected by cropping systems in the tested paddy soils. Based on the results of our studies and existing knowledge bases, we speculate that benefits to rice yield may be obtained by reducing the relative abundance of Nitrospirae and increasing the ratio of abundances of Proteobacteria/Acidobacteria in paddy soils.
Current Approaches to the Management of Usher Syndrome for the Clinician
Authors: Koleilat Alaa , Schimmenti Lisa A. , Poling Gayla L. 
Published: June 2020

PurposeMore than 460 million people suffer from disabling hearing loss worldwide, and about 50%–60% of hearing loss in infants are due to genetics. Usher syndrome is a genetic condition in which children are born deaf or hard of hearing and subsequently develop retinitis pigmentosa. It is the most common cause of deafness and blindness in pediatric populations, and pathogenic variants in 10 different genes are shown to be causative. The purpose of this review article is to advance the understanding of the clinical symptoms of an individual with Usher syndrome and highlight the latest research in the development of new treatments including gene therapy. The care and management of individuals with Usher syndrome require a team of multidisciplinary health care professionals, including an audiologist, a speech-language pathologist, an ophthalmologist, and a medical geneticist. We highlight the importance of early identification for better speech and developmental outcomes, specifically in pediatric individuals.ConclusionThis review empowers audiologists to be aware of early signs of Usher syndrome as they are typically the first point of contact and provides important information for audiologists and other health care professionals involved in the care of individuals with hearing loss and vision loss.