bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concurrent ordination: simultaneous unconstrained and constrained latent variable modeling
Authors: van der Veen Bert , Hui Francis K.C. , Hovstad Knut A. , O’Hara Robert B. 
Published: October 2021

SummaryIn community ecology, unconstrained ordination can be used to indirectly explore drivers of community composition, while constrained ordination can be used to directly relate predictors to an ecological community. However, existing constrained ordination methods do not explicitly account for community composition that cannot be explained by the predictors, so that they have the potential to misrepresent community composition if not all predictors are available in the data.We propose and develop a set of new methods for ordination and Joint Species Distribution Modelling (JSDM) as part of the Generalized Linear Latent Variable Model (GLLVM) framework, that incorporate predictors directly into an ordination. This includes a new ordination method that we refer to as concurrent ordination, as it simultaneously constructs unconstrained and constrained latent variables. Both unmeasured residual covariation and predictors are incorporated into the ordination by simultaneously imposing reduced rank structures on the residual covariance matrix and on fixed-effects.We evaluate the method with a simulation study, and show that the proposed developments outperform Canonical Correspondence Analysis (CCA) for Poisson and Bernoulli responses, and perform similar to Redundancy Analysis (RDA) for normally distributed responses, the two most popular methods for constrained ordination in community ecology. Two examples with real data further demonstrate the benefits of concurrent ordination, and the need to account for residual covariation in the analysis of multivariate data.This article contextualizes the role of constrained ordination in the GLLVM and JSDM frameworks, while developing a new ordination method that incorporates the best of unconstrained and constrained ordination, and which overcomes some of the deficiencies of existing classical ordination methods.
Hydrophobicity in clearwing Lepidoptera: impact of scale micro and nanostructure, and trade-off with optical transparency
Authors: Gomez Doris , Pairraire Jonathan , Pinna Charline , Arias Monica , Houssin Céline , Barbut Jérôme , Berthier Serge , Andraud Christine , Ondarçuhu Thierry , Elias Marianne 
Published: October 2021

AbstractWhile scales ensure hydrophobicity in opaque Lepidoptera, their reduction in clearwing species question hydrophobicity and its dependency on wing microstructures (scale presence, morphology, insertion, coloration) and nanostructures (scale ridge features). By measuring static contact angle (CA) of water droplets at different stages of evaporation in opaque and transparent patches of 23 clearwing species with varied microstructure, we establish for the first time that transparency is costly for hydrophobicity, a cost depending on microstructure: transparent patches lose more hydrophobicity with water evaporation than opaque patches, a loss attenuated for higher scale densities, coloured scales (for erect scales), and when combining two types of scales (piliform and lamellar). Nude membranes show lowest hydrophobicity. Models best predicting CA include microstructures for all scales, and nanostructures only for flat scales. We reveal for the first time that wing hydrophobicity negatively relates to optical transparency. Finally, tropical species have more hydrophobic transparent patches but similarly hydrophobic opaque patches compared to temperate species. All findings are consistent with the physics of hydrophobicity, especially on multiscale roughness, and underline that wings are evolutionary compromises.
Antibacterial 3D-printed PMMA/ceramic composites
Authors: Marin Elia , Mukai Mikiya , Boschetto Francesco , Sunthar Thefye P. M. , Adachi Tetsuya , Zhu Wenliang , Rondinella Alfredo , Lanzutti Alex , Kanamura Narisato , Yamamoto Toshiro , Fedrizzi Lorenzo , Pezzotti Giuseppe 
Published: October 2021

AbstractFollowing the rising interested on 3D-printed technologies, this research explores the possibility to use stereo-lithography to 3D print PMMA resins reinforced with up to 15% in weight of antibacterial ceramic powders. Three different reinforcements were tested, following previous literature data: aluminum nitride, titanium oxide and barium titanate.Between the three powders, the most uniform dispersion was achieved using aluminum nitride. Initial screenings with mixed and cured composite resins showed that between the three composite materials, only aluminum nitride or barium titanate PMMA showed a clear antibacterial effect when compared to the pristine reference, with aluminum nitride being the most effective againstE. coli. When 3D printed using stereo-lithography, the composite containing aluminum nitride showed an even higher degree of dispersion and comparable antibacterial effects. Moreover, aluminum nitride reinforced PMMA resins showed good mechanical properties, comparable to the basic resin, and could be further strengthened by a standard post-curing process.
Drosophila tachykininergic neurons modulate the activity of two groups of receptor-expressing neurons to regulate aggressive tone
Authors: Wohl Margot , Asahina Kenta 
Published: October 2021

