bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organic farming expansion drives natural enemy abundance not diversity in agricultural landscapes
Authors: Muneret Lucile , Auriol Arthur , Bonnard Olivier , Richart-Cervera Sylvie , Thiéry Denis , Rusch Adrien 
Published: July 2019

AbstractOrganic farming is seen as a prototype of ecological intensification able to conciliate crop productivity and biodiversity conservation in agricultural landscapes. However, how natural enemies, an important functional group supporting pest control services, respond to organic farming at different scales and in different landscape contexts remain unclear.Using a hierarchical design within a vineyard-dominated region located in southwestern France, we examine the independent effects of organic farming and semi-natural habitats at the local and landscape scales on natural enemies.We show that the proportion of organic farming is a stronger driver of species abundance than the proportion of semi-natural habitats and is an important facet of landscape heterogeneity shaping natural enemy assemblages. Although our study highlight a strong taxonomic group-dependency about the effect of organic farming, organic farming benefits to dominant species while rare species occur at the same frequency in the two farming systems.Independently of farming systems, enhancing field age, reducing crop productivity, soil tillage intensity and pesticide use are key management options to increase natural enemy biodiversity.Synthesis and Applications. Our study indicates that policies promoting the expansion of organic farming will benefit more to ecological intensification strategies seeking to enhance ecosystem services than to biodiversity conservation.
Precision of auditory responses deteriorates on the way to frontal cortical areas
Authors: López-Jury Luciana , Mannel Adrian , Garcia-Rosales Francisco , Hechavarria Julio C. 
Published: July 2019

AbstractFrontal areas of the mammalian cortex are thought to be important for cognitive control and complex behaviour. These areas have been studied mostly in humans, non-human primates and rodents. In this article, we present a quantitative characterization of response properties of a frontal auditory area responsive to sound in the bat brain, the frontal auditory field (FAF). Bats are highly vocal animals and they constitute an important experimental model for studying the auditory system. At present, little is known about neuronal sound processing in the bat FAF. We combined electrophysiology experiments and computational simulations to compare the response properties of auditory neurons found in the bat FAF and auditory cortex (AC) to simple sounds (pure tones). Anatomical studies have shown that the latter provide feedforward inputs to the former. Our results show that bat FAF neurons are responsive to sounds, however, when compared to AC neurons, they presented sparser, less precise spiking and longer-lasting responses. Based on the results of an integrate-and-fire neuronal model, we speculate that slow, low-threshold, synaptic dynamics could contribute to the changes in activity pattern that occur as information travels through cortico-cortical projections from the AC to the FAF.
A bibliometric analysis of Soil remediation Based on Massive research literature data During 1988-2018
Authors: Hu Ya , Han Jichang , Sun Zenghui , Wang Huanyuan , Liu Xiang , Kong Hui 
Published: July 2019

AbstractSoil is an important part of the ecosystem with significant roles that help human population sustain. Research on prevention and remediation of soil pollution has been carried out when 1985. This study analyzed the 1988–2018 soil remediation dataset in the Web of Science database by bibliometric methods to illustrate the current research trends and hot topics of quantitative analysis and soil remediation in the world. To further identify the major soil contamination topics, we employed social network analysis. The results indicate that the field of soil remediation has entered a stage of rapid progress. The United States has a strong overall strength with the largest number of published articles and larger impact. China ranks second. We identified Journal of hazardous materials as the most influential journal and Chinese academy of sciences as the most influential institution. Academic cooperation showed an increasing trend at the author, institutional, and national levels with an average level of cooperation of 3.57, 1.66, and 1.16, respectively. However, the growth rate of cooperation at the national level is relatively low. In addition, the frequency and co-word analyses of keywords revealed the important research topics. “heavy metals”, “PAH”, “bioremediation”, “Phytoremediation” and “Electrokinetic remediation” were identified as the hot topics. The findings of this study will help researchers understand the status of soil remediation as well as provide guidance for future research.
Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology
Authors: Hughes Travis K , Wadsworth Marc H , Gierahn Todd M , Do Tran , Weiss David , Andrade Priscilla R. , Ma Feiyang , de Andrade Silva Bruno J. , Shao Shuai , Tsoi Lam C , Ordovas-Montanes Jose , Gudjonsson Johann E , Modlin Robert L , Love J Christopher , Shalek Alex K 
Published: July 2019