ABSTRACTNeuropeptides influence animal behaviors through complex molecular and cellular mechanisms, many of which are difficult to predict solely from synaptic connectivity. Here, we uncovered two separate downstream targets that are differentially modulated by the neuropeptide tachykinin, which promotes Drosophila aggression. Tachykinin from a single sexually dimorphic group of neurons recruits two separate downstream groups of neurons. One downstream group, synaptically connected to the tachykinergic neurons, expresses the receptor TkR86C and is necessary for aggression. Tachykinin supports the strength of cholinergic excitatory synaptic transmission between the tachykinergic and TkR86C downstream neurons. The other downstream group expresses the TkR99D receptor and is recruited primarily when tachykinin is over-expressed in the source neurons. This circuit reconfiguration correlates with the quantitative and qualitative enhancement of aggression observed when tachykinin is present in excess. Our data highlight how the amount of neuropeptide released from a small number of neurons can reshape the activity patterns of multiple downstream neural populations.
Combined effects of bird extinctions and introductions in oceanic islands: decreased functional diversity despite increased species richness
Authors: Soares Filipa C. , de Lima Ricardo F. , Palmeirim Jorge M. , Cardoso Pedro , Rodrigues Ana S. L. 
Published: October 2021

AbstractAimWe analyse the functional consequences of the changes in species composition resulting from extinctions and introductions on oceanic island bird assemblages. Specifically, we ask if introduced species have compensated the functional loss resulting from species extinctions.LocationSeventy-four oceanic islands (>100 km2) in the Atlantic, Pacific and Indian Oceans.Time periodLate Holocene.Major taxa studiedTerrestrial and freshwater bird species.MethodsWe compiled a species list per island (extinct and extant, native and introduced), and then compiled traits per species. We used single-trait analyses to assess the effects of past species extinctions and introductions on functional composition. Then, we used probabilistic hypervolumes in trait space to calculate functional richness and evenness of original versus present avifaunas of each island (and net change), and to estimate functional originality of extinct and introduced species.ResultsThe net effects of extinctions and introductions were: an increase in average species richness per island (alpha diversity), yet a decline in diversity across all islands (gamma diversity); an average increase in the prevalence of most functional traits (23 out of 35) yet an average decline functional richness and evenness, associated with the fact that extinct species were functionally more original (when compared to extant natives) than introduced species.Main conclusionsIntroduced species are on average offsetting (and even surpassing) the losses of extinct species per island in terms of species richness, and they are increasing the prevalence of most functional traits. However, they are not compensating the loss of functional richness due to extinctions. Current island bird assemblages are becoming functionally poorer, having lost original species and being composed of functionally more homogeneous species. This is likely to have cascading repercussions on the functioning of island ecosystems.
FOXP4 differentially controls cold-induced beige adipocyte differentiation and thermogenesis
Authors: Wang Fuhua , Xu Shuqin , Chen Tienan , Ling Shifeng , Zhang Wei , Wang Shaojiao , Zhou Rujiang , Xia Xuechun , Yao Zhengju , Li Pengxiao , Zhao Xiaodong , Wang Jiqiu , Guo Xizhi 
Published: October 2021

ABSTRACTBeige adipocytes possess a discrete developmental origin and notable plasticity in thermogenic capacity in response to various environmental cues. But the transcriptional machinery controlling beige adipocyte development and thermogenesis remains largely unknown. By analyzing beige adipocyte-specific knockout mice, we identified a transcription factor, Forkhead Box P4 (FOXP4) that differentially governs beige adipocyte differentiation and activation. Depletion of Foxp4 caused a decline in the frequency of beige preadipocytes by switching their cell fate towards fibroblastic cells at the expense of beige adipocytes. However, we observed that ablation of Foxp4 in differentiated adipocytes profoundly potentiated their thermogenesis upon cold exposure. Of note, the outcome of Foxp4-deficiency on UCP1-mediated thermogenesis was confined to beige adipocytes, rather than to brown adipocytes. Taken together, we submit that FOXP4 primes beige adipocyte cell fate commitment and differentiation by potent transcriptional repression of the thermogenic program.
Electrostatics cause the molecular chaperone BiP to preferentially bind oligomerized states of a client protein
Authors: Kotler Judy L.M. , Wei Wei-Shao , Deans Erin E. , Street Timothy O. 
Published: October 2021