SUMMARYThe development of high-throughput single-cell RNA-sequencing (scRNA-Seq) methodologies has empowered the characterization of complex biological samples by dramatically increasing the number of constituent cells that can be examined concurrently. Nevertheless, these approaches typically recover substantially less information per-cell as compared to lower-throughput microtiter plate-based strategies. To uncover critical phenotypic differences among cells and effectively link scRNA-Seq observations to legacy datasets, reliable detection of phenotype-defining transcripts – such as transcription factors, affinity receptors, and signaling molecules – by these methods is essential. Here, we describe a substantially improved massively-parallel scRNA-Seq protocol we term Seq-Well S^3 (“Second-Strand Synthesis”) that increases the efficiency of transcript capture and gene detection by up to 10- and 5-fold, respectively, relative to previous iterations, surpassing best-in-class commercial analogs. We first characterized the performance of Seq-Well S^3 in cell lines and PBMCs, and then examined five different inflammatory skin diseases, illustrative of distinct types of inflammation, to explore the breadth of potential immune and parenchymal cell states. Our work presents an essential methodological advance as well as a valuable resource for studying the cellular and molecular features that inform human skin inflammation.
Reduction in voluntary activation of elbow and wrist muscles in individuals with chronic hemiparetic stroke
Authors: Garmirian Lindsay R. P. , Dewald Julius P. A. , Acosta Ana Maria 
Published: July 2019

AbstractAfter a stroke, descending drive is impaired due to the loss of corticospinal and corticobulbar projections which causes a reduction in voluntary activation or an inability of the nervous system to activate muscles to their full capacity, which in turn contributes to weakness of the upper extremity. Voluntary activation has not been quantified at specific joints in the upper extremity, in part because directly assessing changes descending drive is difficult. In this study, voluntary activation of elbow and wrist flexors and extensors was assessed in participants with chronic hemiparetic stroke using twitch interpolation. Twitch interpolation uses electrical stimulation to estimate voluntary activation and relies on the principle that there is an inverse relationship between the amplitude of a twitch evoked by a stimulus and the voluntary force output during stimulation (Taylor, 2009). We measured voluntary activation using twitch interpolation as well as maximum voluntary torque (MVT) of the elbow and wrist flexors and extensors in the paretic and non-paretic limb of ten participants post stroke and the dominant and non-dominant limb of 2 control participants. Results show, MVT interlimb differences were significantly greater for stroke participants compared to control, across muscle groups (p≤0.005). For stroke participants, MVT interlimb differences were significantly greater at the wrist compared to the elbow (P=0.003). Voluntary activation was significantly less in the paretic limb compared to the non-paretic, dominant and non-dominant limbs, across participants and muscle groups (p<0.005 for all four muscle groups). For the stroke participants, the voluntary activation interlimb difference was significantly greater for the wrist muscles compared to the elbow muscles (p<0.005). There was a significant positive correlation (r = 0.39, P = .022) between each participant’s impairment level, as measured by a hand specific subscore of the Fugl-Meyer Assessment, and the wrist extensor voluntary activation in the paretic limb but the relationship was not significant for the other muscle groups.
The Cul3 ubiquitin ligase engages Insomniac as an adaptor to impact sleep and synaptic homeostasis
Authors: Li Qiuling , Lim Kayla Y. , Altawell Raad , Verderose Faith , Li Xiling , Dong Wanying , Martinez Joshua , Dickman Dion , Stavropoulos Nicholas 
Published: July 2019

AbstractMutations of the Cullin-3 (Cul3) E3 ubiquitin ligase are associated with autism and schizophrenia, neurological disorders characterized by sleep disturbances and altered synaptic function. Cul3 engages dozens of adaptor proteins to recruit hundreds of substrates for ubiquitination, but the adaptors that impact sleep and synapses remain ill-defined. Here we implicate Insomniac (Inc), a conserved protein required for normal sleep and synaptic homeostasis inDrosophila, as a Cul3 adaptor. Inc binds Cul3 in vivo, and mutations within the N-terminal BTB domain of Inc that weaken Inc-Cul3 associations impair Inc activity, indicating that Inc function requires binding to the Cul3 complex. Deletion of the conserved C-terminus of Inc does not alter Cul3 binding but abolishes Inc activity in the context of sleep and synaptic homeostasis, suggesting that the C-terminal domain of Inc is a substrate recruitment domain. Mutation of a conserved, disease-associated arginine in the Inc C-terminus also abolishes Inc function, suggesting that this residue is vital for recruiting Inc targets. Inc levels are negatively regulated by Cul3 in neurons, consistent with Inc degradation by autocatalytic ubiquitination, a hallmark of Cullin adaptors. These findings link Inc and Cul3 in vivo and indicate that Cul3-Inc complexes are essential for normal sleep and synaptic function. Furthermore, these results indicate that dysregulation of conserved substrates of Cul3-Inc complexes may contribute to altered sleep and synaptic function in autism and schizophrenia associated withCul3mutations.Author SummaryCul3is a highly conserved gene important for brain development and function.Cul3mutations are a risk factor for autism and schizophrenia, neurological disorders associated with disturbed sleep and changes in neuronal synapses. A key challenge in understanding howCul3impacts brain function is elucidating the downstream molecular pathways. Cul3 is a ubiquitin ligase that assembles with dozens of adaptor proteins, which in turn recruit specific protein substrates for ubiquitination. Identifying and characterizing Cul3 adaptors in the nervous system is thus a critical step in understanding Cul3 function. Because Cul3 and its adaptors are conserved through evolution, simpler organisms including the fruit flyDrosophilaprovide powerful systems for identifying and characterizing Cul3 adaptors. We found that the Insomniac (Inc) protein has the properties of a Cul3 adaptor that impacts sleep and synaptic function inDrosophila. These results suggest that human proteins related to Inc may be relevant for changes in sleep and synaptic function in autism and schizophrenia associated with reduced Cul3 activity.
A rapidly evolving polybasic motif modulates bacterial detection by guanylate binding proteins
Authors: Kohler Kristin M. , Kutsch Miriam , Piro Anthony S. , Wallace Graham , Coers Jörn , Barber Matthew F. 
Published: July 2019