AbstractHsp70-family chaperones bind short monomeric peptides with a weak characteristic affinity in the low micromolar range, but can also bind some aggregates, fibrils, and amyloids, with low nanomolar affinity. While this differential affinity enables Hsp70 to preferentially target potentially toxic aggregates, it is unknown how Hsp70s differentiate between monomeric and oligomeric states of a target protein. Here we examine the interaction of BiP (the Hsp70 paralog in the endoplasmic reticulum) with proIGF2, the pro-protein form of IGF2 that includes a long and mostly disordered E-peptide region that promotes proIGF2 oligomerization. We discover that electrostatic attraction enables the negatively charged BiP to bind positively charged E-peptide oligomers with low nanomolar affinity. We identify the specific BiP binding sites on proIGF2, and although some are positively charged, as monomers they bind BiP with characteristically low affinity in the micromolar range. We conclude that electrostatics enable BiP to preferentially recognize oligomeric states of proIGF2. Electrostatic targeting of Hsp70 to aggregates may be broadly applicable, as all the currently-documented cases in which Hsp70 binds aggregates with high-affinity involve clients that are expected to be positively charged.
Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism
Authors: Penny Hugo A. , Domingues Rita G. , Krauss Maria Z. , Melo-Gonzalez Felipe , Dickson Suzanna , Parkinson James , Hurry Madeleine , Purse Catherine , Jegham Emna , Godinho-Silva Cristina , Rendas Miguel , Veiga-Fernandes Henrique , Bechtold David , Grencis Richard K. , Toellner Kai-Michael , Waisman Ari , Swann Jonathan R. , Gibbs Julie E. , Hepworth Matthew R. 
Published: October 2021

ABSTRACTMutualistic interactions with the commensal microbiota are enforced through a range of immune responses that confer metabolic benefits for the host and ensure tissue health and homeostasis. Immunoglobulin (Ig)A responses directly determine the composition of commensal species that colonize the intestinal tract but require significant metabolic resources to fuel antibody production by tissue-resident plasma cells. Here we demonstrate IgA responses are subject to diurnal regulation by dietary-derived metabolic cues and a cell-intrinsic circadian clock. Rhythmicity in IgA secretion conferred oscillatory patterns on the commensal microbial community and its associated metabolic activity, resulting in changes to metabolite availability over the course of the circadian day. Our findings suggest circadian networks comprising intestinal IgA, the diet and the microbiota align to ensure metabolic health.One-Sentence SummaryWe demonstrate diurnal rhythms in intestinal IgA act to cross-regulate oscillations in the abundance of commensal microbes to foster mutualism.
Cyclic constrained immunoreactive peptides from crucial P. falciparum proteins: potential implications in malaria diagnostics
Authors: Vashisht Kapil , Srivastava Sukrit , Vandana  , Das Ram , Sharma Supriya , Bhardwaj Nitin , Anvikar Anupkumar R , Kim Tong-Soo , Na Byoung-Kuk , Shin Ho-Joon , Pandey Kailash C 
Published: October 2021

AbstractMalaria is still a global challenge with significant morbidity and mortality, especially in the African, South-East Asian and Latin American region. Malaria diagnosis is a crucial pillar in the control and elimination efforts, often accomplished by administration of mass-scale Rapid diagnostic tests (RDTs). The inherent limitations of RDTs-failure of detection in low transmission settings, and deletion of one of the target proteins-Histidine rich protein (HRP) are evident from multiple reports; thus necessitating the need to explore novel diagnostic tools/targets. The present study used peptide microarray to screen potential epitopes from 13 antigenic proteins (CSP, EXP1, LSA1, TRAP, AARP, AMA1, GLURP, MSP1, MSP2, MSP3, MSP4, P48/45, HAP2) of P. falciparum. Three cyclic constrained immunoreactive peptides-C6 (EXP1), A8 (MSP2), B7 (GLURP) were identified from 5,458 cyclic constrained peptides (in duplicate) against P. falciparum infected sera. Peptides (C6, A8, B7-cyclic constrained) and (G11, DSQ, NQN-corresponding linear peptides) were fairly immunoreactive towards P. falciparum-infected sera in dot-blot assay. Using indirect ELISA, cyclic constrained peptides (C6 & B7) were found to be specific to P. falciparum infected sera and further, observed to be significantly reactive towards antibodies from field-collected P. falciparum infected sera. Notably, the structural location of the epitopes defines the reactivity, observed by the preferential recognition of cyclic constrained peptides vs linear peptides and corroborated by the homology modeling analysis of selected proteins. In conclusion, the study identified three cyclic constrained immunoreactive peptides (C6, B7 & A8) from P. falciparum secretory/surface proteins and two of them (C6 & B7) were validated for their diagnostic potential with field-collected P. falciparum infected sera samples.
Stretch-induced endogenous electric fields drive neural crest directed collective cell migration in vivo
Authors: Ferreira Fernando , Moreira Sofia , Barriga Elias H. 
Published: October 2021