AbstractCell-autonomous immunity relies on the rapid detection of invasive pathogens by host proteins. Guanylate binding proteins (GBPs) have emerged as key mediators of vertebrate immune defense through their ability to recognize a diverse array of intracellular pathogens and pathogen-containing cellular compartments. Human and mouse GBPs have been shown to target distinct groups of microbes, although the molecular determinants of pathogen specificity remain unclear. We show that rapid diversification of a C-terminal polybasic motif (PBM) in primate GBPs controls recognition of the model cytosolic bacterial pathogen Shigella flexneri. By swapping this membrane-binding motif between primate GBP orthologs, we find that the ability to target S. flexneri has been enhanced and lost in specific lineages of New World monkeys. Single substitutions in rapidly evolving sites of the GBP1 PBM are sufficient to abolish or restore bacterial detection abilities, illustrating a role for epistasis in the evolution of pathogen recognition. We further demonstrate that the squirrel monkey GBP2 C-terminal domain recently gained the ability to target S. flexneri through a stepwise process of convergent evolution. These findings reveal a mechanism by which accelerated evolution of a PBM shifts GBP target specificity and aid in resolving the molecular basis of GBP function in cell-autonomous immune defense.
Asparagine deprivation causes a reversible inhibition of Human Cytomegalovirus acute virus replication
Authors: Lee Chen-Hsuin , Griffiths Samantha , Digard Paul , Pham Nhan T. , Auer Manfred , Haas Juergen , Grey Finn 
Published: July 2019

AbstractAs obligate intracellular pathogens, viruses rely on the host cell machinery to replicate efficiently, with the host metabolism extensively manipulated for this purpose. High throughput siRNA screens provide a systematic approach for the identification of novel host-virus interactions. Here, we report a large-scale screen for host factors important for human cytomegalovirus (HCMV), consisting of 6,881 siRNAs. We identified 47 proviral factors and 68 antiviral factors involved in a wide range of cellular processes including the mediator complex, proteasome function and mRNA splicing. Focused characterisation of one of the hits, asparagine synthetase (ASNS), demonstrated a strict requirement for asparagine for HCMV replication which leads to an early block in virus replication before the onset of DNA amplification. This effect is specific to HCMV, as knockdown of ASNS had little effect on herpes simplex virus-1 or influenza A virus replication, suggesting the restriction is not simply due to a failure in protein production. Remarkably, virus replication could be completely rescued seven days post-infection with addition of exogenous asparagine, indicating that while virus replication is restricted at an early stage, it maintains the capacity for full replication days after initial infection. This study represents the most comprehensive siRNA screen for the identification of host factors involved in HCMV replication and identifies the non-essential amino acid, asparagine as a critical factor in regulating HCMV virus replication. These results have implications for control of viral latency and the clinical treatment of HCMV in patients.ImportanceHCMV accounts for more than 60% of complications associated with solid organ transplant patients. Prophylactic or preventative treatment with antivirals, such as ganciclovir, reduces the occurrence of early onset HCMV disease. However, late onset disease remains a significant problem and prolonged treatment, especially in patients with suppressed immune systems, greatly increases the risk of antiviral resistance. Very few antivirals have been developed for use against HCMV since the licensing of ganciclovir, and of these, the same viral genes are often targeted, reducing the usefulness of these drugs against resistant strains. An alternative approach is to target host genes essential for virus replication. Here we demonstrate that HCMV replication is highly dependent on levels of the amino acid asparagine and knockdown of a critical enzyme involved in asparagine synthesis results in severe attenuation of virus replication. These results suggest that reducing asparagine levels through dietary restriction or chemotherapeutic treatment could limit HCMV replication in patients.
Deer slow down litter decomposition by reducing litter quality in a temperate forest
Authors: Simon Chollet , Morgane Maillard , Juliane Schörghuber , Sue Grayston , Jean-Louis Martin 
Published: July 2019

ABSTRACTIn temperate forest ecosystems, the role of deer in litter decomposition, a key nutrient cycling process, remains debated. Deer may modify the decomposition process by affecting plant cover and thus modifying litter abundance. They can also alter litter quality through differential browsing and affect decomposer ability by changing soil abiotic properties and the nature of decomposer communities. We used two litterbag experiments in a quasi-experimental situation resulting from the introduction of Sitka black-tailed deer Odocoileus odocoileus sitkensis on forested islands of Haida Gwaii (Canada). We investigated the effects of deer on decomposition through their impacts on litter quality and on decomposer ability. After one year, the effect of deer on litter quality resulted in a lower rate of mass loss in litter from litterbags. This mass loss mainly reflected a 21 and 38 % lower rate of carbon (C) and nitrogen (N) loss, respectively. Presence of deer resulted in lower decomposer ability for the rate of carbon loss, but not for nitrogen loss. The level of C loss after one year was 5% higher for litter decomposing on an island without deer. But the change in the rate of carbon loss explained by the effect of deer on decomposer ability was outweighed by the effect deer had on litter quality. Additional effects of deer on the decomposition process through feces deposition were significant but minor. These results question the role the large increase in deer populations observed in temperate forests at continental scales may play in broad scale patterns of C and N cycling.
Model-based cell clustering and population tracking for time-series flow cytometry data
Authors: Minoura Kodai , Abe Ko , Maeda Yuka , Nishikawa Hiroyoshi , Shimamura Teppei 
Published: July 2019

AbstractMotivationModern flow cytometry technology has enabled the simultaneous analysis of multiple cell markers at the single-cell level, and it is widely used in a broad field of research. The detection of cell populations in flow cytometry data has long been dependent on “manual gating” by visual inspection. Recently, numerous software have been developed for automatic, computationally guided detection of cell populations; however, they are not designed for time-series flow cytometry data. Time-series flow cytometry data are indispensable for investigating the dynamics of cell populations that could not be elucidated by static time-point analysis.Therefore, there is a great need for tools to systematically analyze time-series flow cytometry data.ResultsWe propose a simple and efficient statistical framework, named CYBERTRACK (CYtometry-Based Estimation and Reasoning for TRACKing cell populations), to perform clustering and cell population tracking for time-series flow cytometry data. CYBERTRACK assumes that flow cytometry data are generated from a multivariate Gaussian mixture distribution with its mixture proportion at the current time dependent on that at a previous timepoint. Using simulation data, we evaluate the performance of CYBERTRACK when estimating parameters for a multivariate Gaussian mixture distribution, tracking time-dependent transitions of mixture proportions, and detecting change-points in the overall mixture proportion. The CYBERTRACK performance is validated using two real flow cytometry datasets, which demonstrate that the population dynamics detected by CYBERTRACK are consistent with our prior knowledge of lymphocyte behavior.ConclusionsOur results indicate that CYBERTRACK offers better understandings of time-dependent cell population dynamics to cytometry users by systematically analyzing time-series flow cytometry data.
Cyclin-dependent-like kinase 5 is required for pain signalling in both human neurons and mouse models
Authors: La Montanara Paolo , Hervera Arnau , Baltussen Lucas , Hutson Thomas , Palmisano Ilaria , De Virgiliis Francesco , Gao Yunan , Majid Qasim A. , Gorgoraptis Nikos , Wong Kingsley , Downs Jenny , Di Lazzaro Vincenzo , Pizzorusso Tommaso , Ultanir Sila , Leonard Helen , Istvan Nagy , Mazarakis Nicholas D , Di Giovanni Simone 
Published: July 2019

AbstractCyclin-dependent-like kinase 5 (Cdkl5) gene mutations lead to an X-linked disorder that is characterized by infantile epileptic encephalopathy, developmental delay and hypotonia. However, we found that a substantial percentage of these patients also report a previously unrecognised anamnestic deficiency in pain perception. Consistent with a role in nociception, we discovered that Cdkl5 is expressed selectively in nociceptive dorsal root ganglia (DRG) neurons in mice and in iPS-derived human nociceptors. CDKL5 deficient mice display defective epidermal innervation and conditional deletion of Cdkl5 in DRG sensory neurons significantly impairs nociception, phenocopying CDKL5 deficiency disorder in patients. Mechanistically, Cdkl5 interacts with CaMKIIα to control outgrowth as well as TRPV1-dependent signalling, which are disrupted in both Cdkl5 mutant murine DRG and human iPS-derived nociceptors. Together, these findings unveil a previously unrecognized role for Cdkl5 in nociception, proposing an original regulatory mechanism for pain perception with implications for future therapeutics in CDKL5 deficiency disorder.One Sentence SummaryCyclin-dependent-like kinase 5 (Cdkl5) controls nociception in patients and murine models of Cdkl5 deficiency disorder via CaMKII-dependent mechanisms