AbstractDirected collective cell migration (dCCM) is essential for morphogenesis1, 2. Cell clusters migrate in inherently complex in vivo environments composed of chemical, electrical, mechanical as well as topological features. While these environmental factors have been shown to allow dCCM in vitro, our understanding of dCCM in vivo is mostly limited to chemical guidance3. Thus, despite its wide biological relevance, the mechanisms that guide dCCM in vivo remain unclear. To address this, we study endogenous electric fields in relation to the migratory environment of the Xenopus laevis cephalic neural crest, an embryonic cell population that collectively and directionally migrates in vivo4, and whose migratory mode has been linked to cancer invasion and metastasis5. Combining bioelectrical, biomechanical and molecular tools, we show that endogenous electric fields drive neural crest dCCM via electrotaxis in vivo. Moreover, we identify the voltage-sensitive phosphatase 1 (Vsp1) as a key component of the molecular mechanism used by neural crest cells to transduce electric fields into a directional cue in vivo. Furthermore, Vsp1 function is specifically required for electrotaxis, being dispensable for cell motility and chemotaxis. Finally, we reveal that endogenous electric fields are mechanoelectrically established. Mechanistically, convergent extension movements of the neural fold generate membrane tension, which in turn opens stretch-activated channels to mobilise the ions required to fuel electric fields. Overall, our results reveal a mechanism of cell guidance, where electrotaxis emerges from the mechanoelectrical and molecular interplay between neighbouring tissues. More broadly, our data contribute to validate the, otherwise understudied, functions of endogenous bioelectrical stimuli in morphogenetic processes6.
TMAO regulates the rigidity of kinesin-propelled microtubules
Authors: Munmun Tasrina , Kabir Arif Md. Rashedul , Sada Kazuki , Kakugo Akira 
Published: October 2021

AbstractWe demonstrate that the rigidity of the microtubules (MTs), propelled by kinesins in an in vitro gliding assay, can be modulated using the deep-sea osmolyte trimethylamine N-oxide (TMAO). By varying the concentration of TMAO in the gliding assay, the rigidity of the MTs is modulated over a wide range. By employing this approach, we are able to reduce the persistence length of MTs, a measure of MT rigidity, ∼8 fold using TMAO of the concentration of 1.5 M. The rigidity of gliding MTs can be restored by eliminating the TMAO from the gliding assay. This work offers a simple strategy to regulate the rigidity of kinesin-propelled MTs in situ and would widen the applications of biomolecular motors in nanotechnology, materials science, and bioengineering.
PersonaDrive: A Method for the Identification and Prioritization of Personalized Cancer Drivers
Authors: Erten Cesim , Houdjedj Aissa , Kazan Hilal , Taleb Bahmed Ahmed Amine 
Published: October 2021

AbstractMotivationA major challenge in cancer genomics is to distinguish the driver mutations that are causally linked to cancer from passenger mutations that do not contribute to cancer development. The majority of existing methods provide a single driver gene list for the entire cohort of patients. However, since mutation profiles of patients from the same cancer type show a high degree of heterogeneity, a more ideal approach is to identify patient-specific drivers.ResultsWe propose a novel method that integrates genomic data, biological pathways, and protein connectivity information for personalized identification of driver genes. The method is formulated on a personalized bipartite graph for each patient. Our approach provides a personalized ranking of the mutated genes of a patient based on the sum of weighted ‘pairwise pathway coverage’ scores across all the patients, where appropriate pairwise patient similarity scores are used as weights to normalize these coverage scores. We compare our method against three state-of-the-art patient-specific cancer gene prioritization methods. The comparisons are with respect to a novel evaluation method that takes into account the personalized nature of the problem. We show that our approach outperforms the existing alternatives for both the TCGA and the cell-line data. Additionally, we show that the KEGG/Reactome pathways enriched in our ranked genes and those that are enriched in cell lines’ reference sets overlap significantly when compared to the overlaps achieved by the rankings of the alternative methods. Our findings can provide valuable information towards the development of personalized treatments and therapies.AvailabilityAll the code and necessary datasets are available athttps://github.com/abu-compbio/PersonaDrive.Contactcesim.erten@antalya.edu.trorhilal.kazan@antalya.edu.tr
Impact of fluoroquinolones and aminoglycosides on P. aeruginosa virulence factor production and cytotoxicity
Authors: Foulkes Daniel M. , McLean Keri , Sloniecka Marta , Byrne Dominic , Haneef Atikah S. , Winstanley Craig , Berry Neil , Fernig David G. , Kaye Stephen B. 
Published: October 2021

AbstractInfection from the opportunistic pathogen Pseudomonas aeruginosa is one of leading causes of disability and mortality worldwide and the world health organisation has listed it with the highest priority for the need of new antimicrobial therapies. P. aeruginosa strains responsible for the poorest clinical outcomes express either ExoS or ExoU, which are injected into target host cells via the type III secretion system (T3SS). ExoS is a bifunctional cytotoxin that promotes intracellular survival of invasive P. aeruginosa by preventing targeting of the bacteria to acidified intracellular compartments and lysosomal degradation. ExoU is a potent phospholipase which causes rapid destruction of host cell plasma membranes, leading to acute tissue damage and bacterial dissemination. Fluoroquinolones are usually employed as a first line of therapy as they have been shown to be more active against P. aeruginosa in vitro than other antimicrobial classes. However, their overuse over the past decade has caused alarming rates of antibiotic resistance to emerge. In certain clinical situations, aminoglycosides have been shown to be more effective then fluoroquinolones, despite their reduced potency towards P. aeruginosa in vitro. In this study, we evaluated the effects of fluoroquinolones (moxifloxacin and ciprofloxacin) and aminoglycosides (tobramycin and gentamycin) on T3SS expression and toxicity, in corneal epithelial cell infection models. We discovered tobramycin disrupted T3SS expression and inhibited both ExoS and ExoU mediated cytotoxicity, protecting infected HCE-T cells even at concentrations below the minimal inhibitory concentrations (MIC). Fluoroquinolones moxifloxacin and ciprofloxacin, however, upregulated the T3SS and in particular did not subvert the cytotoxic effects of ExoS and ExoU.
Behavioural and molecular characterisation of the Dlg2 haploinsufficiency rat model of genetic risk for psychiatric disorder
Authors: Waldron Sophie , Pass Rachel , Griesius Simonas , Mellor Jack R. , Robinson Emma S. J. , Thomas Kerrie L. , Wilkinson Lawrence S. , Humby Trevor , Hall Jeremy , Dwyer Dominic M. 
Published: October 2021

AbstractGenetic studies implicate disruption to the DLG2 gene in copy number variants as increasing risk for schizophrenia, autism spectrum disorders and intellectual disability. To investigate psychiatric endophenotypes associated with DLG2 haploinsufficiency (and concomitant PSD-93 protein reduction) a novel clinically relevant Dlg2+/- rat was assessed for abnormalities in anxiety, sensorimotor gating, hedonic reactions, social behaviour, and locomotor response to the N-Methyl-D-aspartic acid receptor antagonist phencyclidine. Dlg gene and protein expression were also investigated to assess model validity. Reductions in PSD-93 messenger RNA and protein were observed in the absence of compensation by other related genes or proteins. Behaviourally Dlg2+/- rats show potentiated locomotor response to phencyclidine, as is typical of psychotic disorder models, in the absence of deficits in the other behavioural phenotypes assessed here. This shows that the behavioural effects of Dlg2 haploinsufficiency may specifically relate to psychosis vulnerability but are subtle, providing a contrast to the gross deficits in Dlg2 homozygous models (Winkler, et al., 2018; Yoo et al., 2020a) which do not so specifically model the single chromosome DLG2 deletion in carriers of risk-associated copy number variants.